TMU logo School of Science and Engineering
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
Photosynthetic Microbial Consortia
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 have special interests in the dynamics and functions of photosynthetic bacteria and other bacteria interacting with them in the environment. 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 Katsumi Matsuura e-mail
Asc 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. 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)
  2. 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)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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)
  8. 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)
  9. 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)
  10. 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)
  11. 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)
  12. 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)
  13. 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)
  14. 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)
  15. Takii, S., Hanada, S., Tamaki, H., Ueno, Y., Sekiguchi, Y., Ibe, A., and Matsuura, K. (2007) 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
  16. Yamada, M., Zhang, H., Hanada, S., Nagashima, K.V.P., Shimada, K. and Matsuura, K. (2005) Structural and spectroscopic properties of a reaction center complex from the chlorosome-lacking filamentous anoxygenic phototrophic bacgterium Roseiflexus castenholzii. J. Bacteriol. 187, 1702-1709
  17. Blankenship, R.E. and Matsuura, K. (2003) Antenna Complexes from Green Photosynthetic Bacteria. in Light-Harvesting Antennas in Photosynthesis (Green, B.R. and Parson, W.W. eds.) Kluwer Academic Pub., pp. 195-217
  18. Hanada, S., Shimada, K. and Matsuura, K. (2002) Active and energy-dependent rapid formation of cell aggregates of the thermophilic photosynthetic bacterium Chloroflexus aggregans. FEMS Microbiol Lett, 208, 275-279
  19. Hanada, S., Takaichi, S., Matsuura, K. and Nakamura K. (2002) Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium which lacks chlorosomes. Int J Syst Evol Microbiol, 52, 187-193
  20. Frigaard, N.-U. and Matsuura, K. (1999) Oxygen uncoples light absorption by the chlorosome antenna and photosynthetic electron transfer in the green sulfur bacterium Chlorobium tepidum. Biochim. Biphys. Acta 1412, 108-117
  21. Microbes and Environments, 14, 37-40
  22. Hanada, S., Kawase, Y., Hiraishi, A., Takaichi, S., Matsuura, K., Shimada, K. and Nagashima, K.V.P.(1997) Porphyrobacter tepidarius sp. nov., a moderately thermophylic aerobic photosynthetic bacterium isolated from a hot spring.@Int. J. Syst. Bacteriol., 47, 408-413
  23. Frigaard, N.-U., Takaichi, S., Hirota, M., Shimada, K. and Matsuura, K. (1997) 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
  24. Hanada, S., Hiraishi, A., Shimada, K. and Matsuura K. (1995) Chloroflexus aggregans sp. nov., a filamentous phototrophic bacterium which forms dense cell aggregates by active gliding movement. Int. J. Syst. Bacteriol. 45, 676-681
©2015 Department of Biological Sciences, Tokyo Metropolitan University