Publications [Papers] [Books] [Conference]

[Peer-reviewed papers]

2023
Hirose, S., T. Asano, M. Hamada, S. Morohoshi, T. Kunihiro, and S. Hanada.
Roseomonas fluvialis sp. nov., an aerobic bacteriochlorophyll a-containing freshwater bacterium isolated from river epilithic biofilm.
International Journal of Systematic and Evolutionary Microbiology, 73:005810 (2023)

Alam Md. G., and S. Haruta
Whole-genome sequence of Thermodesulfomicrobium sp. strain WS, isolated from Onikobe geothermal field in Japan
Microbiology Resource Announcements, 12:e0132122 (2023)

2022
Kono, M., J. N. Martinez, T. Sato, and S. Haruta
Draft genome sequence of the thermophilic unicellular cyanobacterium Synechococcus sp. strain C9
Microbiology Resource Announcements, 11:e0029422 (2022)

Muramatsu, S., S. Hirose, T. Iino, M. Ohkuma, S. Hanada, and S. Haruta.
Neotabrizicola shimadae gen. nov., sp. nov., an aerobic anoxygenic phototrophic bacterium harbouring photosynthetic genes in the family Rhodobacteraceae, isolated from a terrestrial hot spring.
Antonie van Leeuwenhoek, 115:731-740 (2022)

Kawai, S., M. Ishikawa, S. Hanada, and S. Haruta
Hydrogenophilus thiooxidans sp. nov., a moderately thermophilic chemotrophic bacterium unable to grow on hydrogen gas, isolated from hot spring microbial mats
International Journal of Systematic and Evolutionary Microbiology, 72:005355 (2022)

Saini, M.K., S. Yoshida, A. Sebastian, E. Hara, H. Tamaki, N.T. Soulier, I. Albert, S. Hanada, M. Tank, and D.A. Bryant.
Elioraea tepida, sp. nov., a moderately thermophilic aerobic anoxygenic phototrophic bacterium isolated from the mat community of an alkaline siliceous hot spring in Yellowstone National Park, WY, USA.
Microorganisms, 10:80 (2022)

2021
Martinez, J. N., A. Nishihara, and S. Haruta
Metagenome-assembled genome sequences recovered from epilithic river biofilm in the Tama River, Japan
Microbiology Resource Announcements, 10:e00664-21 (2021)

Chen, Y., A. Nishihara, T. Iino, M.Ohkuma, and S. Haruta
Caldicellulosiruptor diazotrophicus sp. nov., a thermophilic, nitrogen-fixing fermentative bacterium isolated from a terrestrial hot spring in Japan.
International Journal of Systematic and Evolutionary Microbiology, 71:005014 (2021)

Saini, M. K., A. Sebastian, Y. Shirotori, N. T. Soulier, A. M. Garcia Costas, D. I. Drautz-Moses, S. C. Schuster, I. Albert, S. Haruta, S. Hanada, V. Thiel, M. Tank, and D. A. Bryant.
Genomic and phenotypic characterization of Chloracidobacterium isolates provides evidence for multiple species.
Frontiers in Microbiology, 12:704168 (2021)

Chen, Y., A. Nishihara, and S. Haruta
Nitrogen-fixing ability and nitrogen fixation related genes of thermophilic fermentative bacteria in the genus Caldicellulosiruptor
Microbes and Environments 36:ME21018 (2021)

Kawai, S., J. N. Martinez, M. Lichtenberg, E. Trampe, M. Kuhl, M. Tank, S. Haruta, A. Nishihara, S. Hanada, V. Thiel.
In-situ metatranscriptomic analyses reveal the metabolic flexibility of the thermophilic anoxygenic photosynthetic bacterium Chloroflexus aggregans in a hot spring cyanobacteria-dominated microbial mat.
Microorganisms 9:652 (2021)

2020
Izaki, K. and S. Haruta.
Aerobic production of bacteriochlorophylls in the filamentous anoxygenic photosynthetic bacterium, Chloroflexus aurantiacus in the light.
Microbes and Environments 35:ME20015 (2020)

Lee, J.-Y., S. Haruta, S. Kato, H. C. Bernstein, S. Lindemann, D.-Y. Lee, J. K. Fredrickson, H.-S. Song
Prediction of Neighbor-dependent Microbial Interactions from Limited Population Data
Frontiers in Microbiology 10:3049 (2020)

Miyata, M., R. C. Robinson, T. Q. P. Uyada, Y. Fukumori, S. Fukushima, S. HARUTA, M. Homma, K. Inaba, M. Ito, C. Kaito, K. Kato, T. Kenri, Y. Kinosita, S. Kojima, T. Minamino, H. Mori, S. Nakamura, D. Nakane, K. Nakayama, M. Nishiyama, S. Shibata, K. Shimabukuro, M. Tamakoshi, A. Taoka, Y. Tashiro, I. Tulum, H. Wada, K. Wakabayashi
Tree of motility -History of motility systems in the tree of life-
Genes to Cells 25:6-21 (2020)

Iino, T., S. Kawai, M. Yuki, I. Dekio, M.Ohkuma, S. Haruta
Thermaurantimonas aggregans gen. nov., sp. nov., a moderately thermophilic heterotrophic aggregating bacterium isolated from microbial mats at a terrestrial hot spring
International Journal of Systematic and Evolutionary Microbiology 70:1117-1121 (2020)

Hirose, S., M. Tank, E. Hara, H. Tamaki, K. Mori, S. Takaichi, S. Haruta, S. Hanada
Aquabacterium pictum sp. nov., the first aerobic bacteriochlorophyll a-containing fresh water bacterium in the genus Aquabacterium of the class Betaproteobacteria
International Journal of Systematic and Evolutionary Microbiology 70:596-603 (2020)

2019
Kanno, N., S. Haruta, S. Hanada
Sulfide-dependent photoautotrophy in a filamentous anoxygenic phototrophic bacterium, Chloroflexus aggregans.
Microbes and Environments 34:304-309 (2019)

Kawai, S., A. Nishihara, K. Matsuura, S. Haruta [selected as Editor's Choice Article]
Hydrogen-dependent autotrophic growth in phototrophic and chemolithotrophic cultures of thermophilic bacteria, Chloroflexus aggregans and Chloroflexus aurantiacus, isolated from Nakabusa hot springs.
FEMS Microbiology Letters 366:fnz122 (2019)

Song, H.-S., J.-Y.Lee, S.Haruta, W.C.Nelson, D.-Y.Lee, S.R.Lindemann, J.K.Fredrickson, H.C.Bernstein.
Minimal Interspecies Interaction Adjustment (MIIA): inference of neighbor-dependent interactions in microbial communities.
Frontiers in Microbiology 10:1264 (2019)

Kawai, S., N. Kamiya, K. Matsuura, and S. Haruta.
Symbiotic growth of a thermophilic sulfide-oxidizing photoautotroph and an elemental sulfur-disproportionating chemolithoautotroph and cooperative dissimilatory oxidation of sulfide to sulfate.
Frontiers in Microbiology 10:1150 (2019)

2018
Haruta, S. and K. Yamamoto
Model microbial consortia as tools for understanding complex microbial communities
Current Genomics 19:723-733 (2018)

Nishihara, A., K. Matsuura, M. Tank, S. McGlynn, V. Thiel, and S. Haruta.
Nitrogenase activity in thermophilic chemolithoautotrophic bacteria in the phylum Aquificae isolated under nitrogen-fixing conditions from Nakabusa Hot Springs
Microbes and Environments 33:394-401 (2018)

Nishihara, A., V. Thiel, K. Matsuura, S. McGlynn, S. Haruta.
Phylogenetic diversity of nitrogenase reductase genes and possible nitrogen-fixing bacteria in thermophilic chemosynthetic microbial communities in Nakabusa Hot Springs.
Microbes and Environments 33:357-365 (2018)

Haruta, S., T. Ishimi, S. Fukushima, and S. Morohoshi
Bacterial escaping behavior from predators
Journal of Environmental Biotechnology 18: 9-13(2018)

Kanno, N., K. Matsuura, and S. Haruta
Different metabolomic responses to carbon starvation between light and dark conditions in the purple photosynthetic bacterium, Rhodopseudomonas palustris
Microbes and Environments 33:83-88 (2018)

Wasai, S., N. Kanno, K. Matsuura, and S. Haruta
Increase of salt tolerance in carbon-starved cells of Rhodopseudomonas palustris depending on photosynthesis or respiration
Microorganisms 6:4 (2018)

Shimizu, T., K. Horiguchi, Y. Hatanaka, S. Masuda, K. Shimada, K. Matsuura, and S. Haruta.
Nitrite-reducing ability is related to growth inhibition by nitrite in Rhodobacter sphaeroides f. sp. denitrificans
Bioscience, Biotechnology, and Biochemistry 82:148-151 (2018)

Nishihara, A., S. Haruta, S. McGlynn, V. Thiel, and K. Matsuura
Nitrogen fixation in thermophilic chemosynthetic microbial communities depending on hydrogen, sulfate, and carbon dioxide.
Microbes and Environments 33:10-18 (2018)

2017
Haruta, S., T. Iino, M. Ohkuma, K. Suzuki, and Y. Igarashi
Ca²⁺ in hybridization solutions for fluorescence in situ hybridization facilitate the detection of Enterobacteriaceae.
Microbes and Environments 32:142-146 (2017)

2016
Haruta, S., Y. Saito, and H. Futamata
Editorial: Development of microbial ecological theory: stability, plasticity and evolution of microbial ecosystems.
Frontiers in Microbiology 7:2069 (2016)

Hirose, S., K. Matsuura, and S. Haruta.
Phylogenetically diverse aerobic anoxygenic phototrophic bacteria isolated from epilithic biofilms in Tama River, Japan.
Microbes and Environments 31:299-306 (2016)

Fukushima, S., S. Morohoshi, S. Hanada, K. Matsuura and S. Haruta.
Gliding motility driven by individual cell-surface movements in a multicellular filamentous bacterium Chloroflexus aggregans.
FEMS Microbiology Letters 363:fnw056 (2016)

2015
Shimizu, T., Z. Cheng, K. Matsuura, S. Masuda, and C. E. Bauer
Evidence that altered cis element spacing affects PpsR mediated redox control of photosynthesis gene expression in Rubrivivax gelatinosus.
PLoS ONE 10(6): e0128446 (2015) doi: 10.1371/journal.pone.0128446

Morohoshi, S., K. Matsuura and S. Haruta
Secreted protease mediates interspecies interaction and promotes cell aggregation of the photosynthetic bacterium Chloroflexus aggregans.
FEMS Microbiology Letters 362:1-5 (2015)

2014
Kanno, N., K. Matsuura and S. Haruta.
Differences in survivability under starvation conditions among four species of purple nonsulfur phototrophic bacteria
Microbes and Environments 29:326-328 (2014)

Stolyar,S., Z. Liu, V. Thiel, L. P. Tomsho, N. Pinel, W. C. Nelson, S. R. Lindemann, M. F. Romine, S. Haruta, S. C. Schuster, D. A. Bryant, and Jim K. Fredrickson.
Genome sequence of the thermophilic cyanobacterium Thermosynechococcus sp. strain NK55a.
Genome announcements 2(1):e01060-13 (2014)

2013
Haruta, S., T. Yoshida, Y. Aoi, K. Kaneko and H. Futamata.
Challenges for complex microbial ecosystems: combination of experimental approaches with mathematical modeling.
Microbes and Environments 28:244-250 (2013)

Iino, T., H. Tamaki, S. Tamazawa, Y. Ueno, M. Ohkuma, K. Suzuki, Y. Igarashi and S. Haruta.
Candidatus Methanogranum caenicola: a Novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a methanogenic lineage of the class Thermoplasmata.
Microbes and Environments 28:285-294 (2013)

2012
Hirose, S., K. V. P. Nagashima, K. Matsuura, and S. Haruta.
Diversity of purple phototrophic bacteria, inferred from pufM gene, within epilithic biofilm in Tama River, Japan.
Microbes and Environments 27:327-329 (2012)

Otaki, H., C. R. Everroad, K. Matsuura, and S. Haruta. 　　　2012 Microbes and Environments Award
Production and consumption of hydrogen in hot spring microbial mats dominated by a filamentous anoxygenic photosynthetic bacterium.
Microbes and Environments 27:293-299 (2012)

Everroad, C. R., H. Otaki, K. Matsuura, and S. Haruta.
Diversification of bacterial community composition along a temperature gradient at a thermal spring.
Microbes and Environments 27-374-381 (2012)

Okubo, T., T. Tsukui, H. Maita, S. Okamoto, K. Oshima, T. Fujisawa, A. Saito, H. Futamata, R. Hattori, Y. Shimomura, S. Haruta, S. Morimoto, Y. Wang, Y. Sakai, M. Hattori, S.-I. Aizawa, K. V. P. Nagashima, S. Masuda, T. Hattori, A. Yamashita, Z. Bao, M. Hayatsu, H. Kajiya-Kanegae, I. Yoshinaga, K. Sakamoto, K. Toyota, M. Nakao, M. Kohara, M. Anda, R. Niwa, J.-H. Park, R. Sameshima-Saito, S.-I. Tokuda, S. Yamamoto, S. Yamamoto, T. Yokoyama, T. Akutsu, Y. Nakamura, Y. Nakahira-Yanaka, Y. Takada Hoshino, H. Hirakawa, H. Mitsui, K. Terasawa, M. Itakura, S. Sato, W. Ikeda-Ohtsubo, N. Sakakura, E. Kaminuma, and K. Minamisawa.
Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs.
Microbes and Environments 27:306-315 (2012)

2011
Kubo, K., K. Knittel, R. Amann, M. Fukui, and K. Matsuura.
Sulfur-metabolizing bacterial populations in microbial mats of the Nakabusa hot spring, Japan.
Syst. Appl. Microbiol., 34:293-302 (2011)

岡田久子、倉本宣、渡辺泰徳、松浦克美
多摩川中流域において剥離して流下する藻類由来の有機物負荷量の推定
土木学会論文集Ｇ 67:II_37-43 (2011)

2009
Haruta, S., S. Kato, K. Yamamoto, and Y. Igarashi.
Intertwined inter-species relationships: approaches to untangle the microbial network.
Environ. Microbiol. 11:2963-2969 (2009)

Tsukatani, Y., N. Nakayama, K. Shimada, H. Mino, S. Itoh, K. Matsuura, S. Hanada, and K.V.P. Nagashima.
Characterization of a blue-copper protein, auracyanin, of the filamentous anoxygenic phototrophic bacterium Roseiflexus castenholzii.
Arch. Biochem. Biophys. 490:57-62 (2009)

2008
Takii, S., S. Hanada, Y. Hase, H. Tamaki, Y. Uyeno Y. Sekiguchi, and K. Matsuura,
Desulfovibrio marinisediminis, sp. nov., a novel sulfate-reducing bacterium isolated from coastal marine sediment via enrichment with Casamino acids.
Int. J. Syst. Evol. Microbiol., 58:2433-2438 (2008)

2007
Takii, S., S. Hanada, H. Tamaki, Y. Ueno, Y. Sekiguchi, A. Ibe, and K. Matsuura.
Dethiosulfatibacter aminovorans gen. nov., sp. nov., a novel thiosulfate-reducing bacterium isolated from coastal marine sediment via sulfate-reducing enrichment with Casamino acids.
Int. J. Syst. Evol. Microbiol., 57: 2320-2326 (2007)

before 2005 (A predecessor of Environmenal Microbiology Laboratory)
Yamada, M., H. Zhang, S. Hanada, K.V.P. Nagashima, K. Shimada, and K. Matsuura, K.
Structural and spectroscopic properties of a reaction center complex from the chlorosome-lacking filamentous anoxygenic phototrophic bacgterium Roseiflexus castenholzii.
J. Bacteriol. 187:1702-1709 (2005)

Hanada, S., K. Shimada, and K. Matsuura.
Active and energy-dependent rapid formation of cell aggregates of the thermophilic photosynthetic bacterium Chloroflexus aggregans.
FEMS Microbiol. Lett., 208:275-279 (2002)

Hanada, S., S. Takaichi, K. Matsuura, and K. Nakamura.
Roseiflexus castenholzii gen. nov.,sp. nov., a thermophilic, filamentous, photosynthetic bacterium which lacks chlorosomes.
Int. J. Syst. Evol. Microbiol., 52:187-193 (2002)

Frigaard, N.-U. and K. Matsuura.
Oxygen uncouples light absorption by the chlorosome antenna and photosynthetic electron transfer in the green sulfur bacterium Chlorobium tepidum.
Biochim. Biphys. Acta 1412:108-117 (1999)

Hanada, S., Y. Kawase, A. Hiraishi, S. Takaichi, K. Matsuura, K. Shimada, and K.V.P. Nagashima.
Porphyrobacter tepidarius sp. nov., a moderately thermophylic aerobic photosynthetic bacterium isolated from a hot spring.
Int. J. Syst. Bacteriol., 47:408-413 (1997)

Frigaard, N.-U., S. Takaichi, M. Hirota, K. Shimada, and K. Matsuura.
Quinones in chlorosomes of green sulfur bacteria and their role in the redox-dependent fluorescence studied in chlorosome-like bacteriochlorophyll c aggregates.
Arch. Microbiol. 167:343-349 (1997)

Hanada, S., A. Hiraishi, K. Shimada, and K. Matsuura.
Chloroflexus aggregans sp. nov., a filamentous phototrophic bacterium which forms dense cell aggregates by active gliding movement.
Int. J. Syst. Bacteriol. 45:676-681 (1995)