MF研究者総覧

研究者データベース

詳細
美野　さやか(ミノ　サヤカ)
水産科学研究院　海洋応用生命科学部門　海洋生物工学分野
助教
researchmap個人ページ
Last Updated :2024/05/09

基本情報

所属

  • 水産科学研究院　海洋応用生命科学部門　海洋生物工学分野

職名

  • 助教

学位

  • 博士（水産科学）（北海道大学）

J-Global ID

研究キーワード

  • ゲノム   バイオ燃料   応用微生物   海洋微生物   微生物行動学   分散   微生物生態学   生物地理   化学合成独立栄養微生物   深海底熱水活動域   Epsilonproteobacteria   

研究分野

  • ライフサイエンス / 応用微生物学
  • ライフサイエンス / 生態学、環境学
  • ライフサイエンス / 水圏生命科学

担当教育組織

職歴

  • 2015年04月 - 現在 北海道大学 大学院水産科学研究院 助教
  • 2012年04月 - 2015年03月 日本学術振興会 特別研究員DC1

学歴

  • 2010年04月 - 2015年03月   北海道大学   大学院水産科学院   海洋応用生命科学専攻
  • 2006年04月 - 2010年03月   北海道大学   水産学部   増殖生命科学科

所属学協会

  • 極限環境生物学会   マリンバイオテクノロジー学会   日本微生物生態学会   

研究活動情報

論文

  • 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 2023年11月03日 
    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年10月24日 
    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年09月29日 
    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.
  • Yutaro Inohara, Jiang Chunqi, Sayaka Mino, Tomoo Swabe
    Current microbiology 80 5 143 - 143 2023年03月20日 
    The use of un-utilized feedstock and seawater for material and/or energy production using marine microbial catalysts is one potential option toward contributing to the development of a more sustainable society. Ethanol production from alginate, which is an oxidized polysaccharide present in brown seaweed, is extremely difficult due to the imbalance of reducing power in the microbial cells. Production of ethanol by such means has so far been unsuccessful using marine microbial biocatalysts. To produce ethanol from alginate, an alternative pathway consisting of a pyruvate decarboxylase gene (pdc) and an alcohol dehydrogenase II gene (adhII) derived from Zymomonas mobilis strain ZM4 was implemented into a metabolically engineered bacterium, Vibrio halioticoli, which is a representative marine alginate decomposer. No ethanol from alginate was produced in the wild-type V. halioticoli; however, the engineered V. halioticoli harboring the pdc and adhII operon (Pet operon), designated to the V. halioticoli (Pet), was able to produce 880 mg/L ethanol in maximum from 1.5% alginate for 72 h. The Pet operon also worked on the other marine alginolytic vibrios for ethanol production from alginate. This is the first case of ethanol production from alginate using marine bacterial biocatalysts under seawater-based media.
  • 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年 
    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年 
    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年12月03日 
    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年11月10日 
    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 2022年11月
  • 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年10月 
    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年09月15日 
    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年03月23日 
    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年 
    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年01月 
    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年12月22日 
    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年12月14日 
    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.
  • Sayaka Mino, Taiki Shiotani, Satoshi Nakagawa, Ken Takai, Tomoo Sawabe
    Systematic and applied microbiology 44 1 126170 - 126170 2021年01月 [査読有り][通常論文]
     
    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).
  • Taiki Shiotani, Sayaka Mino, Wakana Sato, Sayo Nishikawa, Masanori Yonezawa, Stefan M. Sievert, Tomoo Sawabe
    PLoS ONE 15 12 December e0241366  2020年12月 [査読有り]
     
    © 2020 Shiotani et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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 60oo (optimum, 60oo), at pH values between 5.4 and 8.6 (optimum, pH 6.6) and in the presence of 2.4–3.2% (w/v) Naol (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 (= JoM 32893T = KoTo 15925T). In addition, it is shown that “Nitratiruptor labii” should be transferred to the genus Nitrtosophilus; the name Nitrosophilus labii comb. nov. (JoM 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 = JoM 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  2020年12月01日 [査読有り]
     
    Copyright 2020 Yamazaki et al. 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.
  • Yohei Yamazaki, Yuichi Sakai, Sayaka Mino, Tomoo Sawabe
    Aquaculture Research 51 9 3602 - 3608 2020年09月 [査読有り]
     
    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年08月15日 [査読有り][通常論文]
     
    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.
  • Mami Tanaka, Daiki Kumakura, Sayaka Mino, Hidetaka Doi, Yoshitoshi Ogura, Tetsuya Hayashi, Isao Yumoto, Man Cai, Yu-Guang Zhou, Bruno Gomez-Gil, Toshiyoshi Araki, Tomoo Sawabe
    Environmental microbiology 22 8 3205 - 3217 2020年08月 [査読有り][通常論文]
     
    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.
  • Juline M Walter, Felipe H Coutinho, Luciana Leomil, Paulo I Hargreaves, Mariana E Campeão, Verônica 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 2020年02月14日 [査読有り][通常論文]
     
    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 CCMR0081T (= CBAS 745T) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081T 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 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.
  • 水素生成マリンビブリオのギ酸水素リアーゼ(FHL)複合体遺伝子群の構造比較
    西川 紗代, 田仲 真実, 美野 さやか, 澤辺 智雄, 小椋 義俊, 林 哲也
    日本細菌学雑誌 75 1 80 - 80 日本細菌学会 2020年01月
  • 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 2020年01月 [査読有り][通常論文]
     
    Two novel strains C4III282T and C4III291 were isolated from seawater collected a site off the Taketomi coral reef. Phylogenetic analysis based on the 16S rRNA sequences revealed that the two strains belong to the genus Vibrio. MLSA using eight protein-coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) showed that C4III282T and C4III291 are closely related to the members of the Ponticus clade, namely Vibrio panuliri JCM 19500T, Vibrio ponticus DSM 16217T, and "Vibrio rhodolitus" G98. ANI and in silico DDH values with members of the Ponticus clade were 77.6-78.7% and 22.2-23.1, respectively. The name Vibrio taketomensis sp. nov. is proposed with C4III282T (CAIM 1928T=DSM 106943T=JCM 33434T) as the type strain.
  • Yohei Yamazaki, Yuichi Sakai, Sayaka Mino, Wataru Suda, Masahira Hattori, Pedro Milet Meirelles, Fabiano Thompson, Tomoo Sawabe
    Environmental microbiology reports 11 6 797 - 807 2019年12月 [査読有り][通常論文]
     
    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 2019年03月 [査読有り][通常論文]
     
    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年 [査読有り][通常論文]
     
    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)).
  • ニッケル輸送体遺伝子型は海洋ビブリオの水素産生能と相関する(Type of nickel transporter genes correlate with ability of hydrogen production in marine vibrios)
    松村 佑太, 美野 さやか, 丸山 史人, 小椋 義俊, 林 哲也, 黒川 顕, 澤辺 智雄
    日本細菌学雑誌 73 1 72 - 72 2018年02月
  • 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 2018年01月 [査読有り][通常論文]
  • Mami Tanaka, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, Tomoo Sawabe
    PeerJ 6 e5018  2018年 [査読有り][通常論文]
     
    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 genome 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 genomes of five Rumoiensis clade species: Vibrio aphrogenes, V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall genome 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 from Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA.
  • 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年 [査読有り][通常論文]
     
    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.
  • Sayaka Mino, Naoki Yoneyama, Satoshi Nakagawa, Ken Takai, Tomoo Sawabe
    Frontiers in bioengineering and biotechnology 6 184 - 184 2018年 [査読有り][通常論文]
     
    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.
  • 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 e0180053  2017年12月 [査読有り][通常論文]
  • 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年12月 [査読有り][通常論文]
  • 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  2017年12月 [査読有り][通常論文]
  • Hisashi Muto, Yoshihiro Takaki, Miho Hirai, Sayaka Mino, Shigeki Sawayama, Ken Takai, Satoshi Nakagawa
    MICROBES AND ENVIRONMENTS 32 4 330 - 335 2017年12月 [査読有り][通常論文]
     
    RNA-based microbiological analyses, e.g., transcriptome and reverse transcription-quantitative PCR, require a relatively large amount of high quality RNA. RNA-based analyses on microbial communities in deep-sea hydrothermal environments often encounter methodological difficulties with RNA extraction due to the presence of unique minerals in and the low biomass of samples. In the present study, we assessed RNA extraction methods for deep-sea vent chimneys that had complex mineral compositions. Mineral-RNA adsorption experiments were conducted using mock chimney minerals and Escherichia coli total RNA solution, and showed that detectable RNA significantly decreased possibly due to adsorption onto minerals. This decrease in RNA was prevented by the addition of sodium tripolyphosphate (STPP), deoxynucleotide triphosphates (dNTPs), salmon sperm DNA, and NaOH. The addition of STPP was also effective for RNA extraction from the mixture of E. coli cells and mock chimney minerals when TRIzol reagent and the RNeasy column were used, but not when the RNeasy PowerSoil total RNA kit was used. A combination of STPP, TRIzol reagent, the RNeasy column, and sonication resulted in the highest RNA yield from a natural chimney. This indirect extraction procedure is simple, rapid, inexpensive, and may be used for large-scale RNA extraction.
  • Ryousuke Nagata, Yoshihiro Takaki, Akihiro Tame, Takuro Nunoura, Hisashi Muto, Sayaka Mino, Shigeki Sawayama, Ken Takai, Satoshi Nakagawa
    SYSTEMATIC AND APPLIED MICROBIOLOGY 40 6 352 - 356 2017年09月 [査読有り][通常論文]
     
    A moderately thermophilic, strictly anaerobic, chemoautotrophic bacterium, designated strain HS1857(T), was isolated from a deep-sea hydrothermal vent at the Noho site in the Mid-Okinawa Trough. Strain HS1857T grew between 35 and 63 degrees C (optimum 55 degrees C), in the presence of 10-55 g1(-1) NaC1 (optimum 25 g1(-1)), and pH 5.5-7.1 (optimum 6.4). Growth occurred with molecular hydrogen as the electron donor and elemental sulfur, nitrate, or selenate as the electron acceptors. Formate could serve as an alternative electron donor with nitrate as an electron acceptor. During growth with nitrate as the electron acceptor, strain HS1857(T) produced ammonium and formed a biofilm. CO2 was utilized as the sole carbon source. The G + C content of the genomic DNA was 33.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain HS1857(T) is a member of the order Nautiliales, showing a sequence similarity of 95.0% with Lebetimonas acidiphila Pd55(T). The fatty acid composition was similar to that of L. acidiphila, which was dominated by C-18:0 (47.0%) and C-18:1 (23.7%). Based on the genomic, chemotaxonomic, phenotypic characteristics, the name Lebetimonas natsushimae sp. nov., is proposed. The type strain is HS1857(T) (=NBRC 112478(T) = DSM 104102(T)). 2017 Elsevier GmbH. All rights reserved.
  • 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 2017年07月 [査読有り][通常論文]
     
    Two phylogenetically distinct Vibrionaceae strains C4I1189(T) and C4V358(T) 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 C411189(T) (=DSM 101554(T) = JCM 31629(T)) (type species) and Thaumasiovibrio subtropicus sp. nov. strain C4V358(T) (=DSM 101555(T) = JCM 31630(T)). Thaumasiovibrio species were phylogenetically distinct from the other Vibrionaceae species based on pyrH gene sequences. The combination of catalase negative, sensitivity to vibriostatic agent 0/129, and green colony formation on TCBS for the phylogenetically affiliated strains was the diagnostic features for the current tentative identification of this genus. (C) 2017 Elsevier GmbH. All rights reserved.
  • 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  2017年06月 [査読有り][通常論文]
     
    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)).
  • 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
    ISME JOURNAL 11 4 909 - 919 2017年04月 [査読有り][通常論文]
     
    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.
  • 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  2016年08月 [査読有り][通常論文]
     
    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.
  • 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 - 335 2016年07月 [査読有り][通常論文]
     
    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 Glade. 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 Glade species. The G + C contents of the Vibrio ishigakensis strains were 47.3-49.1 mol%. 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 Glade species. Sixteen traits (growth temperature range, DNase and lipase production, indole production, and assimilation of 10 carbon compounds) distinguished these strains from Halioticoli Glade species. The names V. ishigakensis sp. nov. is proposed for the species of Halioticoli Glade, with C1T as the type strain (JCM 19231(T) =LMG 28703(T)). (C) 2016 Elsevier GmbH. 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  2016年02月 [査読有り][通常論文]
     
    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.
  • 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 2015年09月 [査読有り][通常論文]
     
    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.
  • 遠藤 祥子, 美野 さやか, 澤辺 智雄
    日本生物工学会大会講演要旨集 平成27年度 201 - 201 (公社)日本生物工学会 2015年09月
  • 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 2015年08月10日 [査読有り][招待有り]
     
    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), fhlA-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.
  • 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 e0136279  2015年08月 [査読有り][通常論文]
     
    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.
  • 目指せ!細菌学の星☆2015 深海底熱水活動域における固有甲殻類血清の性状解析(We'll be the stars of bacteriology! 2015 Hemagglutination activity in the serum of deep-sea vent endemic crab)
    藤吉 奏, 福島 大介, 和辻 智郎, 美野 さやか, 澤辺 智雄, 澤山 茂樹, 高井 研, 中川 聡
    日本細菌学雑誌 70 1 113 - 113 2015年02月
  • 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  2014年11月 [査読有り][通常論文]
  • Sayaka Mino, Hideaki Kudo, Takayuki Arai, Tomoo Sawabe, Ken Takai, Satoshi Nakagawa
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 64 Pt 9 3195 - 3201 2014年09月 [査読有り][通常論文]
     
    A novel mesophilic, strictly hydrogen-oxidizing, sulfur-, nitrate- and thiosulfate-reducing bacterium, designated strain Monchim33(T), was isolated from a deep-sea hydrothermal vent chimney at the Central Indian Ridge. The non-motile, rod-shaped cells were Gram-stain-negative and non-sporulating. Growth was observed between 15 and 37 degrees C (optimum 33 degrees C; 3.2 h doubling time) and between pH 5.4 and 8.6 (optimum pH 6.0). The isolate was a strictly anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. The G+C content of the genomic DNA was 42.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate belonged to the genus Sulfurovum and was closely related to Sulfurovum sp. NBC37-1 and Sulfurovum lithotrophicum 42BK(T) (95.6 and 95.4% similarity, respectively). DNA DNA hybridization demonstrated that the novel isolate could be differentiated genotypically from Sulfurovum sp. NBC37-1 and Sulfurovum lithotrophicum. On the basis of the molecular and physiological traits of the new isolate, the name Sulfurovum aggregans sp. nov. is proposed, with the type strain Monchim33(T) (=JCM 19824(T)=DSM 27205(T)).
  • 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 2014年01月 [査読有り][通常論文]
     
    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.
  • 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 2014年 [査読有り][通常論文]
     
    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.
  • 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 2014年 [査読有り][通常論文]
     
    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.
  • 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 2014年 [査読有り][通常論文]
     
    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.
  • 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 2014年 [査読有り][通常論文]
     
    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.
  • 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 4 414  2013年12月 [査読有り][通常論文]
     
    To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V tritonius sp. nov., which is a member of the "Porteresiae" clade.
  • 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  2013年04月 [査読有り][通常論文]
     
    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.
  • Hiroshi Izumi, Takuro Nunoura, Masayuki Miyazaki, Sayaka Mino, Tomohiro Toki, Ken Takai, Yoshihiko Sako, Tomoo Sawabe, Satoshi Nakagawa
    EXTREMOPHILES 16 2 245 - 253 2012年03月 [査読有り][通常論文]
     
    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)).

書籍

  • Sayaka Mino and Satoshi Nakagawa (担当:分担執筆範囲:Deep-Sea Vent Extremophiles: Cultivation, Physiological Characteristics, and Ecological Significance)
    CRC Press 2018年 (ISBN: 9781498774925)
  • 美野さやか, 海に魅せられた北大の研究者たち (担当:共著)
    海文堂出版 2018年 (ISBN: 9784303800017)
  • 水圏微生物学の基礎
    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 (担当:共著)
    恒星社厚生閣 2015年09月 (ISBN: 4769915683)

その他活動・業績

受賞

  • 2015年03月 北海道大学 大塚賞
     
    受賞者: 美野 さやか
  • 2015年03月 北海道大学大学院水産科学院 はるにれ賞
     
    受賞者: 美野 さやか
  • 2014年 JAMSTEC BLUE EARTH’14 若手奨励賞
     
    受賞者: 美野 さやか
  • 2012年 JAMSTEC BLUE EARTH’12 若手奨励賞
     
    受賞者: 美野 さやか

共同研究・競争的資金等の研究課題

  • 日本学術振興会：科学研究費助成事業
    研究期間 : 2021年04月 -2023年03月 
    代表者 : 美野 さやか
     
    世界各地の深海底熱水孔環境には微生物の一次生産に立脚した独自の生態系が形成される。これまでの多遺伝子座配列解析（MLSA）法を用いた研究から、現場のコスモポリタン微生物であるSulfurimonas属細菌は、海域特有の遺伝的多様性を有することが明らかとなった。しかしながら、 MLSAではゲノム全体の多様性はもとより、遺伝的多様性が微生物の表現型へ与える影響を明らかにするには程遠い。また、現在の分布様式が成立した過程を理解するに至っていない。本研究の目的は、培養依存および培養非依存的手法を組み合わせ、熱水孔環境への適応進化を明らかにするとともに、熱水孔コスモポリタン微生物の分布形成過程を理解することにある。令和3年度は、これまでに研究代表者等が取得した、沖縄トラフ熱水活動域由来Sulfurimonas属に属する分離株から代表株を選別し、Nanoporeシーケンスを活用した完全ゲノムの取得により、ゲノムワイドな変異解析に必要な知見の収集を進め、以下の結果を得た。 ・中部沖縄トラフ熱水孔環境から分離したSulfurimonas autotrophicaのうち、代表株22株のゲノムシーケンスを実施した。このうち8株の完全ゲノムをIlluminaとNanoporeリードを用いたハイブリッドアッセンブリ法により決定した。完全ゲノムが取得できなかった株についても、completenessが96%以上のアセンブリを取得した。
    ・139個のsingle-copy core genes（SCGs）の塩基配列に基づく系統解析の結果、これら22株は遺伝的に二つのクレードにわけられることが明らかになった。この傾向はこれまでのMLSAによる系統解析でも認められていたものであるが、一部の分離株においてMLSAとSCGに基づく系統解析で属するクレードが異なった。
  • 日本学術振興会：科学研究費助成事業 基盤研究(B)
    研究期間 : 2019年04月 -2023年03月 
    代表者 : 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の完全ゲノム比較:得られた完全ゲノムに基づく比較を行い，1)ビブリオ科の共通祖先はhyf型FHLを保有していた可能性が示唆された、2)水素生成能の高いPorteresiaeクレードの2種はhupEが失っていることが示唆された、3)水素生成能に影響するHFLクラスター構造の変異が明らかになった。 ②水素生成マリンビブリオ触媒の能力比較:プロトノフォアを用いたV. tritoniusの細胞生理学実験により，ある種のプロトノフォアで細胞内のギ酸塩漏出に伴う水素生成能の現象が観察された。 この種の細菌の高い水素生成能とギ酸取り込みとの関連性を支持する結果を得た。 ③遺伝子工学：V. tritoniusのFHL要素としてのギ酸脱水素酵素遺伝子産物の構造予測と遺伝子クローニングを進めた。
  • 日本学術振興会：科学研究費助成事業 挑戦的研究(萌芽)
    研究期間 : 2019年06月 -2021年03月 
    代表者 : 澤辺 智雄, 美野 さやか
     
    宿主ー微生物間相互作用の知見拡充に向け，海洋無脊椎動物の一つのモデルとしてナマコ類に着目し，その初期成長に関連する微生物の解析を進め，1)パイオニア微生物あるいは初期定着微生物群の推定，2) 易培養性のパイオニアあるいは初期定着微生物のゲノム情報コレクションの取得，3) 棘皮動物付随細菌のMALDI-TOF-MASSデータベースの整備を進め，多くの新知見を得た。
  • 日本学術振興会：科学研究費助成事業 若手研究(B)
    研究期間 : 2017年04月 -2021年03月 
    代表者 : 美野 さやか
     
    本研究の目的は、深海底熱水活動域に生息するコスモポリタン微生物の環境適応戦略を多角的に明らかにするとともに、熱水孔環境に生息する微生物の遺伝的多様性解析からみる分布様式の理解から新たな海洋循環評価法の基盤を構築することにある。平成30年度は、日本近海の浅海および深海熱水活動域に注目し、1) 沖縄トラフ最南端の浅海熱水フィールド由来試料（堆積物および噴出熱水）の微生物群集構造解析、2) 深海熱水フィールド由来の新たな優占種の分離培養および遺伝子情報解析、3) 新たな浅海熱水フィールドからの試料採取および微生物株の分離培養を中心的に進め、以下の結果を得た。 ・沖縄トラフ最南端に位置する台湾亀山島浅海熱水フィールドの噴出熱水および堆積物を対象とした16Sメタゲノム解析の結果、噴出熱水と堆積物では微生物群集を構成する微生物種が大きく異なった。堆積物試料ではEpsilonproteobacteria綱およびGammaproteobacteria綱が優占しており、Epsilonproteobacteriaの占める割合は熱水孔から離れるにつれて増加する傾向が認められた。 ・八重山諸島竹富島の北東部海域に位置する竹富海底温泉から熱水性試料を採取し、常温菌から好熱菌にわたる10株の分離培養に成功した。この中には、Epsilonproteobacteria綱に属するものは分離されなかったものの、新種の可能性を持つものが含まれていた。 ・沖縄トラフ伊平屋北・伊是名海穴・鳩間海丘熱水フィールドのEpsilonproteobacteria綱Sulfurovum属を新たに分離培養し、MLSA法による遺伝的多様性解析を行った。その結果、深海熱水フィールド間での明確な地理的隔離は認められず、これらの間では遺伝子交流が生じている可能性が示唆された。
  • 日本学術振興会：科学研究費助成事業 基盤研究(B)
    研究期間 : 2016年04月 -2020年03月 
    代表者 : 澤辺 智雄, 美野 さやか
     
    水素社会の形成に向けて水素生成技術基盤の強固化が求められている。研究代表者が見いだした新規マリンビブリオは，海藻に含まれるユニークな炭水化物群を効率よく水素化するため，日本発の海洋生物資源を活用した水素生産技術となり得る。しかし，海洋微生物 を活用したバイオ水素変換技術の基盤，特にマリンビブリオの水素生成能を高める分子育種技術は未成熟であり，水素生産性の向上にはボトルネックとなっている。そこで，本研究では，水素生成能の高いマンビブリオが有する水素生成分子マシナリーの細胞生理学的 特性と遺伝子発現制御の解明および分子育種の進展を目的とした。特に，本年度は，Vibrio tritonius のHyfの特性の解明とアルギン酸から水素を生成可能な新規ビブリオの比較ゲノム解析を進め以下の結果を得た。 1.V.tritonius AM2T株の種々のNaCl濃度下における水素生成キネティクスを測定し，0.5%から1.0% NaCl存在下で水素生成能は高いものの，海水存在下において水素生成が可能である細菌であるとの特徴付けを行った。 2.アルギン酸から水素を生成するV. aphrogenesでは，アルギン酸を基質とした場合の水素生成モル収率がD-グルコースを基質とした場合のそれとほぼ同程度であることを明らかにした。 3. V. ahrogenesと単系統性が強く示唆される全6種の完全ゲノムを取得し，比較ゲノムを行い，アルギン酸から水素を生成する代謝系に関連する遺伝子を保有しているのは，V. aphrogenesのみであることを明らかにした。
  • 日本学術振興会：科学研究費助成事業 挑戦的萌芽研究
    研究期間 : 2016年04月 -2018年03月 
    代表者 : 澤辺 智雄, 美野 さやか
     
    より効率的に海藻原料をバイオ燃料へと生物変換するために，多彩な糖質で構成される海洋バイオマスの効率的利用に適応可能な複数基質の糖化と発酵を統合（一貫バイオプロセス（CBP）化）した生物触媒の開発を行い，①アルギン酸分解性マリンビブリオを核としてポリウロン酸，糖アルコール，グルカンを利用可能な海洋細菌触媒および②増殖能が高いマリンビブリオを核としてガラクトースからもエタノール生産性の高い株を得た。
  • 日本学術振興会：科学研究費助成事業 研究活動スタート支援
    研究期間 : 2015年08月 -2017年03月 
    代表者 : 美野 さやか
     
    本研究の目的は、深海底熱水孔環境に普遍的に優占する化学合成独立栄養微生物を対象に、それらの持つ環境適応能の多角的解明と、それらのもつエネルギー代謝を活かした地球環境修復に向けた基盤構築である。本研究では、系統学的に極めて類似した熱水孔環境微生物株が海域ごとに異なるエネルギー代謝の特徴を持つ傾向にあることを明らかにしたとともに、亜酸化窒素を還元する微生物の取得に成功した。
  • 日本学術振興会：科学研究費助成事業 特別研究員奨励費
    研究期間 : 2012年04月 -2015年03月 
    代表者 : 美野 さやか
     
    本課題は、培養技術を駆使し、深海底熱水活動域に生息する特異な微生物の分離、生態学的研究、および地球環境修復への応用展開を目的としている。 2014年度は、熱水活動域に棲息するN2O還元細菌に近縁な新規微生物の性状解析を行い、新種として提唱した。具体的には、昨年度分離培養に成功した新規化学合成独立栄養細菌の性状を決定し、深海熱水活動域由来の中温性細菌で報告例のない水素酸化-チオ硫酸還元能を有し、近縁種の中では稀な絶対嫌気性細菌であることを明らかにした。本分離株をSulfurovum aggregansとして提唱し、微生物系統分類を扱う国際雑誌IJSEMにて発表した。 また、N2O還元細菌に近縁な化学合成独立栄養細菌集団の種内多様性の解明に向けて、新たな微生物分離株の遺伝子情報を加え、ゲノムレベルの遺伝的多様性解析に成功した。具体的には、昨年度得られた新規沖縄トラフ熱水サイト由来の分離株のもつ11個の遺伝子塩基配列を決定し、これらの分離株を含め、4海域15フィールド（サイト）由来の微生物分離株の種内遺伝的多様性の比較を可能とした。本遺伝子解析から、海域に固有の遺伝的特徴を有する微生物集団が存在することを突き止めた。 さらに、米国Woods Hole Oceanographic Institutionが実施した東太平洋海膨熱水活動域の調査航海に参加し、25種類に及ぶ熱水活動域由来の試料を採取した。これまで本海域由来の分離株が持つ遺伝子情報を上記の遺伝的多様性解析に考慮できておらず、本熱水性試料は全球規模の微生物遺伝的多様性の解明に向けて極めて重要である。これらの熱水性試料から、既に12株以上の分離株を取得しており、今後、新たな分離株を用いてN2O還元能の評価および微生物集団の遺伝的多様性解析に取り組む予定である。

教育活動情報

主要な担当授業

  • 大学院共通授業科目（一般科目）：自然科学・応用科学
    開講年度 : 2021年
    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
  • 教科教育法（理科II）
    開講年度 : 2021年
    課程区分 : 学士課程
    開講学部 : 教育学部
  • 微生物学実験
    開講年度 : 2021年
    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

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