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Tomoo Sawabe
Faculty of Fisheries Sciences　Marine Life Science　Marine Biotechnology and Microbiology
Professor
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Last Updated :2024/05/09

Researcher Profile and Settings

Affiliation

  • Faculty of Fisheries Sciences　Marine Life Science　Marine Biotechnology and Microbiology

Job Title

  • Professor

Degree

  • Master of Fisheries（Hokkaido University）
  • Doctor of Fisheries（Hokkaido University）

URL

J-Global ID

Research Interests

  • アルギン酸分解酵素   アワビ   消化管内細菌   ゲノム   Vibrio halioticoli   Pseudoalteromonas elyakovii   微生物   マコンブプロトプラスト再生   バイオ燃料   アワビ消化管内細菌群   Vibrio   細胞壁再生   エタノール   プロトプラスト   バイオマス   海水依存型発現   分子系統解析   水産学   海産食藻動物   再生可能エネルギー   微生物学   Microbiology   

Research Areas

  • Life sciences / Aquaculture
  • Environmental science/Agricultural science / Environmental policy and society
  • Environmental science/Agricultural science / Environmental impact assessment
  • Life sciences / Marine/Aquatic life sciences

Educational Organization

Academic & Professional Experience

  • 2008/02 - Today Hokkaido Univrsity Faculty of Fisheries Sciences Professor
  • 2002/08 - 2008/01 Hokkaido University Graduate School of Fisheries Sciences Associate Professor
  • 1992/09 - 2002/07 Hokkaido University Graduate School of Fisheries Sciences Assitant Professor

Education

  • 1989/04 - 1991/03  Hokkaido University  Graduate School of Fisheries  Department of Food Sciences
  •        - 1991  Hokkaido University  Graduate School, Division of Fisheries
  • 1985/04 - 1989/03  Hokkaido University  Faculty of Fisheries  Department of Food Sciences
  •        - 1989  Hokkaido University  Faculty of Fisheries

Association Memberships

  • 日本藻類学会   微生物生態学会   生物工学会   マリンバイオテクノロジー学会   日本水産学会   

Research Activities

Published Papers

  • Naoki Takatani, Takashi Maoka, Tomoo Sawabe, Fumiaki Beppu, Masashi Hosokawa
    Applied microbiology and biotechnology 108 (1) 102 - 102 2024/12 
    Bacteria belonging to the genus Algoriphagus have been isolated from various sources, such as Antarctic sea ice, seawater, and sediment, and some strains are known to produce orange to red pigments. However, the pigment composition and biosynthetic genes have not been fully elucidated. A new red-pigmented Algoriphagus sp. strain, oki45, was isolated from the surface of seaweed collected from Senaga-Jima Island, Okinawa, Japan. Genome comparison revealed oki45's average nucleotide identity of less than 95% to its closely related species, Algoriphagus confluentis NBRC 111222 T and Algoriphagus taiwanensis JCM 19755 T. Comprehensive chemical analyses of oki45's pigments, including 1H and 13C nuclear magnetic resonance and circular dichroism spectroscopy, revealed that the pigments were mixtures of monocyclic carotenoids, (3S)-flexixanthin ((3S)-3,1'-dihydroxy-3',4'-didehydro-1',2'-dihydro-β,ψ-caroten-4-one) and (2R,3S)-2-hydroxyflexixanthin ((2R,3S)-2,3,1'-trihydroxy-3',4'-didehydro-1',2'-dihydro-β,ψ-caroten-4-one); in particular, the latter compound was new and not previously reported. Both monocyclic carotenoids were also found in A. confluentis NBRC 111222 T and A. taiwanensis JCM 19755 T. Further genome comparisons of carotenoid biosynthetic genes revealed the presence of eight genes (crtE, crtB, crtI, cruF, crtD, crtYcd, crtW, and crtZ) for flexixanthin biosynthesis. In addition, a crtG homolog gene encoding 2,2'-β-hydroxylase was found in the genome of the strains oki45, A. confluentis NBRC 111222 T, and A. taiwanensis JCM 19755 T, suggesting that the gene is involved in 2-hydroxyflexixanthin synthesis via 2-hydroxylation of flexixanthin. These findings expand our knowledge of monocyclic carotenoid biosynthesis in Algoriphagus bacteria. KEY POINTS: • Algoriphagus sp. strain oki45 was isolated from seaweed collected in Okinawa, Japan. • A novel monocyclic carotenoid 2-hydroxyflexixanthin was identified from strain oki45. • Nine genes for 2-hydroxyflexixanthin biosynthesis were found in strain oki45 genome.
  • Sayaka Mino, So Fukazawa, Jiro Tsuchiya, Jesse C. McNichol, Stefan M. Sievert, Shogo Yamaki, Yasuhiro Ando, Tomoo Sawabe
    International Journal of Systematic and Evolutionary Microbiology 73 (11) 1466-5026 2023/11/03 
    A novel mesophilic, hydrogen- and thiosulfate-oxidizing bacterium, strain ISO32T, was isolated from diffuse-flow hydrothermal fluids from the Crab Spa vent on the East Pacific Rise. Cells of ISO32T were rods, being motile by means of a single polar flagellum. The isolate grew at a temperature range between 30 and 55 °C (optimum, 43 °C), at a pH range between 5.3 and 7.6 (optimum, pH 5.8) and in the presence of 2.0–4.0 % NaCl (optimum, 2.5 %). The isolate was able to grow chemolithoautotrophically with molecular hydrogen, thiosulfate or elemental sulfur as the sole electron donor. Thiosulfate, elemental sulfur, nitrate and molecular oxygen were each used as a sole electron acceptor. Phylogenetic analysis of 16S rRNA gene sequences placed ISO32T in the genus Hydrogenimonas of the class Epsilonproteobacteria, with Hydrogenimonas thermophila EP1-55–1 %T as its closest relative (95.95 % similarity). On the basis of the phylogenetic, physiological and genomic characteristics, it is proposed that the organism represents a novel species within the genus Hydrogenimonas, Hydrogenimonas cancrithermarum sp. nov. The type strain is ISO32T (=JCM 39185T =KCTC 25252T). Furthermore, the genomic properties of members of the genus Hydrogenimonas are distinguished from those of members of other thermophilic genera in the orders Campylobacterales (Nitratiruptor and Nitrosophilus) and Nautiliales (Caminibacter, Nautilia and Lebetimonas), with larger genome sizes and lower 16S rRNA G+C content values. Comprehensive metabolic comparisons based on genomes revealed that genes responsible for the Pta–AckA pathway were observed exclusively in members of mesophilic genera in the order Campylobacterales and of the genus Hydrogenimonas. Our results indicate that the genus Hydrogenimonas contributes to elucidating the evolutionary history of Epsilonproteobacteria in terms of metabolism and transition from a thermophilic to a mesophilic lifestyle.
  • Juanwen Yu, Chunqi Jiang, Ryota Yamano, Shotaro Koike, Yuichi Sakai, Sayaka Mino, Tomoo Sawabe
    Animal microbiome 5 (1) 54 - 54 2023/10/24 
    BACKGROUND: Microbiome in early life has long-term effects on the host's immunological and physiological development and its disturbance is known to trigger various diseases in host Deuterostome animals. The sea cucumber Apostichopus japonicus is one of the most valuable marine Deuterostome invertebrates in Asia and a model animal in regeneration studies. To understand factors that impact on host development and holobiont maintenance, host-microbiome association has been actively studied in the last decade. However, we currently lack knowledge of early life core microbiome during its ontogenesis and how it benefits the host's growth. RESULTS: We analyzed the microbial community in 28 sea cucumber samples from a laboratory breeding system, designed to replicate aquaculture environments, across six developmental stages (fertilized eggs to the juvenile stage) over a three years-period to examine the microbiomes' dynamics and stability. Microbiome shifts occurred during sea cucumber larval ontogenesis in every case. Application of the most sophisticated core microbiome extraction methodology, a hybrid approach with abundance-occupancy core microbiome analyses (top 75% of total reads and > 70% occupation) and core index calculation, first revealed early life core microbiome consisted of Alteromonadaceae and Rhodobacteraceae, as well as a stage core microbiome consisting of pioneer core microbe Pseudoalteromonadaceae in A. japonicus, suggesting a stepwise establishment of microbiome related to ontogenesis and feeding behavior in A. japonicus. More interestingly, four ASVs affiliated to Alteromonadaceae and Rhodobacteraceae were extracted as early life core microbiome. One of the ASV (ASV0007) was affiliated to the Sulfitobactor strain BL28 (Rhodobacteraceae), isolated from blastula larvae in the 2019 raring batch. Unexpectedly, a bioassay revealed the BL28 strain retains a host growth-promoting ability. Further meta-pangenomics approach revealed the BL28 genome reads were abundant in the metagenomic sequence pool, in particular, in that of post-gut development in early life stages of A. japonicus. CONCLUSION: Repeated rearing efforts of A. japonicus using laboratory aquaculture replicating aquaculture environments and hybrid core microbiome extraction approach first revealed particular ASVs affiliated to Alteromonadaceae and Rhodobacteraceae as the A. japonicus early life core microbiome. Further bioassay revealed the growth promoting ability to the host sea cucumber in one of the core microbes, the Sulfitobactor strain BL28 identified as ASV0007. Genome reads of the BL28 were abundant in post-gut development of A. japonicus, which makes us consider effective probiotic uses of those core microbiome for sea cucumber resource production and conservation. The study also emphasizes the importance of the core microbiome in influencing early life stages in marine invertebrates. Understanding these dynamics could offer pathways to improve growth, immunity, and disease resistance in marine invertebrates.
  • Yutaro Kimura, Yutaka Fukuda, Rumi Otsu, Juwanen Yu, Sayaka Mino, Satoru Misawa, Satoshi Maruyama, Yuta Ikeda, Remi Miyamachi, Hiroshi Noguchi, Satoshi Kato, Yasuhito Yamamoto, Tomoo Sawabe
    Environmental microbiology 2023/09/29 
    Polybutylene succinate (PBS) is an eco-friendly green plastic. However, PBS was shown as being non-biodegradable in marine environments, and up until now, only a limited number of PBS-degrading marine microbes have been discovered. We first set up in vitro PBS- and PBSA (polybutylene succinate adipate)-plastispheres to characterize novel PBS-degrading marine microbes. Microbial growth and oxygen consumption were observed in both PBS- and PBSA-plastispheres enriched with natural seawater collected from Usujiri, Hokkaido, Japan, and Vibrionaceae and Pseudoalteromonadaceae were significantly enriched on these films. Further gene identification indicated that vibrios belonging to the Gazogenes clade possess genes related to a PBS degrading enzyme (PBSase). The PBS degradation assay for six Gazogenes clade vibrios identified Vibrio ruber, Vibrio rhizosphaerae, and Vibrio spartinae as being capable of degrading PBS. We further identified the gene responsible for PBSase from the type strain of V. ruber, and the purified recombinant vibrio PBSase was found to have low-temperature adaptation and was active under high NaCl concentrations. We also provided docking models between the vibrio PBSase and PBS and PBSA units to show how vibrio PBSase interacts with each substrate compared to the Acidovorax PBSase. These results could contribute to a more sustainable society through further utilization of PBS in marine environments and plastic recycling.
  • Ryota Yamano, Juanwen Yu, Alfabetian Harjuno Condro Haditomo, Chunqi Jiang, Sayaka Mino, Jesús L Romalde, Kyuhee Kang, Yuichi Sakai, Tomoo Sawabe
    PloS one 18 (6) e0286693  2023 
    The genus Thalassotalea is ubiquitous in marine environments, and up to 20 species have been described so far. A Gram-staining-negative, aerobic bacterium, designated strain PTE2T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PTE2T was closely related to Thalassotalea sediminis N211T (= KCTC 42588T = MCCC 1H00116T) with 97.9% sequence similarity. ANI and in silico DDH values against Thalassotalea species were 68.5-77.0% and 19.7-24.6%, respectively, indicating the novelty of PTE2T. Based on genome-based taxonomic approaches, strain PTE2T (= JCM 34608T = KCTC 82592T) is proposed as a new species, Thalassotalea hakodatensis sp. nov.
  • Rika Kudo, Ryota Yamano, Juanwen Yu, Shotaro Koike, Alfabetian Harjuno Condro Haditomo, Mayanne A M de Freitas, Jiro Tsuchiya, Sayaka Mino, Fabiano Thompson, Jesús L Romalde, Hisae Kasai, Yuichi Sakai, Tomoo Sawabe
    PloS one 18 (8) e0290060  2023 
    A Gram-staining-negative, oxidase-positive, strictly aerobic rod-shaped bacterium, designated strain PT1T, was isolated from the laboratory-reared larvae of the sea cucumber Apostichopus japonicus. A phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT1T was closely related to Neptuniibacter marinus ATR 1.1T (= CECT 8938T = DSM 100783T) and Neptuniibacter caesariensis MED92T (= CECT 7075T = CCUG 52065T) showing 98.2% and 98.1% sequence similarity, respectively. However, the average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values among these three strains were 72.0%-74.8% and 18.3%-19.5% among related Neptuniibacter species, which were below 95% and 70%, respectively, confirming the novel status of PT1T. The average amino acid identity (AAI) values of PT1T showing 74-77% among those strains indicated PT1T is a new species in the genus Neptuniibacter. Based on the genome-based taxonomic approach, Neptuniibacter victor sp. nov. is proposed for PT1T. The type strain is PT1T (JCM 35563T = LMG 32868T).
  • So Fukazawa, Sayaka Mino, Jiro Tsuchiya, Satoshi Nakagawa, Ken Takai, Tomoo Sawabe
    Archives of microbiology 205 (1) 12 - 12 2022/12/03 
    A novel bacterium, strain MOT50T, was isolated from the chimney structure at the Iheya North field in the Mid-Okinawa Trough. The cells were motile short rods with a single polar flagellum. Growth was observed between 40 and 65 ℃ (optimum, 52 ℃), at pH values between 5.0 and 7.1 (optimum, pH 6.1) and in the presence of 2.0-4.0% NaCl (optimum, 2.5%). The isolates utilized molecular hydrogen, thiosulfate, or elemental sulfur as the sole electron donor. Thiosulfate, elemental sulfur, nitrate, and molecular oxygen are utilized as the sole electron acceptor. Ammonium is required as a nitrogen source. Thiosulfate, elemental sulfur, sulfate, or sulfite serves as a sulfur source for growth. The G + C content of the genomic DNA was 28.9%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain MOT50T belonged to the genus Nitrosophilus of the class "Campylobacteria", and its closest relative was Nitrosophilus labii HRV44T (97.20%). On the basis of the phylogenetic, physiological, and molecular characteristics, it is proposed that the organism represents a novel species within the genus Nitrosophilus, Nitrosophilus kaiyonis sp. nov. The type strain is MOT50T (= JCM 39187T = KCTC 25251T).
  • Yunato Kuroyanagi, Jiro Tsuchiya, Chunqi Jiang, Sayaka Mino, Hisae Kasai, Daisuke Motooka, Tetsuya Iida, Masataka Satomi, Tomoo Sawabe
    Frontiers in Marine Science 9 2022/11/10 
    Light is one of the most critical stimuli in the majority of living organisms. In the last two decades, blue light (BL) has become a major subject of attention because of developments in light-emitting diodes (LED). The effects of BL on eukaryotic organisms and phototrophic prokaryotes have been well studied, but the knowledge of its effects on non-phototrophic prokaryotes remains unclear. Since BL can penetrate seawater, it is expected that most prokaryotes living in the ocean possess molecular mechanisms which protect against BL. The aim of this study is to assess the molecular mechanisms of Vibrio parahaemolyticus cells against BL as a marine bacterial model compared to other wavelength light exposures. Physiological and transcriptomic analyses of BL-exposed cells compared to other light treated cells revealed the highest ROS fold change, the highest number of differentially expressed genes (DEGs), and up-regulation in the gene responsible to not only compatible solute such as glycine betaine and ectoine but also iron-sulfur biosynthesis related to ROS formation. Furthermore, red light (RL) up-regulated the expression of cryptochrome DASH, a protein known to be excited by BL, and orange light (OL) decreased the expression of thermostable direct hemolysin (TDH), suggesting that OL attenuates the virulence of V. parahaemolyticus. In addition, the expression of VtrA (V. parahaemolyticus type III secretion system 2 (T3SS2) regulator A) but not VtrB (V. parahaemolyticus T3SS2 regulator B) increased under both light treatments, indicating that light exposure is unlikely to be involved in T3SS2-mediated pathogenicity. These results expand our knowledge on unique light responses in non-phototrophic marine prokaryotes.
  • Yuta Matsumura, Kazumich Sato, Chunqi Jiang, Sayaka Mino, Tomoo Swabe
    Current Microbiology 79 (12) 0343-8651 2022/11
  • Md Ali Amatul-Samahah, Aslah Mohamad, Nurhidayu Al-Saari, Mohd Zamri-Saad, Mohamad Noor Amal Azmai, Mohd Termizi Yusof, Md Yasin Ina-Salwany, Mami Tanaka, Sayaka Mino, Tomoo Sawabe
    Data in brief 44 108533 - 108533 2022/10 
    Vibriosis accounts for 66.7% of diseases reported in groupers' cultures and affects almost all stages of growth. The disease could lead up to mortality up to 50% mortality, and it was reported that high stocking density and poor fish handling were among the factors that contributed to the disease dissemination. V. harveyi has been reported to be among the causative agent and has caused acute mortality in cage groupers. In this study, we report the genome of V. harveyi VH1 isolated from a diseased tiger grouper Epinephelus fuscoguttatus, reared in a cage farm located in the coastal area of Langkawi.
  • Chunqi Jiang, Hisae Kasai, Sayaka Mino, Jesús L Romalde, Tomoo Sawabe
    Environmental microbiology 24 (10) 4587 - 4606 2022/09/15 
    The Splendidus clade is the largest clade in Vibrionaceae, and its members are often related to mortality of marine animals with huge economic losses. The molecular bases of their pathogenicity and virulence, however, remain largely unknown. In particular, the complete genome sequences of the Splendidus clade species are rarely registered, which is one of the obstacles to predict core and/or unique genes responsible to their adaptation and pathogenicity, and to perform a fine scale meta-transcriptome during bacterial infection to their hosts. In this study, we obtained the complete genomes of all type strains in the Splendidus clade and revealed that 1) different genome sizes (4.4-5.9 Mb) with V. lentus the biggest and most of them had several big plasmids, likely because of the different features on mobilome elements, 2) the Splendidus clade consists of 19 species except V. cortegadensis, and 3 sub-clades (SC) were defined with the 15 most closely related members as SC1; 3) different carbohydrate degradation preferences may be the result of environmental adaptation, 4) a broad prediction of virulence factors (VFs) revealed core and species unique VF genes. This article is protected by copyright. All rights reserved.
  • Chunqi Jiang, Sayaka Mino, Tomoo Sawabe
    Frontiers in Marine Science 9 2022/03/23 
    Vibrionaceae is one of the most diverse bacterial families and is currently classified into over 50 clades, some members of which play an important role in the symbiotic relationships with humans and animals. Halioticoli clade, which currently consists of 10 species: 8 species associated with the gut of abalone (symbiotic), 1 species (V. breoganii) from bivalves, and 1 species (V. ishigakensis) from subtropical seawater (planktonic). To accelerate studies in the evolution, ecogenomics, and biotechnology of Halioticoli clade species, the genomic backbones and pangenome analyses based on complete genome sequences are needed. Genome sizes of Halioticoli clade species ranged from 3.5 Mb to 4.8 Mb, with V. ishigakensis the biggest. The evolutionary relationships using multilocus sequence analysis based on eight housekeeping genes and 125 single-copy core genes revealed a division of five sub-clades in this clade; 1) V. breoganii, V. comitans, V. inusitatus and V. superstes, 2) V. ezurae, V. neonatus, and V. halioticoli, 3) V. rarus, 4) V. gallicus, and 5) V. ishigakensis. The pan-genomic analysis combined with function and metabolism estimations showed that the planktonic group (sub-clade 5) contained the greatest number of specific genes, and more genes responsible for carbohydrate metabolisms, especially the genes encoding D-galactonate degradation. These results demonstrated that the genome expanded by acquiring more abilities for utilizing various carbohydrates during the evolution from symbiotic to a planktonic lifestyle. Moreover, according to Carbohydrate-Active enZYmes (CAZy) profiling, genes encoding alginate degrading enzymes (aly), classified into PL6, PL7, PL15, and PL17 were common in the ten genomes, but sub-clade 1 had the most. Meanwhile, sub-clade 1and 5 also possessed abundant genes related to macroalgae substrates degradation (GHs), which are also responsible for the genome expansion of sub-clade 1 and 5.
  • Ryota Yamano, Juanwen Yu, Chunqi Jiang, Alfabetian Harjuno Condro Haditomo, Sayaka Mino, Yuichi Sakai, Tomoo Sawabe
    PloS one 17 (8) e0271174  2022 
    A Gram-staining-negative, aerobic bacterium, designated strain PT3T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT3T was closely related to Amphritea ceti RA1T (= KCTC 42154T = NBRC 110551T) and Amphritea spongicola MEBiC05461T (= KCCM 42943T = JCM 16668T) both with 98.3% sequence similarity, however, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (in silico DDH) values among these three strains were below 95% and 70%, respectively, confirming the novelty of PT3T. Furthermore, the average amino acid identity (AAI) values of PT3T against other Amphritea species were on the reported genus delineation boundary (64-67%). Multilocus sequence analysis using four protein-coding genes (recA, mreB, rpoA, and topA) further demonstrated that PT3T, Amphritea ceti and Amphritea spongicola formed a monophyletic clade clearly separate from other members of the genus Amphritea. Three strains (PT3T, A. ceti KCTC 42154T and A. spongicola JCM 16668T) also showed higher similarities in their core genomes compared to those of the other Amphritea spp. Based on the genome-based taxonomic approach, Aliamphritea gen. nov. was proposed together with the reclassification of the genus Amphritea and Aliamphritea ceti comb. nov. (type strain RA1T = KCTC 42154T = NBRC 110551T), Aliamphritea spongicola comb. nov. (type strain MEBiC05461T = KCCM 42943T = JCM 16668T), and Aliamphritea hakodatensis sp. nov. (type strain PT3T = JCM 34607T = KCTC 82591T) were suggested.
  • Juanwen Yu, Yuichi Sakai, Sayaka Mino, Tomoo Sawabe
    FRONTIERS IN MARINE SCIENCE 9 2022/01 
    There is a lot of evidence indicating pioneer microbes in early life having various effects on later host biology. Because of the influential phylogenetic position of sea cucumber, which is a deep branching clade in Deuterostomia, the attention on the microbiome in sea cucumber has been increasing. Although microbes in sea cucumber have been reported in several studies, there is a lack of knowledge regarding the pioneer microbiota in the early life stages of sea cucumber. In this study, microbiota changes during the larval development of sea cucumber were assessed using a laboratory rearing system. Microbial community structure was likely to be related to the developmental stage and significant alterations were detected in the late auricularia stage. The relative abundances of Oceanospirillales, Alteromonadales, and Rhodobacterales significantly varied after gut formation. A total of 257 strains were isolated from larval developmental stages of sea cucumber and affiliated to 124 ASVs in the metagenomic analysis. This data demonstrates for the first-time dynamic changes of sea cucumber microbiota in the developmental stages in early life.
  • Alfabetian Harjuno Condro Haditomo, Masanori Yonezawa, Juanwen Yu, Sayaka Mino, Yuichi Sakai, Tomoo Sawabe
    Frontiers in Marine Science 8 2021/12/22 [Refereed][Not invited]
     
    Sea urchin is an indicator of coastal environmental changes in the global warming era, and is also a model organism in developmental biology and evolution. Due to the depletion of wild resources, new aquaculture techniques for improving stocks have been well studied. The gut microbiome shapes various aspects of a host’s physiology. However, these microbiome structures and functions on sea urchins, particularly Mesocentrotus nudus and Strongylocentrotus intermedius which are important marine bioresources commonly found in Japan, have not been fully investigated yet. Using metagenomic approaches including meta16S and shotgun metagenome sequencings, the structures, functions, and dynamics of the gut microbiome of M. nudus and S. intermedius, related to both habitat environment and host growth, were studied. Firstly, a broad meta16S analysis revealed that at the family level, Psychromonadaceae and Flavobacteriaceae reads (38–71%) dominated in these sea urchins, which is a unique feature observed in species in Japan. Flavobacteriaceae reads were more abundant in individuals after rearing in an aquarium with circulating compared to one with running water. Campylobacteraceae and Vibrionaceae abundances increased in both kinds of laboratory-reared sea urchins in both types of experiments. 2-weeks feeding experiments of M. nudus and S. intermedius transplanted from the farm to laboratory revealed that these gut microbial structures were affected by diet rather than rearing environments and host species. Secondly, further meta16S analysis of microbial reads related to M. nudus growth revealed that at least four Amplicon Sequence Variant (ASV) affiliated to Saccharicrinis fermentans, which is known to be a nitrogen (N2) fixing bacterium, showed a significant positive correlation to the body weight and test diameter. Interestingly, gut microbiome comparisons using shotgun metagenome sequencing of individuals showing higher and lower growth rates revealed a significant abundance of “Nitrate and nitrite ammonification” genes in the higher-grown individuals under the circulating water rearing. These findings provide new insights on the structure-function relationship of sea urchin gut microbiomes beyond previously reported nitrogen fixation function in sea urchin in 1950s; we discovered a nitrate reduction function into ammonium for the growth promotion of sea urchin.
  • Chunqi Jiang, Mami Tanaka, Sayo Nishikawa, Sayaka Mino, Jesús L Romalde, Fabiano L Thompson, Bruno Gomez-Gil, Tomoo Sawabe
    Current microbiology 79 (1) 10 - 10 2021/12/14 
    Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of species has doubled compared to the previous vibrio evolutionary update (Vibrio Clade 2.0) (Sawabe et al. 2014). In this study, "Vibrio Clade 3.0," the second update of the molecular phylogenetic analysis was performed based on nucleotide sequences of eight housekeeping genes (8-HKGs) retrieved from genome sequences, including 22 newly determined genomes. A total of 51 distinct clades were observed, of which 21 clades are newly described. We further evaluated the delineation powers of the clade classification based on nucleotide sequences of 34 single-copy genes and 11 ribosomal protein genes (11-RPGs) retrieved from core-genome sequences; however, the delineation power of 8-HKGs is still high and that gene set can be reliably used for the classification and identification of Vibrionaceae. Furthermore, the 11-RPGs set proved to be useful in identifying uncultured species among metagenome-assembled genome (MAG) and/or single-cell genome-assembled genome (SAG) pools. This study expands the awareness of the diversity and evolutionary history of the family Vibrionaceae and accelerates the taxonomic applications in classifying as not-yet-cultured taxa among MAGs and SAGs.
  • Yuki Ohama, Kotaro Aoki, Sohei Harada, Tatsuya Nagasawa, Tomoo Sawabe, Lisa Nonaka, Kyoji Moriya, Yoshikazu Ishii, Kazuhiro Tateda
    mSphere 6 (5) e0059321  2021/10/27 
    Although Shewanella spp. are most frequently isolated from marine environments; more rarely, they have been implicated in human infections. Shewanella spp. are also recognized as the origin of genes for carbapenem-hydrolyzing class D β-lactamases. Due to the spread globally among Enterobacterales in recent years, risk assessments of both clinical and environmental Shewanella strains are urgently needed. In this study, we analyzed the whole-genome sequences of 10 clinical isolates and 13 environmental isolates of Shewanella spp. and compared them with those of Shewanella species strains registered in public databases. In addition, the levels of blaOXA-55-like transcription and β-lactamase activity of a carbapenem-resistant Shewanella algae isolate were compared with those of carbapenem-susceptible S. algae clade isolates. All clinical isolates were genetically identified as S. algae clade (S. algae, Shewanella chilikensis, and Shewanella carassii), whereas all but one of the environmental isolates were identified as various Shewanella spp. outside the S. algae clade. Although all isolates of the S. algae clade commonly possessed an approximately 12,500-bp genetic region harboring blaOXA-55-like, genetic structures outside this region were different among species. Among S. algae clade isolates, only one showed carbapenem resistance, and this isolate showed a high level of blaOXA-55-like transcription and β-lactamase activity. Although this study documented the importance of the S. algae clade in human infections and the relationship between enhanced production of OXA-55-like and resistance to carbapenems in S. algae, further studies are needed to elucidate the generalizability of these findings. IMPORTANCE Shewanella spp., which are known to carry chromosomally located blaOXA genes, have mainly been isolated from marine environments; however, they can also cause infections in humans. In this study, we compared the molecular characteristics of clinical isolates of Shewanella spp. with those originating from environmental sources. All 10 clinical isolates were genetically identified as members of the Shewanella algae clade (S. algae, S. chilikensis, and S. carassii); however, all but one of the 13 environmental isolates were identified as Shewanella species members outside the S. algae clade. Although all the S. algae clade isolates possessed an approximately 12,500-bp genetic region harboring blaOXA-55-like, only one isolate showed carbapenem resistance. The carbapenem-resistant isolate showed a high level of blaOXA-55-like transcription and β-lactamase activity compared with the carbapenem-susceptible isolates. To confirm the clinical significance and antimicrobial resistance mechanisms of the S. algae clade members, analysis involving more clinical isolates should be performed in the future.
  • Sayaka Mino, Taiki Shiotani, Satoshi Nakagawa, Ken Takai, Tomoo Sawabe
    Systematic and applied microbiology 44 (1) 126170 - 126170 0723-2020 2021/01 
    A novel thermophilic bacterium, strain SSM-sur55T, was isolated from a chimney structure at the Urashima site on the Southern Mariana Trough in the Pacific Ocean. Growth was observed at temperatures between 25 and 60°C (optimum, 55°C; 180min doubling time), at pH values between 5.3 and 7.2 (optimum, pH 5.9) and in the presence of between 1.6 and 5.6% (w/v) NaCl (optimum, 3.2%). The isolate used molecular hydrogen as its sole energy source, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and elemental sulfur as its sole sulfur source. Thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur was utilized as its sole electron acceptor. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SSM-sur55T belonged to the genus Hydrogenimonas of the class "Campylobacteria", and its closest relative was Hydrogenimonas thermophila EP1-55-1%T (94.9%). On the basis of the phylogenetic, physiological and molecular characteristics, strain SSM-sur55T represents a novel species within the genus Hydrogenimonas, for which the name Hydrogenimonas urashimensis sp. nov. is proposed, with the type strain SSM-sur55T (JCM 19825=KCTC 15926).
  • Yohei Yamazaki, Yuichi Sakai, Sayaka Mino, Tomoo Sawabe
    AQUACULTURE RESEARCH 51 (9) 3602 - 3608 1355-557X 2020/09 
    To fill in the gaps in knowledge as to how individual sea cucumber Apostichopus japonicus behave consuming eukaryotic food sources in natural environments, eukaryotic communities in the faeces of sea cucumbers and sediments were analysed through one whole year based on 16S rRNA gene sequencing of the organelle genomes. A total of 390 eukaryotic features were obtained, and 99.7% of the features were assigned to chloroplasts. The eukaryotic communities in faeces and sediments showed seasonal fluctuations through one whole year based on Bray-Curtis distance and community composition. Comparison of eukaryotic communities between faeces and sediments showed that 12 families including Chaetocerotaceae and Laminariaceae were more abundant in faeces than in sediments, suggesting that sea cucumbers may choose sediment containing these algal taxa more often compared with others in natural environments. All features of Laminariaceae were assigned to Saccharina japonica, which is consistent with the fact that this alga is one of the most suitable diets in the aquaculture of A. japonicus. Assessments of individual 16S amplicon sequences of both faecal and sediment samples could be an alternative tool to help us understand dynamic feeding behaviours of sea cucumber populations in contributing to bioresource conservation and development of a superior approach to aquaculture.
  • Muneyuki Fukushi, Sayaka Mino, Hirohisa Tanaka, Satoshi Nakagawa, Ken Takai, Tomoo Sawabe
    iScience 23 (9) 101462 - 101462 2020/08/15 
    Nitrous oxide (N2O) is a potent greenhouse gas and has significantly increased in the atmosphere. Deep-sea hydrothermal fields are representative environments dominated by mesophilic to thermophilic members of the class Campylobacteria that possess clade II nosZ encoding nitrous oxide reductase. Here, we report a strain HRV44T representing the first thermophilic campylobacterium capable of growth by H2 oxidation coupled to N2O reduction. On the basis of physiological and genomic properties, it is proposed that strain HRV44T (=JCM 34002 = DSM 111345) represents a novel species of the genus Nitratiruptor, Nitratiruptor labii sp. nov. The comparison of the N2O consumption ability of strain HRV44T with those of additional Nitratiruptor and other campylobacterial strains revealed the highest level in strain HRV44T and suggests the N2O-respiring metabolism might be the common physiological trait for the genus Nitratiruptor. Our findings provide insights into contributions of thermophilic Campylobacteria to the N2O sink in deep-sea hydrothermal environments.
  • Juline M. Walter, Felipe H. Coutinho, Luciana Leomil, Paulo I. Hargreaves, Mariana E. Campeao, Veronica V. Vieira, Beatriz S. Silva, Giovana O. Fistarol, Paulo S. Salomon, Tomoo Sawabe, Sayaka Mino, Masashi Hosokawa, Hideaki Miyashita, Fumito Maruyama, Marcel C. van Verk, Bas E. Dutilh, Cristiane C. Thompson, Fabiano L. Thompson
    MICROBIAL ECOLOGY 80 (2) 249 - 265 0095-3628 2020/08 [Refereed][Not invited]
     
    Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081(T) (= CBAS 745(T)) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081(T) exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 degrees C, with scant growth at 30 degrees C). These characteristics provide insights into their widespread distribution in reef systems.
  • Mami Tanaka, Daiki Kumakura, Sayaka Mino, Hidetaka Doi, Yoshitoshi Ogura, Tetsuya Hayashi, Iseo Yumoto, Man Cai, Yu-Guang Zhou, Bruno Gomez-Gil, Toshiyoshi Araki, Tomoo Sawabe
    ENVIRONMENTAL MICROBIOLOGY 22 (8) 3205 - 3217 1462-2912 2020/08 [Refereed][Not invited]
     
    Members of the family Vibrionaceae are generally found in marine and brackish environments, playing important roles in nutrient cycling. The Rumoiensis clade is an unconventional group in the genus Vibrio, currently comprising six species from different origins including two species isolated from non-marine environments. In this study, we performed comparative genome analysis of all six species in the clade using their complete genome sequences. We found that two non-marine species, Vibrio casei and Vibrio gangliei, lacked the genes responsible for algal polysaccharide degradation, while a number of glycoside hydrolase genes were enriched in these two species. Expansion of insertion sequences was observed in V. casei and Vibrio rumoiensis, which suggests ongoing genomic changes associated with niche adaptations. The genes responsible for the metabolism of glucosylglycerate, a compound known to play a role as compatible solutes under nitrogen limitation, were conserved across the clade. These characteristics, along with genes encoding species-specific functions, may reflect the habit expansion which has led to the current distribution of Rumoiensis clade species. Genome analysis of all species in a single clade give us valuable insights into the genomic background of the Rumoiensis clade species and emphasize the genomic diversity and versatility of Vibrionaceae.
  • Taiki Shiotani, Sayaka Mino, Wakana Sato, Sayo Nishikawa, Masanori Yonezawa, Stefan M Sievert, Tomoo Sawabe
    PloS one 15 (12) e0241366  1932-6203 2020 
    A novel bacterium, strain EPR55-1T, was isolated from a deep-sea hydrothermal vent on the East Pacific Rise. The cells were motile rods. Growth was observed at temperatures between 50 and 60°C (optimum, 60°C), at pH values between 5.4 and 8.6 (optimum, pH 6.6) and in the presence of 2.4-3.2% (w/v) NaCl (optimum, 2.4%). The isolate used molecular hydrogen as its sole electron donor, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and thiosulfate, sulfite (0.01 to 0.001%, w/v) or elemental sulfur as its sole sulfur source. Nitrate, nitrous oxide (33%, v/v), thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur could serve as the sole electron acceptor to support growth. Phylogenetic analyses based on both 16S rRNA gene sequences and whole genome sequences indicated that strain EPR55-1T belonged to the family Nitratiruptoraceae of the class "Campylobacteria", but it had the distinct phylogenetic relationship with the genus Nitratiruptor. On the basis of the physiological and molecular characteristics of the isolate, the name Nitrosophilus alvini gen. nov. sp. nov. is proposed, with EPR55-1T as the type strain (= JCM 32893T = KCTC 15925T). In addition, it is shown that "Nitratiruptor labii" should be transferred to the genus Nitrtosophilus; the name Nitrosophilus labii comb. nov. (JCM 34002T = DSM 111345T) is proposed for this organism. Furthermore, 16S rRNA gene-based and genome-based analyses showed that Cetia pacifica is phylogenetically associated with Caminibacter species. We therefore propose the reclassification of Cetia pacifica as Caminibacter pacificus comb. nov. (DSM 27783T = JCM 19563T). Additionally, AAI thresholds for genus classification and the reclassification of subordinate taxa within "Campylobacteria" are also evaluated, based on the analyses using publicly available genomes of all the campylobacterial species.
  • Yohei Yamazaki, Yuichi Sakai, Juanwen Yu, Sayaka Mino, Tomoo Sawabe
    PeerJ 8 e10260  2167-8359 2020 
    Sea cucumbers possess the remarkable capacity to regenerate their body parts or organs. Regeneration of host organs and/or body parts involves reconstruction of the host associated microbiota, however, the dynamics and contribution of microbiota to the regeneration process are largely unknown due to a lack of experimental models. To track the dynamics of individual gut microbiomes during gut regeneration, both caged mariculture and laboratory isolator systems of sea cucumbers (Apostichopus japonicus) were developed and longitudinal meta16S analyses were performed. Under natural environmental conditions in the caged mariculture system, both bacterial and eukaryotic communities in sea cucumbers' guts appeared to be reconstructed within 4 months after evisceration. Using the laboratory isolator, which can trace daily dynamics, we found that fecal microbiota collected before evisceration were clearly different from those collected after evisceration. We also identified eight key bacteria, belonging to Alteromonadaceae, Rhodobacteraceae, Oceanospirillaceae and family-unassigned Gammaproteobacteria, suggesting that these bacteria might interact with the host during the gut regeneration process. Six of the eight key bacteria were isolated for further bioassay using the isolator developed in this study to test whether these isolates affect gut regeneration.
  • Mami Tanaka, Bi Hongyu, Chunqi Jiang, Sayaka Mino, Pedro Milet Meirelles, Fabiano Thompson, Bruno Gomez-Gil, Tomoo Sawabe
    SYSTEMATIC AND APPLIED MICROBIOLOGY 43 (1) 126048 - 126048 0723-2020 2020/01 [Refereed][Not invited]
     
    Two novel strains C4III282(T) and C4III291 were isolated from seawater collected a site off the Taketomi coral reef. Phylogenetic analysis based on the I 6 rRNA sequences revealed that the two strains belong to the genus Vibrio. MLSA using eight protein-coding genes (ftsZ, gapA, gyrB, mreB, pyres, recA, rpoA, and topA) showed that C4III282(T) and C4III291 are closely related to the members of the Ponticus Glade, namely Vibrio panuliri JCM I9500(T), Vibrio ponticus DSM 16217(T), and "Vibrio rhodolitus" G98. ANI and in silico DDH values with members of the Ponticus Glade were 77.6-78.7% and 22.2-23.1, respectively. The name Vibrio taketomensis sp. nov. is proposed with C4III282(T) (CAIM 1928(T)=DSM 106943(T)=JCM 33434(T)) as the type strain. (C) 2019 Elsevier GmbH. All rights reserved.
  • Yohei Yamazaki, Yuichi Sakai, Sayaka Mino, Wataru Suda, Masahira Hattori, Pedro Milet Meirelles, Fabiano Thompson, Tomoo Sawabe
    ENVIRONMENTAL MICROBIOLOGY REPORTS 11 (6) 797 - 807 1758-2229 2019/12 [Refereed][Not invited]
     
    Deposit-feeding sea cucumbers repeat ingestion of sediments and excretion of faeces daily and consequently increase bacterial abundance in sediments and promote organic matter mineralization. Such ecological roles are expected to be collaborative activities of sea cucumbers and the gut microbiota. Here, we performed a spatiotemporally broad 16S rRNA gene analysis using 109 samples from sea cucumber faeces and habitat sediments to explore potential contribution of their gut microbiota to the ecological roles. Most operational taxonomic units (OTUs) observed in the faecal samples were shared with the sediment samples, nevertheless faecal and sediment microbiota differed from each other in UniFrac analysis. Lower bacterial diversity and increased relative abundance of specific OTUs in the faecal microbiota strongly suggest selective enrichment of ingested sediment microbiota in their guts. Interestingly, representative faecal OTUs were more abundant in sea cucumber-populated sediments than in un-inhabited sediments, indicating bacteria selectively enriched in the guts were spread on ambient sediments via faeces. Moreover, the predicted microbial community metabolic potential showed a higher abundance of genes related to carbohydrate and xenobiotics metabolisms in faeces than in sediments. Our study suggests the repeated selective enrichment transforms ambient sediment microbial communities and maintains the host's ecological roles by promoting organic matter mineralization.
  • M Y Ina-Salwany, Nurhidayu Al-Saari, Aslah Mohamad, Fathin-Amirah Mursidi, Aslizah Mohd-Aris, M N A Amal, Hisae Kasai, Sayaka Mino, Tomoo Sawabe, M Zamri-Saad
    Journal of aquatic animal health 31 (1) 3 - 22 0899-7659 2019/03 [Refereed][Not invited]
     
    Current growth in aquaculture production is parallel with the increasing number of disease outbreaks, which negatively affect the production, profitability, and sustainability of the global aquaculture industry. Vibriosis is among the most common diseases leading to massive mortality of cultured shrimp, fish, and shellfish in Asia. High incidence of vibriosis can occur in hatchery and grow-out facilities, but juveniles are more susceptible to the disease. Various factors, particularly the source of fish, environmental factors (including water quality and farm management), and the virulence factors of Vibrio, influence the occurrence of the disease. Affected fish show weariness, with necrosis of skin and appendages, leading to body malformation, slow growth, internal organ liquefaction, blindness, muscle opacity, and mortality. A combination of control measures, particularly a disease-free source of fish, biosecurity of the farm, improved water quality, and other preventive measures (e.g., vaccination) might be able to control the infection. Although some control measures are expensive and less practical, vaccination is effective, relatively cheap, and easily implemented. In this review, the latest knowledge on the pathogenesis and control of vibriosis, including vaccination, is discussed.
  • Nurhidayu Al-Saari, Eri Amada, Yuta Matsumura, Mami Tanaka, Sayaka Mino, Tomoo Sawabe
    PeerJ 7 e6769  2019 [Refereed][Not invited]
     
    Biohydrogen is one of the most suitable clean energy sources for sustaining a fossil fuel independent society. The use of both land and ocean bioresources as feedstocks show great potential in maximizing biohydrogen production, but sodium ion is one of the main obstacles in efficient bacterial biohydrogen production. Vibrio tritonius strain AM2 can perform efficient hydrogen production with a molar yield of 1.7 mol H2/mol mannitol, which corresponds to 85% theoretical molar yield of H2 production, under saline conditions. With a view to maximizing the hydrogen production using marine biomass, it is important to accumulate knowledge on the effects of salts on the hydrogen production kinetics. Here, we show the kinetics in batch hydrogen production of V. tritonius strain AM2 to investigate the response to various NaCl concentrations. The modified Han-Levenspiel model reveals that salt inhibition in hydrogen production using V. tritonius starts precisely at the point where 10.2 g/L of NaCl is added, and is critically inhibited at 46 g/L. NaCl concentration greatly affects the substrate consumption which in turn affects both growth and hydrogen production. The NaCl-dependent behavior of fermentative hydrogen production of V. tritonius compared to that of Escherichia coli JCM 1649 reveals the marine-adapted fermentative hydrogen production system in V. tritonius. V. tritonius AM2 is capable of producing hydrogen from seaweed carbohydrate under a wide range of NaCl concentrations (5 to 46 g/L). The optimal salt concentration producing the highest levels of hydrogen, optimal substrate consumption and highest molar hydrogen yield is at 10 g/L NaCl (1.0% (w/v)).
  • Mami Tanaka, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, Tomoo Sawabe
    PEERJ 6 e5018  2167-8359 2018/06 [Refereed][Not invited]
     
    Whole genome sequence comparisons have become essential for establishing a robust scheme in bacterial taxonomy. To generalize this genome-based taxonomy, fast, reliable, and cost-effective gnome sequencing methodologies are required. MinION, the palm -sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minimal laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae and compared Nanopore- only assemblies to complete gnomes of fiw Rumoiensis clade species: Vibrio aphrogenes, V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall gnome relatedness indices (OGRI) and multilocus sequence analysis (MLSA) based on Nanopore-only assembly and Illumina or hybrid assemblies revealed that errors in Nanopore-only assembly do not Influence average nucleotide identity (ANI), in silico DNA -DNA hybridization (DDH), G+C content, or MLSA tree topology in Vibrionaceae. Our results show that the genome sequences frorn Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA.
  • A K M Rohul Amin, Mami Tanaka, Nurhidayu Al-Saari, Gao Feng, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, Pedro M Meirelles, Fabiano L Thompson, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
    Systematic and applied microbiology 41 (1) 62 - 63 0723-2020 2018/01 [Refereed][Not invited]
  • Sayaka Mino, Naoki Yoneyama, Satoshi Nakagawa, Ken Takai, Tomoo Sawabe
    Frontiers in bioengineering and biotechnology 6 184 - 184 2018 [Refereed][Not invited]
     
    Nitrous oxide (N2O) is a greenhouse gas and also leads to stratospheric ozone depletion. In natural environments, only a single N2O sink process is the microbial reduction of N2O to N2, which is mediated by nitrous oxide reductase (NosZ) encoded by nosZ gene. The nosZ phylogeny has two distinct clades, clade I and formerly overlooked clade II. In deep-sea hydrothermal environments, several members of the class Campylobacteria are shown to harbor clade II nosZ gene and perform the complete denitrification of nitrate to N2; however, little is known about their ability to grow on exogenous N2O as the sole electron acceptor. Here, we obtained an enrichment culture from a deep-sea hydrothermal vent in the Southern Mariana Trough, which showed a respiratory N2O reduction with H2 as an electron donor. The single amplicon sequence variant (ASV) presenting 90% similarity to Hydrogenimonas species within the class Campylobacteria was predominant throughout the cultivation period. Metagenomic analyses using a combination of short-read and long-read sequence data succeeded in reconstructing a complete genome of the dominant ASV, which encoded clade II nosZ gene. This study represents the first cultivation analysis that shows the occurrence of N2O-respiring microorganisms in a deep-sea hydrothermal vent and provides the opportunity to assess their capability to reduce N2O emission from the environments.
  • Pedro Milet Meirelles, Ana Carolina Soares, Louisi Oliveira, Luciana Leomil, Luciana Reis Appolinario, Ronaldo Bastos Francini-Filho, Rodrigo Leão de Moura, Renato Tenan de Barros Almeida, Paulo S Salomon, Gilberto Menezes Amado-Filho, Ricardo Kruger, Eduardo Siegle, Diogo A Tschoeke, Isao Kudo, Sayaka Mino, Tomoo Sawabe, Cristiane C Thompson, Fabiano L Thompson
    Frontiers in microbiology 9 2203 - 2203 2018 [Refereed][Not invited]
     
    Local and global stressors have affected coral reef ecosystems worldwide. Switches from coral to algal dominance states and microbialization are the major processes underlying the global decline of coral reefs. However, most of the knowledge concerning microbialization has not considered physical disturbances (e.g., typhoons, waves, and currents). Southern Japan reef systems have developed under extreme physical disturbances. Here, we present analyses of a three-year investigation on the coral reefs of Ishigaki Island that comprised benthic and fish surveys, water quality analyses, metagenomics and microbial abundance data. At the four studied sites, inorganic nutrient concentrations were high and exceeded eutrophication thresholds. The dissolved organic carbon (DOC) concentration (up to 233.3 μM) and microbial abundance (up to 2.5 × 105 cell/mL) values were relatively high. The highest vibrio counts coincided with the highest turf cover (∼55-85%) and the lowest coral cover (∼4.4-10.2%) and fish biomass (0.06 individuals/m2). Microbiome compositions were similar among all sites and were dominated by heterotrophs. Our data suggest that a synergic effect among several regional stressors are driving coral decline. In a high hydrodynamics reef environment, high algal/turf cover, stimulated by eutrophication and low fish abundance due to overfishing, promote microbialization. Together with crown-of-thorns starfish (COTS) outbreaks and possible of climate changes impacts, theses coral reefs are likely to collapse.
  • Feng Gao, Nurhidayu Al-Saari, A K M Rohul Amin, Kazumichi Sato, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Paulo Iiboshi Hargreaves, Pedro Milet Meirelles, Fabiano L Thompson, Cristiane Thompson, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
    Systematic and applied microbiology 40 (8) 516 - 516 2017/12 [Refereed][Not invited]
  • Mami Tanaka, Shoko Endo, Fumihito Kotake, Nurhidayu Al-Saari, A. K. M. Rohul Amin, Gao Feng, Sayaka Mino, Hidetaka Doi, Yoshitoshi Ogura, Tetsuya Hayashi, Wataru Suda, Masahira Hattori, Isao Yumoto, Toko Sawabe, Tomoo Sawabe, Toshiyoshi Araki
    PLOS ONE 12 (12) e0189555  1932-6203 2017/12 [Refereed][Not invited]
     
    [This corrects the article DOI: 10.1371/journal.pone.0180053.].
  • A K M Rohul Amin, Mami Tanaka, Nurhidayu Al-Saari, Gao Feng, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, Pedro M Meirelles, Fabiano L Thompson, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
    Systematic and applied microbiology 40 (5) 290 - 296 0723-2020 2017/07 [Refereed][Not invited]
     
    Two phylogenetically distinct Vibrionaceae strains C4II189T and C4V358T isolated from reef seawater off Ishigaki Island, Japan, in 2014 were studied with advanced genome-based taxonomy approaches. All aspects of phylogenetic (16S rRNA phylogeny, MLSA), phenotypic and genetic (ANI, DDH, AAI, and the number of core genes) cohesions between the two identified species were high enough to propose them as members of a new genus within the family Vibrionaceae. Consequently, an eighth genus Thaumasiovibrio gen. nov. is proposed that contains two new species Thaumasiovibrio occultus sp. nov. strain C4II189T (=DSM 101554T=JCM 31629T) (type species) and Thaumasiovibrio subtropicus sp. nov. strain C4V358T (=DSM 101555T=JCM 31630T). Thaumasiovibrio species were phylogenetically distinct from the other Vibrionaceae species based on pyrH gene sequences. The combination of catalase negative, sensitivity to vibriostatic agent O/129, and green colony formation on TCBS for the phylogenetically affiliated strains was the diagnostic features for the current tentative identification of this genus.
  • Mami Tanaka, Shoko Endo, Fumihito Kotake, Nurhidayu Al-Saari, A. K. M. Rohul Amin, Gao Feng, Sayaka Mino, Hidetaka Doi, Yoshitoshi Ogura, Tetsuya Hayashi, Wataru Suda, Masahira Hattori, Isao Yumoto, Toko Sawabe, Tomoo Sawabe, Toshiyoshi Araki
    PLOS ONE 12 (6) e0180053  1932-6203 2017/06 [Refereed][Not invited]
     
    A novel strain Vibrio aphrogenes sp. nov. strain CA-1004(T) isolated from the surface of seaweed collected on the coast of Mie Prefecture in 1994 [1] was characterized using poly phasic taxonomy including multilocus sequence analysis (MLSA) and a genome based comparison. Both phylogenetic analyses on the basis of 16S rRNA gene sequences and MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the strain could be placed in the Rumoiensis Glade in the genus Vibrio. Sequence similarities of the 16S rRNA gene and the multilocus genes against the Rumoiensis Glade members, V. rumoiensis, V. algivorus, V. casei, and V. litoralis, were low enough to propose V. aphrogenes sp. nov. strain CA-1004(T) as a separate species. The experimental DNA-DNA hybridization data also revealed that the strain CA-1004(T) was separate from four known Rumoiensis Glade species. The G+C content of the V. aphrogenes strain was determined as 42.1% based on the genome sequence. Major traits of the strain were non motile, halophilic, fermentative, alginolytic, and gas production. A total of 27 traits (motility, growth temperature range, amylase, alginase and lipase productions, and assimilation of 19 carbon compounds) distinguished the strain from the other species in the Rumoiensis Glade. The name V. aphrogenes sp. nov. is proposed for this species in the Rumoiensis Glade, with CA-1004(T) as the type strain (JCM 31643(T) = DSM 103759(T)).
  • Tomoo Sawabe, James D Oliver
    International journal of systematic and evolutionary microbiology 67 (3) 759 - 760 2017/04 [Refereed][Not invited]
  • Sayaka Mino, Satoshi Nakagawa, Hiroko Makita, Tomohiro Toki, Junichi Miyazaki, Stefan M Sievert, Martin F Polz, Fumio Inagaki, Anne Godfroy, Shingo Kato, Hiromi Watanabe, Takuro Nunoura, Koichi Nakamura, Hiroyuki Imachi, Tomo-O Watsuji, Shigeaki Kojima, Ken Takai, Tomoo Sawabe
    The ISME journal 11 (4) 909 - 919 1751-7362 2017/04 [Refereed][Not invited]
     
    Rich animal and microbial communities have been found at deep-sea hydrothermal vents. Although the biogeography of vent macrofauna is well understood, the corresponding knowledge about vent microbial biogeography is lacking. Here, we apply the multilocus sequence analysis (MLSA) to assess the genetic variation of 109 Sulfurimonas strains with ⩾98% 16S rRNA gene sequence similarity, which were isolated from four different geographical regions (Okinawa Trough (OT), Mariana Volcanic Arc and Trough (MVAT), Central Indian Ridge (CIR) and Mid-Atlantic Ridge (MAR)). Sequence typing based on 11 protein-coding genes revealed high genetic variation, including some allele types that are widespread within regions, resulting in 102 nucleotide sequence types (STs). This genetic variation was predominantly due to mutation rather than recombination. Phylogenetic analysis of the 11 concatenated genes showed a clear geographical isolation corresponding to the hydrothermal regions they originated from, suggesting limited dispersal. Genetic differentiation among Sulfurimonas populations was primarily influenced by geographical distance rather than gas composition of vent fluid or habitat, although in situ environmental conditions of each microhabitat could not be examined. Nevertheless, Sulfurimonas may possess a higher dispersal capability compared with deep-sea hydrothermal vent thermophiles. This is the first report on MLSA of deep-sea hydrothermal vent Epsilonproteobacteria, which is indicative of allopatric speciation.
  • Mami Tanaka, Shoko Endo, Fumihito Kotake, Nurhidayu Al-Saari, A K M Rohul Amin, Gao Feng, Sayaka Mino, Hidetaka Doi, Yoshitoshi Ogura, Tetsuya Hayashi, Wataru Suda, Masahira Hattori, Isao Yumoto, Toko Sawabe, Tomoo Sawabe, Toshiyoshi Araki
    PloS one 12 (12) e0189555  1932-6203 2017 [Refereed][Not invited]
     
    [This corrects the article DOI: 10.1371/journal.pone.0180053.].
  • Feng Gao, Nurhidayu Al-Saari, A K M Rohul Amin, Kazumichi Sato, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Paulo Iiboshi Hargreaves, Pedro Milet Meirelles, Fabiano L Thompson, Cristiane Thompson, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
    Systematic and applied microbiology 39 (5) 330 - 5 0723-2020 2016/07 [Refereed][Not invited]
     
    Five novel strains showing non-motile, alginolytic, halophilic and fermentative features were isolated from seawater samples off Okinawa in coral reef areas. These strains were characterized by an advanced polyphasic taxonomy including genome based taxonomy using multilocus sequence analysis (MLSA) and in silico DNA-DNA similarity (in silico DDH). Phylogenetic analyses on the basis of 16S rRNA gene sequences revealed that the isolates could be assigned to the genus Vibrio, however they were not allocated into any distinct cluster with known Vibrionaceae species. MLSA based on eight protein-coding genes (gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA) showed the vibrios formed an outskirt branch of Halioticoli clade. The experimental DNA-DNA hybridization data revealed that the five strains were in the range of being defined as conspecific but separate from nine Halioticoli clade species. The G+C contents of the Vibrio ishigakensis strains were 47.3-49.1mol%. Both Amino Acid Identity and Average Nucleotide Identity of the strain C1(T) against Vibrio ezurae HDS1-1(T), Vibrio gallicus HT2-1(T), Vibrio halioticoli IAM 14596(T), Vibrio neonatus HDD3-1(T) and Vibrio superstes G3-29(T) showed less than 95% similarity. The genome-based taxonomic approach by means of in silico DDH values also supports the V. ishigakensis strains being distinct from the other known Halioticoli clade species. Sixteen traits (growth temperature range, DNase and lipase production, indole production, and assimilation of 10 carbon compounds) distinguished these strains from Halioticoli clade species. The names V. ishigakensis sp. nov. is proposed for the species of Halioticoli clade, with C1(T) as the type strain (JCM 19231(T)=LMG 28703(T)).
  • Toko Sawabe, Wataru Suda, Kenshiro Ohshima, Masahira Hattori, Tomoo Sawabe
    JOURNAL OF INFECTION AND PUBLIC HEALTH 9 (3) 362 - 365 1876-0341 2016/05 [Refereed][Not invited]
     
    Insufficient chloric sterilization of children's paddling pool waters increases the risk of diarrheal illness. Therefore, we investigated the micro biota changes after children use pools. First, we applied 16S rRNA gene-based metagenome analysis to understand the dynamics of microbiota in pool water, especially with respect to the bio-contamination by potential pathogens. Proteobacteria were major taxa detected in every pool water sample after children spent time in the pool. In more detail, Gammaproteobacteria comprised the dominant class, which was followed by Betaproteobacteria. Five phyla, Bacteroidetes, Firmicutes, Actinobacteria and Deinococcus-Thermus phyla were minor groups. The pool water microbiota are likely to be a consortium of intestinal and skin microbiota from humans. Interestingly, the ratio of Gammaproteobacteria and Betaproteobacteria differed according to the age of the children who used the pool, which means the pool water was additionally contaminated by soil microbiota as a result of the children's behavior. Furthermore, potential pathogens, such as Campylobacter spp., Comamonas testosteroni and Burkholderia pseudomallei, were also found. Considering the standard plate counts, the abundances of these human pathogens are unlikely to be a sufficiently infectious dose. We suggest the importance of sanitary measures in paddling pool waters to reduce bio-contamination from both humans and the environment. (C) 2015 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Limited. All rights reserved.
  • Yohei Yamazaki, Pedro Milet Meirelles, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Fabiano L. Thompson, Yuichi Sakai, Toko Sawabe, Tomoo Sawabe
    SCIENTIFIC REPORTS 6 21631 - 21631 2045-2322 2016/02 [Refereed][Not invited]
     
    Gut microbiome shapes various aspects of a host's physiology, but these functions in aquatic animal hosts have yet to be fully investigated. The sea cucumber Apostichopus japonicus Selenka is one such example. The large growth gap in their body size has delayed the development of intensive aquaculture, nevertheless the species is in urgent need of conservation. To understand possible contributions of the gut microbiome to its host's growth, individual fecal microbiome comparisons were performed. High-throughput 16S rRNA sequencing revealed significantly different microbiota in larger and smaller individuals; Rhodobacterales in particular was the most significantly abundant bacterial group in the larger specimens. Further shotgun metagenome of representative samples revealed a significant abundance of microbiome retaining polyhydroxybutyrate (PHB) metabolism genes in the largest individual. The PHB metabolism reads were potentially derived from Rhodobacterales. These results imply a possible link between microbial PHB producers and potential growth promotion in Deuterostomia marine invertebrates.
  • A K M R Amin, Gao Feng, Nurhidayu Al-Saari, Pedro M Meirelles, Yohei Yamazaki, Sayaka Mino, Fabiano L Thompson, Toko Sawabe, Tomoo Sawabe
    Frontiers in microbiology 7 1185 - 1185 2016 [Refereed][Not invited]
     
    Coral reefs perform a major role in regulating marine biodiversity and serve as hotspot for highly dynamic and diverse microbiomes as holobionts. Corals around Ishigaki, however, are at risk due to tremendous stressors including elevation of seawater temperature, eutrophication and so on. However, no information is currently available on how Vibrio diversity fluctuates spatially and temporally due to environmental determinants in Ishigaki coral reef ecosystems. The aim of this study is to elucidate spatiotemporal Vibrio diversity dynamic at both community and population levels and to assess the environmental drivers correlated to Vibrio abundance and diversity. The Vibrio community identified based on pyrH gene phylogeny of 685 isolates from seawater directly connecting to Ishigaki coral holobionts consisted of 22 known and 12 potential novel Vibrionaceae species. The most prominent species were V. hyugaensis, V. owensii and V. harveyi followed by V. maritimus/V. variabillis, V. campbellii, V. coralliilyticus, and Photobacterium rosenbergii. The Vibrio community fluctuations, assessed by PCoA with UniFrac distance and clustering with Euclidiean distance were varied less not only by year but also by site. Interestingly, significant positive correlation was observed between rising seawater temperature and the abundance of V. campbellii (r = 0.62; P < 0.05) whereas the opposite was observed for V. owensii (r = -0.58; P < 0.05) and the C6 group of V. hyugaensis (r = -0.62; P < 0.05). AdaptML-based microhabitat differentiation revealed that V. harveyi, V. campbellii, P. rosenbergii, and V. coralliilyticus populations were less-ecologically distinctive whereas V. astriarenae and V. ishigakensis were ecologically diverse. This knowledge could be important clue for the future actions of coral conservation.
  • So Fujiyoshi, Hiroaki Tateno, Tomoo Watsuji, Hideyuki Yamaguchi, Daisuke Fukushima, Sayaka Mino, Makoto Sugimura, Tomoo Sawabe, Ken Takai, Shigeki Sawayama, Satoshi Nakagawa
    MICROBES AND ENVIRONMENTS 30 (3) 228 - 234 1342-6311 2015/09 [Refereed][Not invited]
     
    In deep-sea hydrothermal environments, most invertebrates associate with dense populations of symbiotic microorganisms in order to obtain nutrition. The molecular interactions between deep-sea animals and environmental microbes, including their symbionts, have not yet been elucidated in detail. Hemagglutinins/lectins, which are carbohydrate-binding proteins, have recently been reported to play important roles in a wide array of biological processes, including the recognition and control of non-self materials. We herein assessed hemagglutination activity in the serum of a deep-sea vent endemic crab, Shinkaia crosnieri, which harbors chemosynthetic epibionts on its plumose setae. Horse and rabbit erythrocytes were agglutinated using this serum (opt. pH 7.5 and opt. temperature 15 degrees C). Agglutinating activity was inhibited by eight kinds of sugars and several divalent cations, did not require any divalent metal ions, and remained detectable even after heating the serum at 100 degrees C for 30 min. By using fluorescently labeled serum, we demonstrated that deep-sea crab serum components bound to the epibionts even in the presence of sugars. This study represents the first immunological assessment of a deep-sea vent endemic crab and demonstrated the possibility of a non-lectin-mediated symbiont-host interaction.
  • Yuta Matsumura, Hidayu Al-saari, Sayaka Mino, Satoshi Nakagawa, Fumito Maruyama, Yoshitoshi Ogura, Tetsuya Hayashi, Ken Kurokawa, Toko Sawabe, Tomoo Sawabe
    INTERNATIONAL JOURNAL OF HYDROGEN ENERGY 40 (30) 9137 - 9146 0360-3199 2015/08 [Refereed][Not invited]
     
    Vibrio tritonius strain AM2 shows high-yield hydrogen production even under saline conditions (1.7 mol hydrogen/mol mannitol). However, the molecular mechanism of efficient hydrogen production has never been studied in the genus Vibrio. The aim of this study is to identify the genes responsible for hydrogen evolution in V. tritonius and the gene expression pattern. Complete genome analysis revealed an existence of a single 24-kb gene cluster containing 21 genes, which are essential for the formation of an energy-conserving formate hydrogen lyase (FHL) complex, to be more specific the vibrio FHL was structurally rather similar to the hyf (hydrogenase four) gene cluster found in Escherichia coli. Moreover, genes responsible to the formate dehydrogenase (FDH-H), fh1A-type transcriptional activator and hydrogenase maturation proteins (hyp) were also located downstream of the vibrio hyf gene cluster to form a "super-gene-set" of the FHL complex gene cluster. The vibrio gene for the large subunit of the FHL complex hyfG possessed typical motifs coordinating the [NiFe] center at the active site, which indicates the V. tritonius hydrogenase was able to be classified as a [NiFe]-hydrogenase. Furthermore, transcriptional analysis revealed that the expression level of the hyfG gene slightly increased upon pH decrease, which correlates to the pH-dependent hydrogen production of V. tritonius. Therefore, we can conclude that the FHL complex of V. tritonius is key enzyme in the hydrogen production under acidic conditions. Moreover hyfABCDEFGHIJ-hycI-hydN-fdhF and hyp genes could be co-transcribed respectively during the efficient hydrogen production state. Details of the gene cluster are discussed here. Copyright (C) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.
  • Nurhidayu Al-Saari, Feng Gao, Amin A. K. M. Rohul, Kazumichi Sato, Keisuke Sato, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Pedro M. Meirelles, Fabiano L. Thompson, Cristiane Thompson, Gilberto M. A. Filho, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
    PLOS ONE 10 (8) 1932-6203 2015/08 [Refereed][Not invited]
     
    Advances in genomic microbial taxonomy have opened the way to create a more universal and transparent concept of species but is still in a transitional stage towards becoming a defining robust criteria for describing new microbial species with minimum features obtained using both genome and classical polyphasic taxonomies. Here we performed advanced microbial taxonomies combined with both genome-based and classical approaches for new agarolytic vibrio isolates to describe not only a novel Vibrio species but also a member of a new Vibrio clade. Two novel vibrio strains (Vibrio astriarenae sp. nov. C7(T) and C20) showing agarolytic, halophilic and fermentative metabolic activity were isolated from a seawater sample collected in a coral reef in Okinawa. Intraspecific similarities of the isolates were identical in both sequences on the 16S rRNA and pyrH genes, but the closest relatives on the molecular phylogenetic trees on the basis of 16S rRNA and pyrH gene sequences were V. hangzhouensis JCM 15146(T) (97.8% similarity) and V. agarivorans CECT 5085(T) (97.3% similarity), respectively. Further multilocus sequence analysis (MLSA) on the basis of 8 protein coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) obtained by the genome sequences clearly showed the V. astriarenae strain C7(T) and C20 formed a distinct new clade protruded next to V. agarivorans CECT 5085(T). The singleton V. agarivorans has never been included in previous MLSA of Vibrionaceae due to the lack of some gene sequences. Now the gene sequences are completed and analysis of 100 taxa in total provided a clear picture describing the association of V. agarivorans into pre-existing concatenated network tree and concluded its relationship to our vibrio strains. Experimental DNA-DNA hybridization (DDH) data showed that the strains C7(T) and C20 were conspecific but were separated from all of the other Vibrio species related on the basis of both 16S rRNA and pyrH gene phylogenies (e.g., V. agarivorans CECT 5085(T), V. hangzhouensis JCM 15146(T) V. maritimus LMG 25439(T), and V. variabilis LMG 25438(T)). In silico DDH data also supported the genomic relationship. The strains C7(T) also had less than 95% average amino acid identity (AAI) and average nucleotide identity (ANI) towards V. maritimus C210, V. variabilis C206, and V. mediterranei AK1(T), V. brasiliensis LMG 20546(T), V. orientalis ATCC 33934(T), and V. sinaloensis DSM 21326. The name Vibrio astriarenae sp. nov. is proposed with C7 as the type strains. Both V. agarivorans CECT 5058(T) and V. astriarenae C7(T) are members of the newest clade of Vibrionaceae named Agarivorans.
  • Pedro M. Meirelles, Gilberto M. Amado-Filho, Guilherme H. Pereira-Filho, Hudson T. Pinheiro, Rodrigo L. de Moura, Jean-Christophe Joyeux, Eric F. Mazzei, Alex C. Bastos, Robert A. Edwards, Elizabeth Dinsdale, Rodolfo Paranhos, Eidy O. Santos, Tetsuya Iida, Kazuyoshi Gotoh, Shota Nakamura, Tomoo Sawabe, Carlos E. Rezende, Luiz M. R. Gadelha, Ronaldo B. Francini-Filho, Cristiane Thompson, Fabiano L. Thompson
    PLOS ONE 10 (6) 1932-6203 2015/06 [Refereed][Not invited]
     
    Seamounts are considered important sources of biodiversity and minerals. However, their biodiversity and health status are not well understood; therefore, potential conservation problems are unknown. The mesophotic reefs of the Vitoria-Trindade Seamount Chain (VTC) were investigated via benthic community and fish surveys, metagenomic and water chemistry analyses, and water microbial abundance estimations. The VTC is a mosaic of reef systems and includes fleshy algae dominated rhodolith beds, crustose coralline algae (CCA) reefs, and turf algae dominated rocky reefs of varying health levels. Macro-carnivores and larger fish presented higher biomass at the CCA reefs (4.4 kg per frame) than in the rhodolith beds and rocky reefs (0.0 to 0.1 kg per frame). A larger number of metagenomic sequences identified as primary producers (e.g., Chlorophyta and Streptophyta) were found at the CCA reefs. However, the rocky reefs contained more diseased corals (>90%) than the CCA reefs (similar to 40%) and rhodolith beds (similar to 10%). Metagenomic analyses indicated a heterotrophic and fast-growing microbiome in rocky reef corals that may possibly lead to unhealthy conditions possibly enhanced by environmental features (e.g. light stress and high loads of labile dissolved organic carbon). VTC mounts represent important hotspots of biodiversity that deserve further conservation actions.
  • Cristiane C. Thompson, Gilda R. Amaral, Mariana Campeao, Robert A. Edwards, Martin F. Polz, Bas E. Dutilh, David W. Ussery, Tomoo Sawabe, Jean Swings, Fabiano L. Thompson
    ARCHIVES OF MICROBIOLOGY 197 (3) 359 - 370 0302-8933 2015/04 [Refereed][Not invited]
     
    Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.
  • Naoki Takatani, Tomoo Sawabe, Takashi Maoka, Kazuo Miyashita, Masashi Hosokawa
    BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 4 (2) 174 - 179 1878-8181 2015/04 [Refereed][Not invited]
     
    Gillisia lirtinaea strain DSM 15749 (=R-8282(T), =LMG21470,=CIP108418) is a Gram-negative, strictly aerobic, psychrophilic, and non-photosynthetic bacterium that belongs to the family Flavobacteriaceae, which was isolated from a microbial mat in Lake Fryxell, Antarctica (Van. Trapp en eI. al., 2004). The bacteriurn shows yellow colored colony, but the cat otenoid composition has never been determined yet. In this study, we elucidated the structure of carotenoids produced by the strain DSM 15749. G. lirtinaea strain DSM 15749 synthesized a novel monocyclic-type carotenoid, 3 ''-hydroxy-2'-isopentenylsaproxanthin ((3R, 2'S')-2 '-(3-hydroxy-3-methylbutyl)-3 '', 4'-didehydro-1', 2'-dihydro-beta, Psi-carotene-3, 1'-diol), as well as (3R, TR)-zeaxanthin. Furthermore, another monocyclic carotenoid, 2'-isopentenylsaproxanthin, was also detected in the strain DSM 15749. 3 ''-Hydroxy-2'-isopentenylsaproxanthin is "Chimera'like unique structures, in that one end group forms the same structure of zeaxanthin, and the other end group is the same as bacterioruberin which is produced by several extremophilic bacteria and archaea. This structure involved the hydroxy derivative of 2'-isopentenylsaproxanthin. The present study is the First report about the carotenoids produced by the genus Gillisto, of the family Flavobacteriaceae. (C) 2015 Elsevier Ltd. All rights reserved.
  • Nelson Alves Junior, Pedro Milet Meirelles, Eidy de Oliveira Santos, Bas Dutilh, Genivaldo G. Z. Silva, Rodolfo Paranhos, Anderson S. Cabral, Carlos Rezende, Tetsuya Iida, Rodrigo L. de Moura, Ricardo Henrique Kruger, Renato C. Pereira, Rogerio Valle, Tomoo Sawabe, Cristiane Thompson, Fabiano Thompson
    ARCHIVES OF MICROBIOLOGY 197 (2) 165 - 179 0302-8933 2015/03 [Refereed][Not invited]
     
    Microbial oceanography studies have demonstrated the central role of microbes in functioning and nutrient cycling of the global ocean. Most of these former studies including at Southwestern Atlantic Ocean (SAO) focused on surface seawater and benthic organisms (e.g., coral reefs and sponges). This is the first metagenomic study of the SAO. The SAO harbors a great microbial diversity and marine life (e.g., coral reefs and rhodolith beds). The aim of this study was to characterize the microbial community diversity of the SAO along the depth continuum and different water masses by means of metagenomic, physical-chemical and biological analyses. The microbial community abundance and diversity appear to be strongly influenced by the temperature, dissolved organic carbon, and depth, and three groups were defined [1. surface waters; 2. sub-superficial chlorophyll maximum (SCM) (48-82 m) and 3. deep waters (236-1,200 m)] according to the microbial composition. The microbial communities of deep water masses [South Atlantic Central water, Antarctic Intermediate water and Upper Circumpolar Deep water] are highly similar. Of the 421,418 predicted genes for SAO metagenomes, 36.7 % had no homologous hits against 17,451,486 sequences from the North Atlantic, South Atlantic, North Pacific, South Pacific and Indian Oceans. From these unique genes from the SAO, only 6.64 % had hits against the NCBI non-redundant protein database. SAO microbial communities share genes with the global ocean in at least 70 cellular functions; however, more than a third of predicted SAO genes represent a unique gene pool in global ocean. This study was the first attempt to characterize the taxonomic and functional community diversity of different water masses at SAO and compare it with the microbial community diversity of the global ocean, and SAO had a significant portion of endemic gene diversity. Microbial communities of deep water masses (236-1,200 m) are highly similar, suggesting that these water masses have very similar microbiological attributes, despite the common knowledge that water masses determine prokaryotic community and are barriers to microbial dispersal. The present study also shows that SCM is a clearly differentiated layer within Tropical waters with higher abundance of phototrophic microbes and microbial diversity.
  • Thiago Bruce, Astria D. Ferrão-Gonzales, Yutaka Nakashimada, Yuta Matsumura, Fabiano Thompson, Tomoo Sawabe
    Springer Handbook of Marine Biotechnology 1163 - 1180 2015/01/01 [Refereed][Not invited]
     
    Biofuels represent a viable alternative to the use of fossil fuels. They contribute to the reduction of greenhouse gas emission and do not compete with agricultural land. However, biofuels are not yet capable of replacing the current energy matrix based on fossil fuels because they cannot compete with standard fuels such as diesel and gasoline. Therefore, innovation is necessary to promote technical, economical, and environmental viability of biofuels. For this purpose, the marine realm is a promising source of bioresources to promote innovation in biofuel production. The marine biomass can be converted into biofuels such as biodiesel, bioethanol, and biogases (i. e, methane and hydrogen) through microbial activity. Microbial diversity plays a fundamental role in marine ecosystems by recycling of organic matter, which is a reflection of the vast genetic diversity associated to the marine microbial species available for biotechnological exploitation. The present study provides an overview of the importance of microbial fuels and presents innovative findings which can be applied to the production of biofuels in the near future.
  • Tomoo Sawabe, Yoshitoshi Ogura, Yuta Matsumura, Gao Feng, A. K. M. Rohul Amin, Sayaka Mino, Satoshi Nakagawa, Toko Sawabe, Ramesh Kumar, Yohei Fukui, Masataka Satomi, Ryoji Matsushima, Fabiano L. Thompson, Bruno Gomez Gil, Richard Christen, Fumito Maruyama, Ken Kurokawa, Tetsuya Hayashi
    FRONTIERS IN MICROBIOLOGY 5 583  1664-302X 2014/11 [Refereed][Not invited]
  • Tomoo Sawabe, Masataka Satomi, Koji Yamazaki, Shinichi Kawamoto, Masahira Hattori, Wataru Suda, Kageyasu Takanashi, Takashi Sasahira, Takashi Kuda, Hajime Takahashi, Bon Kimura, Masashi Ohtsubo, Kenji Isshiki
    NIPPON SUISAN GAKKAISHI 日本水産学会 80 (6) 1002 - 1008 0021-5392 2014/11 [Refereed][Not invited]
  • Hooi Jun Ng, Mario Lopez-Perez, Hayden K. Webb, Daniela Gomez, Tomoo Sawabe, Jason Ryan, Mikhail Vyssotski, Chantal Bizet, Francois Malherbe, Valery V. Mikhailov, Russell J. Crawford, Elena P. Ivanova
    PLOS ONE 9 (9) 1932-6203 2014/09 [Refereed][Not invited]
     
    Two non-pigmented, motile, Gram-negative marine bacteria designated R9SW1(T) and A3d10(T) were isolated from sea water samples collected from Chazhma Bay, Gulf of Peter the Great, Sea of Japan, Pacific Ocean, Russia and St. Kilda Beach, Port Phillip Bay, the Tasman Sea, Pacific Ocean, respectively. Both organisms were found to grow between 4 degrees C and 40 degrees C, between pH 6 to 9, and are moderately halophilic, tolerating up to 20% (w/v) NaCl. Both strains were found to be able to degrade Tween 40 and 80, but only strain R9SW1(T) was found to be able to degrade starch. The major fatty acids were characteristic for the genus Marinobacter including C-16:0, C-16:1 omega 7c, C-18:1 omega 9c and C-18:1 omega 7c. The G+C content of the DNA for strains R9SW1(T) and A3d10(T) were determined to be 57.1 mol% and 57.6 mol%, respectively. The two new strains share 97.6% of their 16S rRNA gene sequences, with 82.3% similarity in the average nucleotide identity (ANI), 19.8% similarity in the in silico genome-to-genome distance (GGD), 68.1% similarity in the average amino acid identity (AAI) of all conserved protein-coding genes, and 31 of the Karlin's genomic signature dissimilarity. A phylogenetic analysis showed that R9SW1(T) clusters with M. algicola DG893(T) sharing 99.40%, and A3d10(T) clusters with M. sediminum R65(T) sharing 99.53% of 16S rRNA gene sequence similarities. The results of the genomic and polyphasic taxonomic study, including genomic, genetic, phenotypic, chemotaxonomic and phylogenetic analyses based on the 16S rRNA, gyrB and rpoD gene sequence similarities, the analysis of the protein profiles generated using MALDI-TOF mass spectrometry, and DNA-DNA relatedness data, indicated that strains R9SW1(T) and A3d10(T) represent two novel species of the genus Marinobacter. The names Marinobacter salarius sp. nov., with the type strain R9SW1(T) (= LMG 27497(T) = JCM 19399(T) = CIP 110588(T) = KMM 7502(T)) and Marinobacter similis sp. nov., with the type strain A3d10(T) (= JCM 19398(T) = CIP 110589(T) = KMM 7501(T)), are proposed.
  • Yuta Matsumura, Kazumichi Sato, Nurhidayu Al-Saari, Satoshi Nakagawa, Tomoo Sawabe
    International Journal of Hydrogen Energy 39 (14) 7270 - 7277 0360-3199 2014/05/05 [Refereed][Not invited]
     
    To achieve more stable bio-hydrogen (bioH2) production from non-food feedstocks, stable feedstock preparations of marine biomass and an efficient bioH2 system using marine bacteria under saline conditions are two important key technologies that needed to be developed. Vibrio tritonius strain AM2, which was isolated from the gut of a marine invertebrate, was cultured under various conditions in marine broth (at initial 2.25% (w/v) NaCl) supplemented with mannitol, a seaweed carbohydrate, to evaluate its hydrogen production. The maximum molar yield of bioH2 was recorded as 1.7 mol H2/mol mannitol at pH 6 and 37 °C. The mannitol-grown cells had higher yields of bioH2 than the glucose-grown cells in the pH range 5.5-7.5. Compared to glucose, mannitol might be a better substrate for bioH 2 production using strain AM2. Fermentation product profiling revealed that strain AM2 might be utilising the formate-hydrogen pathway for bioH2 production. Furthermore, strain AM2 was able to produce hydrogen from powdered brown macroalgae containing 31.1% dry weight of mannitol. The molar yield of hydrogen reached 1.6 mol H2/mol mannitol contained in the seaweed feedstock. In conclusion, strain AM2 has the ability to produce hydrogen from mannitol with high yields even under saline conditions. Copyright © 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.
  • N. Rameshkumar, Ramya Krishnan, Elke Lang, Yuta Matsumura, Toko Sawabe, Tomoo Sawabe
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 64 545 - 550 1466-5026 2014/02 [Refereed][Not invited]
     
    A Gram-stain-negative, strictly aerobic, slightly halophilic, non-motile and rod-shaped bacterial strain, designated P2E16(T), was isolated from mangrove (Avicennia marina) rhizosphere, collected at Devipattinam mangroves, Tamil Nadu, India. Strain P2E16(T) grew optimally at pH 7.0-8.0, at 25-28 degrees C and in the presence of 2-3% (w/v) NaCl. 16S rRNA gene analysis showed that strain P2E16(T) was phylogenetically closely related to the genus Zunongwangia, with Zunongwangia pro funda SM-A87(T) as the closest related type strain (98.2 % 16S rRNA gene sequence similarity) and less than 93% 16S rRNA gene sequence similarity to all other members of the family Flavobacteriaceae. Strain P2E16(T) contained MK-6 as the major respiratory quinone,phosphatidylethanolamine as the predominant polar lipid and iso-C-15:0 (17.8%), iso-C-17:0 3-OH (15.1 %), C-15:0 (12.8%), iso-C-17:1 omega 9c (9.8%), iso-C-15:1 G (9.0%), and summed feature 3 (comprising C-16:1 omega 7c and/or iso-C-15:0 2-OH; 7.1 %) as the major fatty acids. The DNA G+C content was 34.3 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness and low DNA-DNA relatedness demonstrated that strain P2E16(T) was distinct from the type strain of Zunongwangia pro funda. On the basis of these presented data, strain P2E16(T) is considered to represent a novel species of the genus Zunongwangia, for which the name Zunongwangia mangrovi sp. nov. is proposed. The type strain is P2E16(T) (=DSM 24499(T)=LMG 26237(T)=KCTC 23496(T)). An emended description of the genus Zunongwangia is also provided.
  • Satoshi Nakagawa, Shigeru Shimamura, Yoshihiro Takaki, Yohey Suzuki, Shun-ichi Murakami, Tamaki Watanabe, So Fujiyoshi, Sayaka Mino, Tomoo Sawabe, Takahiro Maeda, Hiroko Makita, Suguru Nemoto, Shin-Ichiro Nishimura, Hiromi Watanabe, Tomo-O Watsuji, Ken Takai
    ISME JOURNAL 8 (1) 40 - 51 1751-7362 2014/01 [Refereed][Not invited]
     
    Deep-sea vents harbor dense populations of various animals that have their specific symbiotic bacteria. Scaly-foot gastropods, which are snails with mineralized scales covering the sides of its foot, have a gammaproteobacterial endosymbiont in their enlarged esophageal glands and diverse epibionts on the surface of their scales. In this study, we report the complete genome sequencing of gammaproteobacterial endosymbiont. The endosymbiont genome displays features consistent with ongoing genome reduction such as large proportions of pseudogenes and insertion elements. The genome encodes functions commonly found in deep-sea vent chemoautotrophs such as sulfur oxidation and carbon fixation. Stable carbon isotope (C-13)-labeling experiments confirmed the endosymbiont chemoautotrophy. The genome also includes an intact hydrogenase gene cluster that potentially has been horizontally transferred from phylogenetically distant bacteria. Notable findings include the presence and transcription of genes for flagellar assembly, through which proteins are potentially exported from bacterium to the host. Symbionts of snail individuals exhibited extreme genetic homogeneity, showing only two synonymous changes in 19 different genes (13 810 positions in total) determined for 32 individual gastropods collected from a single colony at one time. The extremely low genetic individuality in endosymbionts probably reflects that the stringent symbiont selection by host prevents the random genetic drift in the small population of horizontally transmitted symbiont. This study is the first complete genome analysis of gastropod endosymbiont and offers an opportunity to study genome evolution in a recently evolved endosymbiont.
  • Giselle S. Cavalcanti, Gustavo B. Gregoracci, Eidy O. dos Santos, Cynthia B. Silveira, Pedro M. Meirelles, Leila Longo, Kazuyoshi Gotoh, Shota Nakamura, Tetsuya Iida, Tomoo Sawabe, Carlos E. Rezende, Ronaldo B. Francini-Filho, Rodrigo L. Moura, Gilberto M. Amado-Filho, Fabiano L. Thompson
    ISME JOURNAL 8 (1) 52 - 62 1751-7362 2014/01 [Refereed][Not invited]
     
    Rhodoliths are free-living coralline algae (Rhodophyta, Corallinales) that are ecologically important for the functioning of marine environments. They form extensive beds distributed worldwide, providing a habitat and nursery for benthic organisms and space for fisheries, and are an important source of calcium carbonate. The Abrolhos Bank, off eastern Brazil, harbors the world's largest continuous rhodolith bed (of similar to 21 000 km(2)) and has one of the largest marine CaCO3 deposits (producing 25 megatons of CaCO3 per year). Nevertheless, there is a lack of information about the microbial diversity, photosynthetic potential and ecological interactions within the rhodolith holobiont. Herein, we performed an ecophysiologic and metagenomic analysis of the Abrolhos rhodoliths to understand their microbial composition and functional components. Rhodoliths contained a specific microbiome that displayed a significant enrichment in aerobic ammonia-oxidizing betaproteobacteria and dissimilative sulfate-reducing deltaproteobacteria. We also observed a significant contribution of bacterial guilds (that is, photolithoautotrophs, anaerobic heterotrophs, sulfide oxidizers, anoxygenic phototrophs and methanogens) in the rhodolith metagenome, suggested to have important roles in biomineralization. The increased hits in aromatic compounds, fatty acid and secondary metabolism subsystems hint at an important chemically mediated interaction in which a functional job partition among eukaryal, archaeal and bacterial groups allows the rhodolith holobiont to thrive in the global ocean. High rates of photosynthesis were measured for Abrolhos rhodoliths (52.16 mu mol carbon m(-2)s(-1)), allowing the entire Abrolhos rhodolith bed to produce 5.65 x 10(5) tons C per day. This estimate illustrates the great importance of the Abrolhos rhodolith beds for dissolved carbon production in the South Atlantic Ocean.
  • SAWABE TOMOO, SATOMI MASATAKA, YAMAZAKI KOJI
    NSUGAF The Japanese Society of Fisheries Science 80 (6) 1002 - 1002 0021-5392 2014
  • Naoki Takatani, Masato Nakanishi, Pedro Meirelles, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Masashi Hosokawa, Kazuo Miyashita, Fabiano L. Thompson, Ako Niwa, Toko Sawabe, Tomoo Sawabe
    Genome Announcements 2 (6) 2169-8287 2014 [Refereed][Not invited]
     
    Here, we present the draft genome sequence of a novel carotenoid 2'-isopentenylsaproxanthin producer, Jejuia pallidilutea strain 11shimoA1, isolated from the surface of seaweed in Japan, and the ethyl methanesulfonate-induced pigmentation mutants. This genomic information will help to not only elucidate the 2'-isopentenylsaproxanthin biosynthetic pathway but also understand the evolution of flavobacteria.
  • Masato Nakanishi, Pedro Meirelles, Ryohei Suzuki, Naoki Takatani, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Masashi Hosokawa, Kazuo Miyashita, Fabiano L. Thompson, Ako Niwa, Toko Sawabe, Tomoo Sawabe
    Genome Announcements 2 (6) 2169-8287 2014 [Refereed][Not invited]
     
    Here, we present the draft genome sequences of six carotenoid producers affiliated with Nonlabens spp. isolated from marine environments in both the northern and southern parts of Japan. The genomic information will help to elucidate the function and evolution of carotenoid synthetic gene clusters not only in the genus Nonlabens but also in the family Flavobacteriaceae.
  • Nurhidayu Al-saari, Pedro Milet Meirelles, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Fabiano L. Thompson, Bruno Gomez-Gil, Toko Sawabe, Tomoo Sawabe
    Genome Announcements 2 (5) 2169-8287 2014 [Refereed][Not invited]
     
    Here, the draft genome sequences of two Vibrionaceae, Vibrio ponticus C121 and Photobacterium aphoticum C119, which were isolated from the coral reef vicinity in Okinawa, Japan, are reported. The genome provides further insight into the genomic plasticity, biocomplexity, and ecophysiology, including pathogenicity and evolution, of these genera.
  • Naoki Takatani, Masato Nakanishi, Pedro Meirelles, Sayaka Mino, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Masashi Hosokawa, Kazuo Miyashita, Fabiano L. Thompson, Ako Niwa, Toko Sawabe, Tomoo Sawabe
    Genome Announcements 2 (6) 2169-8287 2014 [Refereed][Not invited]
     
    Here, we present the draft genome sequences of a zeaxanthin-producing flavobacterium, Algibacter lectus strains SS8 and NR4, isolated from coastal sediment and rock surfaces in Hakodate, Japan, respectively. This genomic information represents the first Algibacter genome sequences, which will help us to elucidate the biology and evolution of Flavobacteriaceae bacteria.
  • Elena P. Ivanova, Hooi Jun Ng, Hayden K. Webb, Gao Feng, Kenshiro Oshima, Masahira Hattori, Moriya Ohkuma, Alexander F. Sergeev, Valery V. Mikhailov, Russell J. Crawford, Tomoo Sawabe
    Genome Announcements 2 (3) 2169-8287 2014 [Refereed][Not invited]
     
    Here, we present the draft genomes of Marinobacter similis A3d10T, a potential plastic biodegrader, and Marinobacter salarius R9SW1T, isolated from radioactive waters. This genomic information will contribute information on the genetic basis of the metabolic pathways for the degradation of both plastic and radionuclides.
  • N. Takatani, K. Nishida, T. Sawabe, T. Maoka, K. Miyashita, M. Hosokawa
    Applied Microbiology and Biotechnology 98 (15) 6633 - 6640 1432-0614 2014 [Refereed][Not invited]
     
    Carotenoids are a class of naturally occurring pigment, carrying out important biological functions in photosynthesis and involved in environmental responses including nutrition in organisms. Saproxanthin and myxol, which have monocyclic carotenoids with a γ-carotene skeleton, have been reported to show a stronger antioxidant activity than those with β-carotene and zeaxanthin. In this research, a yellow-orange bacterium of strain 11shimoA1 (JCM19538) was isolated from a seaweed collected at Nabeta Bay (Shizuoka, Japan). The 16S rRNA gene sequence of strain 11shimoA1 revealed more than 99.99 % similarity with those of Jejuia pallidilutea strains in the family Flavobacteriaceae. Strain 11shimoA1 synthesized two types of carotenoids. One of them was (3R, 3′R)-zeaxanthin with dicyclic structure and another was identified as (3R, 2′S)-2′-isopentenylsaproxanthin, a novel monocyclic carotenoid with pentenyl residue at C-2′ position of saproxanthin, using FAB-MS, 1H NMR, and CD analyses. Culturing strain 11shimoA1 in an alkaline medium at pH 9.2 resulted in a markedly increased in production of 2′-isopentenylsaproxanthin per dry cell weight, but a decreased in zeaxanthin production as compared to their respective production levels in medium with pH 7.0. These carotenoids are likely to play some roles in the adaptation of the bacterium to the environmental conditions. © 2014 Springer-Verlag.
  • Gizele D. Garcia, Gustavo B. Gregoracci, Eidy de O. Santos, Pedro M. Meirelles, Genivaldo G. Z. Silva, Rob Edwards, Tomoo Sawabe, Kazuyoshi Gotoh, Shota Nakamura, Tetsuya Iida, Rodrigo L. de Moura, Fabiano L. Thompson
    MICROBIAL ECOLOGY 65 (4) 1076 - 1086 0095-3628 2013/05 [Refereed][Not invited]
     
    Coral health is under threat throughout the world due to regional and global stressors. White plague disease (WP) is one of the most important threats affecting the major reef builder of the Abrolhos Bank in Brazil, the endemic coral Mussismilia braziliensis. We performed a metagenomic analysis of healthy and WP-affected M. braziliensis in order to determine the types of microbes associated with this coral species. We also optimized a protocol for DNA extraction from coral tissues. Our taxonomic analysis revealed Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, and Actinomycetes as the main groups in all healthy and WP-affected corals. Vibrionales, members of the Cytophaga-Flavobacterium-Bacteroides complex, Rickettsiales, and Neisseriales were more abundant in the WP-affected corals. Diseased corals also had more eukaryotic metagenomic sequences identified as Alveolata and Apicomplexa. Our results suggest that WP disease in M. braziliensis is caused by a polymicrobial consortium.
  • Sayaka Mino, Hiroko Makita, Tomohiro Toki, Junichi Miyazaki, Shingo Kato, Hiromi Watanabe, Hiroyuki Imachi, Tomo-o Watsuji, Takuro Nunoura, Shigeaki Kojima, Tomoo Sawabe, Ken Takai, Satoshi Nakagawa
    FRONTIERS IN MICROBIOLOGY 4 107  1664-302X 2013/04 [Refereed][Not invited]
     
    Deep-sea hydrothermal vent fields are areas on the seafloor with high biological productivity fueled by microbial chemosynthesis. Members of the Aquificales genus Persephone//a are obligately chemosynthetic bacteria, and appear to be key players in carbon, sulfur, and nitrogen cycles in high temperature habitats at deep-sea vents. Although this group of bacteria has cosmopolitan distribution in deep-sea hydrothermal ecosystem around the world, little is known about their population structure such as intraspecific genomic diversity, distribution pattern, and phenotypic diversity. We developed the multi-locus sequence analysis (MLSA) scheme for their genomic characterization. Sequence variation was determined in five housekeeping genes and one functional gene of 36 Persephone//a hydrogeraphrla strains originated from the Okinawa Trough and the South Mariana Trough (SNT). Although the strains share >98.7% similarities in 16S rRNA gene sequences, MLSA revealed 35 different sequence types (ST), indicating their extensive genomic diversity. A phylogenetic tree inferred from all concatenated gene sequences revealed the clustering of isolates according to the geographic origin. In addition, the phenotypic clustering pattern inferred from whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TO F/MS) analysis can be correlated to their MLSA clustering pattern. This study represents the first MLSA combined with phenotypic analysis indicative of allopatric speciation of deep-sea hydrothermal vent bacteria.
  • Masaki Enomoto, Satoshi Nakagawa, Tomoo Sawabe
    MICROBES AND ENVIRONMENTS 27 (3) 300 - 305 1342-6311 2012/09 [Refereed][Not invited]
     
    Marine invertebrates interact with various microorganisms ranging from pathogens to symbionts. One-to-one symbiosis between a single microbial species and a single host animal has served as a model for the study of host-microbe interactions. In addition, increasing attention has recently been focused on the complex symbiotic associations, e. g., associations between sponges and their symbionts, due to their biotechnological potential; however, relatively little is known about the microbial diversity associated with members of the phylum Echinodermata. Here, for the first time, we investigated microbial communities associated with a commercially important holothurian species, Apostichopus japonicus, using culture-dependent and -independent methods. Diverse and abundant heterotrophs, mostly Gammaproteobacteria members, were cultured semi-quantitatively. Using the cloning and sequencing technique, different microbial communities were found in different holothurian tissues. In the holothurian coelomic fluid, potentially metabolically active and phylogenetically unique members of Epsilonproteobacteria and Rickettsiales were discovered. This study suggests that coelomic fluids of marine invertebrates, at least those inhabiting intertidal areas where physical and chemical conditions fluctuate, provide microbes with unique and stable habitats.
  • Kentaro Niwa, Hideaki Aono, Tomoo Sawabe
    NIPPON SUISAN GAKKAISHI 78 (5) 951 - 957 0021-5392 2012/09 [Refereed][Not invited]
     
    A simple method using a syringe to collect digestive fluid from the gut of the disc abalone Haliotis discus discus is described. The activities of polysaccharide degrading enzymes and bacterial microflora were compared between the digestive fluid (DF) collected by using a syringe and the digestive diverticulum homogenate (DH) collected by the conventional dissection method. Specific activities of alginate lyase, cellulase and beta-1,4-mannanase of DF were higher than those of DH. Viable bacterial count of DF was lower (1.0 x 10(7) CFU/mL) than that of DH (2.1 x 10(8) CFU/g). Microflora analysis of isolates using the 16S rRNA gene indicated that DF and DH showed a similar microflora composition, in which vibrios including Vibrio halioticoli and V. ezurae were predominant. The present method may be useful to determine changes in the digestive activity and the gut microflora of abalone without sacrificing individuals.
  • Susumu Yoshizawa, Yasuhiro Tsuruya, Youhei Fukui, Tomoo Sawabe, Akira Yokota, Kazuhiro Kogure, Melissa Higgins, Jeremy Carson, Fabiano L. Thompson
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 62 1864 - 1870 1466-5026 2012/08 [Refereed][Not invited]
     
    Six isolates of a facultatively anaerobic bacterium were recovered in culture from marine invertebrates and vertebrates, including packhorse lobster (Jasus verreauxi, abalone (Haliotis sp.) and Atlantic salmon (Salmo salar), between 1 994 and 2002. The bacteria were Gramnegative, rod-shaped and motile by means of more than one polar flagellum, oxidase-positive, catalase-positive and able to grow in the presence of 0.5-8.0% NaCl (optimum 3.0-6.0 %) and at 10-37 degrees C (optimum 25-30 degrees C). On the basis of 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA) using five loci (2443 bp; gyrB, pyrH, ftsZ, mreB and gapA), the closest phylogenetic neighbours of strain TCFB 0772(T) were the type strains of Vibrio communis (99.8 and 94.6% similarity, respectively), Vibrio owensii (99.8 and 94.1 %), Vibrio natriegens (99.4 and 88.8 %), Vibrio parahaemolyticus (99.4 and 90.3 %), Vibrio rotiferianus (99.2 and 94.4%), Vibrio alginolyticus (99.1 and 89.3%) and Vibrio campbellii (99.1 and 92.3%). DNA DNA hybridization confirmed that the six isolates constitute a unique taxon that is distinct from other known species of Vibrio. In addition, this taxon can be readily differentiated phenotypically from other Vibrio species. The six isolates therefore represent a novel species, for which the name Vibrio jasicida sp. nov. is proposed; the novel species is represented by the type strain TCFB 0772(T) (=JCM 16453(T) =LMG 25398(T)) (DNA G+C content 45.9 mol%) and reference strains TCFB 1977 (=JCM 16454) and TCFB 1000 (=JCM 16455).
  • Hiroshi Izumi, Takuro Nunoura, Masayuki Miyazaki, Sayaka Mino, Tomohiro Toki, Ken Takai, Yoshihiko Sako, Tomoo Sawabe, Satoshi Nakagawa
    EXTREMOPHILES 16 (2) 245 - 253 1431-0651 2012/03 [Refereed][Not invited]
     
    A novel heterotrophic, thermophilic bacterium, designated strain AC55(T), was isolated from a deep-sea hydrothermal vent chimney at the Hatoma Knoll in the Okinawa Trough, Japan. Cells of strain AC55(T) were non-motile, long rods (2.0- to 6.8-mu m long and 0.3- to 0.6-mu m wide). The strain was an obligatory anaerobic heterotroph capable of fermentative growth on complex proteinaceous substances. Elemental sulfur was reduced to hydrogen sulfide but did not stimulate growth. Growth was observed between 37 and 60A degrees C (optimum 55A degrees C), pH 5.5 and 8.5 (optimum pH 6.6), and in the presence of 1.5-4.5% (w/v) NaCl (optimum 2.5%, w/v). Menaquinone-7 and -8 were the major respiratory quinones. The G + C content of the genomic DNA from strain AC55(T) was 51.6 mol%. The 16S rRNA gene sequence analysis revealed that strain AC55(T) was the first cultivated representative of Acidobacteria subdivision 10. Based on the physiological and phylogenetic features of the novel isolate, the genus name Thermotomaculum gen. nov. is proposed, with Thermotomaculum hydrothermale sp. nov. as the type species. The type strain is AC55(T) (=JCM 17643(T) = DSM 24660(T) = NBRC 107904(T)).
  • Kentaro Niwa, Hideaki Aono, Tomoo Sawabe
    Nippon Suisan Gakkaishi (Japanese Edition) 日本水産學會 78 (5) 951 - 957 0021-5392 2012 [Refereed][Not invited]
     
    A simple method using a syringe to collect digestive fluid from the gut of the disc abalone Haliotis discus discus is described. The activities of polysaccharide degrading enzymes and bacterial microflora were compared between the digestive fluid (DF) collected by using a syringe and the digestive diverticulum homogenate (DH) collected by the conventional dissection method. Specific activities of alginate lyase, cellulase and β-1,4-mannanase of DF were higher than those of DH. Viable bacterial count of DF was lower (1.0×107 CFU/mL) than that of DH (2.1×108 CFU/g). Microflora analysis of isolates using the 16S rRNA gene indicated that DF and DH showed a similar microflora composition, in which vibrios including Vibrio halioticoli and V. ezurae were predominant. The present method may be useful to determine changes in the digestive activity and the gut microflora of abalone without sacrificing individuals.
  • Haruo Sugita, Tomoo Sawabe, Mamoru Yoshimizu
    Nippon Suisan Gakkaishi (Japanese Edition) 公益社団法人 日本水産学会 78 (4) 779 - 779 0021-5392 2012 [Refereed][Not invited]
  • 澤辺桃子, 澤辺智雄
    New Food Industry 食品資材研究会 53 (8) 57 - 66 0547-0277 2011 [Refereed][Not invited]
  • SHIMIZU Shigemasa, KUBOSAWA Yosuke, MATSUURA Misato, KAWAI Yuji, YAMAZAKI Koji
    Japanese Journal of Food Microbiology 日本食品微生物学会 28 (1) 29 - 36 1340-8267 2011 [Refereed][Not invited]
     
    Conventional plating methods for enumerating Staphylococcus aureus are time-consuming and labor-intensive. Rapid methods for specific quantification are desirable. Fluorescence in situ hybridization with filter-cultivation (FISHFC) method has been already developed to enumerate viable specific microorganisms such as Listeria monocytogenes, Clostridium perfringens and Vibrio parahaemolyticus. The purpose of this study was to develop and estimate FISHFC method for S. aureus quantitative detection in food samples. Alexa Fluor® 546-labeled oligonucleotide probe, STA68, was newly designed from the 16S rRNA gene sequences of S. aureus. STA68-conferred fluorescence was observed for S. aureus but not for any other organisms, suggesting that STA68 probe is highly specific for S. aureus. Results were achievable within 12 hours by FISHFC method, containing with 10 hours cultivation, as compared to more than 3 days required for confirmation of S. aureus by conventional plating methods. When inoculated to BPW and food samples, the numbers of viable counts determined by FISHFC method were not significantly different to those obtained by the conventional plating method (p>0.05). This result suggests that FISHFC method was preferable for the specific, rapid and accurate quantification of viable S. aureus in food.
  • Ryohei Aoi, Shigemasa Shimizu, Koji Yamazaki, Tomoo Sawabe, Yuji Kawai
    JOURNAL OF THE JAPANESE SOCIETY FOR FOOD SCIENCE AND TECHNOLOGY-NIPPON SHOKUHIN KAGAKU KOGAKU KAISHI 日本食品科学工学会 58 (10) 483 - 489 1341-027X 2011 [Refereed][Not invited]
     
    Conventional plate counting for Escherichia coli is time consuming, and more rapid and specific quantification methods are desired. The fluorescence in situ hybridization with filter cultivation (FISHFC) method has already been developed to specifically detect viable microorganisms such as Listeria monocytogenes, Clostridium perfringens and Staphylococcus aureus. The purpose of this study was to develop and estimate the accuracy of the FISHFC method for E. coli detection in food samples. An Alexa Fluor (R) 647-labeled oligonucleotide probe. ECO636. targeting a species-specific sequence of E. coli 16SrRNA was designed. ECO636-conferred fluorescence was observed for E coli and Shigella spp. micro-colonies, but not for any other organisms. This suggests that the ECO636 probe is highly specific for E. coli and Shigella spp. This assay using the FISHFC method can be completed within 9 hours, including a 7-hour cultivation period, and is much faster compared to standard plating methods, which require more than 4 days, for the confirmation of E. coli. Viable E. coli counts in food samples determined by the FISHFC method were not significantly different to those obtained by the conventional plate counting method p > 0.051 These results suggest that the proposed FISHFC method is more rapid than and equally as reliable as the standard methods used for estimating viable E. coli numbers as indicators of food contamination in food.
  • Sawabe T
    Nihon saikingaku zasshi. Japanese journal of bacteriology 2-4 65 (2) 333 - 342 0021-4930 2010/12 [Refereed][Not invited]
     
    ビブリオは，コレラ菌，腸炎ビブリオ及びビブリオ・バルニフィカスというヒト病原性種を含むことから，病原微生物学から環境微生物学までにおける幅広い学術分野でモデル微生物として活発に研究されている細菌群である。コレラ菌の発見から156年を経過した今でも，新種のビブリオが発見され続けており，自然界におけるビブリオの種多様性は驚くほど高い。1965年にM. Véonによって作られたビブリオ科（Vibrionaceae）は，6属，103種が包含される巨大な分類群となっている。ビブリオで新種が記載され続ける背景には，株の遺伝的多様性を精密に検出する指紋鑑定法や個体識別法が取り入れられたことにある。また，個体識別の過程で得られる多座位の遺伝子配列を解析することにより，ビブリオの進化の系譜や種分化機構の推定も試みられるようになってきた。さらに，ビブリオをモデルとしたゲノム情報に基づく分類規範の構築も始まっている。本稿ではビブリオの分類の歴史を紐解きながら，ビブリオの多様性と進化に関する最新の成果をまとめて紹介する。
  • 澤辺桃子, 澤辺智雄
    函館短期大学紀要 函館短期大学 38 (38) 13 - 18 2010 [Refereed][Not invited]
  • Youhei Fukui, Sei-Ichi Saitoh, Tomoo Sawabe
    ENVIRONMENTAL MICROBIOLOGY 12 (1) 124 - 133 1462-2912 2010/01 [Refereed][Not invited]
     
    P>Vibrio harveyi is an emerging pathogen that causes mass mortality in a wide variety of marine animal species; however, it is still unclear which environmental determinants correlate V. harveyi dynamics and the bacterium-mediated death of marine animal life. We conducted a correlation analysis over a 5-year period (2003-2007) analysing the following data: V. harveyi abundance, marine animal mortality and environmental variables (seawater temperature, salinity, pH, chlorophyll a, rainfall and total viable bacterial counts). The samples were collected from a coastal area in northern Japan, where deaths of a marine gastropod species (Haliotis discus hannai) have been reported. Our analysis revealed significant positive correlations between average seawater temperature and average V. harveyi abundance (R = 0.955; P < 0.05), and between average seawater temperature and V. harveyi-mediated abalone death (R = 0.931; P < 0.05). Based on the regression model, n degrees C rise in seawater temperature gave rise to a 21n-fold increase in the risk of mortality caused by V. harveyi infection. This is the first report providing evidence of the strong positive correlation between seawater temperature and V. harveyi-mediated death of marine species.
  • 澤辺 智雄
    化学と生物 公益社団法人 日本農芸化学会 47 (1) 4 - 6 0453-073X 2009 [Refereed][Not invited]
  • 澤辺桃子, 大坪雅史, 澤辺智雄
    The Bulletin of Hakodate Junior College 函館短期大学 35 (35) 51 - 56 2009 [Refereed][Not invited]
  • NIWA Kentaro, AONO Hideaki, SAWABE Tomoo
    Aquaculture Science 水産増殖談話会 57 (4) 557 - 565 0371-4217 2009 [Refereed][Not invited]
     
    In order to elucidate the nutritional physiology on Kuro abalone Haliotis discus discus, activities of digestive enzymes were measured, and the three major polysaccharide degrading enzymes were purified and characterized.
    Lipase, protease and polysaccharide degrading enzyme activities were detected from both digestive fluid and homogenate of digestive diverticulum of the abalone. The enzyme activities of alginate lyase, cellulase and mannanase were rather higher than the other enzyme activities. An alginate lyase, a cellulase and a mannanase were electrophoretically purified. MW of there purified enzymes were 27.5, 64.6, and 38.1 kDa, optimal temperatures were 40, 40 and 55°C, and optimal pH were 7.0, 5.0 and 5.0, respectively.
  • Hayden K. Webb, Russell J. Crawford, Tom Sawabe, Elena P. Ivanova
    MICROBES AND ENVIRONMENTS 24 (1) 39 - 42 1342-6311 2009 [Refereed][Not invited]
     
    Plastic debris causes extensive damage to the marine environment, largely due to its ability to resist degradation. Attachment on plastic surfaces is a key initiation process for their degradation. The tendency of environmental marine bacteria to adhere to poly(ethylene terephthalate) (PET) plastic surfaces as a model material was investigated. It was found that the overall number of heterotrophic bacteria in a sample of sea water taken from St. Kilda Beach, Melbourne, Australia, was significantly reduced after six months from 4.2-4.7 x 10(3) cfu mL(-1) to below detectable levels on both full-strength and oligotrophic marine agar plates. The extinction of oligotrophs after six months was detected in all samples. In contrast, the overall bacterial number recovered on full strength marine agar from the sample flasks with PET did not dramatically reduce. Heterotrophic bacteria recovered on full-strength marine agar plates six months after the commencement of the experiment were found to have suitable metabolic activity to survive in sea water while attaching to the PET plastic surface followed by the commencement of biofilm formation.
  • Tomoo Sawabe, Ai Yoshizawa, Yuko Kawanishi, Eriko Komatsu-Takeda, Satoshi Nakagawa, Toko Sawabe, Masashi Ootubo, Masataka Satomi, Yutaka Yano, Koji Yamazaki
    MICROBES AND ENVIRONMENTS 24 (3) 259 - 264 1342-6311 2009 [Refereed][Not invited]
     
    A one-step multi-probe FISH method of detecting viable Vibrio parahaemolyticus was developed. Three candidate regions, corresponding to Helix 440+441, Helix 588, and Helix 1241 in 16S rRNA, were selected for detection, the thermodynamic parameters (Delta G(overall)) of the probes were optimized, and VP437, VP612 and VP1253, whose fluorescence were 1.7 to 11.3 times that of Delta G(overall)-unadjusted sequences, were designed. The addition of competitive oligo-nucleotides to reactions with VP612 and VP1253 strengthened the specificity of the probes. The three probes were labeled with FITC, TAMRA, and Cy5, respectively, and using a mixture of the probes and six competitive oligo-nucleotides, one-step FISH was applied to the species-specific detection of V. parahaemolyticus including epidemic strains of O3:K6 and O4:K68 serotypes. V. alginolyticus, V. rotiferianus, and V. campbellii were not detected in the reaction. Microcolonies (30-80 mu m in diameter) of V. parahaemolyticus were observed within 6 hours at 37 degrees C on seawater agar plates in both fresh and heat-damaged V. parahaemolyticus. Viable bacterial counts based on the proposed method were significantly different from those measured with typical vibrio selective media (CHROMagar Vibrio and TCBS).
  • Tomoo Sawabe, Shinichi Koizumi, Youhei Fukui, Satoshi Nakagawa, Elena P. Ivanova, Kumiko Kita-Tsukamoto, Kazuhiro Kogure, Fabiano L. Thompson
    MICROBES AND ENVIRONMENTS 24 (4) 281 - 285 1342-6311 2009 [Refereed][Not invited]
     
    The Vibrio splendidus clade is the biggest in Vibrionales composed of 11 described species (25). Diversification of these species may have occurred 260 million years ago. The main driving forces of speciation in this clade have never been studied. Population biological parameters (population base recombination rate (rho), population base mutation rate (theta), and index of association (Ia)) were determined among 16 strains of 9 defined species in the Splendidus cluster. A comparison of individual gene phylogeny indicated significant incongruence in tree topology, which suggests the occurrence of recombination between species. Homologous recombination between species was detected at four loci. However, the mutation rate theta was higher than the recombination rate rho, suggesting that mutation is the main driving force in the diversification of V. splendidus-related species.
  • N. Rameshkumar, Youhei Fukui, Tomoo Sawabe, Sudha Nair
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 58 1608 - 1615 1466-5026 2008/07 [Refereed][Not invited]
     
    Two facultatively anaerobic, nitrogen-fixing bacteria (strains MSSRF30(T) and MSSRF31) were isolated from a mangrove-associated wild rice (Porteresia coarctata Tateolka). These strains were determined to be nitrogen-fixers using the acetylene reduction assay and by PCR detection of a nifH gene amplicon. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel strains were most closely related to Vibrio fluvialis LMG 7894(T) (96.8 % gene sequence similarity), Vibrio furnissii LMG 7910(T) (96.8 % sequence similarity) and Vibrio tubiashii CIP 102760(T) (96.7% sequence similarity). Further multilocus sequence analysis using recA, pyrH, rpoA and nifH genes also showed low levels of sequence similarities (83-93 %) with all species of the genus Vibrio with validly published names. A multigene phylogenetic tree using concatenated sequences of the four genes (16S rRNA, rpoA, recA and pyrH) showed that strains MSSRF30T and MSSRF31 occupied a distinct phylogenetic position, forming a long branching that was not clustered with-any other recognized Vibrio species. The fatty acid profile also suggested that the novel strains belonged to the genus Vibrio. The results of physiological and biochemical tests, genomic fingerprinting and DNA-DNA hybridization analyses clearly differentiated both novel strains from their closest phylogenetic neighbours, Vibrio cholerae IID6019, Vibric, mimicus LMG 7896(T), V. fluvialis LMG 7894(T) and V. furnissii LMG 7910(T). Several phenotypic traits enabled the differentiation of strain MSSRF30T from other species of the genus Vibrio. The DNA G + C content of strain MSSIRF30(T) was 44.4 +/- 3.1 mol%. Based on genotypic, phenotypic, chemotaxonomic, phylogenetic and DNA-DNA hybridization analyses, the name Vibrio porteresiae sp. nov. (type strain rVISSRF30(T) =LMG 24061(T) =DSM 19223(T)) is proposed for this novel taxon.
  • 自然界におけるビブリオ－その多様性、進化、生態
    澤辺 智雄
    化学療法の領域 (株)医薬ジャーナル社 24 (6) 24 - 32 0913-2384 2008 [Refereed][Not invited]
     
    コレラ菌の発見から154年を経過した今でも新種のビブリオが相次いで発見され、自然界におけるビブリオの多様性は驚くほど高い。1965年にM.Veronによって作られたビブリオ科は、現在、6属、96種が包含される巨大な分類群に成長している。ここまで種数が増えた背景には、ビブリオの分類に染色体上の遺伝子変異を精密に検出する指紋鑑定や個体識別の方法が取り入れられたことにある。また個体識別で得られた遺伝子配列を基に、種分化や進化の系譜もたどれるようになってきた。最新の分子系統解析で、ビブリオには少なくとも14の単系統群があり、その共通祖先は6億年前に、そしてそのいくつかは魚類の爆発的進化が生じた3億5千万年以降に大きく種分化した可能性が示されている。(著者抄録)
  • 澤辺 智雄
    IFO Res. Commun. 22 17 - 26 2008 [Refereed][Not invited]
  • Youhei Fukui, Tomoo Sawabe
    MICROBES AND ENVIRONMENTS 23 (2) 172 - 176 1342-6311 2008 [Refereed][Not invited]
     
    Vibrio harveyi cause mass mortalities of cultured marine fish. To address the ecology of V. harveyi in aquaculture, intensive monitoring is needed. We first optimized a quantitative real-time PCR method to determine V. harveyi abundance. The designed TaqMan probe and primers based on the 16S rRNA gene were specific at 68 degrees C of annealing and extension. Furthermore, the method using a chelating resin method was able to enumerate 1.7 x 10(2) CFU/ml in breeding seawater at an abalone farm. This method represents a good tool for monitoring the ecology of V. harveyi in marine environments within 5 h.
  • Tomoo Sawabe, Kumiko Kita-Tsukamoto, Fabiano L. Thompson
    JOURNAL OF BACTERIOLOGY 189 (21) 7932 - 7936 0021-9193 2007/11 [Refereed][Not invited]
     
    We performed the first broad study aiming at the reconstruction of the evolutionary history of vibrios by means of multilocus sequence analysis of nine genes. Overall, 14 distinct clades were recognized using the SplitsTree decomposition method. Some of these clades may correspond to families, e.g., the clades Salinivibrio and Photobacteria, while other clades, e.g., Splendidus and Harveyi, correspond to genera. The common ancestor of all vibrios was estimated to have been present 600 million years ago. We can define species of vibrios as groups of strains that share >95% gene sequence similarity and >99.4% amino acid identity based on the eight protein-coding housekeeping genes. The gene sequence data were used to refine the standard online electronic taxonomic scheme for vibrios (http://www.taxvibrio.incc.br).
  • Fabiano L. Thompson, Bruno Gomez-Gil, Ana Teresa Ribeiro Vasconcelos, Tomoo Sawabe
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY 73 (13) 4279 - 4285 0099-2240 2007/07 [Refereed][Not invited]
     
    Identification and classification of Vibrio species have relied upon band pattern methods (e.g., amplified fragment length polymorphism) and DNA-DNA hybridization. However, data generated by these methods cannot be used to build an online electronic taxonomy. In order to overcome these limitations, we developed the first standard multilocus sequence scheme focused on the ubiquitous and pathogenic Vibrio harveyi species group (i.e., V. harveyi, V. campbellii, V. rotiferianus, and a new as yet unnamed species). We examined a collection of 104 isolates from different geographical regions and hosts using segments of seven housekeeping genes. These two species formed separated clusters on the basis of topA, pyrH, ftsZ, and mreB gene sequences. The phylogenetic picture obtained by the other three loci, i.e., gyrB, recA, and gapA, was more complex though. V. campbellii appeared nested within V. harveyi in the recA trees, whereas V. harveyi formed a tight nested cluster within V. campbellii by gapA. The gyrB gene had no taxonomic resolution and grouped the two species together. The fuzziness observed in these three genes seems not be related to recombination but to low divergence due to the accumulation of only a few substitutions. In spite of this, the concatenated sequences provided evidence that the two species form two separated clusters. These clusters did not arise by recombination but by accumulation of point mutations. V. harveyi and V. campbellii isolates can be readily identified through the open database resource developed in this study (http://www.taxvibrio.Incc.br/). We argue that the species should be defined by evolutionary criteria. Strains of the same species will share at least 95% concatenated sequence similarity using the seven loci, and, most importantly, cospecific strains will form cohesive readily recognizable phylogenetic clades.
  • Tomoo Sawabe, Yusuke Fujimura, Kentaro Niwa, Hideaki Aono
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 57 916 - 922 1466-5026 2007/05 [Refereed][Not invited]
     
    Nine alginolytic, facultatively anaerobic, non-motile bacteria were isolated from the guts of the abalones Haliotis discus discus, H. gigantea, H. madaka and H. rufescens. Phylogenetic analyses based on 16S rRNA gene sequences indicated that these bacteria were closely related to Vibrio superstes G3-29(T) (98.6-99.3% sequence similarity). DNA-DNA hybridization and phylogenetic analysis based on the gapA gene demonstrated that six strains constituted one bacterial species, two strains represented a second species and one strain represented a third species. The three novel bacterial species were different from all currently known vibrios. The names Vibrio comitans sp. nov. (type strain GHG2-1(T) =LMG 23416(T) = NBRC 102076(T); DNA G+C content 45.0-48.0 mol%), Vibrio inusitatus sp. nov. (type strain RW14(T) =LMG 23434(T) = NBRC 102082(T); DNA G + C content 43.1-43.7 mol%) and Vibrio rarus sp. nov. (type strain RW22(T) =LMG 23674(T) =NBRC 102084(T); DNA G + C content 43.8 mol%) are proposed to encompass these new taxa. Several phenotypic features were revealed that discriminate V. comitans, V. rarus and V. inusitatus from other Vibrio species.
  • Tomoo Sawabe, Youhei Fukui
    NIPPON SUISAN GAKKAISHI 73 (2) 310 - 312 0021-5392 2007/03 [Refereed][Not invited]
  • Tomoo Sawabe, Sahoko Inoue, Youhei Fukui, Kaoru Yoshie, Yutaka Nishihara, Hiroki Miura
    MICROBES AND ENVIRONMENTS 22 (3) 300 - 308 1342-6311 2007 [Refereed][Not invited]
     
    Sixty thousand of deaths among cultured Ezo abalone Haliotis discus hannai occurred within a few days at an abalone farm in Japan in the middle of August, 2002. Dead animals were characterized by a hemolymphatic edema around the major circulatory system. Vibrios showing swarming motility dominated in the edema. The pathogenic vibrios were identified as Vibrio harveyi based on a phylogenetic analysis and a phenotypic characterization. In both immersion and injection experiments, the swarming vibrios fulfilled Koch's postulates as a pathogen for Ezo abalone. Using a GFP-tagged V. harveyi S20, a clump of bacterium was detected on the gills of the abalone within 48 hours after contact with the bacterium. This is the first report of V. harveyi infection in Ezo abalone Haliotis discus hannai.
  • Youhei Fukui, Tomoo Sawabe
    MICROBES AND ENVIRONMENTS 22 (1) 1 - 10 1342-6311 2007 [Refereed][Not invited]
     
    Vibrio harveyi strains are pathogenic to a wide range of marine fish and shellfish, having a significant negative economic impact on aquaculture worldwide. However, a reliable and rapid method of detecting V. harveyi has yet to be established. We aimed to construct an improved one-step detection method for V. harveyi. Reanalysis of 16S rRNA gene sequences of type strains of V. harveyi revealed a unique consensus region compared to related Vibrio species. Using a VHARF-VHARR primer set from this region, a V. harveyi-specific PCR-based detection method was established and could differentiate V. harveyi from related species such as V. campbellii, V. rotiferianus, and V. alginolyticus. Furthermore, the new method (optimal amplification with 20 core cycles of (94 degrees C-30 s, 60 degrees C-30 s, 72 degrees C-30 s)) could be applied to the identification of V. harveyi strains of colonies. This PCR was able to detect V. harveyi grown on plates in the environment within 3 days without bacterial isolation, DNA extraction, or the assistance of biochemical tests. The specificity and rapidity of the detection is reliable enough to understand the ecology of V. harveyi in environments, and to predict outbreaks of mass mortality caused by V. harveyi in aquaculture.
  • T. Sawabe, Y. Fukui, E. V. Stabb
    LETTERS IN APPLIED MICROBIOLOGY 43 (5) 514 - 522 0266-8254 2006/11 [Refereed][Not invited]
     
    Aim: Our goal was to develop a simple system for tagging wild-type marine bacteria with gfp. Methods and Results: Escherichia coli strain CC118 lambda pir carrying the conjugative helper plasmid pEVS104 and the gfp-containing plasmid pKV111 was used to transfer gfp to Vibrio recipients. Four different media were tested for their ability to support the growth of recipients, but not the E. coli donor, to allow powerful enrichment of gfp-tagged wild-type vibrios from mating mixes. Forty-three vibrio strains, representing 39 different species, were successfully tagged with gfp using the conjugative transfer from E. coli followed by selective outgrowth at 15 degrees C on ZoBell 2216E agar containing 0.5% sodium alginate. Using this outgrowth medium, colonies of GFP-expressing vibrio clones were detectable within 4 days. The percentage of visibly fluorescent cells in three representative GFP-tagged vibrios was higher at 15 degrees C than at 20 or 25 degrees C (c. 50% vs. 45% or 40%, respectively), and was also higher during the aerobic rather than the anaerobic culturing (c. 50% vs. 35%, respectively). Conclusions: We found a simple selective outgrowth technique that enabled us to isolate a wide variety of GFP-tagged marine vibrios following the conjugative transfer of gfp from E. coli. Significance and Impact of the Study: Tagging cells with GFP and related fluorescent proteins is a powerful approach for investigating the bacteria in situ, particularly during the colonization of hosts. The simple and cost-effective outgrowth condition described in this study could be applied to construct a wide variety gfp-tagged marine bacteria.
  • Fabiano L. Thompson, Karl E. Klose, Brian Austin, Yan Boucher, Peter Dawyndt, Dirk Gevers, Shah M. Faruque, Bruno Gomez-Gil, John F. Heidelberg, Tetsuya Iida, Didier Mazel, Diane McDougald, G. Balakrish Nair, Frans Ollevier, John H. Paul III, Martin Polz, Tomoo Sawabe, Ana C. P. Vicente, Rita R. Colwell, Jean Swings
    Journal of Bacteriology 188 (13) 4592 - 4596 0021-9193 2006/07 [Refereed][Not invited]
  • T Yamase, T Sawabe, K Kuma, K Tajima
    FISH PATHOLOGY 41 (1) 1 - 6 0388-788X 2006/03 [Refereed][Not invited]
     
    Tenacibaculum sp., the causative bacterium of spotting disease of short-spined sea urchin Storongylocentrotus intermedius, has been known to enter into the viable but non-culturable (VBNC) state in 75% Herbst's artificial seawater at 5 degrees C. Previous studies indicated that elevation of water temperature or addition of iron induced the resuscitation of the bacterium from the VBNC state. The present study revealed that the resuscitation period from the VBNC state was further prolonged when Tenacibaculum sp. in the VBNC state was resuscitated under the presence of iron, catalase and the homogenate of the sea urchin. Environmental waters around a sea urchin hatchery in Hokkaido, Japan often contained iron at concentrations over 0.34 mg/L in summer. The infection experiment showed that the VBNC cells activated with iron produced the spotting disease to healthy sea urchins. These results suggest that the VBNC cells of Tenacibaculum sp. resuscitated during summer under iron-rich environment are associated with outbreaks of the disease.
  • R Taniguchi, T Sawabe, K Tajima
    FISH PATHOLOGY 41 (1) 13 - 17 0388-788X 2006/03 [Refereed][Not invited]
     
    We examined the adhesion of Tenacibaculum sp., the causative bacterium of spotting disease of short-spined sea urchin Stronglycentroutus intermedius, to the host. The number of adhesive cells of Tenacibaculum sp. strain F-2 isolated from diseased sea urchin was about 30 times more than those of two stains of non-pathogenic marine Cytophaga. sp. isolated from healthy sea urchins. The adhesion of Tenacibaculum sp. F-2 to the sea urchins was inhibited by about 90% when the sea urchins were pre-treated with 0.1% D-galactose or D-xylose for 1h. With this treatment, all sea urchins remained asymptomatic and were still alive at 7 1h day after being immersed with 10(6) or 10(7) CFU/mL Tenacibaculum sp. F-2 for 1 h at 23 degrees C, while mortality of control reached 100%. These results indicate that carbohydrate treatment of the sea urchin is useful to control the disease.
  • Tomohisa Yamase, Tomoo Sawabe, Kensi Kuma, Kenichi Tajima
    Fish Pathology 41 (1) 1 - 6 0388-788X 2006/03 [Refereed][Not invited]
     
    Tenacibaculum sp., the causative bacterium of spotting disease of short-spined sea urchin Storongylocentrotus intermedius, has been known to enter into the viable but non-culturable (VBNC) state in 75% Herbst's artificial seawater at 5°C. Previous studies indicated that elevation of water temperature or addition of iron induced the resuscitation of the bacterium from the VBNC state. The present study revealed that the resuscitation period from the VBNC state was further prolonged when Tenacibaculum sp. in the VBNC state was resuscitated under the presence of iron, catalase and the homogenate of the sea urchin. Environmental waters around a sea urchin hatchery in Hokkaido, Japan often contained iron at concentrations over 0.34 mg/L in summer. The infection experiment showed that the VBNC cells activated with iron produced the spotting disease to healthy sea urchins. These results suggest that the VBNC cells of Tenacibaculum sp. resuscitated during summer under iron-rich environment are associated with outbreaks of the disease. © 2006 The Japanese Society of Fish Pathology.
  • FL Thompson, Y Barash, T Sawabe, G Sharon, J Swings, E Rosenberg
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 56 365 - 368 1466-5026 2006/02 [Refereed][Not invited]
     
    The taxonomic position of the coral pathogen strain CBMAI 722(T) was determined on the basis of molecular and phenotypic data. We clearly show that the novel isolate CBMAI 722 T is a member of the family Colwelliaceae, with Thalassomonas ganghwensis as the nearest neighbour (95% 16S rRNA gene sequence similarity). CBMAI 722(T) can be differentiated from its nearest neighbour on the basis of phenotypic and chemotaxonomic features, including the utilization of cellobiose and L-arginine, the production of alginase and amylase, but not oxidase, and the presence of the fatty acids 12:0 3-OH and 14:0, but not 10:0 or 15:0. The DNA G + C content of CBMAI 722(T) is 39.3 mol%. We conclude that this strain represents a novel species for which we propose the name Thalassomonas loyana sp. nov., with the type strain CBMAI 722(T) (=LMG 22536(T)). This is the first report of the involvement of a member of the family Colwelliaceae in coral white plague-like disease.
  • Enhanced expression of active recombinant alginate lyase AlyPEEC cloned from a marine bacteriu Pseudoalteromonas elyakovii in Escherichia coli by calcium compounds
    Sawabe, T, Takahasi, H. Saeki, H, Niwa, K, Aono, H
    Enzyme and Microbial Technology 40 285 - 291 2006 [Refereed][Not invited]
  • MM Rahman, T Somsiri, R Tanaka, T Sawabe, K Tajima
    FISH PATHOLOGY 40 (4) 151 - 159 0388-788X 2005/12 [Refereed][Not invited]
     
    The study was conducted to develop a PCR and an improved PCR-RFLP analysis method for rapid species-identification of Aeromonas genospecies. The forward and reverse primers for PCR were designed from the complementary sequences of the 16S rDNA of all 15-recognized Aeromonas genospecies to amplify a 1206-bp PCR product. The PCR amplified the expected product from the DNA template of type or reference strains of all recognized Aeromonas genospecies as well as 106 Aeromonas strains, while no PCR product was obtained from any of the non-Aeromonas strains tested. The PCR-RFLP analysis using the restriction enzymes (Alul, Mbol, Pvull, Pstl and Narl) provided identification of almost all Aeromonas species. However, the Aeromonas sp. T8 group and A. caviae exhibited a similar RFLP pattern. Some selected biochemical tests were found to be helpful for differentiation of the two species.
  • SHIMIZU Tomoko, SHINOZAKI Daisuke, KASAI Hisae, SAWABE Tomoo, WATANABE Kenichi, YOSHIMIZU Mamoru
    Aquaculture Science 水産増殖談話会 53 (3) 275 - 278 0371-4217 2005/09/20 [Not refereed][Not invited]
     
    Effect of manipulation of dietary rotifer Brachionus plicatilis bacterial flora on the intestinal bacterial flora of Japanese flounder Paralichthys olivaceus larvae was investigated. Manipulation was done by disinfecting rotifer eggs to reduce viable bacterial counts and then by inoculating hatched rotifers with non-sucrose fermenting Vibrio splendidus strain V-15 to make the bacterium dominant in the rotifers. Flounder larvae were fed the manipulated rotifers and intestinal bacterial flora of the fish was monitored. The dominant intestinal bacterial flora of the flounder became Vibrio spp. These results indicate that intestinal bacterial flora of flounder can be artificially controlled by manipulating bacterial flora in diets.
  • Elena P. Ivanova, Richard Christen, Tomoo Sawabe, Yulia V. Alexeeva, Anatoly M. Lysenko, Victor P. Chelomin, Valery V. Mikhailov
    Microbes and Environments 20 (4) 200 - 207 1347-4405 2005 [Refereed][Not invited]
     
    Over the last decade, taxonomic surveys have recovered sixteen strains of Halomonas-like marine het-erotrophic bacteria from different ecological habitats. The sixteen strains were isolated from three N.W. Pacific Ocean habitats: seawater, the mussel Crenomytilus grayanus and the degraded thallus of brown alga Fucus evanescens. These strains were subjected to a taxonomic investigation of their phenotypic/physiological, genetic, and phylogenetic features. Analysis indicates these bacteria belong to Cobetia marina. The study found all strains tolerated CdCl2 concentrations up to 875 mM. Taxonomically, the sixteen strains belong to the same species, nevertheless, their physiological features revealed distinguishing characteristics. For instance, strain KMM 296, recovered from the mussel Crenomytilus grayanus, was distinct from other C. Marina strains by its ability to produce highly active alkaline phosphatase. The majority of C. Marina strains that were isolated from degraded alga thallus appeared to have a particular metabolic specialisation by utilizing a range of easily assimilable monosaccharides. Notably, despite a high level of genetic similarity (80% of DNA relatedness), the phenotypic features of the strains isolated from degraded alga thallus differed with the type strain C. Marina LMG 2217T. These differences suggest an ecologically adapted population of C. Marina at a subspecies level. © 2005, Japanese Society of Microbial Ecology & The Japanese Society of Soil Microbiology. All rights reserved.
  • R Sato, T Sawabe, H Saeki
    JOURNAL OF FOOD SCIENCE 70 (1) C58 - C62 0022-1147 2005/01 [Refereed][Not invited]
     
    The production of alginate lyase using genetically modified Escherichia coli was superior to the purification of alginate lyase from a culture medium of Pseudoalteromonas elyakovii regarding production efficiency. When alginate oligosaccharide (AO) prepared using genetic recombinant alginate lyase was introduced to fish myofibrillar proteins, the protein obtained high water solubility and improved thermal stability, similarly to AO prepared using wild-type lyase. Therefore, the use of genetic recombinant technology for the production of alginate lyase would be useful for the functional improvement of fish myofibrillar proteins by conjugation with AO.
  • R Tanaka, M Ootsubo, T Sawabe, Y Ezura, K Tajima
    AQUACULTURE 241 (1-4) 453 - 463 0044-8486 2004/11 [Refereed][Not invited]
     
    The compositions of bacterial communities in the gut of abalone were determined using the 16S rDNA clone library and fluorescence in situ hybridization (FISH). Sequencing of cloned 16S rDNA amplicons revealed a diverse community comprised Alpha-, Gamma- and Epsilonproteobacteria, and Mollicutes in the gut of artificial diet-fed abalone, and majority of Mollicutes, Fusobacteria, Alpha-and Gammaproteobacteria, in the gut of starved abalone. Biodiversity of gut bacterial community was rather high in artificial diet fed abalones than in Laminaria fed and starved animals. While, in situ abundance of the community composition determined by FISH revealed that 54% of 4',6-diamidino-2-phenylindole (DAPI)-stained bacteria were hybridized with a probe for Gammaprotcobacteria and 40% of DAPI-stained bacteria appeared to be of the Vibrio group. Alphaproteobacteria, which was frequent in clone libraries, was less abundant in artificial diet fed abalones determined by FISH. Our data show that the Vibrio group can be a dominant component in the gut microflora, of abalone. (C) 2004 Elsevier B.V. All rights reserved.
  • Marina Taniguchi, Toshinori Kanehisa, Tomoo Sawabe, Richard Christen, Tsutomu Ikeda
    Journal of Plankton Research 26 (10) 1249 - 1255 0142-7873 2004/10 [Refereed][Not invited]
     
    Monophylies of Neocalanus cristatus, Neocalanus plumchrus and Neocalanus flemingeri were revealed by nucleotide sequences of mitochondrial 16S rRNA gene (410 bp) but not of nuclear 18S rDNA gene (1802 bp). Intraspecific variations in mitochondrial 16S rRNA of N. cristatus collected from geographically distant regions were very low (< 0.5%).
  • T Sawabe, K Hayashi, J Moriwaki, Y Fukui, FL Thompson, J Swings, R Christen
    SYSTEMATIC AND APPLIED MICROBIOLOGY 27 (5) 527 - 534 0723-2020 2004/09 [Refereed][Not invited]
     
    Five alginolytic, facultative anaerobic, non-motile bacteria were isolated from the gut of Japanese abalones (Haliotis discus discus, H. diversicolor diversicolor and H. diversicolor aquatilis). Phylogenetic analyses based on 16S rRNA gene and gap gene sequences indicated that these strains are closely related to V. balioticoli. DNA-DNA hybridizations, FAFLP fingerprintings, and phylogenies of gap and 16S rRNA gene sequences showed that the five strains represent two species different from all currently described vibrios. The names Vibrio neonatus sp. nov. (IAM 15060(T) = LMG 19973(T) = HDD3(_)1(T); Mol% G+C of DNA is 42.1-43.9), and Vibrio ezurae sp. nov. (IAM 15060(T) = LMG 19973(T) = HDD3-1(T); mol% G+C of DNA is 43.6-44.8) are proposed to encompass these new taxa. The two new species can be differentiated from V balioticoli on the basis of several features, including beta-galactosidase activity, assimilation of glycerol, D-mannose and D-gluconate.
  • EP Ivanova, OI Nedashkovskaya, T Sawabe, NV Zhukova, GM Frolova, DV Nicolau, VV Mikhailov, JP Bowman
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 54 1089 - 1093 1466-5026 2004/07 [Refereed][Not invited]
     
    Four marine bacterial strains, designated KMM 3587(T), KMM 3586, KMM 3821 and KMM 3822, were isolated from the sipuncula Phascolosoma japonicum, a common inhabitant of Troitza Bay in the Gulf of Peter the Great (Sea of Japan region), and from an unidentified hydrocoral species collected in Makarov Bay (Iturup Islands), Kuril Islands, North-West Pacific Ocean. The strains were characterized to clarify their taxonomic position. 16S rRNA gene sequences of KMM 3587(T) and KMM 3586 indicated 99% similarity to Shewanella colwelliana. Despite such a high level of 16S rRNA gene sequence similarity, DNA-DNA hybridization experiments demonstrated only 45-52% binding with DNA of S. colwelliana ATCC 39565 T. The DNA G + C contents of the novel strains were 45 mol% and the shared level of DNA hybridization was conspecific (81-97%), indicating that they represent a single genospecies. The novel strains were mesophilic (able to grow at 10-34degreesC), neutrophilic and haemolytic, and able to degrade gelatin, casein and Tween 20, 40 and 80, but not starch, agar, elastin, alginate or chitin. The major fatty acids were i13: 0, i15:0, 16:0, 16:1omega7 and 17:1omega8 (68.9% of total). The major isoprenoid quinones were Q7 (47-62%) and Q8 (26-47%). Eicosapentaenoic acid was produced in minor amounts. Based on these data, the strains are assigned to a novel species, Shewanella affinis sp. nov. (type strain KMM 3587(T)=CIP 107703(T) = ATCC BAA-642(T)).
  • T Sawabe, K Hayashi, J Moriwaki, FL Thompson, J Swings, P Potin, R Christen, Y Ezura
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 54 843 - 846 1466-5026 2004/05 [Refereed][Not invited]
     
    Five alginolytic, facultatively anaerobic, non-motile bacteria were isolated from the gut of the abalone Haliotis tuberculata. Phylogenetic analyses based on 16S rDNA data indicated that these strains are related to Vibrio wodanis, Vibrio salmonicida, Vibrio logei and Vibrio fischeri (but with <97% 16S rRNA gene sequence similarity). DNA-DNA hybridization and fluorescence amplified fragment length polymorphism fingerprinting demonstrated that the five strains constituted a single species that was different from all currently known vibrios. The name Vibrio gallicus sp. nov. (type strain, CIP 107863(T) = LMG 21878(T) = HT2-1(T); DNA G + C content, 43.6-44.3 mol%) is proposed for this novel taxon. Several phenotypic features were disclosed that discriminated V. gallicus from other Vibrio species: V gallicus can be differentiated from Vibrio halioticoli on the basis of four traits (β-galactosidase test and assimilation of three carbon compounds) and from Vibrio superstes by 16 traits.
  • EP Ivanova, NM Gorshkova, T Sawabe, NV Zhukova, K Hayashi, VV Kurilenko, Y Alexeeva, Buljan, V, DV Nicolau, VV Mikhailov, R Christen
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 54 475 - 480 1466-5026 2004/03 [Refereed][Not invited]
     
    On the basis of data from phenotypic and genotypic characterization and analysis of 16S rRNA gene sequences, two novel species belonging to the genus Sulfitobacter are described. Strains KMM 3584(T), a pale-yellowish, non-motile strain isolated from a starfish (Stellaster equestris), and KMM 3554(T), which is motile by means of a single subpolar flagellum and was isolated from sea grass (Zostera marina), are marine, Gram-negative, aerobic, rod-shaped organisms. Both strains have the ability to degrade gelatin, but not casein, chitin, agar, DNA, Tween 80 or starch. Strain KMM 3584(T) decomposed alginate and grew at NaCl concentrations of 1-8% and temperatures of 12-37 degreesC, whereas strain KMM 3554(T) grew in 1-12% NaCl and at temperatures of 10-30 degreesC. The predominant fatty acid was 18:1 omega7, amounting to up to 80% of the total fatty acids. The other characteristic feature was the presence of 18:2 isomers. The DNA G + C contents of KMM 3584(T) and KMM 3554(T) were respectively 60(.)0 and 63(.)7 mol%. The level of DNA similarity between the two strains was 33%. DNA from KMM 3584(T) and KMM 3554(T) had hybridization values of 5-24% and 10-41%, respectively, with DNA from the type strains of Sulfitobacter pontiacus, Sulfitobacter brevis, Sulfitobacter mediterraneus and Staleya guttiformis. It is proposed that strains KMM3584(T) (= LMG 20554(T) ATCC BAA-321(T)) and KMM 3554(T) (= LMG 20555(T) = ATCC BAA-320(T)) represent two novel species, Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively.
  • Hironori Fujishima, Toshiko Gamano, Yukako Taoka, Tomoo Sawabe, Yutaka Itabashi
    Nippon Suisan Gakkaishi (Japanese Edition) 70 (2) 200 - 202 0021-5392 2004/03 [Refereed][Not invited]
  • K Hayashi, J Moriwaki, T Sawabe, FL Thompson, J Swings, N Gudkovs, R Christen, Y Ezura
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 53 1813 - 1817 1466-5026 2003/11 [Refereed][Not invited]
     
    Five alginolytic, facultatively anaerobic, non-motile bacteria were isolated from the gut of abalones Haliotis laevigata and Haliotis rubra. Phylogenetic analyses based on 16S rDNA data indicated that these strains are related closely to Vibrio halioticoli (98 % 1 6S rDNA sequence similarity). DNA-DNA hybridization and fluorescent amplified fragment length polymorphism fingerprinting demonstrated that the five strains constituted a single species that was different from all currently known vibrios. The name Vibrio superstes sp. nov. (type strain, LMG 21323(T) = \AM 15009(T) = G3-29(T) ; DNA G + C content, 48(.)0-48(.)9 mol%) is proposed to encompass this novel taxon. Several phenotypic features were disclosed that discriminate V superstes from other Vibrio species: V. superstes sp. nov. and V. halioticoli can be differentiated on the basis of 17 traits (indole production, beta-galactosidase test and assimilation of 15 carbon compounds).
  • R Tanaka, Sugimura, I, T Sawabe, M Yoshimizu, Y Ezura
    FISHERIES SCIENCE 69 (5) 951 - 958 0919-9268 2003/10 [Refereed][Not invited]
     
    Development of gut microflora in abalone Haliotis discus hannai cultured at two abalone farms in Japan was similar: (i) gut microflora of juvenile abalones fed on microalgae matched microflora cultured from seawater; and (ii) gut microflora changed coincident with the abalone switching food sources from microalgae to algal pellets. After abalone reached 4 months of age, the gut microflora was replaced by algal polysaccharide-degrading bacteria, which were almost entirely characterized as facultative anaerobes. Dominant species were alginolytic, non-motile fermenters (NMF) and Vibrio spp. The gut microflora seemed to be stable in abalone older than 1 year, with NMF bacteria dominating. Ninety-six percent of the NMF isolates were identified as Vibrio halioticoli by species-specific identification using the colony hybridization method. These results show that abalone H. discus hannai has a unique developmental process in which gut microflora shifts to alginate-degrading bacteria, especially V, halioticoli.
  • R Sato, S Katayama, T Sawabe, H Saeki
    JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 51 (15) 4376 - 4381 0021-8561 2003/07 [Refereed][Not invited]
     
    Carp myofibrillar protein (Mf) was conjugated with alginate oligosaccharide (AO) through the Maillard reaction under low relative humidity, and the functional properties of the Mf-AO conjugate were investigated under different NaCl concentrations and pH levels. Mf became highly solubilized at lower NaCl concentrations by conjugation with AO, with a slight loss of available lysine. The thermal stability of Mf was effectively improved by conjugation with AO. Heat treatment at 80 degreesC for 2 h had no effect on the solubility of the Mf-AO conjugate attached to 227 mug/mg of AO regardless of the NaCl concentration and pH. Furthermore, the Mf-AO conjugate showed excellent emulsion-forming ability regardless of NaCl concentration. The improved functionalities of Mf by conjugation with AO remained even at a nearly isoelectric point. These results indicate that conjugation with AO through the Maillard reaction is an effective way to prepare high-functional food material from fish muscle protein.
  • EP Ivanova, T Sawabe, NV Zhukova, NM Gorshkova, OI Nedashkovskaya, K Hayashi, GM Frolova, AF Sergeev, KG Pavel, VV Mikhailov, DV Nicolau
    SYSTEMATIC AND APPLIED MICROBIOLOGY 26 (2) 293 - 301 0723-2020 2003/06 [Refereed][Not invited]
     
    Although bacteria of the genus Shewanella belong to one of the readily cultivable groups of "Gammaproteobacteria", little is known about the occurrence and abundance of these microorganisms in the marine ecosystem. Studies revealed that of 654 isolates obtained from marine invertebrates (ophiuroid Amphiopholis kochii, sipuncula Phascolosoma japonicum, and holothurian Apostichopus japonicus, Cucumaria japonica), seawater and sediments of the North-West Pacific Ocean (i.e. the Sea of Japan and Iturup Is, Kurile Islands), 10.7% belonged to the genus Shewanella. The proportion of viable Shewanella species varied from 4% to 20% depending on the source of isolation. From the isolation study, representative strains of different phenotypes (from seventy presumptive Shewanella strains) were selected for detailed characterization using phenotypic, chemotaxonomic, and phylogenetic testing. 16S rDNA sequence-based phylogenetic analysis confirmed the results of tentative identification and placed the majority of these strains within only a few species of the genus Shewanella with 98-99% of 16S rDNA sequences identity mainly with S. japonica and S. colwelliana, suggesting that the strains studied might belong to these species. Numerically dominant strains of S. japonica were metabolically active and produced protemases (gelatinases, caseinases), lipases, amylases, agarases, and alginases. Shewanella strains studied demonstrated weak antimicrobial and antifungal activities that might be an indication of their passive role in the colonization on living and non-living surfaces.
  • T Sawabe, N Setoguchi, S Inoue, R Tanaka, M Ootsubo, M Yoshimizu, Y Ezura
    AQUACULTURE 219 (1-4) 671 - 679 0044-8486 2003/04 [Refereed][Not invited]
     
    Acetic acid, which is converted from cellulose by means of the metabolism of their gut microbes, is an important oxidizable energy source and precursors of anabolism in ruminant animals and xylophagus insects. However, acetic acid production from algal polysaccharides by means of the metabolism of gut microbes of marine herbivorous invertebrates is not well studied. Abundance of Vibrio halioticoli, which is a dominant alginolytic gut microbe of abalone Haliotis discus hannai, in the gut of various marine herbivorous invertebrates and major fermentation products from alginate of these strains were investigated in this study. V halioticoli strains were detected from the gut of three species of the Japanese abalone, Haliotis discus discus, Haliotis diversicolor aquatilis, and Haliotis diversicolor diversicolor, and a South African abalone, Haliotis midae, with a range of 40-65% amongst these microflora. The bacterium was also found in the gut of a turban shell, Turbo cornutus, of which occupation rate was 16%. Furthermore, acetic acid and formic acid were detected as major fermentation products of alginate in these V halioticoli strains. It is suggested that the abundant populations of V halioticoli in the gut of Haliotis abalone may have a great role for converting alginate to acetic acid. (C) 2003 Elsevier Science B.V. All rights reserved.
  • EP Ivanova, T Sawabe, K Hayashi, NM Gorshkova, NV Zhukova, OI Nedashkovskaya, VV Mikhailov, DV Nicolau, R Christen
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 53 577 - 582 1466-5026 2003/03 [Refereed][Not invited]
     
    Two marine bacterial strains, KMM 3582(T) and KMM 3589, isolated respectively from sediments of the South China Sea and sea water of the Sea of Japan, have been characterized. Comparative 16S rDNA sequence-based phylogenetic analysis placed the two strains in a separate branch of the gamma-Proteobacteria within the members of the genus Shewanella. KMM 3582 T showed the highest similarity (97(.)1 and 97(.)4%, respectively) to Shewanella pealeana and Shewanella gelidimarina. The G + C contents of the DNAs of the two strains studied were 45(.)0 mol%. The level of DNA-DNA relatedness between the two strains was 82%, indicating that they represent a single genospecies. These organisms were slightly pinkish, Gram-negative, polarly flagellated, facultatively anaerobic, mesophilic (with temperature range from 4 to 30degreesC), neutrophilic: and haemolytic and were able to degrade alginate, gelatin and DNA. The novel organisms were susceptible to gentamicin, lincomycin, oleandomycin, streptomycin and polymyxin. The predominant fatty acids were characteristic for shewanellae: 13:0-i, 15:0-i, 16:0 and 16:1omega7. Eicosapentaenoic acid, 20:5omega3, was not detected. Phylogenetic evidence, together with phenotypic characteristics, showed that the two bacteria constitute a novel species of the genus Shewanella. The name Shewanella fidelis sp. nov. is proposed, with the type strain KIMM 3582(T) (=LMG 20551(T) =ATCC BAA-318(T)).
  • M Ootsubo, T Shimizu, R Tanaka, T Sawabe, K Tajima, Y Ezura
    JOURNAL OF APPLIED MICROBIOLOGY 95 (6) 1182 - 1190 1364-5072 2003 [Refereed][Not invited]
     
    Aims: A fluorescent in situ hybridization (FISH) technique using an Enterobacteriaceae-specific probe (probe D) to target 16S rRNA was improved in order to enumerate, within a single working day, Enterobacteriaceae present in food and environmental water samples. Methods and Results: In order to minimize the time required for the FISH procedure, each step of FISH with probe D was re-evaluated using cultured Escherichia coli. Five minutes of ethanol treatment for cell fixation and hybridization were sufficient to visualize cultured E. coli, and FISH could be performed within 1 h. Because of the difficulties in detecting low levels of bacterial cells by FISH without cultivation, a FISH technique for detecting microcolonies on membrane filters was investigated to improve the bacterial detection limit. FISH with probe D following 6 h of cultivation to grow microcolonies on a 13 mm diameter membrane filter was performed, and whole Enterobacteriaceae microcolonies on the filter were then detected and enumerated by manual epifluorescence microscopic scanning at magnification of x100 in ca 5 min. The total time for FISH with probe D following cultivation(FISHFC) was reduced to within 7 h. FISHFC can be applied to enumerate cultivable Enterobacteriaceae in food (above 100 cells g(-1)) and environmental water samples (above 1 cell ml(-1)). Conclusions: Cultivable Enterobacteriaceae in food and water samples were enumerated accurately within 7 h using the FISHFC method. Significance and Impact of the Study: A FISHFC method capable of evaluating Enterobacteriaceae contamination in food and environmental water within a single working day was developed.
  • EP Ivanova, NM Gorshkova, T Sawabe, K Hayashi, NI Kalinovskaya, AM Lysenko, NV Zhukova, DV Nicolau, TA Kuznetsova, VV Mikhailov, R Christen
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 52 2113 - 2120 1466-5026 2002/11 [Refereed][Not invited]
     
    On the basis of phenotypic and genotypic characteristics and 16S rDNA sequence analysis, a novel species belonging to the genus Pseudomonas sensu stricto was identified. The saprophytic, fluorescent bacterium, designated KMM 3447(T), was isolated from a drinking water reservoir near Vladivostok City, Russia. The novel organism was a Gram-negative, aerobic, rod-shaped bacterium that produced a cyclic depsipeptide with surface-active properties. It degraded casein, but did not degrade gelatin, starch, agar or Tween 80. The bacterium was also haemolytic. Growth of the novel bacterium occurred between 4 and 35 degreesC. The predominant cellular fatty acids of the novel pseudomonad were C-16:0, C16:1(n-7), C18:1(n-7) and C-17:0 cyclo; branched fatty acids were only found in trace amounts. The G+C content of the novel bacterium was 61.0 mol%. 16S rDNA sequence analysis indicated that the novel bacterium had a clear affiliation with Pseudomonas fluorescens and species closely related to this recognized pseudomonad. DNA-DNA hybridization experiments showed that the novel bacterium bound at low levels (27-53 %) with the DNA of the type strains of its nearest phylogenetic relatives, namely Pseudomonas tolaasii, Pseudomonas veronii, Pseudomonas orientalis and Pseudomonas rhodesiae, indicating that the novel bacterium represented a novel species within the genus Pseudomonas, for which the name Pseudomonas extremorientalis is proposed; the type strain is KMM 3447(T) (= LMG 19695(T)).
  • EP Ivanova, T Sawabe, AM Lysenko, NM Gorshkova, K Hayashi, NV Zhukova, DV Nicolau, R Christen, VV Mikhailov
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 52 1759 - 1766 1466-5026 2002/09 [Refereed][Not invited]
     
    On the basis of phenotypic and genotypic characteristics and analysis of 16S rRNA sequences, two novel species belonging to the genus Pseudoalteromonas are described. A pale-orange-pigmented strain, KMM 3548(T), isolated from a sponge and a non-pigmented strain, KMM 520(T), isolated from sea water are marine, Gram-negative, aerobic, rod-shaped organisms. One of the strains, KMM 520(T), had bipolar flagella. Both strains had the ability to degrade gelatin, DNA and Tween 80 but not chitin or agar. Strain KMM 520(T) decomposed elastin and grew at NaCl concentrations of 1-8%, while strain KMM 3548T grew at 1-6% NaCl. The temperature range for both strains was 4-30degreesC. The DNA G+C contents were 46.3 (KMM 520(T)) and 41.1 mol % (KMM 3548(T)). The level of DNA relatedness between the two strains was 20%. DNA from strain KMM 520(T) showed 8-34% genetic relatedness and that of KMM 3548(T) showed 17-53% relatedness to the DNA of other type strains of the genus Pseudoalteromonas. 16S rRNA analysis indicated a clear affiliation of these novel bacteria with the genus Pseudoalteromonas. The type strains of the novel species are Pseudoalteromonas translucida sp. nov. KMM 520(T) (=LMG 19696(T)=ATCC BAA-315(T)) and Pseudoalteromonas paragorgicola sp. nov. KMM 3548(T) (=LMG 19694(T) = ATCC BAA-322(T)).
  • T Sawabe, FL Thompson, J Heyrman, M Cnockaert, K Hayashi, R Tanaka, M Yoshimizu, B Hoste, J Swings, Y Ezura
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY 68 (8) 4140 - 4144 0099-2240 2002/08 [Refereed][Not invited]
     
    When analyzed by fluorescent amplified fragment length polymorphism and repetitive extragenic palindrome-PCR fingerprinting, a total of 47 Vibrio halioticoli strains isolated from four Japanese abalone species and one turban shell species formed three clusters that roughly reflect the different species of host abalone from which they were isolated. The V. halioticoli isolates from turban shells were distributed evenly among the clusters. Representative isolates from two clusters were deemed separate species or subspecies by DNA-DNA hybridization.
  • Y Sogabe, K Tajima, R Tanaka, T Sawabe, Y Ezura
    NIPPON SUISAN GAKKAISHI 68 (2) 201 - 206 0021-5392 2002/03 [Refereed][Not invited]
     
    The causative bacteria, Vibrio spp., have been isolated from the diseased sea urchin Strongylocentrotus intermedius at low water temperatures. To develop a specific identification method for the pathogens, species-specific nucleotide sequences in the 16S rRNA of Vibrio spp., were determined. We designed two PCR primers, DA2F and SK1F, based on the nucleotide sequences: DA2F forward primer (nucleotide numbers 456 to 476 in Escherichia coli 16S rRNA) for Date isolates and Sk1F for-ward primer (nucleotide numbers 455 to 478 in E. coli 16S rRNA) for Shiriuchi and Shikabe isolates. The PCR product with about 1kbp was obtained in all causative bacteria from Date, Shiriuchi, Shikabe Breeding Centers and some of Vibrio reference strains by amplification with DA2F-1540R primer set, however, those from three Breeding Centers differed from the reference strains in the case of growth at 30degreesC. PCR amplification with SK1F-1540R primer set was able to differentiate the causative bacteria from Date and those from Shiriuchi and Shikabe. These results indicate that PCR amplification with two primers is useful for identification of Vibrio spp., which are the pathogens of cultured sea urchin.
  • EP Ivanova, IY Bakunina, T Sawabe, K Hayashi, YV Alexeeva, NV Zhukova, DV Nicolau, TN Zvaygintseva, VV Mikhailov
    MICROBIAL ECOLOGY 43 (2) 242 - 249 0095-3628 2002/03 [Refereed][Not invited]
     
    The heterotrophic microbial enrichment community established during degradation of brown algae Fucus evanescens was characterized. A two-species bacterial community of marine culturable gamma-proteobacteria consisted of Pseudoalteromonas and Halomonas. The first member of the community, Pseudoalteromonas sp., was highly metabolically active, had bacteriolytic and hemolytic activities, produced proteinases (gelatinase and caseinase), lipases, DNases, and fucoidanhydrolases, laminaranases, alginases, pustulanases, beta-glucosiclases, beta-galactosidases, beta-N-acetylglucosaminidases, and beta-xylosidases. The second member of the community, Halomonas marina, produced only caseinase and DNase, and it did not hydrolyze algal polysaccharides. Both members of the studied bacterial community utilized a range of easily assimilable monosaccharides and other low molecular weight organic substances. The results provide an evidence of the complex metabolic interrelations between two members of this culturable community. One of them Pseudoalteromonas sp., most likely plays the major role in the initial stages of algal degradation; the other one, H. marina, resistant to the bacteriolytic activity of the former, is able to utilize the products of degradation of polysaccharides.
  • R Tanaka, M Ootsubo, T Sawabe, K Tajima, J Vandenberghe, Y Ezura
    FISHERIES SCIENCE 68 (1) 227 - 229 0919-9268 2002/02 [Refereed][Not invited]
  • EP Ivanova, T Sawabe, YV Alexeeva, AM Lysenko, NM Gorshkova, K Hayashi, NV Zukova, R Christen, VV Mikhailov
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 52 229 - 234 1466-5026 2002/01 [Refereed][Not invited]
     
    Eleven non-pigmented strains of Gram-negative, aerobic, marine bacteria with polar flagella were isolated from the thallus of the brown alga Fucus evanescens collected in the Kraternaya Bight of the Kurile Islands in the Pacific Ocean. These organisms were conspecific and exhibited high levels of genetic relatedness (up to 91 %). The G+C contents of the DNAs of these strains were 42.9-43.3 mol%. These halophilic bacteria had bacteriolytic, proteolytic and haemolytic activities and degraded algal polysaccharides, synthesizing a number of glycoside hydrolases (fucoidanases, laminaranases, alginases, agarases, pullulanases, beta-glucosidases, beta-galactosidases, beta-N- acetylglucosaminidases and beta-xylosidases). By 16S rDNA analysis, the bacteria were shown to belong to the genus Pseudoalteromonas, a member of the gamma-subclass of the Proteobacteria. DNA from the strains isolated from the brown alga showed 27-54 % genetic relatedness with respect to DNAs of other type strains of the genus Pseudoalteromonas. The phenotypic characteristics, together with the genetic evidence, indicate that this group of epiphytic bacteria represents a distinct species, Pseudoalteromonas issachenkonii sp. nov., for which the type strain is KMM 3549(T) (= LMG 19697(T)= CIP 106858(T)).
  • EP Ivanova, T Sawabe, AM Lysenko, NM Gorshkova, Svetashev, VI, DV Nicolau, N Yumoto, T Taguchi, S Yoshikawa, R Christen, VV Mikhailov
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 52 235 - 240 1466-5026 2002/01 [Refereed][Not invited]
     
    On the basis of phenotypic and genotypic characteristics and analysis of 16S rRNA sequences, a novel species belonging to the genus Pseudoalteromonas is described. Two pale-orange-pigmented strains, KMM 300(T) and KMM 290, isolated respectively from a mussel, Crenomytilus grayanus, and a scallop, Patinopecten yessoensis, are marine, Gram-negative, aerobic, rod-shaped bacteria that produce a number of antimicrobial compounds. The strains are able to degrade gelatin, elastin, starch, DNA and Tween 80. Chitin and agar are not degraded. The isolates from marine invertebrates grew at NaCl concentrations of 1-9 % and a temperature range of 10-35 degreesC and did not utilize most of the wide range of carbohydrates tested, with the exception of D-glucose, cellobiose and sucrose. The DNA G+C content was 48.4-48.9 moll %. The level of DNA homology of the two strains was 98 %. DNA from the strains isolated from marine invertebrates showed 5-15 % genetic relatedness to the DNA of other type strains of the genus Pseudoalteromonas. 16S rRNA analysis indicated a clear affiliation of the novel bacteria to other species of the genus. The strains are assigned to a novel species, Pseudomonas ruthenica sp. nov., with the type strain KMM 300(T) (= LMG 19699(T) = CIP 106857(T)).
  • EP Ivanova, LS Shevchenko, TL Sawabe, AM Lysenko, Svetashev, VI, NM Gorshkova, M Satomi, R Christen, VV Mikhailov
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 52 263 - 271 1466-5026 2002/01 [Refereed][Not invited]
     
    A marine, Gram-negative, aerobic bacterium that produced cytotoxic, lemon-yellow, chromopeptide pigments that inhibited the development of sea urchin eggs has been isolated from the Australian sponge Fascaplysinopsis reticulata Hentschel. The cells of the organism were rod-shaped with a single polar flagellum and they required NaCl for growth (0.5-10%) with optimum growth at 1-3% NaCl. The temperature for growth was 10-37 degreesC, with optimum growth at 25-30 degreesC. Growth occurred at pH values from 6.0 to 10.0, with optimum growth at pH 6.8-8.0. Major phospholipids were phosphatidylethanolamine, phosphatidylglycerol and lyso-phosphatidylethanolamine. Of 26 fatty acids with 11-19 carbon atoms that were detected, 16:1omega7, 16:0, 17:1omega8 and 18:1omega7 were predominant. The DNA G+C content was 38.9 mol%. All of these phenotypic and chemotaxonomic characters place the organism in the genus Pseudoalteromonas (Gauthier et al., 1995). These data are consistent with the phylogenetic analyses that confirmed that strain KMM 636(T) is a member of the Pseudoalteromonas cluster in the gamma-subclass of the Proteobacteria. DNA-DNA hybridization experiments revealed that the levels of relatedness between the DNA of the strain studied and DNAs of type strains of the species that clustered together (on the basis of 16S rDNA sequences) and [Pseudoalteromonas aurantia] NCIMB 2033 ranged from 19 to 35%, and that the DNA-DNA homology between [P. aurantia] NCIMB 2033 and other phylogenetically and/or phenotypically similar type strains ranged from 32 to 52%. According to the polyphasic evidence presented in this study, it is proposed that strain KMM 636(T) (= LMG 19692(T) = CIP 106859(T)) be classified as Pseudoalteromonas maricaloris sp. nov. and [P. aurantia] NCIMB 2033 be reclassified as Pseudoalteromonas flavipulchra NCIMB 2033(T) (= KMM 3630(T) = LMG 20361(T)) sp. nov.
  • M Ootsubo, T Shimizu, R Tanaka, T Sawabe, K Tajima, M Yoshimizu, Y Ezura, T Ezaki, H Oyaizu
    JOURNAL OF APPLIED MICROBIOLOGY 93 (1) 60 - 68 1364-5072 2002 [Refereed][Not invited]
     
    Aims: To develop oligonucleotide probes for visualizing bacteria belonging to Enterobacteriaceae. Methods and Results: 24-mer oligonucleotide probe (probe D) was designed by comparison of 16S rDNA sequences of 35 species of Enterobacteriaceae, eight species of Vibrionaceae and six species of Pasteurellaceae. The sequence of the probe corresponding to the complementary sequence of a position 1251-1274 of Escherichia coli 16S rRNA was found to be a highly conserved region of 16S rDNA sequence in Enterobacteriaceae different from that of Vibrionaceae and Pasteurellaceae. The fluorescent dye-labelled probe was tested for the specificity by in situ hybridization and epifluorescence microscopy. Seventy-six out of 78 strains belonging to Enterobacteriaceae were visualized in an optimal hybridization condition. No bacterial strains belonging to Vibrionaceae (31 strains) and Gram-positive bacteria (three strains) were visualized. Conclusions: In situ hybridization using probe D allows the detection of bacterial cells belonging to Enterobacteriaceae without false positive reaction. Significance and Impact of the Study: In situ hybridization techniques using the probe D are potential tools for detecting Enterobacteriaceae in food and water samples.
  • T Sawabe, H Takahashi, Y Ezura, P Gacesa
    CARBOHYDRATE RESEARCH 335 (1) 11 - 21 0008-6215 2001/09 [Refereed][Not invited]
     
    A gene (alyPEEC) encoding an alginate lyase of Pseudoalteromonas elyakovii IAM 14594 was cloned using the plasmid vector pUC118 and expressed in Escherichia coli. Sequencing of a 3.0kb fragment revealed a 1,197bp open reading frame encoding 398 amino acid residues. The calculated molecular mass and isoelectric point of the alyPEEC gene product are 43.2 kDa and pI 5.29. A region G(165) to V-194 in the AlyPEEC internal sequence is identical to the N-terminal amino acid sequence of the previously purified extracellular alginate lyase of P. elyakovii, and the calculated molecular mass (25.4 kDa) and isoelectric point (pI 4.78) of the region resembled those of the purified enzyme. Expression of enzymically-active alginate lyase from alyPEEC required growth of recombinant E. coli in LB broth containing 50% (v/v) artificial seawater (ASW). Alginate lyase activity with broad substrate specificity was detected in both 42 and 30 kDa products. Subcloning of the region G(165) to N-398 of AlyPEEC corresponding to the 30 kDa protein confirmed that this region of the alyPEEC gene encoded the active site of the enzyme. A region A(32) to G(164) corresponding to about 13 kDa of the N-terminal region of AlyPEEC showed about 30% identity to a putative chitin binding domain of Streptomyces chitinases, but did not exhibit any catalytic activity. (C) 2001 Elsevier Science Ltd. All rights reserved.
  • J Kraiwattanapong, T Ooi, S Kinoshita, Sugimura, I, T Sawabe, Y Ezura
    WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY 16 (3) 219 - 224 0959-3993 2000/04 [Refereed][Not invited]
     
    Sixteen alginate lyases whose primary sequences have been reported were compared, and classified into the following three groups on the basis of the identity of their primary sequences. Strong homology (> 50%): A-AlgL, A-AlgL*, P-AlgL, P-AlgL*, and AlgA; weak homology (> 20%): ALY, AlxM, P-Aly, K-Aly, AlyPG, AlgVGI, AlgVGII, and AlgVGIII; little homology (< 20%): ALYII, Al-III, and AlgVMI. Using hydrophobic cluster analysis (HCA), a secondary structure prediction method, the sixteen alginate lyases were placed into the following classes. Class 1: AlgA, A-AlgL, A-AlgL*, P-AlgL, and P-AlgL*; Class 2: AlgVMI and Al-III; Class 3: ALY and AlxM; Class 4A: ALYII, K-Aly, P-Aly, and AlyPG; Class 4B: AlgVGI and AlgVGII; Class 5: AlgVGIII, which is put in a class of its own, because it is unlike any of the other alginate lyases.
  • T Sawabe, M Narita, R Tanaka, M Onji, K Tajima, Y Ezura
    NIPPON SUISAN GAKKAISHI 66 (2) 249 - 254 0021-5392 2000/03 [Refereed][Not invited]
     
    Spot-disease of Laminaria fronds has been occasionally observed in coastal areas of Hokkaido Japan. A huge outbreak of the disease occurred in Laminaria japonica near the southeastern part of Hokkaido in 1998. Three bacterial strains showing Laminaria-frond degrading activity were isolated from the spot-wounded fronds of L. japonica collected at Minamikayabe, Hokkaido, Japan. All the strains were tentatively identified as Alteromonas strain, and two of them were identified as Pseudoalteromonas elyakovii, of which the species included an alginolytic marine bacterium isolated from a spot-disease of Laminaria japonica var, ochotensis occurring at Rishiri Island at 1985. The phenotypic and genotypic characterizations of the Laminaria-frond degrading bacteria were described.
  • M Onji, T Sawabe, Y Ezura
    FISHERIES SCIENCE 66 (1) 38 - 43 0919-9268 2000/02 [Refereed][Not invited]
     
    Eighteen samples of virus-like growth suppression agents against the marine phytoplankton Alexandrium catenella, Gymnodinium mikimotoi and Tetraselmis sp., obtained from the coastal waters at the mouth of Funka Bay, Hokkaido, Japan, from 1993 to 1995, were characterized on size estimation, heat stability, nuclease sensitivity, proteinase K sensitivity, stability under acidic condition, titration, diethyl ether sensitivity, and ultraviolet (UV) sensitivity. All agents were affected by heating at 50 degrees C for 30 min, exposure to acidic conditions below pH 5.0, passing through a 0.05 mu m filter, RNase treatment, and irradiation of UV dosage at 5 x 10(4) mu W/s per cm(2). The growth suppression effects of 11 agents from Tetraselmis sp, and A. catenella disappeared after proteinase K treatment, however, seven agents from G. mikimotoi were unaffected by this treatment. Furthermore, 11 agents against Tetraselmis sp. and A. catenella were collected from the bottom fraction by ultracentrifugation, while seven agents against G, mikimotoi were collected from the upper fraction, not from the precipitated fraction. These results suggest that at least two types exist in the virus-like agents showing growth suppression for phytoplankton.
  • Kenshi Kuma, Akira Katsumoto, Naonobu Shiga, Tomoo Sawabe, Katsuhiko Matsunaga
    Marine Chemistry 71 (1-2) 111 - 123 0304-4203 2000 [Refereed][Not invited]
     
    Vertical distributions of size-fractionated Fe concentrations (< 0.025-μm, 0.025-0.22-μm, < 0.22-μm and > 0.22-μm fractions) and Fe(III) hydroxide solubilities were studied during a spring phytoplankton bloom (February to April, 1995) in Funka Bay, Japan. 'Soluble Fe' (< 0.025-μm fraction) concentrations were approximately 70% of the < 0.22-μm Fe fraction with the exception of a few deeper samples. During the spring bloom, the vertical profiles of soluble Fe were variable (0.3-13 nM), probably resulting from temporal variations of atmospheric input, bottom sediment resuspension, decomposition of sinking organic matter and biological removal in this bay water. High 'colloidal Fe' (0.025-0.22-μm fraction) concentrations (5-8 nM) were found in subsurface water near the shelf sediment interface (50-80-m depths, bottom depth of 92 m) after the spring bloom. The vertical changes of Fe(III) hydroxide solubilities appeared to have a small variation with low values (0.2-0.3 nM) throughout the water column during intense vertical mixing before the bloom, and to increase slightly during the beginning of the bloom (0.3-0.4 nM). The highest Fe(III) solubilities (0.8-0.86 nM) were found in the surface waters (2-10-m depths) during and after the peak of bloom. The high Fe(III) solubilities may be due to higher concentrations, or a stronger affinity of natural organic Fe(III) chelators that were possibly released by phytoplankton or bacteria. (C) 2000 Published by Elsevier Science B.V.
  • R Sato, T Sawabe, H Kishimura, K Hayashi, H Saeki
    JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 48 (1) 17 - 21 0021-8561 2000/01 [Refereed][Not invited]
     
    Alginate oligosaccharide (AO) was conjugated with carp myofibrillar protein (Mf) by using the controlled Maillard reaction, and the change in the solubility of Mf in low ionic strength media as affected by the glycosylation was investigated. AO was prepared by degrading sodium alginate using alginate lyase, which was purified from the culture supernatant of Pseudoalteromonas elyakovii. When a lyophilized Mf and AO mixture was incubated at 40 degrees C and 65% relative humidity, the conjugation of AO was confirmed at myosin heavy chain, actin, and tropomyosin. When > 30 mu g/mg of AO was conjugated to Mf, the protein solubility in a low ionic strength medium was greatly improved without significant loss of available lysine. These results indicate that the conjugation with AO is a superior manner for improving the water solubility of Mf in view of its nutritional aspect.
  • M Onji, T Sawabe, Y Ezura
    FISHERIES SCIENCE 65 (5) 687 - 693 0919-9268 1999/10 [Refereed][Not invited]
     
    Filtrable pathogens infecting the phytoplankton Alexandrium catenella and Tetraselmis sp. were screened from coastal seawater on the mouth of Funka flay, Hokkaido, Japan from 1993 to 1994. Growth suppression against these phytoplankton species was observed in the seawater samples collected during September and October 1993. The growth of A. catenella was suppressed from 40 to 45%, and that of Tetraselmis sp. was suppressed from 20 to 30%. Re-inoculation of the culture filtrate of growth-suppressed phytoplankton after passing the culture through a 0.22-mu m filter also caused growth suppression of the fresh culture. However, these effects disappeared after several treatments including heating at 50 degrees C for 30 min, exposure to acidic conditions below pH 5.0, passing through a 0.05-mu m filter, and Proteinase K and RNase treatment. Cell free extracts of the growth-suppressed phytoplankton caused the same extent of growth suppression. Electron microscopic observation of A. catenella cells that were lead to the growth suppression revealed that the cells were severely damaged, whereas no virus-like particles or bacterial cells were observed. Growth suppression was observed in a fresh culture of A. catenella and an axenic culture of Gymnodinium mikimotoi by the growth suppressed Tetraselmis sp. culture filtrate, and the A. catenella culture filtrate affected the growth of Tetraselmis sp. and an axenic culture of G. mikimotoi. However, the growth suppression or inhibition was not observed in fresh cultures of Prorocentrum micans, P. minimum, A. tamarense, G. mikimotoi, Chattonella antiqua, C. marina, and Heterosigma akashiwo. These results suggested that unique filterable pathogens might be found in the seawater samples.
  • K Takeuchi, K Tajima, MM Iqbal, T Sawabe, Y Ezura
    FISHERIES SCIENCE 65 (2) 264 - 268 0919-9268 1999/04 [Refereed][Not invited]
     
    Identification of the causative bacteria Vibrio spp., which were isolated from diseased sea urchin Strongylocentrotus intermedius and their rearing cages at low seawater temperatures at Date, Shiriuchi and Shikabe Fisheries Breeding Centers in Hokkaido was undertaken based on their biochemical properties, DNA-DNA homology and serological analysis. All fifteen strains, five from each Breeding Center were almost identical in biochemical properties except indole production. However, the strains isolated at Date differed from the strains at Shiriuchi and Shikabe in DNA-DNA homology and analysis of thermostable and thermolabile antigenic compositions. These results indicated that the strains from Shiriuchi and Shikabe belonged to the same species but they were different from those of Date. Moreover, the causative Vibrio spp. differed in biochemical, genotypical and serological properties from any strains of Vibrio spp. isolated from the intestine of healthy sea urchin and any of type strains of the genus Vibrio.
  • Yumoto, I, H Iwata, T Sawabe, K Ueno, N Ichise, H Matsuyama, H Okuyama, K Kawasaki
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY 65 (1) 67 - 72 0099-2240 1999/01 [Refereed][Not invited]
     
    A novel facultatively psychrophilic bacterium, strain S-1, which exhibits extraordinarily high catalase activity was isolated from the drain pool of a fish product processing plant that uses H2O2 as a bleaching and microbicidal agent. The catalase activity of the isolate was 1 or 2 orders of magnitude higher than those of Corynebacterium glutamicum, Staphylococcus aureus, Pseudomonas fluorescens, and five other species tested in this study. The strain seemed to possess only one kind of catalase, according to the results of polyacrylamide gel electrophoresis of the cell extract, The optimum temperature for catalase activity was about 30 degrees C, which was about 20 degrees C lower than that for bovine catalase activity. Electron microscopic observation revealed that the surface of the microorganism was covered by blebs, Although the isolate was nonflagellated, its taxonomic position on the basis of physiological and biochemical characteristics and analysis of 16S rRNA sequence and DNA-DNA relatedness data indicated that strain S-l is a new species belonging to the genus Vibrio. Accordingly, we propose the name Vibrio rumoiensis. The type strain is S-l (FERM P-14531).
  • MM Iqbal, K Tajima, T Sawabe, K Nakano, Y Ezura
    FISH PATHOLOGY 33 (4) 255 - 263 0388-788X 1998/10 [Refereed][Not invited]
     
    The phenotypic properties and genotypic characteristics of 44 aeromonads isolated from fish affected by epizootic ulcerative syndrome (EUS) in Southeast Asia were investigated. Among the 13 A. hydrophila phenospecies 9 were genotypically identical to A. hydrophila (HGl) and 4 were A. veronii biotype sobria (HG8Y) or A. veronii biotype sobria-related genospecies. All the 6 A. veronii biotype sobria phenospecies were placed in the same genospecies, A. veronii biotype sobria. Of the 12 A. jandaei phenospecies, 5 were A. veronii biotype sobria or A. veronii biotype sobria-related genospecies and 7 were A. jandaei genospecies. Of 13 Aeromonas isolates unspeciated by phenotyping 9 were genotypically identical to A. hydrophila or very similar to A. hydrophila and 2 isolates were A. veronii biotype sobria or very similar to A. veronii biotype sobria; 2 isolates could not be identified to genospecies level. These results strongly suggest that Aeromonas species from fish affected by EUS could not correctly be identified to the species level using various published biochemical schemes; it needs genetic identification like DNA-DNA hybridization.
  • T Sawabe, H Makino, M Tatsumi, K Nakano, K Tajima, MM Iqbal, Yumoto, I, Y Ezura, R Christen
    INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY 48 769 - 774 0020-7713 1998/07 [Refereed][Not invited]
     
    An aerobic, polarly flagellated marine bacterium that produces a prodigiosin-like pigment was isolated from the red-spotted culture beds of Laminaria japonica. Five isolates had unique bacteriolytic activity for both Gram-positive and -negative bacteria, which had never been observed among Alteromonas or spot related species, The isolates were identified as the causative agent or reo disease of L. japonica seeds. The phenotypic features of the isolates were similar to these of Pseudoalteromonas rubra ATCC 29570(T), but they could be differentiated using 10 traits (growth at 37 degrees C, requirement for organic growth factors, bacteriolytic activity, utilization of sucrose, N-acetylglucosamine, fumarate, succinate, D-galactose, L-proline and acetate). The G+C content of DNAs from the isolates was 44-46 mol%. The isolates constitute a new species, distinct from the other Alteromonas and Pseudoalteromonas species, as shown by DNA-DNA hybridization experiments and phylogenetic clustering of 16S rRNA gene sequences, for which the name Pseudoalteromonas bacteriolytica sp. nov. (type strain = IAM 14595(T)) is proposed. A set of phenotypic features which differentiate this new species from closely related Pseudoalteromonas and Alteromonas species is provided.
  • T Sawabe, C Sawada, E Suzuki, Y Ezura
    FISHERIES SCIENCE 64 (2) 320 - 324 0919-9268 1998/04 [Refereed][Not invited]
     
    Intracellular homo-and hetero-polymeric blocks degrading enzyme activity incapable of degrading intact sodium alginate was detected in Alteromonas sp. strain H-4. The enzyme activity for polyM and MG blocks was highest during the late log phase of the bacterium and was not induced by the addition of sodium alginate to the culture medium. The activity for MG random block was as high as that for polyM, but that for polyG block was half and that for sodium alginate was one fifth. At least 4 kinds of enzyme activities, a polyM specific, a MG-polyM specific, and two kinds of polyG specific enzymes, were detected from the crude intracellular fraction, but a trace spot for sodium alginate. Analysis of reaction products using a partially purified preparation of the enzyme indicated that the enzyme generated a saturated diuronate and an unsaturated polyuronide from polyM block. These results suggest that the intracellular enzymes can degrade only oligosaccharides generated from high molecular alginate by the extracellular alginate lyase and may have an important role in the alginate metabolism of the bacterium.
  • Yumoto, I, K Yamazaki, T Sawabe, K Nakano, K Kawasaki, Y Ezura, H Shinano
    INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY 48 565 - 571 0020-7713 1998/04 [Refereed][Not invited]
     
    Novel Cram-negative alkaliphilic strains were isolated from soil obtained from Atsuma, Hokkaido, Japan. The isolates were strictly aerobic rods that produced subterminally located ellipsoidal spores. Chemotaxonomic characteristics of the isolates included the presence of meso-diaminopimelic acid in the cell wall and a DNA G+C content of 40.2-40.9 mol%. The major isoprenoid quinone was menaquinone-7 and the cellular fatty acid profile consisted of a significant amount of 15.C branched-chain acids, iso-C-15:0 and anteiso-C-15:0. The growth rate was higher at ph 8-10 than at ph 7. Comparative sequence analysis of 16S rDNA of 14 alkaliphilic Bacillus strains indicates that the isolated strain has an equidistant relationship to three already defined rRNA groups of alkaliphilic Bacillus species. Based on the morphological and physiological characteristics, as well as phylogenetic position as determined by 16S rDNA analysis and DNA-DNA relatedness data, it is concluded that these isolates should be designated as a new species, for which the name Bacillus horti is proposed. The type strain is K13(T)(= JCM 9943(T)).
  • T Sawabe, Y Ezura, H Yamamoto
    PLANT CELL REPORTS 17 (2) 109 - 112 0721-7714 1997/12 [Refereed][Not invited]
     
    A continuous-flow culture system was developed for culturing Laminaria japonica protoplasts. Protoplasts were settled on 5-mu m pore size nylon mesh fixed inside a 50-ml plastic syringe, and cultured in Provasoli's enriched seawater with iodine medium with a gentle upward flow generated by a peristaltic pump. In the culture system, 50% of the protoplasts regenerated their cell wall within 24 hours and almost all protoplasts regenerated a cell wall after 3 days culture. After cell wall regeneration, a number of cells divided and regenerated into sheet-shaped thalli. The thalli transferred to a tissue culture flask developed into sporophyte-like plantlets within 1 month. Plantlets then differentiated into blade, stipe, and holdfast, with a proper mucilage canal.
  • T Yoshinaka, M Yoshimizu, T Sawabe, Y Ezura
    FISHERIES SCIENCE 63 (4) 592 - 595 0919-9268 1997/08 [Refereed][Not invited]
     
    A method based on reverse transcription (RT)-polymerase chain reaction (PCR) was established for detection and identification of infectious hematopoietic necrosis virus (IHNV). A set of primers was prepared for amplification of a 510 bp nucleotide which encodes a region of IHNV nucleoprotein (N) gene. The PCR product was confirmed as the IHNV specific nucleotide by southern hybridization with an oligonucleotide probe synthesized from the N gene. The PCR was able to amplify the target sequence from five representative strains of IHNV from Japan and North America. There was no PCR product from five other fish rhabdoviruses. Viruses from ovarian fluid of masu salmon collected at Shibetsu River, Ichani River in Hokkaido and kidney tissue of rainbow trout in Aichi Prefecture were isolated and identified using the RT-PCR.

Books etc

  • 濵﨑 恒二, 木暮 一啓, 澤 辺智雄, 澤辺 桃子, 鈴木 聡, 砂村 倫成, 永田 俊, 春田 伸, 福田 秀樹, 美野 さやか, 和田 実, 濵﨑 恒二, 木暮 一啓 (Joint work)
    恒星社厚生閣 2015/09 (ISBN: 4769915683) 280
  • The Prokaryotes 4th edition
    B. Gomez-Gil, C.C. Thompson, Y. Matsumura, T. Sawabe, T. Iida, R. Christen, F.T. Thompson, T. Sawabe (ContributorFamily Vibrionaceae)
    Springer 2014
  • 海藻バイオ燃料
    澤辺 智雄 (Contributorマリンビブリオを活用した海藻からのエタノール生産)
    CMC出版 2011
  • The Biology of Vibrios
    SAWABE Tomoo (ContributorThe mutual partnership between Vibrio halioticoli and abalones)
    ASM Press 2006
  • Thompson, Fabiano Lopes, Austin, B. (Brian), Swings, J. G., American Society for Microbiology 
    ASM Press 2006 (ISBN: 1555813658) xiii, 423 p.

Works

  • 養殖コンブの疾病調査
    2000
  • Research on disease of Laminaria
    2000

MISC

Awards & Honors

  • 2000/04 日本水産学会 日本水産学会奨励賞

Research Grants & Projects

  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2019/04 -2023/03 
    Author : 澤辺 智雄, 美野 さやか
     
    化石燃料代替エネルギー生産技術開発は，学術的・社会的要請が高い地球規模課題である。海洋バイオマスのエネルギー変換技術の開発もその一つであるが，アルギン酸などの難燃料化成分が多く，その完全変換にはさらなる技術革新が必要である。我々が見いだした新規マリンビブリオは，Hyf複合体を核とするギ酸水素リアーゼ（FHL）複合体を介した独特の水素代謝を示し，海藻由来の種々の糖を水素化する。しかし，マリンビブリオ触媒の水素生成能を高める分子育種基盤の構築は発展途上であり，海洋バイオ水素生産性向上のボトルネックでもある。Hyf複合体の分子レベルで特徴を理解するためには，マリンビブリオは恰好の生物材料であるため，本研究では，マリンビブリオが有する活性型Hyf複合体の特徴を理解し，多彩な海洋バイオマスからのより効率的な水素生成が可能な海洋微生物触媒の構築にフィードバックさせる知見を得ることを目的に研究を進めた。その結果以下の成果を得た。 ①バイオ水素生成マリンビブリオ全種の完全ゲノムの取得 水素生成能が観察されているほぼ全種を含む17種のビブリオ科細菌の完全ゲノムを取得した。遺伝子構造に基づき，主に3タイプに分かれることを明らかにした。 ②水素生成マリンビブリオ触媒の能力比較 上記17種のうち，水素生成が確認できる12種について，グルコースを基質とした場合の水素生成プロファイルを調べたところ，ギ酸の再取り込み量が水素生成と相関することを明らかにした。
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Research (Exploratory)
    Date (from‐to) : 2019/06 -2021/03 
    Author : Sawabe Tomoo
     
    Using sea cucumber as a model of marine invertebrate, 1) pioneer and/or first colonizer candidates were mined, 2) these bacterial strains and genome data were collected, and 3) these MALDI-TOF-MASS data were accumulated.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2016/04 -2020/03 
    Author : Sawabe Tomoo
     
    Aims of the study are to understand physiology and genomics of hydrogen production marine vibrios. We did achieve 1) optimized synthetic medium, 2) physiological and genome comparison among hydrogen producing marine vibrios, 3) a RNA-Seq, and 4) effects of nitrogen fixation on hydrogen production. We also discovered a new marine vibrio which is capable of producing hydrogen from alginate.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research
    Date (from‐to) : 2016/04 -2018/03 
    Author : Sawabe Tomoo
     
    An aim of the study is to develop marine microbial biocatalysts implemented multiple substrate utilizing phenotypes based on consolidated biological processing (CBP) in efficient biofuel production. We created new marine vibrio biocatalysts showing 1) polyuronide-sugar alcohol-glucan utilizing phenotype and 2) higher ethanol producing phenotype from D-galactose.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research
    Date (from‐to) : 2014/04 -2016/03 
    Author : Sawabe Tomoo, HOSOKAWA MASASHI
     
    An aim of the study is to develop light-driven marine vibrio biocatalysts in efficient biofuel production. We performed 1) gene expression of a Nonlabens sediminis proteorhdopsin gene, and 2) a cloning of a myxol synthetic gene cluster of Nonlabens ulvanivorans. We also accumulated fundamental knowledge on CRISPR/Cas system for further developments of a genome editing approach working in marine vibrio cells.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2013/04 -2016/03 
    Author : Sawabe Tomoo, HOSOKAWA MASASHI, NAKAGAWA SATOSHI
     
    Aims of the study are to establishment of 1) continuous culture system and 2) biorefinery of hydrogen producing marine vibrios as biocatalysts. We did succeeded 1) continuous hydrogen production for 70 days with appropriate hydrogen producing rates and yields, 2) alginate-hydrogen conversion using 2 kinds of biocatalysts, and 3) bioprospects of new and rare carotenoid producers and their genome information.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research
    Date (from‐to) : 2011 -2013 
    Author : SAWABE Tomoo, HOSOKAWA Masashi, NAKAGAWA Satoshi
     
    In maintaining a sustainable ecosystem in this period of global warming, development of key technologies in the field of renewable energy sources has become an important challenge; a method of biofuel production from marine biomass could be one of the most crucial technologies in the future. In this study, we performed global transcriptome, fermentation product profiling, and metabolic engineering to design marine vibrio cells with efficient ethanol production from marine biomass.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research
    Date (from‐to) : 2011 -2012 
    Author : NAKAGAWA Satoshi, TAKAI Ken, SAWAB Tomoo, SUZUKI Yohey
     
    The main objective of this study is to reveal mechanisms by which deep-sea vent animals and their symbionts sense and respond to environmental fluctuations. By using the high-throughput sequencing technique, meta-transcriptome analysis from a deep-seahydrothermal vent gastropod species was performed. This study lead to the identification of biological processes underlying physiological adaptation to deep-sea vent environments.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2009 -2012 
    Author : SAWABE Tomoo, OJIMA Takao, NAKAGAWA Satoshi
     
    In maintaining a sustainable ecosystem in this period of global warming, development of key technologies in the field of renewable energy sources has become an important challenge; a method of biofuel production from marine biomass could be one of the mostcrucial technologies in the future. In this study, we investigated genome wide metabolic pathway prediction, functional analysis of the genes responsible for the alginate degradation and ethanol production, and the transcriptomic analysis in two unique marine vibrios, both of which are capable of producing bioethanol from seaweed carbohydrates. We successfully reconstructed the metabolic pathway with functional and transcriptomic information as a marine vibrio platform.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (A)
    Date (from‐to) : 2008 -2010 
    Author : NAKAGAWA Satoshi, TAKAI Ken, MAKITA Hiroko, SAWABE Tomoo
     
    The main objective of this study is to reveal the molecular mechanisms underlying symbiont-host relationship in deep-sea hydrothermal vent environments. We have focused on sugar chains, glycans. We have succeeded in detection, profiling, structure determination of glycans for both symbionts and their host animals. Glycans having quite unique structures were identified.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2007 -2010 
    Author : OJIMA Takao, INOUE Akira, TANAKA Hiroyuki, SAWABE Tomoo
     
    Herbivorous marine gastropods like abalone and sea hare possess various polysaccharide-degrading enzymes which can degrade seaweeds' polysaccharides such as alginate, laminaran, mannan, xylane, and cellulose to oligo- and monosaccharides. These saccharides are considered to be metabolized via glycolytic pathway and TCA cycle. In the present study, we isolated several polysaccharide-degrading enzymes, e.g., alginate lyase, laminarinase and mannanase, from abalone and sea hare and investigated their biological roles in the metabolism of seaweeds' polysaccharides in gastropods.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2005 -2008 
    Author : YOSHIMIZU Mamoru, TAJIMA Kenichi, NISHIZAWA Toyohiko, SAWABE Tomoo, KASAI Hisae
     
    20℃以上に調温した0.3mg/Lの塩素を含む電解海水あるいは中圧紫外線処理海水を用い、V. alginolyticus優勢キートセロスを給餌しながら浄化すれば、カキが痩せることなく、大腸菌、ノロウイルスおよびV. parahaemolyticusを排除できると考えられる。さらに安全性を確保するために2,000気圧の高静水圧をかけて脱殻を行えば、安全性はより向上する。
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2003 -2005 
    Author : KUDO Isao, MONTANI Shigeru, SAITOH Sei-ichi, SAWABE Tomoo
     
    Chemical substances and biochemical parameters were measured in the subarctic coastal region which receives fresh water and nutrients from the Tokachi River, one of the largest river in Japan. River discharge increased ten times after April due to a spring thaw and continued until June. In the coastal region, nutrients were depleted after a spring bloom which occurred in April. River plume area showed an elevated concentration of nutrients and iron originated from the Tokachi River. High concentration of chlorophyll a was observed only in the river plume because outside the plume nutrients were depleted. The mainstream of the Tokachi River and its tributaries showed different concentration of nutrients. This may be attributed to the different type of land use, i.e., farming, dairy farming, forest and city sewage plants. We also investigated the heterotrophic microbial process (microbial loop) which is related to the fate of organic carbon produced by phytoplankton. The abundance of heterotrophic bacteria was higher in the river plume than off shore region. Dissolved organic carbon was also higher in the plume. Riverine organic matter may accelerate the growth of heterotrophic bacteria in the plume. The mortality of bacteria was investigated by a dilution culture experiment. Virus infection was accounted for more than 80% of the mortality. The regenerated organic carbon may contribute to the further bacterial production.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2002 -2004 
    Author : YOSHIMIZU Mamoru, TAJIMA Kenichi, NISHIZAWA Toyohiko, SAWABE Tomoo
     
    Oysters (Crassestrea gigas) harvested from major cultivation areas are commonly contaminated with Escherichia coli. Also, some places, oyster concentrates small rounded structured virus (SRSV ; norovirus). It's very important to remove the E.coli, food born bacteria and norovirus. E.coli has to be removed from oysters during oyster purification by re-laying in a non-polluted seawater. Although sodium hypochlorite or UV irradiation is used to disinfect seawater, it's difficult to treat large volumes of seawater. Recently the bactericidal and virucidal effects of hypochlorite produced by electrolysis of seawater were examined against pathogenic bacteria and viruses. SRSV (norovirus) is not able to replicate in the established cell line, and its difficult to determine the virus infectivity. This virus is belonging to family Caliciviridae, and cat pathogenic virus ; FCV that is able to replicate in cat cell line. In this study, virucidal effects of UV irradiation, hypochlorite and high pressure on FCV infectivity were studied to eliminate the FCV from oyster. Stability of FCV in sea water and intestinal contents of oyster was also studied. FCV was inactivated at the dose of 1.0x10^4 micro W・sec/cm^2, electrolyzed seawater chlorine concentration controlled at 0.20〜0.4mg/L, and 800MPa・40℃・5min FCV infectivity decreased rapidly in sea water at the temperature 20℃ or high. In the intestinal contents of oyster, FCV was inactivated by antiviral substances produced by intestinal bacteria. These results indicate that combination of 3 conditions ; (1)using a electrolyzed sea water containing the 0.3 mg/L hypochlorite, (2)harvest in sea water at the temperature 20℃ or high, (3)remove the shell using a 800 MPa・at 40℃ for 5 min. Seawater electrolyzers have ability to treat large volumes of water and cost performance of this method is better than that of UV irradiation. From these results, it is considered that electrolysis of seawater could be a useful method for post harvest elimination of norovirus from oysters.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2001 -2004 
    Author : YOSHIMIZU Mamoru, SAWABE Tomoo, UENISHI Toshio
     
    In Japan, because many seafood products are distributed without being heated, generally there is a danger of their quality deteriorating sharply with the passage of time at each stage after fishing. This makes temperature control important in order to inhibit growth of pathogens and spoilage organisms. Reliable hygiene and sanitation controls at all stages from fishing until products reach consumers are vital. The basic approach involves, at every stage from fishing, prevention of products pathogens, maintaining temperatures below set levels, thoroughly controlling the water and ice used, preventing damage to raw material, and minimal processing time. Clean crushed ice is stored in a sanitary ship hold. Fish are preserved in the hold filled with clean seawater and ice. Establishment of seawater disinfection method is very important, because Eschericia coli and coli forms were isolated from seawater in almost of all fishing port. A pathogen-free water source is essential, and treatment with ultraviolet light is used widely. UV treatment is limited the volume. Hypochlorite produced by electrolysis of seawater showed bactericidal and virucidal effects. This method can easily treat large volumes of seawater, and is suitable for disinfecting sea water for hygiene and sanitation at a fishing port. Dssinfection of seawater pomp up from the fishing port was investigated using electrolyzed seawater. Viable bacterial counts of electrolyzed seawater from port were decreased and this water was useful to disinfect the deck and hatch of fishing boat, fish selection board, quay, and the market floor at a fishing port.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2001 -2003 
    Author : ITABASHI Yutaka, ANDO Yasuhiro, SAWABE Tomoo
     
    The aim of this study was to clarify the distribution and physiological function of unusual glycerophospho- and glycolipids in marine organisms. For this purpose, chiral phase HPLC, reversed-phase HPLC and reversed-phase HPLC in conjunction with electrospray ionization mass spectrometry(ESI-MS) were applied to the separation and identification of stereoisomeric and regio-isomeric glycerolipids. Using these techniques, we found an unnatural phosphatidylglycerol (1,2-diacyl-sn-glycero-3-phospho-3'-sn-glycerol, R, R configurations at the two chiral centers) from various kinds of microorganisms including marine bacteria. The R, R isomer content increased with increasing culture temperature. The results strongly suggest that the bacteria adapt to temperature by alternating not only the degree of unsaturation but also the stereoisomer composition of phosphatidylglycerols. In the present study, we also investigated the separation and identification of the reverse isomers of glycerophospholipids (PtdCho,PtdEtn,PtdIno) and glycoglycerolipids (MGDG,DGDG,SQDG) by reversed-phase HPLC/ESI-MS. These glycerolipids were chromatographed as intact forms or 3,5-dinitrophenylurethanes of the 1,2-diacyl-sn-glycerols derived from the parent molecules. Excellent resolution was achieved for reverse isomers of very different pairs of acyl groups, such as 20:5-16:0 and 22:6-16:0, on highly efficient C18 columns. Using the method, we analyzed the glycerolipids from some fish and marine algae, and found that only MGDG from marine red algae, such as Porphyra yezoensis and Gracilaria verrucosa, gave two clearly resolved peaks, representing the reverse isomers of 20:5(sn-1)/16:0(sn-2) and 16:0(sn-1)/20:5(sn-2), and 20:4(sn-1)/16:0(sn-2) and 16:0(sn-1)/20:5(sn-2), respectively. The present method provides the first direct demonstration of the occurrence of reverse isomers in natural glycoglycerolipids and should be helpful in promoting work on the biosynthetic pathway and physiological importance of the reverse isomers in the red algae.
  • 日本学術振興会：科学研究費助成事業 若手研究(B)
    Date (from‐to) : 2001 -2002 
    Author : 澤辺 智雄
     
    本年度の成果は以下の通り。 1.アワビ消化管内細菌叢の抗生物質添加飼料を用いた人工的置換 Vibrio halioticoliは、ペニシリン系、セファロスポリン系、およびクロラムフェニコール(CP)に高い感受性を示した。この中で最小発育阻止濃度の低いベンジルペニシリン(PCG)とCPをそれぞれ0.5-50mg/50gおよび1.5-150mg/50g飼料となるように混合したアワビ配合飼料を1ヶ月間エゾアワビに給餌し、アワビ消化管からのV. halioticoliの除去を試みた。その結果、50mg PCGおよび150mg CP添加飼料給餌区でV. halioticoliの比率は30%から0.04%に減少し、総菌数は10^8cells/9(消化管)から2桁減少した。しかし、生菌数は減少せず10^6CFU/g(消化管)を維持していたが、飼育試験終了時にはPolaribacter sp.が優占し、細菌叢は変化した。次に、アワビ消化管内細菌叢の完全除去を目指し、PCG-CP添加飼料給餌区で残存したPolaribacter sp.に高い感受性を示すセフォタキシム(CTX)を添加したPCG-CP-CTX添加飼料を調製し、飼育試験を試みたが、総菌数および生菌数を著しく減少させる条件を見いだすまでには至らなかった。 2.緑色蛍光タンパク質(GFP)標識V. halioticoliにおけるGFP発現条件の検討 GFP標識V. halioticoli株について細胞単位でのGFP蛍光発現条件の至適化やGFP発現細胞の検出限界時間などを検討した。その結果、GFP発現細胞の比率は培養温度15℃で高く、また、嫌気培養条件(ガスパック法)下においては、好気条件下よりも比率は10%低下するものの、GFP発現細胞は観察された。さらに、15℃-好気条件下でGFPを発現させた細胞は、15-25℃下では滅菌海水中で4日以内までは正確に検出できた。このGFP標識株を用いたトレーサー実験が今後の課題となった。
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
    Date (from‐to) : 2000 -2002 
    Author : TAJIMA Kenichi, SAWABE Tomoo
     
    The survival in low water temperature, detection method in VBNC state and resuscitation from VBNC condition of the bacterium Flexibacter sp., the pathogen of spotting disease of sea urchin Strongylocentrotus intermedius, were examined. The important results obtained were as follwos: 1. The pathogen lost its colony forming ability in 75% ASW at 5℃ after 15 days of incubation. This state was clarified as VBNC state. In VBNC state the bacterial cells became short rod or round in shape and lost its pathogenicity to sea urchin. 2. A primer set was constructed based on the 16S rRNA sequences for detection of the bacterium. The primer set was specific for the bacterium. 3. The VBNC cells resuscitated by temperature up-shift from 5° to 25℃ in 75% ASW in the presence of 0.0017% (approximately 60μM Fe) ferric chloride solution and in 75% ASW containing homogenated sea urchin. The morphology of the resuscitated cell was similar to that of the original cell, they showed positive reaction in agglutination test against rabbit antiserum moreover, the cells regained pathogenicity to sea urchin. From the above results it is clear that during low water temperature the cells enter into VBNC state, but survive in that condition by adhering to surface fo sea urchin. The findings also clearly indicate that when the water temperature increases the VBNC cells resuscitate and cause disease to the sea urchin.
  • Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
    Date (from‐to) : 2000 -2001 
    Author : SAEKI Hiroki, SAWABE Tomoo, NAKAMURA Soichiro
     
    Fish meat has excellent food functionalities such as gel-forming ability, emulsifying ability, and water-holding ability. However, fish myofibrillar ptotein (Mf) is thermally and chemically less stable than that of other vertebrates and its functional properties are rapidly impaired with progress of protein denaturation. To improve the functional properties and the thermal stability, Mf was conjugated with alginate oligosaccharide (AO : Mean degree of polymerization=6) through the Maillard reaction under controlled humidity states. 1. The improved functional changes of Mf by the conjugation with AO are as follows : (1) The solubility of Mf in low salt concentration (<0.16M) was significantly improved by conjugation with AO and the ionic strength dependence of the solubility was completely lost. (2) The water soluble Mf thus obtained had excellent thermal stability (no aggregation at 80 ℃ for 3h). (3) The emulsifying properties of Mf was also improved by conjugation with AO. (4) Good digestivity of Mf was remained after the conjugation. 2. Bactertial mutagenesis tests and animal dose test were examined to evaluate the food safety of Mf-AO conjugate. (1) No mutagenecity of Mf-AO conjugate was confirmed by rec-assey and Ames-test. (2) Mf-AO conjugate was nontoxic for oral administration to rats. The results of this study indicate that the conjugation with AO with alginate oligosaccharide through the Maillard reaction is a good manner to improve food functionalities of fish meat as a foodstuff.
  • 日本学術振興会：科学研究費助成事業 奨励研究(A)
    Date (from‐to) : 1999 -2000 
    Author : 澤辺 智雄
     
    本年度は、海洋細菌由来のプラスミッドの探索とそれらのプラスミッドを用いた形質転換の可能性について検討し、以下の結果を得た。 1.海洋細菌由来新規プラスミッドベクターの探索 海水試料から分離した100株の海洋細菌からプラスミッド様核酸を保持するの菌株の探索を行い、5菌株がプラスミッド様核酸を有していた。前年度の成果により、3菌株のプラスミッド保持菌株を見いだしたが、本研究課題で計8菌株が得られた。これら8菌株のプラスミド様核酸に抗生物質耐性マーカー遺伝子が存在するか否かを調べるために、エレクトロポレーション法により、大腸菌JM109株の形質転換を試みた。その結果、OM918-2-6株およびH8株のプラスミッドが、大腸菌内で複製可能で、しかもアンピシリン耐性遺伝子がコードされている可能性が示唆された。 2.Pseudoalteromonas elyakoviiのアルギン酸分解酵素遺伝子を高発現する海洋細菌宿主の探索 P.elyakoviiからクローン化したアルギン酸分解酵素遺伝子alyPEECを挿入した3種類のプラスミッド(pTPB24、pTPB31、pCD11)を用い、2種のアルギン酸非分解性海洋細菌P.haloplanktis IAM12915^TおよびP.tetraodonis IAM14610^Tをエレクトロポレーション法により、形質転換することを試みたが、いずれのプラスミッドとも両海洋細菌で複製しえなかった。 本研究で見いだされたアンピシリン耐性プラスミッドの遺伝子地図の作成とこれらのプラスミッドを安定して保持、複製できる海洋細菌宿主の探索が急務となった。
  • Ministry of Education, Culture, Sports, Science and Technology：Grants-in-Aid for Scientific Research(基盤研究(B))
    Date (from‐to) : 1997 -2000 
    Author : Yoshio EZURA, Tomoo SAWABE, Mamoru YOSHIMIZU, Kenichi TAJIMA
     
    Aim of the project has been orientated to clarify physiological and ecological functions of gut microbes living in gut of marine herbivores. The project has directed to obtain many excellent results for understanding an abalone-gut microbes interaction as follows ;1. Changes of the gut microflora of abalone were corresponding to a time when a feeding behavior of abalone was changed.2. One of the dominant microbes in the gut of abalone was Vibrio halioticoli, which was identified as a new species of Vibrio.3. Three kinds of V.halioticoli specific identification methods were developed based on 1) 16S rDNA PCR/RFLP, 2) colony hybridization, and 3) in situ PCR.4. Use of the V.halioticoli-specific identification method clarified the interesting distribution.1) V.halioticoli was distributed in seawater in/around an abalone farm, and likely to attach on a surface of microalgae. The bacterium may be reached with the microalgae into the gut of abalone. A change of gut environments creating by a change of the feeding behavior caused the bacterium dominancy in the gut.2) V.halioticoli was also distributed in abalones, H.discus discus, H.diversicolor supertexta, and H.diversicolor diversicolor ; and a turban shell, Turbo cornatus, living in Japan. The bacterium was not isolated from Australian, South African and French abalones.5. Fingerprinting analysis suggested an occurrence of host specific polymorphism among V.halioticoli strains isolated from various abalones.6. Four genes encoding alginate degrading enzymes of V.halioticoli IAM14596^T were cloned and sequenced.7. Preliminary experiment for an artificial substitution of gut microflora of abalone Haliotis discuss hannai using antibiotics-containing diet resulted that an occupation rate of V.halioticoli in the gut of the abalone was decreased below 0.1%.8. Main fermentation products from alginate by V.halioticoli IAM 1459^T were determined as acetic acid and formic acid.
  • Ministry of Education, Culture, Sports, Science and Technology：Grants-in-Aid for Scientific Research(基盤研究(B))
    Date (from‐to) : 1997 -2000 
    Author : Mamoru YOSHIMIZU, 渡辺 研一, 三村 元, 上西 敏夫, Tomoo SAWABE, Yoshio EZURA, Toshio UENISHI, Kenichi WATANABE, Hajime MIMURA
     
    Water supplies often provide an efficient means for the introduction and spread of infectious desease. Pathogen-free water sources are often essential for success in aquaculture. The surface waters commonly used in aquaculture come from coastal waters or rivers and may contain the fish pathogens. Such open water supplies should be used prior treatment to kill the fish pathogens. Disinfection of wastewater before discharging is better for the environment.Usually, the treatment systems make use of high efficiency sand filters to clarify the water before treatment with ultraviolet(UV)light or ozonation. Fish pathogens are divided into 2 groups based on their sensitivity to UV and TROs. Sensitive viruses include infectious hematopoietic necrosis virus(IHNV), Oncorhynchus masou virus(OMV), lymphocystis virus(LCDV)and Japanese flounder rhabdovirus(HIRRV), and Gram-negative bacteria. These microorganisms are inactivated or killed by treatment with 10^4μW・sec/cm^2(UV dose)or 0.1mg/L(TROs)for 1min. Resistant viruses include infectious pancreatic necrosis virus(IPNV), marine birnavirus, reovirus and fish nodavirus, Gram-positive bacteria, fungi and parasite which are inactivated with a dose of 106μ W・sec/m^2 or 0.5mg/L(TROs)for 1min. Ozonated seawater containing TROs is toxic to fixh, thus it should be removed by charcoal before using.Bactericidal and virucidal effects of hypochlorite produced by Electrolysis of seawater(salt water)are examined. More than 99.99% cells of V.anguillarum and A.salmonicida were killed when the bacteria were exposed to 0.1 mg/L hypochlorite for 1 min. Yellowtail ascites virus(YAV)and hirame rhabdovirus(HIRRV)were inactivated>99099% after treatment with 0.58 mg/L hypochlorite for 1 min. Using for wastewater, more than 99% of viable bacteria in waste-seawater was reduced treated with 0.5mg/L of total residual chlorite for 1min. The bactericidal effects of electrolysis were almost same as that of ultraviolet irradiation(1.0×10^5μW・sec/cm^2)or ozonization(TROs 0.5mg/L, 1min)of seawater. This method is easy to treat large volume of water, so it suits to disinfection of wastewater.
  • 文部科学省：科学研究費補助金(奨励研究(A))
    Date (from‐to) : 1996 -1996 
    Author : 澤辺 智雄
     
    本年度に得られた成果は以下の通りである。I.ウニ・アワビ消化管由来アルギン酸分解菌の種構成と分解特異性エゾバフンウニ消化管から分離したアルギン酸分解菌はその一般性状からVibrio属と同定されたものが大半を占めていたが、代表株についてDNA-DNA相同性を測定した結果、少なくとも2菌種以上が混在していることが明らかとなった。一方、エゾアワビ消化管から分離したアルギン酸分解菌は非運動性のVibrio属類似細菌が主体をなしていた。これらの菌群は16SrDNA塩基配列による分子系統解析およびアルギン酸分解性Vibrio属標準株とのDNA-DNA相同性を測定した結果、Vivrio属の新種であることが明らかとなった。また、ウニ消化管由来アルギン酸分解菌のアルギン酸分解特異性はアルギン酸を構成するpolyMおよびpolyGいずれのホモポリマーとも分解する菌株が30%以上を占めているのに対し、アワビ分離株ではpolyGブロックに対する分解性の強い菌株が30-70%占めていた。ウニ自体はアルギン酸分解酵素を分泌しないことから、消化管内細菌がアルギン酸分解の大部分を担っていると考えられた。一方、アワビはpolyM特異的な分解酵素を分泌することから、アワビ消化酵素で分解されにくい部分を分解する消化管内細菌が定住していることが示唆された。II.アルギン酸分解酵素の特性ウニ由来アルギン酸分解菌代表株Ud10株は基質特異性を示さないNaCl要求性の強い酵素を誘導的に産生していた。一方、アワビ由来アルギン酸分解菌A431株はpolyG特異的分解酵素以外にも、基質特異性の異なる6種類以上の酵素を産生しており、その中でpolyMに強い特異性を示す分解活性画分およびpolyGに強い特異性を示す分解活性画分の部分精製物について酵素化学的性状を調べた。それぞれの画分の至適反応温度は40℃および30℃と異なっていたが、至適反応温度(pH7.5)および塩類の要求性(100mM NaCl)は同様の性質を示した。
  • 文部科学省：科学研究費補助金(基盤研究(C))
    Date (from‐to) : 1996 -1996 
    Author : 久万 健志, 志賀 直信, 澤辺 智雄
     
    1、(1)紫外線を照射して有機物を除去した海水の含水酸化鉄の溶解度(20℃)は、天然海水に比べ著しく低く、その値は【less than or equal】0.1nMであった。(2)含水酸化鉄の溶解度の高い沿岸水(天然有機リガンドを含む)と紫外線を照射して得られた溶解度の低い沿岸水(有機リガンドを除去した)における沿岸性植物プランクトン(珪藻)の鉄添加増殖実験から、紫外線を照射した海水ではその増殖速度は遅くなる。このことは、天然海水に存在する有機リガンドが溶存鉄濃度を高め、より生物に使われやすい溶存形態になっていると思われる。2、(1)北海道噴火湾でのスプリングブルーム前の鉛直混合期(2月上旬)には、海水における含水酸化鉄の溶解度は低く、ほぼ一定値(0.2-0.3nM)を示した。しかしながら、ブルーム最盛期(3月中旬)には20m以浅で最大値(0.7-0.8nM)に達し、ブルーム終了後においても高い溶解度が維持された。これは、植物プランクトン、バクテリア等から放出された有機リガンドによるものと推察され、藻類による鉄の取り込みに重要な影響を与えていると考えられる。しかしながら、溶解度とクロロフィル-a濃度とは必ずしも相関性がなく、すべての植物プランクトンが有機リガンドを放出しているとは考えられない。(2)ブルーム前後における珪藻類優占種の変動は、ブルーム前から最盛期(2月〜3月中旬)にかけてThalassiosira nordenskioldiiが最も優占し、最盛期以降(3月中旬以降)にChaetoceros compressumやChaetoceros concavicorneに遷移した。このことは、ある種の植物プランクトンが有機リガンドを放出している可能性を示している。またある種の海産性バクテリアにもシドロフォアのような有機リガンドを放出することが確認された。以上の結果から、沿岸海水には3価鉄と溶存有機鉄錯体を形成する有機リガンドが存在しており、沿岸域での生物生産に重要な役割を果たしていると
  • Ministry of Education, Culture, Sports, Science and Technology：Grants-in-Aid for Scientific Research(一般研究(B), 基盤研究(B))
    Date (from‐to) : 1994 -1996 
    Author : Mamor YOSHIMIZU, Toyohiko NISHIZAWA, Tomoo SAWABE, Kenichi TAJIMA, Yoshio EZURA
     
    Viral disease is a serious problems of fish in hatchery. Especially, viral nervous necrosis of marine fish and infectious hematopoietic necrosis of salmonids are difficult to control. In this study, we studied and established the highly sensitive and specific diagnostic method to detect the virus specific gene using polymerase chain reaction (PCR) method. Results obtained in this study are summarized as follow.1. Striped jack nervous necrosis virus (SJNNV) coat protein gene and infectious hematopoietic necrosis virus (IHNV) N protein gene were amplified by polymerase chain reaction (PCR) an could apply for the specific and sensitive diagnosis of VNN and IHN.2. Rainbow trout embryo (RTE-2) and sea bass kidney (SBK-2) cell lines were selected for the isolation of IHNV and NNV.3. Method of the simultaneous detection and identification of both IHNV and infectious pancreatic necrosis virus (IPNV) in a single PCR reaction was developed.4. Fish nodaviruses were clasified into 4 clusters by molecular phylo-genetic analysis of the coat protein gene.5. Combination of RT-PCR and antibody screening by ELISA was effective method for the identification of nervous necrosis viurs carriers in a flounder brood stock.
  • 文部科学省：科学研究費補助金(奨励研究(A))
    Date (from‐to) : 1995 -1995 
    Author : 澤辺 智雄
     
    本年度に得られた成果は以下の通りである。1.海産微細藻類感染ウイルスの探索と特性北海道噴火湾沿岸海水から海産微細藻類の増殖に影響を与えるウイルスの探索を試み、濃縮した海水の0.45μmろ過性画分に渦鞭毛藻、Alexandrium catenella、Gymnodinium mikimotoiおよびProrocentrum sp.の3藻類の増殖を抑制する現象を見出した。A.catenellaおよびG.mikimotoiに対し増殖抑制効果を示すろ過性因子は、今年度(1995年)と昨年度の9月〜10月に採水した海水に認められ、その抑制効果は40〜90%の範囲であった。また、Prorocentrum sp.に対し増殖抑制効果を示すろ過性因子は1993年9月〜10月に採水した海水に見い出され、その抑制効果は20〜30%であったが、今年度は観察されなかった。いずれの藻類増殖抑制因子とも孔径0.45μmおよび孔径0.22μmのフィルターを通過させた後でも抑制効果は持続した。同様の増殖抑制因子は調査を行なった3年間とも9月〜10月にのみ見出され、季節変動が観察された。Prorocentrum sp.、A.catenellaおよびG.mikimotoiの各増殖抑制因子は0.22μm以上の孔径のフィルターを増殖抑制効果の低減なしに通過したが、孔径0.05μmフィルターでのろ過では増殖抑制効果が消失した。さらに、1993年の海水試料から検出されたProrocentrum sp.、A.catenellaの増殖抑制因子は50℃、30分の加熱およびRNase処理により増殖抑制効果が消失した。また、超遠心沈降画分のネガティブ染色像の観察により長さ約400nm、幅約30nmの屈曲棒状のウイルス様構造体が観察された。これらの特性から、本藻類増殖抑制因子が植物ウイルスに多く見られる屈曲棒状のRNAウイルスである可能性が示唆された。II.海産大型藻類感染ウイルス培養系の構築マコンブプロトプラストの連続培養系を考案し、プロトプラストの再生率を向上させることができた。この培養系はマコンブ感染ウイルスの分離に応用が期待される。
  • 文部科学省：科学研究費補助金(奨励研究(A))
    Date (from‐to) : 1993 -1993 
    Author : 澤辺 智雄
     
    海洋細菌Alteromonas sp.H-4株の培養上清から精製したアルギン酸分解酵素を5mM HEPES-25mM MgCl_2-50%天然海水-0.7Mマンニトールに対し透析し、アルギン酸分解活性を30U/mlに調整し、1.5%Cellulase Onozuka R-10(Yakult本社)を添加したものを細胞壁分解酵素液とし、マコンブ芽胞体からプロトプラストの単離を試みた。15℃で反応を行った結果、約1時間後からプロトプラストの遊離が認められ、反応3時間後には藻体1g当たり4.5×10^6cells、5時間後には1.3×10^7cellsのプロトプラストが得られた。得られたプロトプラストは球形、黄金色で10〜25mumの大きさであった。また、ニュートラルレッド染色法によりほとんどの細胞が生存していることが確認された。さらにプロトプラストの収量と生存率を高める反応条件を検討した結果、プロトプラストの単離にはアルギン酸分解酵素の他にセルラーゼが必須であり、高張液の組成は海水濃度が50%、MgCl_2濃度は50〜100mM、緩衝液成分は5mMHEPES、マンニトールの濃度は0.5Mとした場合が至適であった。本条件下(MgCl_2濃度は25mM、反応3時間)で得られたプロトプラストの収量は5.2×10^6cells/g、生存率は98%であった。対照として市販のアワビアセトンパウダー(Sigma社)をアルギン酸分解酵素源とし、同一条件下で反応を行った場合ではプロトプラストの単離が認められず、Alteromonas sp.の産生するアルギン酸分解酵素の有効性が明らかとなった。また、マコンブプロトプラストの培養を試み、培養液への抗生物質の添加はプロトプラストの再生に悪影響を及ぼすことが明らかとなった。上記の至適培養条件下で単離したプロトプラストをProvasoliのESI培地で5℃、35001x、12h:12h明暗周期の条件下で培養を行ったところ、培養2〜3日目に細胞壁が再生し、6日目から分裂細胞が観察され始め、その後さらに繰り返し分裂した細胞も認められた。本結果からマコンブプロトプラスト培養系の確立が進展すると期待される。
  • 水産無脊椎動物の腸内細菌に関する研究
  • 海洋細菌の産生するアルギン酸分解酵素に関する研究
  • Studies on intestinal microflora of marine invertebrates
  • Studies on alginate degrading enzymes produced by marin bacteria.

Educational Activities

Teaching Experience

  • Inter-Graduate School Classes(General Subject):Natural and Applied Sciences
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 大学院共通科目
    キーワード : 水産科学，海洋生物学，生物多様性，生物資源, 環境, 資源探査, 漁業技術, 持続可能性, 環境保全, 養殖, 遺伝学, 生命工学, 微生物学, 化学，食糧科学,生物安全性
  • Inter-Graduate School Classes(General Subject):Natural and Applied Sciences
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 大学院共通科目
    キーワード : Bioinformatics, Biology, Marine Microbiology
  • Career Management Seminar
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 水産科学院
    キーワード : キャリアマネジメント（Career Management）、　研究マネジメント（Research Management）、すべての仕事に必要な基本スキル（Transferable Skills）、イノベーション　（Innovation）、マーケティング（Marketing）、知的財産（Intellectual Property）、プレゼンテーション（Presentation）、アントレプレナーシップ（Entrepreneurship）、発想法（Method of thinking）、企業における研究開発（Industrial R&D）、リーダーシップ（Leadership）、グローバル人材（Global Human Resource）
  • Step-up career education I
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 水産科学院
    キーワード : 企業　研究開発　実際の業務　キャリアパス　多様性
  • Step-up career education II
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 水産科学院
    キーワード : 企業　研究開発　実際の業務　キャリアパス　多様性
  • Introduction to Fisheries Sciences Ⅱ
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 水産科学院
    キーワード : 水産科学，海洋生物学，生物多様性，生物資源, 環境, 資源探査, 漁業技術, 持続可能性, 環境保全, 養殖, 遺伝学, 生命工学, 微生物学, 化学，食糧科学,生物安全性
  • Introduction to Fisheries Sciences Ⅰ
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 水産科学院
    キーワード : 水産科学，海洋生物学，生物多様性，生物資源, 環境, 資源探査, 漁業技術, 持続可能性, 環境保全, 養殖, 遺伝学, 生命工学, 微生物学, 化学，食糧科学,生物安全性
  • Advanced Marine Biotechnology and Microbiology Ⅰ
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 水産科学院
    キーワード : 生化学、微生物学、細胞工学、魚病学、微生物生態学、分子生物学、酵素化学
  • Advanced Marine Biotechnology and Microbiology Ⅱ
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 水産科学院
    キーワード : 生化学、微生物学、細胞工学、魚病学、微生物生態学、分子生物学、酵素化学
  • Inter-Graduate School Classes(General Subject):Inter-Disciplinary Sciences
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 大学院共通科目
    キーワード : 企業　研究開発　実際の業務　キャリアパス　多様性
  • Inter-Graduate School Classes(General Subject):Inter-Disciplinary Sciences
    開講年度 : 2021
    課程区分 : 修士課程
    開講学部 : 大学院共通科目
    キーワード : キャリアマネジメント（Career Management）、　研究マネジメント（Research Management）、すべての仕事に必要な基本スキル（Transferable Skills）、イノベーション　（Innovation）、マーケティング（Marketing）、知的財産（Intellectual Property）、プレゼンテーション（Presentation）、アントレプレナーシップ（Entrepreneurship）、発想法（Method of thinking）、企業における研究開発（Industrial R&D）、リーダーシップ（Leadership）、グローバル人材（Global Human Resource）
  • Introduction to Oceanography
    開講年度 : 2021
    課程区分 : 学士課程
    開講学部 : 水産学部
    キーワード : 海底地形、海洋大循環、熱/物質循環、プランクトン、海底資源、海洋観測、海洋法、海洋生物資源の保全
  • Environment and People
    開講年度 : 2021
    課程区分 : 学士課程
    開講学部 : 全学教育
    キーワード : 生物資源，資源利用，機能性，マリンバイオマス，環境保全，マリンバイオテクノロジー，有効利用，高度利用，ゼロエミッション，SDGs
  • Health and Society
    開講年度 : 2021
    課程区分 : 学士課程
    開講学部 : 全学教育
    キーワード : 魚、海藻、食生活、加工保蔵、嗜好性、栄養成分、機能性、健康、安全性
  • Marine Microbiology
    開講年度 : 2021
    課程区分 : 学士課程
    開講学部 : 水産学部
    キーワード : 微生物、多様性、物質循環、マリンバイオテクノロジー
  • Microbiology
    開講年度 : 2021
    課程区分 : 学士課程
    開講学部 : 水産学部
    キーワード : 細菌、真菌、ウイルス、海洋微生物、微生物生態、病原性、免疫、
  • Laboratory Works on Microbiology
    開講年度 : 2021
    課程区分 : 学士課程
    開講学部 : 水産学部
    キーワード : 微生物、細菌計数、細菌同定、細菌特異検出、細胞培養、ウイルス培養
  • English for Fisheries Sciences I
    開講年度 : 2021
    課程区分 : 学士課程
    開講学部 : 水産学部
    キーワード : 水産生命科学英語、水産技術英語
  • Environment and People
    開講年度 : 2021
    課程区分 : 学士課程
    開講学部 : 全学教育
    キーワード : 海、河川、生命、細胞、遺伝子、魚、海藻、微生物、代謝、進化

Campus Position History

  • 2015年4月1日 
    - 
    2017年3月31日 
    企画・経営室室員

Position History

  • 2015年4月1日 
    - 
    2017年3月31日 
    企画・経営室室員

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