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Department of Biological Sciences
Molecular Neuroscience
Developmental Biology
Cellular Genetics
Molecular Genetics
Plant Development and Physiology
Cellular Biochemistry
Evolutionary Genetics
Plant Environmental Responses
Environmental Microbiology
Animal Ecology
Plant Ecology
Systematic Zoology
Systematic Botany
Photo Environmental Microbiology Laboratory
Microorganisms (bacteria and archaea) are responsible for material cycling and environmental conservation in our planet. We will clarify the ecophysiological roles of microorganisms in the soil and hydrosphere and explore their possible application in urban areas. We are trying to understand microbial ecosystems by integrating individual microbial relationships into microbial networks as well as by elucidating the ecophysiology of each microbe.
Prof Shin Haruta e-mail
Population dynamics of photosynthetic bacteria in the environment
1. Distribution, species composition and their changes due to environmental conditions for photosynthetic bacteria in the soil and hydrosphere (main measuring methods are the detection and sequencing of photosynthetic genes).
2. Functions of photosynthetic bacteria for material cycling and interactions with other bacteria in the soil and hydrosphere (main measuring methods are measurement of oxidation-reduction reaction and mixed culture with various bacteria).
3. Environmental stress responses of photosynthetic bacteria
(main measuring methods are measurement of survivability and omics).
4. Evolution of photosynthetic bacteria and their photosynthetic functions (genetic analysis, comparative molecular biology on many species including new species and reproduction of the process of evolution via genetic manipulation).
Characterization of microbial communities determined by interspecies interactions
The physiological characteristics of microorganisms are affected by various environmental factors in nature. Various species of microorganisms exist by interacting with each other in microbial ecosystems. We will clarify mechanisms of microbial community development and material cycling functions of the communities, specially focusing on hot spring microbial mats.
Microbial mats develop in hot spring waters, and these areas are locations of complex biogeochemical cycles. Studies on microbial communities in the mats will be useful to understand the formation and evolution of structured microbial populations both today and in the past.
Research interests include:
1. Composition and spatial distribution of microorganisms in the microbial mats.
2. Ecophysiology of microbes in microbial ecosystems
3. Ecophysiological functions of microbial communities
4. Material cycling functions within the microbial mats and their biogeochemical significance.
5. Interbacterial interactions affecting the physiological functions of microbial communities.
Ecophysiology of microorganisms in natural environments
Most microorganisms do not actively grow in natural environments. In order to understand microbial roles in nature, it is important to clarify physiology and metabolism of the non-growing state. These studies will lead us to unveil unknown microorganisms and functions. We are applying omics approaches as well as analysis of survivability.
1. Tolerance against various environmental stresses
2. Adaptation to nutrient and energy starvation
3. Maintenance energy for viability
Exploration of unknown bacteria and dynamics in environments
The bacteria currently isolated are considered to account for less than one percent of the total number of species of bacteria which constitute environmental ecosystems. We will explore useful bacteria for environmental purification and environmental conservation. Such exploration requires patience because of the limitation of classical isolation culture methods. However, through efficient exploration by planning new isolation strategies, good results are expected to be achieved quickly.
1. Cultivation and isolation of novel bacteria or archaea useful for environmental purification or environmental conservation.
2. Systematic and evolutionary lineages of the novel isolates.
3. Distribution and ecophysiology of the novel isolates in environments.
Recent Publications
  1. 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)
  2. 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 (2020)
  3. Kawai, S., A. Nishihara, K. Matsuura, S. Haruta. 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 (2019)
  4. 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)
  5. 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)
  6. Haruta, S. and K. Yamamoto. Model microbial consortia as tools for understanding complex microbial communities. Current Genomics 19:723-733 (2018)
  7. 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 (2018)
  8. 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 (2018)
  9. 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 (2018)
  10. 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 (2018)
  11. 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 (2018)
  12. 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 (2018)
  13. 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)
  14. 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)
  15. 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)
  16. 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)
  17. 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)
  18. 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)
  19. 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)
  20. 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)
  21. 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)
  22. 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)
  23. 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)
  24. Otaki, H., C. R. Everroad, K. Matsuura, and S. Haruta. Production and consumption of hydrogen in hot spring microbial mats dominated by a filamentous anoxygenic photosynthetic bacterium. Microbes and Environments 27:293-299 (2012)
  25. 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)
  26. 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)
  27. 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)
  28. 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)
  29. Haruta, S. and Y. Igarashi. Network study of interspecies relationships will open new aspects of microbial ecology. pp.7-10, In: Progress in Environmental Microbiology. Myung-Bo Kim (ed), Nova Science Publishers, Inc., New York (2008)
©2015 Department of Biological Sciences, Tokyo Metropolitan University