博士（農学）, 東北大学

微生物多様性

群集構造解析

メタオミクス

プロテオミクス

ゲノム微生物学

微生物生態学

Genomic Microbiology

Protenomics

Community structure

Soil microbiology

Life Science, Ecology and environment

Life Science, System genome science

Life Science, Genome biology

Environmental Science/Agriculture Science, Landscape science

Environmental Science/Agriculture Science, Environmental agriculture

Master's degree program, Graduate School of Environmental Science

Doctoral (PhD) degree program, Graduate School of Environmental Science

N2O Reduction by Gemmatimonas aurantiaca and Potential Involvement of Gemmatimonadetes Bacteria in N2O Reduction in Agricultural Soils.
Mamoru Oshiki; Yuka Toyama; Toshikazu Suenaga; Akihiko Terada; Yasuhiro Kasahara; Takashi Yamaguchi; Nobuo Araki
Microbes and Environments, 37, 2, Japanese Society of Microbial Ecology, 2022, [Peer-reviewed]
Scientific journal

Possible Involvement of a Tetrathionate Reductase Homolog in Dissimilatory Arsenate Reduction by Anaeromyxobacter sp. PSR-1
Fumika Muramatsu; Mimori Tonomura; Mikina Yamada; Yasuhiro Kasahara; Shigeki Yamamura; Takao Iino; Seigo Amachi
Applied and Environmental Microbiology, American Society for Microbiology, 25 Sep. 2020, [Peer-reviewed], [International Magazine]
English, Scientific journal, Anaeromyxobacter sp. strain PSR-1, a dissimilatory arsenate [As(V)]-reducing bacterium, can utilize As(V) as a terminal electron acceptor for anaerobic respiration. A previous draft genome analysis revealed that strain PSR-1 lacks typical respiratory As(V) reductase genes (arrAB), which suggested the involvement of another protein in As(V) respiration. Dissimilatory As(V) reductase activity of strain PSR-1 was induced under As(V)-respiring conditions, and was localized predominantly in the periplasmic fraction. The activity was visualized on partially-denaturing gel electrophoresis, and liquid chromatography-tandem mass spectrometry analysis identified proteins involved in the active band. Among these proteins, a protein annotated as molybdopterin-dependent oxidoreductase (PSR1_00330) exhibited the highest sequence coverage of 76%. Phylogenetic analysis revealed that this protein was a homolog of tetrathionate reductase catalytic subunit TtrA. However, the crude extract of strain PSR-1 did not show significant tetrathionate reductase enzyme activity. Comparative proteomic analysis revealed that the protein PSR1_00330 and a homolog of tetrathionate reductase electron transfer subunit TtrB (PSR1_00329) were expressed abundantly and specifically under As(V)-respiring conditions, respectively. The genes encoding PSR1_00330 and PSR1_00329 formed an operon-like structure along with a c-type cytochrome gene, and their transcription was upregulated under As(V)-respiring conditions. These results suggest that the protein PSR1_00330, which lacks tetrathionate reductase activity, functions as a dissimilatory As(V) reductase in strain PSR-1. Considering the wide distribution of TtrA homologs among bacteria and archaea, they may play a hitherto unknown role along with conventional respiratory As(V) reductase (Arr) in the biogeochemical cycling of arsenic in nature.


IMPORTANCE Dissimilatory As(V)-reducing prokaryotes play significant roles in arsenic release and contamination in groundwater and threaten the health of people worldwide. Generally, such prokaryotes reduce As(V) by means of a respiratory As(V) reductase designated as Arr. However, some dissimilatory As(V)-reducing prokaryotes such as Anaeromyxobacter sp. strain PSR-1 lack genes encoding Arr, suggesting the involvement of other protein in As(V) reduction. In this study, by using multiple proteomic and transcriptional analyses, it was found that the dissimilatory As(V) reductase of strain PSR-1 was a protein closely related to the tetrathionate reductase catalytic subunit (TtrA). Tetrathionate reductase is known to play a role in anaerobic respiration of Salmonella on tetrathionate, but strain PSR-1 showed neither growth on tetrathionate nor significant tetrathionate reductase enzyme activity. These results suggest the possibility that TtrA homologs encoded in a wide variety of archaeal and bacterial genomes might function as dissimilatory As(V) reductases.

A novel dimethylsulfoxide reductase family of molybdenum enzyme, Idr, is involved in iodate respiration by Pseudomonas sp . SCT
Chihiro Yamazaki; Sumie Kashiwa; Ayaka Horiuchi; Yasuhiro Kasahara; Shigeki Yamamura; Seigo Amachi
Environmental Microbiology, 22, 6, 2196, 2212, Wiley, Jun. 2020, [Peer-reviewed], [International Magazine]
English, Scientific journal, Pseudomonas sp. strain SCT is capable of using iodate (IO3- ) as a terminal electron acceptor for anaerobic respiration. A possible key enzyme, periplasmic iodate reductase (Idr), was visualized by active staining on non-denaturing gel electrophoresis. Liquid chromatography-tandem mass spectrometry analysis revealed that at least four proteins, designated as IdrA, IdrB, IdrP1 , and IdrP2 , were involved in Idr. IdrA and IdrB were homologues of catalytic and electron transfer subunits of respiratory arsenite oxidase (Aio); however, IdrA defined a novel clade within the dimethylsulfoxide (DMSO) reductase family. IdrP1 and IdrP2 were closely related to each other and distantly related to cytochrome c peroxidase. The idr genes (idrABP 1 P 2 ) formed an operon-like structure, and their transcription was upregulated under iodate-respiring conditions. Comparative proteomic analysis also revealed that Idr proteins and high affinity terminal oxidases (Cbb3 and Cyd), various H2 O2 scavengers, and chlorite (ClO2- ) dismutase-like proteins were expressed specifically or abundantly under iodate-respiring conditions. These results suggest that Idr is a respiratory iodate reductase, and that both O2 and H2 O2 are formed as by-products of iodate respiration. We propose an electron transport chain model of strain SCT, in which iodate, H2 O2 , and O2 are used as terminal electron acceptors.

Expression of Genes and Proteins Involved in Arsenic Respiration and Resistance in Dissimilatory Arsenate-Reducing Geobacter sp. Strain OR-1
Tatsuya Tsuchiya; Ayaka Ehara; Yasuhiro Kasahara; Natsuko Hamamura; Seigo Amachi
Applied and Environmental Microbiology, 85, 14, American Society for Microbiology, 17 May 2019, [Peer-reviewed]
Scientific journal,
The reduction of arsenate [As(V)] to arsenite [As(III)] by dissimilatory As(V)-reducing bacteria, such as Geobacter spp., may play a significant role in arsenic release from anaerobic sediments into groundwater. The biochemical and molecular mechanisms by which these bacteria cope with this toxic element remain unclear. In this study, the expression of several genes involved in arsenic respiration (arr) and resistance (ars) was determined using Geobacter sp. strain OR-1, the only cultured Geobacter strain capable of As(V) respiration. In addition, proteins expressed differentially under As(V)-respiring conditions were identified by semiquantitative proteomic analysis. Dissimilatory As(V) reductase (Arr) of strain OR-1 was localized predominantly in the periplasmic space, and the transcription of its gene (arrA) was upregulated under As(V)-respiring conditions. The transcription of the detoxifying As(V) reductase gene (arsC) was also upregulated, but its induction required 500 times higher concentration of As(III) (500 μM) than did the arrA gene. Comparative proteomic analysis revealed that in addition to the Arr and Ars proteins, proteins involved in the following processes were upregulated under As(V)-respiring conditions: (i) protein folding and assembly for rescue of proteins with oxidative damage, (ii) DNA replication and repair for restoration of DNA breaks, (iii) anaplerosis and gluconeogenesis for sustainable energy production and biomass formation, and (iv) protein and nucleotide synthesis for the replacement of damaged proteins and nucleotides. These results suggest that strain OR-1 copes with arsenic stress by orchestrating pleiotropic processes that enable this bacterium to resist and actively metabolize arsenic.


IMPORTANCE Dissimilatory As(V)-reducing bacteria, such as Geobacter spp., play significant roles in arsenic release and contamination in groundwater and threaten the health of people worldwide. However, the biochemical and molecular mechanisms by which these bacteria cope with arsenic toxicity remain unclear. In this study, it was found that both respiratory and detoxifying As(V) reductases of a dissimilatory As(V)-reducing bacterium, Geobacter sp. strain OR-1, were upregulated under As(V)-respiring conditions. In addition, various proteins expressed specifically or more abundantly in strain OR-1 under arsenic stress were identified. Strain OR-1 actively metabolizes arsenic while orchestrating various metabolic processes that repair oxidative damage caused by arsenic. Such information is useful in assessing and identifying possible countermeasures for the prevention of microbial arsenic release in nature.

Identification of nitrogen-fixing Bradyrhizobium associated with roots of field-grown sorghum by metagenome and proteome analyses.
Minamisawa, K; S. Hara; T. Morikawa; S. Wasai; Y. Kasahara; T. Koshiba; K. Yamazaki; T. Fujiwara; T. Tokunaga
Frontiers in Microbiology, 10, 407, Mar. 2019, [Peer-reviewed]
English, Scientific journal

Thiocyanate Degradation by a Highly Enriched Culture of the Neutrophilic Halophile Thiohalobacter sp. Strain FOKN1 from Activated Sludge and Genomic Insights into Thiocyanate Metabolism
Mamoru Oshiki; Toshikazu Fukushima; Shuichi Kawano; Yasuhiro Kasahara; Junichi Nakagawa
Microbes and Environments, 34, 4, 402, 412, Japanese Society of Microbial Ecology, 2019, [Peer-reviewed]
Scientific journal

Understory Dwarf Bamboo Affects Microbial Community Structures and Soil Properties in a Betula ermanii Forest in Northern Japan
Bihe Kong; Lei Chen; Yasuhiro Kasahara; Akihiro Sumida; Kiyomi Ono; Jan Wild; Arata Nagatake; Ryusuke Hatano; Toshihiko Hara
MICROBES AND ENVIRONMENTS, 32, 2, 103, 111, Jun. 2017, [Peer-reviewed]
English, Scientific journal

Genes essential for the morphogenesis of the Shiga toxin 2-transducing phage from Escherichia coli O157:H7
Shakhinur Islam Mondal; Md Rakibul Islam; Akira Sawaguchi; Md Asadulghani; Tadasuke Ooka; Yasuhiro Gotoh; Yasuhiro Kasahara; Yoshitoshi Ogura; Tetsuya Hayashi
Scientific Reports, 6, 1, Dec. 2016, [Peer-reviewed]
English, Scientific journal

Proteome analysis of Pseudomonas putida F1 genes induced in soil environments
Hajime Morimoto; Ryosuke Kadoya; Kazuhiro Takahashi; Yasuhiro Kasahara
ENVIRONMENTAL MICROBIOLOGY REPORTS, 8, 5, 825, 832, Oct. 2016, [Peer-reviewed]
English, Scientific journal

土壌プロテオミクスから考える微生物生態系機能
笠原 康裕
土と微生物, 70, 2, 41, 44, 2016, [Peer-reviewed]
Japanese, Scientific journal

Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants
Zhihua Bao; Takashi Okubo; Kengo Kubota; Yasuhiro Kasahara; Hirohito Tsurumaru; Mizue Anda; Seishi Ikeda; Kiwamu Minamisawa
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80, 16, 5043, 5052, Aug. 2014, [Peer-reviewed]
English, Scientific journal

An essential enzyme for phospholipid synthesis associates with the Bacillus subtilis divisome
Hiraku Takada; Sanae Fukushima-Tanaka; Masato Morita; Yasuhiro Kasahara; Satoru Watanabe; Taku Chibazakura; Hiroshi Hara; Kouji Matsumoto; Hirofumi Yoshikawa
MOLECULAR MICROBIOLOGY, 91, 2, 242, 255, Jan. 2014, [Peer-reviewed]
English, Scientific journal

Gene expression profiling of Pseudomonas putida F1 after exposure to aromatic hydrocarbon in soil by using proteome analysis
Hajime Morimoto; Masayoshi Kuwano; Yasuhiro Kasahara
ARCHIVES OF MICROBIOLOGY, 195, 12, 805, 813, Dec. 2013, [Peer-reviewed]
English, Scientific journal

Genome-wide analytical approaches using semi-quantitative expression proteomics for aromatic hydrocarbon metabolism in Pseudomonas putida F1
Yasuhiro Kasahara; Hajime Morimoto; Masayoshi Kuwano; Ryo Kadoya
JOURNAL OF MICROBIOLOGICAL METHODS, 91, 3, 434, 442, Dec. 2012, [Peer-reviewed]
English, Scientific journal

Application of nested PCR-DGGE (denaturing gradient gel electrophoresis) for the analysis of ciliate communities in soils
Satoshi Shimano; Mitsuo Sambe; Yasuhiro Kasahara
Microbes and Environments, 27, 2, 136, 141, 2012, [Peer-reviewed]
English, Scientific journal

The Oligomeric States of the Photosystems and the Light-Harvesting Complexes in the Chl b-Less Mutant
Atsushi Takabayashi; Katsunori Kurihara; Masayoshi Kuwano; Yasuhiro Kasahara; Ryouichi Tanaka; Ayumi Tanaka
PLANT AND CELL PHYSIOLOGY, 52, 12, 2103, 2114, Dec. 2011, [Peer-reviewed]
English, Scientific journal

Detection of Effects of a High Trophic Level Predator, Sorex unguiculatus (Soricidae, Mammalia), on a Soil Microbial Community in a Cool Temperate Forest in Hokkaido, Using the ARISA Method
Kana Yamamoto; Satoshi D. Ohdachi; Yasuhiro Kasahara
MICROBES AND ENVIRONMENTS, 25, 3, 197, 203, Sep. 2010, [Peer-reviewed]
English, Scientific journal

Linkage between Light Microscopic Observations and Molecular Analysis by Single-Cell PCR for Ciliates
Satoshi Shimano; Mitsuo Sanbe; Yasuhiro Kasahara
MICROBES AND ENVIRONMENTS, 23, 4, 356, 359, 2008, [Peer-reviewed]
English, Scientific journal

A taxon-specific oligonucleotide primer set for PCR detection of soil ciliate.
Tunjung Puitika; Y. Kasahara; N. Miyoshi; Y. Sato; S. Shimano
Microbes & Environ, 22, 78, 81, 2007, [Peer-reviewed]
English, Scientific journal

A taxon-specific oligonucleotide primer set for PCR-based detection of soil ciliate
Tunjung Puitika; Yasuhiro Kasahara; Norikazu Miyoshi; Yoshinori Sato; Satoshi Shimano
MICROBES AND ENVIRONMENTS, 22, 1, 78, 81, 2007, [Peer-reviewed]
English, Scientific journal

カバークロップが土壌微生物相に及ぼす影響について(2005年度大会一般講演要旨)
昭日 格図; 小松崎 将一; 佐藤 嘉則; 太田 寛行; 笠原 康裕
土と微生物, 59, 2, 136, 136, 日本土壌微生物学会, 2005
Japanese

Degradation profiles of branched nonylphenol isomers by Sphingobium amiense and Sphingomonas cloacae
Y Ikunaga; SI Miyakawa; M Hasegawa; Y Kasahara; O Kodama; H Ohta
SOIL SCIENCE AND PLANT NUTRITION, 50, 6, 871, 875, Dec. 2004, [Peer-reviewed]
English, Scientific journal

Electrophoretic mobility of Bacillus subtilis knockout mutants with and without flagella
S Okuda; R Igarashi; Y Kusui; Y Kasahara; H Morisaki
JOURNAL OF BACTERIOLOGY, 185, 13, 3711, 3717, Jul. 2003, [Peer-reviewed]
English, Scientific journal

Chromosome DNA fragmentation and excretion caused by defective prophage gene expression in the early-exponential-phase culture of Bacillus subtilis
R Shingaki; Y Kasahara; T Inoue; S Kokeguchi; K Fukui
CANADIAN JOURNAL OF MICROBIOLOGY, 49, 5, 313, 325, May 2003, [Peer-reviewed]
English, Scientific journal

Essential Bacillus subtilis genes
K Kobayashi; SD Ehrlich; A Albertini; G Amati; KK Andersen; M Arnaud; K Asai; S Ashikaga; S Aymerich; P Bessieres; F Boland; SC Brignell; S Bron; K Bunai; J Chapuis; LC Christiansen; A Danchin; M Debarbouille; E Dervyn; E Deuerling; K Devine; SK Devine; O Dreesen; J Errington; S Fillinger; SJ Foster; Y Fujita; A Galizzi; R Gardan; C Eschevins; T Fukushima; K Haga; CR Harwood; M Hecker; D Hosoya; MF Hullo; H Kakeshita; D Karamata; Y Kasahara; F Kawamura; K Koga; P Koski; R Kuwana; D Imamura; M Ishimaru; S Ishikawa; Ishio, I; D Le Coq; A Masson; C Mauel; R Meima; RP Mellado; A Moir; S Moriya; E Nagakawa; H Nanamiya; S Nakai; P Nygaard; M Ogura; T Ohanan; M O'Reilly; M O'Rourke; Z Pragai; HM Pooley; G Rapoport; JP Rawlins; LA Rivas; C Rivolta; A Sadaie; Y Sadaie; M Sarvas; T Sato; HH Saxild; E Scanlan; W Schumann; JFML Seegers; J Sekiguchi; A Sekowska; SJ Seror; M Simon; P Stragier; R Studer; H Takamatsu; T Tanaka; M Takeuchi; HB Thomaides; Vagner, V; JM van Dijl; K Watabe; A Wipat; H Yamamoto; M Yamamoto; Y Yamamoto; K Yamane; K Yata; K Yoshida; H Yoshikawa; U Zuber; N Ogasawara
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100, 8, 4678, 4683, Apr. 2003, [Peer-reviewed]
English, Scientific journal

Distribution and Characterization of Antibiotic Resistant Bacteria in the Sediment of Southern Basin of Lake Biwa
Daisuke Miyake; Yasuhiro Kasahara; Hisao Morisaki
Microbes and Environments, 18, 1, 24, 31, 2003, [Peer-reviewed]
English, Scientific journal

Induction of L-form-like cell shape change of Bacillus subtilis under microculture conditions.
Shingaki, R; Y. Kasahara; M. Iwano; M. Kuwano; T. Takatsuka; T. Inoue; S. Kokeguchi; K. Fukui
Microbiology, 149, 2501, 2511, 2003, [Peer-reviewed]
English, Scientific journal

The electrophoretic mobility of Bacillus subtilis knockout mutants with and without flagella.
Okuda, S; R. Igarashi; Y. Kusui; Y. Kasahara; H. Morisaki
J. Bacteriology, 149, 2501, 2511, 2003, [Peer-reviewed]
English, Scientific journal

Proteomics characterization of novel spore proteins of Bacillus subtilis
R Kuwana; Y Kasahara; M Fujibayashi; H Takamatsu; N Ogasawara; K Watabe
MICROBIOLOGY-SGM, 148, 3971, 3982, Dec. 2002, [Peer-reviewed]
English, Scientific journal

Two separate DNA sequences within oriC participate in accurate chromosome segregation in Bacillus subtilis
R Kadoya; AKM Hassan; Y Kasahara; N Ogasawara; S Moriya
MOLECULAR MICROBIOLOGY, 45, 1, 73, 87, Jul. 2002, [Peer-reviewed]
English, Scientific journal

Phylogenetic Analysis of Bacterial Populations Found in Groundwater and an Acidic Stream Draining from an Abandoned Coal Mine
In-Gi Kim; Yasuhiro Kasahara; Kyung-Sook Whang
Microbes and Environments, 16, 3, 169, 176, 2001, [Peer-reviewed]
English, Scientific journal

Organic nutrient-dependent degradation of branched nonylphenol by Sphingomonas sp. YT isolated from a river sediment sample.
Ynte P. de Vries; Y. Takahara; Y. Ikunaga; Y. Ushiba; M. Hasegawa; Y. Kasahara; H. Shimomura; S. Hayashi; Y. Hirai; H. Ohta
Microbes & Environ., 45, 4, 73, 87, Japanese Society of Microbial Ecology, 2001, [Peer-reviewed]
English, Scientific journal, A conventional enrichment culture on branched nonylphenol (NP) with diluted nutrient broth as an additional source of organic nutrients yielded a bacterial strain able to degrade branched NP. The isolate (designated YT) was identified as Sphingomonas sp. based on an analysis of its 16S ribosomal RNA genes and cellular lipids. The degradation of NP by strain YT occurred primarily during the exponential phase of cell growth in cultures on a yeast extract-mineral salts medium. The degree of degradation was directly proportional to the amount of yeast extract present in the medium and no significant growth occurred when NP was the sole source of carbon and energy. Gas chromatography-mass spectrometry (GC-MS) of resting cell suspensions incubated with branched NP revealed that the degradation did not yield any metabolites containing aromatic residues but only branched alcohols. When a linear NP was used as the target substrate, GS-MS of the suspensions indicated the appearance of a hydroxylated linear NP as an intermediate during the degradation. Strain YT is expected to attack NP by an initial oxidative cleavage of the phenol ring.

The essential two-component regulatory system encoded by yycF and yycG modulates expression of the ftsAZ operon in Bacillus subtilis
K Fukuchi; Y Kasahara; K Asai; K Kobayashi; S Moriya; N Ogasawara
MICROBIOLOGY-UK, 146, 1573, 1583, Jul. 2000, [Peer-reviewed]
English, Scientific journal

Regulation of the transport system for C-4-dicarboxylic acids in Bacillus subtilis
K Asai; SH Baik; Y Kasahara; S Moriya; N Ogasawara
MICROBIOLOGY-UK, 146, 263, 271, Feb. 2000, [Peer-reviewed]
English, Scientific journal

Identification and expression of the Bacillus subtilis fructose-1,6-bisphosphatase gene (fbp)
Y Fujita; KI Yoshida; Y Miwa; N Yanai; E Nagakawa; Y Kasahara
JOURNAL OF BACTERIOLOGY, 180, 16, 4309, 4313, Aug. 1998, [Peer-reviewed]
English, Scientific journal

The complete genome sequence of the Gram-positive bacterium Bacillus subtilis
F Kunst; N Ogasawara; Moszer, I; AM Albertini; G Alloni; Azevedo, V; MG Bertero; P Bessieres; A Bolotin; S Borchert; R Borriss; L Boursier; A Brans; M Braun; SC Brignell; S Bron; S Brouillet; CV Bruschi; B Caldwell; Capuano, V; NM Carter; SK Choi; JJ Codani; IF Connerton; NJ Cummings; RA Daniel; F Denizot; KM Devine; A Dusterhoft; SD Ehrlich; PT Emmerson; KD Entian; J Errington; C Fabret; E Ferrari; D Foulger; C Fritz; M Fujita; Y Fujita; S Fuma; A Galizzi; N Galleron; SY Ghim; P Glaser; A Goffeau; EJ Golightly; G Grandi; G Guiseppi; BJ Guy; K Haga; J Haiech; CR Harwood; A Henaut; H Hilbert; S Holsappel; S Hosono; MF Hullo; M Itaya; L Jones; B Joris; D Karamata; Y Kasahara; M KlaerrBlanchard; C Klein; Y Kobayashi; P Koetter; G Koningstein; S Krogh; M Kumano; K Kurita; A Lapidus; S Lardinois; J Lauber; Lazarevic, V; SM Lee; A Levine; H Liu; S Masuda; C Mauel; C Medigue; N Medina; RP Mellado; M Mizuno; D Moestl; S Nakai; M Noback; D Noone; M OReilly; K Ogawa; A Ogiwara; B Oudega; SH Park; Parro, V; TM Pohl; D Portetelle; S Porwollik; AM Prescott; E Presecan; P Pujic; B Purnelle; G Rapoport; M Rey; S Reynolds; M Rieger; C Rivolta; E Rocha; B Roche; M Rose; Y Sadaie; T Sato; E Scanlan; S Schleich; R Schroeter; F Scoffone; J Sekiguchi; A Sekowska; SJ Seror; P Serror; BS Shin; B Soldo; A Sorokin; E Tacconi; T Takagi; H Takahashi; K Takemaru; M Takeuchi; A Tamakoshi; T Tanaka; P Terpstra; A Tognoni; Tosato, V; S Uchiyama; M Vandenbol; F Vannier; A Vassarotti; A Viari; R Wambutt; E Wedler; H Wedler; T Weitzenegger; P Winters; A Wipat; H Yamamoto; K Yamane; K Yasumoto; K Yata; K Yoshida; HF Yoshikawa; E Zumstein; H Yoshikawa; A Danchin
NATURE, 390, 6657, 249, 256, Nov. 1997, [Peer-reviewed]
English, Scientific journal

Characterization of an lrp-like (lrpC) gene from Bacillus subtilis
C Beloin; S Ayora; R Exley; L Hirschbein; N Ogasawara; Y Kasahara; JC Alonso; F LeHegarat
MOLECULAR & GENERAL GENETICS, 256, 1, 63, 71, Sep. 1997, [Peer-reviewed]
English, Scientific journal

Advances in soil microbial ecology and the biodiversity
T Hattori; H Mitsui; H Haga; N Wakao; S Shikano; K Gorlach; Y Kasahara; A ElBeltagy; R Hattori
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY, 72, 1, 21, 28, Jul. 1997, [Peer-reviewed]
English, Scientific journal

Nucleotide sequence and analysis of the phoB-rrnE-groESL region of the Bacillus subtilis chromosome
Y Sadaie; K Yata; M Fujita; H Sagai; M Itaya; Y Kasahara; N Ogasawara
MICROBIOLOGY-UK, 143, 1861, 1866, Jun. 1997, [Peer-reviewed]
English, Scientific journal

Sequence analysis of the groESL-cotA region of the Bacillus subtilis genome, containing the restriction/ modification system genes
Yasuhiro Kasahara; Sumiko Nakai; Naotake Ogasawara; Katsunori Yata; Yoshito Sadaie
DNA Research, 4, 5, 335, 339, Universal Academy Press Inc., 1997, [Peer-reviewed]
English, Scientific journal

Sequence analysis of the 36-kb region between gntZ and trnY genes of bacillus subtilis genome
Yasuhiro Kasahara; Sumiko Nakai; Naotake Ogasawara
DNA Research, 4, 2, 155, 159, Universal Academy Press Inc., 1997, [Peer-reviewed]
English, Scientific journal

Sequence analysis of a 25-kb segment in the 17°-19° region of the Bacillus subtilis chromosome containing ada locus
Hongtu Liu; Koki Haga; Yasuhiro Kasahara; Naotake Ogasawara; Hideo Takahashi; Hirofumi Yoshikawa
DNA Research, 4, 5, 325, 328, Universal Academy Press Inc., 1997, [Peer-reviewed]
English, Scientific journal

Determination of a 17484 bp nucleotide sequence around the 39 degrees region of the Bacillus subtilis chromosome and similarity analysis of the products of putative ORFs
E Akagawa; K Kurita; T Sugawara; K Nakamura; Y Kasahara; N Ogasawara; K Yamane
MICROBIOLOGY-UK, 141, 3241, 3245, Dec. 1995, [Peer-reviewed]
English, Scientific journal

HYDROPHOBICITY OF THE CELLS OF FAST-GROWING AND SLOW-GROWING BACTERIA ISOLATED FROM A GRASSLAND SOIL
Y KASAHARA; H MORISAKI; T HATTORI
JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY, 39, 4, 381, 388, Aug. 1993, [Peer-reviewed]
English, Scientific journal

THE CELL-SURFACE CHARGE OF FAST-GROWING AND SLOW-GROWING BACTERIA ISOLATED FROM GRASSLAND SOIL
H MORISAKI; Y KASAHARA; T HATTORI
JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY, 39, 1, 65, 74, Feb. 1993, [Peer-reviewed]
English, Scientific journal

THE CHANGES IN THE SURFACE CHARACTERISTICS OF PSEUDOMONAS-SYRINGAE INDUCED BY A PLASMID
H MORISAKI; Y KASAHARA; S TANIGAWA; T HATTORI
JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY, 38, 2, 165, 177, Apr. 1992, [Peer-reviewed]
English, Scientific journal

ANALYSIS OF BACTERIAL-POPULATIONS IN A GRASSLAND SOIL ACCORDING TO RATES OF DEVELOPMENT ON SOLID MEDIA
Y KASAHARA; T HATTORI
FEMS MICROBIOLOGY ECOLOGY, 86, 2, 95, 101, Dec. 1991, [Peer-reviewed]
English, Scientific journal

動物の死骸は誰のもの？: 死肉食性昆虫と雑食性食肉目の消費型競争
橋詰茜; 松島義治; 幸田良介; 笠原康裕; 大舘智志; 中島啓裕, 日本生態学会第68回全国大会講演要旨, Mar. 2021

火熱撹乱による森林土壌の細菌と真菌群集の応答と回復
笠原康裕; 高橋一弘; 小椋義俊; 三木 健; 新井大輔; 林哲也; 佐藤雅志, 第14回日本ゲノム微生物学会年会講演要旨, Mar. 2020

細菌のヨウ素酸呼吸には新規鉄硫黄モリブデンタンパクIdrが関与する
柏澄江, 山崎千尋, 笠原康裕, 天知誠吾, 日本農芸化学会大会講演要旨集(Web), 33rd, Mar. 2020

火熱撹乱による森林土壌微生物群集の応答と回復
笠原康裕; 高橋一弘; 小椋義俊; 森本一; 三木 健; 新井大輔; Larry Lopez; 林哲也; 佐藤雅志, 日本土壌微生物学会2019年度大会講演要旨（札幌）, Jun. 2019

オーミック解析に基づくソルガム根窒素固定細菌の特
原新太郎; 森川峻志; 和才沙和; 笠原康裕; 小柴太一; 山崎清志; 藤原徹; 徳永毅; 南澤究, 日本土壌肥料学会講演要旨集, 64, 26, 29 Aug. 2018
Japanese

環境オミックス解析によるソルガム根の窒素固定Bradyrhizobium属細菌の同定
原新太郎; 森川峻志; 新井沙和; 笠原康裕; 小柴太一; 山崎清志; 藤原徹; 徳永毅; 南澤究, 日本ゲノム微生物学会年会要旨集, 12th, 62, 05 Mar. 2018
Japanese

ソルガム根の窒素固定活性とその原因窒素固定細菌の探索
森川峻志; 原新太郎; 新井沙和; 笠原康裕; 小柴太一; 山崎清志; 藤原徹; 徳永毅; 南澤究, 植物微生物研究会研究交流会講演要旨集, 27th, 103 (JA),104 (EN), Dec. 2017
Japanese

ソルガム根の窒素固定活性とその原因窒素固定細菌のOmic解析による同定
南澤究; 原新太郎; 森川峻志; 笠原康裕; 小柴太一; 山崎清志; 藤原徹; 徳永毅, 植物微生物研究会研究交流会講演要旨集, 27th, 23 (JA),24 (EN), Dec. 2017
Japanese

ソルガム根の窒素固定活性とその原因窒素固定細菌の探索
森川峻志; 原新太郎; 笠原康裕; 小柴太一; 山崎清志; 藤原徹; 徳永毅; 南澤究, 日本微生物生態学会大会(Web), 2017, ROMBUNNO.P‐323 (WEB ONLY), 2017
Japanese

異化的ヒ酸還元細菌によるヒ素ストレス応答機構の発現解析
土屋達哉; 笠原康裕; 濱村奈津子; 天知誠吾, 日本微生物生態学会大会(Web), 31st, 2016

水稲根メタン酸化細菌の窒素固定能のメタプロテオーム解析,組織局在性と分離まで
包智華; 篠田亮; 大久保卓; 久保田健吾; 笠原康裕; 池田成志; 浅川晋; 南澤究, 日本微生物生態学会大会(Web), 30th, JS5-3 (WEB ONLY), 2015
Japanese

水稲根メタン酸化細菌は非マメ科植物の根粒菌か?
南澤究; BAO Zhihua; 池田成志; 大久保卓; 今泉(安楽)温子; 常田岳志; 久保田健吾; 笠原康裕; LIU Dongyan; 浅川晋, 植物微生物研究会研究交流会講演要旨集, 24th, (JA)6,(EN)7, Dec. 2014
Japanese

S3-1-21 水稲根における窒素固定メタン酸化細菌のメタプロテオーム同定と組織局在性(ミニシンポジウム S3-1,3-1 土壌生物の生態と機能,2014年度東京大会)
包 智華; 大久保 卓; 窪田 健吾; 笠原 康裕; 鶴丸 博人; 按田 瑞恵; 池田 成志; 南澤 究, 日本土壌肥料学会講演要旨集, 60, 35, 35, 09 Sep. 2014
一般社団法人日本土壌肥料学会, Japanese

根粒菌シグマ因子RpoH1の制御を受ける機能未知遺伝子の鉄硫黄タンパク質生合成への関与
佐々木祥平; 門屋亨介; 笠原康裕; 南澤究; 三井久幸, 日本ゲノム微生物学会年会要旨集, 8th, 2014

ASL5の過剰発現はシロイヌナズナ花茎の重力屈性変異atlazy1を抑圧する
佐々木秋; 佐藤敦子; 綿引雅昭; 門屋亨介; 笠原康裕; 山本興太朗, 日本植物生理学会年会要旨集, 54th, 175, 14 Mar. 2013
Japanese

P-25 Proteome analysis of the response of Pseudomonas putida F1 to aromatic hydrocarbon in soil(Poster Session)
MORIMOTO HAJIME; KUWANO MASAYOSHI; KASAHARA YASUHIRO, 日本微生物生態学会講演要旨集, 26, 107, 107, 2010
日本微生物生態学会, English

04-066 Effect of higher trophic level predator, long-clawed shrews (Sorex nguiculatus) on microbial community(Soil ecosystem)
Yamamoto Kana; Odachi Satoshi; Kasahara Yasuhiro, 日本微生物生態学会講演要旨集, 24, 91, 91, 2008
日本微生物生態学会, Japanese

PA-66 Proteome analysis on viable but nonculturable (VBNC) state of Escherichia coli.(GENETIC ANALYSIS,Session A,(1) Poster presentations)
Sonoda Sachiko; Kuwano Masayoshi; Sasakura Asako; Sato Hiroki; Kasahara Yasuhiro, 日本微生物生態学会講演要旨集, 21, 112, 112, 2005
日本微生物生態学会, Japanese

土壌微生物学におけるポストゲノム研究の現状と将来
福井 学; 南澤 究; 笠原康裕; 町田雅之; 早津雅仁; 妹尾啓史, 日本土壌肥料学雑誌, 76, 4, 523, 529, 2005
Japanese Society of Soil Science and Plant Nutrition, Japanese, Introduction other

ポストゲノム微生物研究における展開 : 枯草菌のプロテオミクス(I 土壌微生物学におけるポストゲノム研究の現状と将来, 2004年度シンポジウムならびに受賞記念講演講演要旨集)
笠原 康裕, 日本土壌肥料学会講演要旨集, 50, 203, 203, 14 Sep. 2004
一般社団法人日本土壌肥料学会, Japanese

B-7 枯草菌の胞子蛋白質のプロテオーム解析(遺伝子解析,B会場,口頭発表)
笠原 康裕; 桑名 利津子; 高松 宏治; 渡部 一仁; 小笠原 直毅, 日本微生物生態学会講演要旨集, 17, 57, 57, 2001
日本微生物生態学会, Japanese

Systematic phenotypic analysis of mutants of Bacillus subtilis
KOBAYASHI Kazuo; ASAI Kei; KASAHARA Yasuhiro; MORIYA Shigeki; OGASAWARA Naotake, 日本分子生物学会年会プログラム・講演要旨集, 21, 247, 247, 01 Dec. 1998
Japanese

枯草菌ゲノムのLRP相同遺伝子の機能解析
笠原 康裕; 守家 成紀; 小笠原 直毅, 日本分子生物学会年会プログラム・講演要旨集, 19, 572, 572, 01 Aug. 1996
Japanese

環境変動による土壌微生物生態系の影響
笠原 康裕, 低温科学便覧（北海道大学低温科学研究所編）
丸善出版, 2015, [Contributor]

微生物ってなに？
日科技連, 2006

微生物生態学入門
日科技連, 2004

PCR Tips
秀潤社, 2000

基礎生化学実験法、第4巻核酸・遺伝子実験
東京化学同人, 2000

動物の死骸は誰のもの？: 死肉食性昆虫と雑食性食肉目の消費型競争
橋詰茜; 松島義治; 幸田良介; 笠原康裕; 大舘智志; 中島啓裕
日本生態学会第68回全国大会, 19 Mar. 2021, Japanese, Poster presentation
17 Mar. 2021 - 21 Mar. 2021

火熱撹乱による森林土壌の細菌と真菌群集の応答と回復
笠原康裕; 高橋一弘; 小椋義俊; 三木 健; 新井大輔; 林哲也; 佐藤雅志
第14回日本ゲノム微生物学会年会, 07 Mar. 2020, Japanese, Poster presentation
06 Mar. 2020 - 08 Mar. 2020

火熱撹乱による森林土壌微生物群集の応答と回復
笠原康裕; 高橋一弘; 小椋義俊; 森本一; 三木 健; 新井大輔; Larry Lopez; 林哲也; 佐藤雅志
日本土壌微生物学会2019年度大会（札幌）, 15 Jun. 2019, Japanese, Poster presentation
15 Jun. 2019 - 16 Jun. 2019

肉の腐敗にどう抗うか？－微生物への対抗ともう１つの戦略－
橋詰 茜; 山中康如; 笠原康裕; 大舘智志; 幸田良介; 中島啓裕
第66回日本生態学会大会, 15 Mar. 2019, Japanese, Poster presentation
[Domestic Conference]

ソルガム根の窒素固定活性とその原因窒素固定細菌のOmic解析による同定
南澤 究; 原新太郎; 森川峻志; 笠原康裕; 小柴太一; 山崎清志; 藤原 徹; 徳永 毅
第27回植物微生物研究会, Sep. 2017, Oral presentation
20 Sep. 2017 - 22 Sep. 2017, [Domestic Conference]

メタゲノム解析に基づくソルガム根の窒素固定細菌の分離
森川峻志、原新太郎、新井沙和、笠原康裕、小柴太一、山崎清志、藤原 徹、徳永 毅、南澤 究
第27回植物微生物研究会, Sep. 2017, Japanese, Poster presentation
[Domestic Conference]

メソルガム根の窒素固定活性とその原因窒素固定細菌の探索
森川峻志、原新太郎、笠原康裕、小柴太一、山崎清志、藤原 徹、徳永 毅、南澤 究
環境微生物系学会合同大会2017, Aug. 2017, Poster presentation
[Domestic Conference]

ゲノム科学から見えてくる微生物によるヒ素循環
天知誠吾、土屋達哉、笠原康裕、濱村奈津子
JpGU-AGU Joint Meeting 2017, May 2017, Nominated symposium
[Domestic Conference]

Microbial community structure and soil properties in the rhizosphere of understory dwarf bamboo in Betula ermanii forest, northern Japan.
Bihe Kong; Lei Chen; Yasuhiro Kasahara; Akihiro Sumida; Kiyomi Ono; Arata Nagatake; Ryusuke Hatano; Jan Wild; Toshihiko Hara
第31回日本微生物生態学会, Oct. 2016, Poster presentation

異化的ヒ酸還元細菌によるヒ素ストレス応答機構の発現解析
土屋達哉、笠原康裕、濱村奈津子、天知誠吾
第31回日本微生物生態学会, Oct. 2016, Poster presentation
[Domestic Conference]

土壌プロテオミクスから考える微生物生態系機能
笠原康裕
日本土壌微生物学会2016年度大会, Jun. 2016, Invited oral presentation
[Invited], [Domestic Conference]

Understory dwarf bamboo affects microbial structure and soil properties in a Betula ermanii forest in northern Japan
Bihe Kong; Lei Chen; Yasuhiro Kasahara; Akihiro Sumida; Kiyomi Ono; Jan Wild; Arata Nagatake; Ryusuke Hatano; Toshihiko Hara
日本生態学会第64回大会, Mar. 2016, English, Oral presentation

異化的ヒ酸還元細菌によるヒ素ストレス応答の網羅的解析
土屋達哉; 笠原康裕; 天知誠吾
日本農芸化学会2016年度大会, Mar. 2016, Oral presentation

プロテオーム解析を用いたPseudomonas putida F1株の土壌特異的発現遺伝子の同定と特性解析
森本 一、門屋亨介、高橋一弘、笠原康裕
第10回日本ゲノム微生物学会年会, Mar. 2016, Poster presentation
[Domestic Conference]

Proteome analysis of the response of Pseudomonas putida F1 to aromatic hydrocarbon in soil
第26回日本微生物生態学会, 2010, Poster presentation

Micro-eukaryote diversity in soil environments of a grass field.
ISEP, 2010, Poster presentation

ゲノム未解析株のプロテオーム解析の評価
第4回日本ゲノム微生物学会年会, 2010, Poster presentation

間接タンパク質抽出法を用いた土壌メタプロテオミクスの基盤構築
第4回日本ゲノム微生物学会年会, 2010, Poster presentation

半定量的発現プロテオミクスによる芳香族分解の代謝経路解析
第4回日本ゲノム微生物学会年会, 2010

環境変動と土壌微生物群集変動
第56回日本生態学会大会, 2009

大腸菌のVBNC状態関与遺伝子のゲノムワイドスクリーニング
第3回ゲノム微生物学会年会, 2009, Poster presentation

Biodiversity of micro-eukaryotes in soil environments of a grass field.
Canadian Society for Ecology and Evolution (CSEE) 2009 meeting, 2009, Poster presentation

シングルセルPCR法による繊毛虫類の塩基配列解析
日本土壌動物学会第31回大会, 2008, Poster presentation

土壌微生物群集に対する高次捕食者トガリネズミの効果（予報）
第24回日本微生物生態学会, 2008, Poster presentation

Ciliate community analysis of agricultural soil based on SSU rDNA with new taxon-specific primer
59th Annual Meeting, and the International Society for Evolutionary Protistology, 2008, Poster presentation

Soil ciliate diversity in upland soil studied by molecular and culturing approaches
日本微生物生態学会, 2007

Effect of phylogenetic diversity using multiple displacement amplification for bacterial community structure.
日本微生物生態学会, 2007

難培養性細菌のゲノム解析を目指して－１細胞微量ゲノム増幅法の検討－
日本土壌微生物学会, 2006, Poster presentation

環境由来DNA配列に基づいた土壌原生生物の群集解析法に関する検討
日本土壌動物学会, 2006

細菌1細胞からのゲノム解析を目指して －微量DNA増幅法の検討
ワークショップ微生物ゲノム研究のフロンティア, 2006, Poster presentation

Analysis of soil ciliates community using 18S rDNA
日本微生物生態学会, 2005, Poster presentation

大腸菌の生きているが培養不能（VBNC）状態のプロテオーム解析
日本微生物生態学会, 2005, Poster presentation

枯草菌ペリクルの形成因子の同定
日本微生物生態学会, 2005, Poster presentation

枯草菌のペリクル形成過程の顕微鏡学的およびプロテオーム解析
日本微生物生態学会, 2005, Poster presentation

Degradation profiles of alkylphenols by two strains belong to the Sphingomonas group.
International Symposium on Microbial Ecology, 2004, Poster presentation

Community Analysis of Ciliates in Soil Based on 18S rDNA
日本微生物生態学会, 2004, Poster presentation

枯草菌ペリクル構造体の形成過程と発現蛋白質プロファイル
日本微生物生態学会, 2004, Poster presentation

ポストゲノム微生物研究における展開－枯草菌のプロテオミクス－
日本土壌肥料学会, 2004

環境分子生物学特論Ⅰ, 2024年, 修士課程, 環境科学院

分子生物学基礎論, 2024年, 修士課程, 環境科学院

分子生物学基礎論, 2024年, 修士課程, 環境科学院

環境と人間, 2024年, 学士課程, 全学教育

一般教育演習(ﾌﾚｯｼｭﾏﾝｾﾐﾅｰ), 2024年, 学士課程, 全学教育

一般教育演習(ﾌﾚｯｼｭﾏﾝｾﾐﾅｰ), 2024年, 学士課程, 全学教育

Elucidation of the structure and contribution of soil bacterial communities responsible for soil functions during the recovery period after forest fire disturbance
Grants-in-Aid for Scientific Research
Apr. 2024 - Mar. 2027
笠原 康裕; 小椋 義俊
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Hokkaido University, Principal investigator, 24K15270

火熱撹乱による森林土壌細菌生態系の回復メカニズムの解明
Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)
Apr. 2021 - Mar. 2024
笠原 康裕; 小椋 義俊
山火事は生態系にとって重大な撹乱であり、土壌微生物にも多大な影響を与える。火災後の土壌生態系の回復に微生物が重要な役割を果たしているが、微生物群集の回復メカニズムは群集の構造・多様性・遷移に関する経時的な解析データの不足により未解明である。さらに生態系機能レベルの群集集合の研究不足も回復メカニズムの理解を阻んでいる。本研究は、火入れ後の回復過程における細菌群集と細菌機能群の構造変化を経時的に解析し、一連の解析結果から、構造と機能の関連性を見いだし、細菌群集の回復の変化とメカニズムを明らかにすることである。
細菌群集代謝プロファイル解析として、基質31種類が入った96穴プレートEcoPlateを用いて、土壌の基質分解能の有無を発色から判断し、代謝プロファイル解析を行う。さらに、発色ウェルから、DNAとRNAを同時に抽出する。DNAについて16SrDNA遺伝子を増幅、解読し、同定と組成解析を行う。抽出RNAについて、RNA-seq解析を行い、ネットワーク分析や群集機能解析を行う。
本年度は、EcoPlateの発色ウェルからDNAとRNAの同時抽出の検討を行った。プレートでの試料について、土壌そのままと土壌懸濁液のどちらかの適正を判断するため、接種、培養、判定、回収を行い、解析能やウェルから扱いや簡便性を評価した。これより、土壌懸濁液の使用に決定した。核酸抽出では、DNAの次世代シークエンス解析やRNAのRNA-seq解析が可能な質量を得るための、ウェル数（１か3）の比較を行った。これより１ウェルからでも解析が可能である。本研究では、試料間やウェル間のばらつきをできるだけ避けるために、３ウェルをまとめて処理することにした。これより、次年度の機能解析の方法を確立することができ、解析を進めていく。
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Hokkaido University, Principal investigator, 21K12203

Cross-kingdom competitions among microbes, arthropods, and vertebrates for animal carcasses
Grants-in-Aid for Scientific Research
01 Apr. 2018 - 31 Mar. 2021
NAKASHIMA Yoshihiro
In this study, we studied how species interactions among distantly-related organisms affect the limited resources by using vertebrate carcasses as a model. Specifically, we observed the carcass fate of a raccoon in the summer 2018-2021 and quantified the effects of consumption by necrophagous insects and microbes on the time to detection and the consumption rate by vertebrate scavengers. The results showed that consumption by fly larvae (especially Chrysomya pinguis) and microbes greatly limited the carcasses available for consumption by mammalian carnivores (red fox and raccoon dog), while the activities of the fly larvae accelerated the detection of carcasses by the carnivores.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (C), Nihon University, 18K06430

熱撹乱による森林土壌微生物生態系の維持機構の包括的解析
科学研究費補助金
Apr. 2014 - Mar. 2018
笠原 康裕
日本学術振興会, Principal investigator, Competitive research funding

土壌プロテオミクスによる自然環境下の細菌個生態学的研究
科学研究費補助金
Apr. 2013 - Mar. 2015
笠原 康裕
日本学術振興会, Principal investigator, Competitive research funding

北方森林土壌において温暖化が及ぼす微生物と原生生物の群集構造変化と連鎖関係
科学研究費補助金
Apr. 2008 - Mar. 2012
笠原 康裕
日本学術振興会, Principal investigator, Competitive research funding

Post-genomics of microbial community in natural environment.
Basic Science Research Program
2005 - 2010
Competitive research funding

寒冷圏生態系機能モニタリングシステムの構築
先導的研究助成
Apr. 2008 - Mar. 2009
笠原 康裕
北海道大学低温科学研究所, Principal investigator, Competitive research funding

環境プロテオミクスに基づく汚染土壌修復法の開発
シーズ発掘試験（発掘型）研究
Apr. 2008 - Mar. 2009
笠原 康裕
科学技術振興機構, Principal investigator, Competitive research funding

電熱線大規模埋設実験による落葉広葉樹林生態系の温暖化に対する応答の解明
科学研究費補助金
Apr. 2007 - Mar. 2009
日本学術振興会, Competitive research funding

低温生態系微生物の相互作用ネットワークの解明
リーダーシップ研究助成
Apr. 2007 - Mar. 2008
笠原 康裕
北海道大学低温科学研究所, Principal investigator, Competitive research funding

Study of the inhibitory effect of branched-chain fatty acids on carrier-lipid-dependent biosynthesis and transport of bacterial cell wall materialas.
Grants-in-Aid for Scientific Research
2007 - 2008
SHINGAKI Ryuji; KASAHARA Yasuhiro; INOUE Tetsuyoshi
細胞膜を構成する主要脂肪酸として一部の細菌が持つメチル分岐を有した脂肪酸のある種の分子(12-メチルテトラデカン酸ならびに13-メチルテトラデカン酸)がグラム陽性菌に対して示す抗菌作用と、一部のグラム陰性菌が示すswarming運動性阻害活性について解析を行い、C-55キャリアーリピド依存的に行われる細胞壁物質や菌体外多糖様物質の合成・輸送を阻害する機構を解析した。
Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists (B), Okayama University, 19790322

Phylogenetic analysis of unculturable bacterial cells
0104 (Japanese Only)
2005 - 2008
Competitive research funding

Genetic analysis of pellicle formation of Bacillus subtills
Basic Science Research Program
2003 - 2008
Competitive research funding

北方森林土壌の微生物および原生生物の群集構造解析
科学研究費補助金
2008
Competitive research funding

Development of methodology for rhizosphere research
Grants-in-Aid for Scientific Research
2005 - 2007
TOSHIFUMI Murakami; OYANAGI Atsushi; NAKAMAOTO Tomomi; SHIMANO Satoshi
Root is a very important organ, which absorbs water and nutrients from soil, and is affected by the environment or soil organisms. However, the methods of research have not yet been developed well, and the ecology of rhizosphere is still obscure. Our project aimed at development of methods of root and soil organisms.
The root staining method by pressure-injection of dye for field grown plant was developed. By using this method, relationship between roots of neighboring plants of field grown tomato was clarified. The method was modified for monocotyledonous plant ; the leaf sheath near the ground was filled with resin.
The experimental model system of wet injury (puddling and leveling method) was developed to know the genetic characteristics of wheat root under excess water condition in soil. It was clarified that the tolerance of water injury of Mizutakamoji (Agropyron humidum) and rye were higher than wheat.
A sampling method was developed to know the vertical and horizontal distribution of soil organisms and factors controlling them. Roots enhanoed the activity of soil organisms more in a tilled plot than that in a non-tilled plot. The microcosm method using a litter bag was developed for evaluating the effect of soil organisms on the decomposition of organic matter and nutrient absorption by roots.
The PCR-DGGE method for analyzing community structure of soil ciliate was developed. The method can detect more species in soil compared to miauscopic method.
The ecology of soil ciliate, predator of bacteria, was investigated by molecular biological method based on environmental DNA for analyzing community structure of bacteria.
Our developed methods for root system and soil organisms would contribute to clarify the interaction between root and soil organisms.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), National Agricultural Research Organization, 17380196

Analysis of 2000-yr eruption-affected soil microbial ecosystem of Miyake-jima Island
Grants-in-Aid for Scientific Research
2005 - 2007
OHTA Hiroyuki; KUBOTA Masatsugu; KASAHARA Yasuhiro; HIGASHI Teruo; KAMIJYO Takashi; NANBA Kenji
Miyake-jima Island is situated on western rim of the Pacific Ocean, about 180 km south of Tokyo. Mt. Oyama in the island erupted from July to September 2000, ejecting large amounts of volcanic ash and finally forming a large collapsed crater. Since the formation of the new crater, a large quantity of volcanic gas containing high concentrations of SO_2 and H_2S has been emitted. This study was aimed to characterize such volcano-affected soil ecosystems by culture-based and molecular genetic methods. We focused on the lithotrophic and heterotrophic bacterial communities in the 2000 volcanic ash deposits from an essentially unvegetated site near the crater. The pH of samples ranged from 3.0 to 3.6 and the contents of carbon and nitrogen were 0.03% and 0.01%, respectively. Total microscopic counts of bacteria were between 10^7 and 10^9/g and plate counts of heterotrophic bacteria were 10^6/g. Phylogenetic analysis of isolates and 16S rDNA clone library analysis revealed that the predominant bacteria were Thiomonas (41% of isolates and 5% of clones), Leptospirillum (39% of clones) and Acidithiobacillus (15% of clones). Further, the intact volcanic ash samples had activites of CO_2 and N_2 fixation and the clone library analyses targeting RubisCo and nitrogenase reductase genes revealed the predominance of the genes of Leptospirillum and Acidithiobacillus. The volcanic ash sample was subjected to stable isotope probing by using ^<15>N_2 to demonstrate the occurrence of N_2 fixation by these bacteria. Our results suggested that chemolithoautotrophic bacteria such as Fe oxidizers could be the pioneer organisms in the microbial ecosystem of the fresh volcanic ash deposit and contribute to the accumulation of carbon and nitrogen in the fresh volcanic deposits.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), Ibaraki University, 17310018

土壌中における大腸菌O157の培養不可能（VBNC）状態のモニタリング解析
科学研究費補助金
Apr. 2004 - Mar. 2006
笠原 康裕
日本学術振興会, Principal investigator, Competitive research funding

低温生態系微生物の相互作用ネットワークの解明
2005
Competitive research funding

Protein-protein interaction network supporting growth and differentiation of Bacillus subtilis
Grants-in-Aid for Scientific Research
2000 - 2004
OGASAWARA Naotake; KANATA Shigehiko; KAWAMURA Fujio; YOSHIKAWA Hirofumi; WATABE Kazuhito; SATO Thutomu
1) We newly constructed about 300 mutants of the genes identified by genome sequencing, to complete the international mutant construction project, and reported that 271 genes are essential for the B. subtilis growth at 37℃ in LB medium.
2) Among essential genes without known function, we have found that yacA encodes an RNA-modifying enzyme responsible for lysidine formation and yneS, together with plsX, is essential for the first step of phospholipids biosynthesis. In addition, one of the essential GTP binding proteins, YlqF, has been demonstrated to participate in the last step of 50S ribosome subunit assembly.
3) We have attempted to construct knock out mutant of each of 57 ribosome protein genes, and found that 22 are dispensable for the growth.
4) We have systematically analyzed the synthetic lethality of double knockout of paralogous gene pairs, and found that the polA-yacP double mutant is lethal due to the defect in removal of primer RNA of Okazaki fragments.
5) By combination of proteome, transcriptome and genetic analysis, in addition to 119 genes previously reported, we have newly identified 175 genes that are expressed specifically during sporulation, and determined sigma factors responsible for their expression. We have also analyzed the localization of GFP fusions of about 90 spore proteins, and found at least 10 different the localization patterns.
6) We have attempted the analysis of protein-protein interaction network by using yeast two-hybrid analysis and mass spectroscopic analysis of in vivo protein complex, and identified several interesting interactions; anti-sigma proteins regulating activities of ECF sigma factors, Rap proteins regulating ComK responsible for competence development, YheIH involved in regulation of phosphor-relay inducing initiation of sporulation, YlqF interacting with FtsZ and involved in cell division, and YabA interacting with DnaA and DnaA and regulating initiation of genome replication.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research on Priority Areas, Nara Institute of Science and Technology, 12206007

Study on interaction and intracellular distribution of proteins regulating the cell cycle progression in Bacillus subtilis
Grants-in-Aid for Scientific Research
1999 - 2002
OGASAWARA Naotake; KOBAYASHI Kazuo; KASAHARA Yasuhiro; MORIYA Shigeki
(1) Initiation of chromosome replication starts with formation of a complex of initiator protein DnaA and the oriC sequence. Then, DNA helicase, DnaC, is loaded on the complex by the action of DnaB, DnaD and DnaI proteins. We showed that DnaI acts as a helicase loader and DnaD interact with DnaA.
(2) DnaA was distributed throughout the cytoplasm, but both DnaB and DnaI seemed to be localized near the outer or inner edges of the nucleoids at initiation of replication, together with oriC. Furthermore, DnaX (a component of DNA polymerase) foci were detected near either of the edges of the nucleoids at the onset of replication, suggesting that the replisome is recruited into oriC near either edge of the nucleoids to initiate chromosome replication in B.subtilis.
(3) We obtained results indicating that, if the DnaA level increases with progression of the replication cycle, it could act as a rate-limiting factor of replication initiation in B.subtilis. We found that SpoOJ contributes to the positioning of the chromosomal oriC region. In addition, the spoOJ mutant produced a significant proportion of cells with increased chromosome content Furthermore we demonstrated that Soj interferes with tight control of replication initiation and causes early and asynchronous initiation and SpoOJ counteracts this Soj function in wild-type cells. Additionally we found that essential GTP-binding proteins, Bex and YqeH, appeared to participate in the regulation of initiation of chromosome replication.
(4) We demonstrated that the two DNA sequences in and downstream of the dnaA gene participate in correct positioning of the replication origin region within the cell and that this function is associated with accurate chromosome segregation in B.subtilis.
(5) When visualized simultaneously, SMC and the replisome were often in similar regions of the cell. Persistence of SMC foci did not depend on ongoing replication, but did depend on ScpA and ScpB, two proteins interacting with SMC. Our results indicate that SMC is bound to many sites on the chromosome and a concentration of SMC is localized near replication forks, perhaps there to bind and organize newly replicated DNA.
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B), NARA INSTITUTE OF SCIENCE AND TECHNOLOGY, 11480212

Metaproteomcs
Competitive research funding

繊毛虫検出用プライマー及びそれを用いる繊毛虫の検出方法
Patent right