nagata

Toshi Nagata
Professor
Atmosphere and Ocean Research Institute
The University of Tokyo
5-1-5 Kashiwanoha, Kashiwa
Chiba 277-8564, Japan
Email: nagata_at_aori.u-tokyo.ac.jp

Education

1981: B.S., Biology, Tokyo Metropolitan University
1983: M.S., Biology (Zoology), Kyoto University
1987: Doctor of Science, Biology (Zoology), Kyoto University

Professional Positions

1989 – 1991: Postdoctoral Research Fellow, College of Marine Studies, University of Delaware (USA)
Advisor: Professor David Kirchman
1991 – 1995: Assistant Professor, Institute of Hydrospheric and Atmospheric Science, Nagoya University
1995 – 2000: Associate Professor, Ocean Research Institute, The University of Tokyo
2000 – 2008: Professor, Center for Ecological Research, Kyoto University
2008 –2010 : Professor, Ocean Research Institute, The University of Tokyo
2010- present: Professor, Atmosphere and Ocean Research Institute, The University of Tokyo

Research Interests

My research interests cover a broad range of topics in marine biogeochemistry and ecology. Current research themes include organic matter-microbe interactions in marine environments. This research investigates how microbes degrade and transform organic matter to affect carbon and nitrogen cycles in marine systems. I am also interested in the application of isotope methods to investigate the ecology of marine organisms and biogeochemical processes. This includes exploring the application of radiocarbon and compound specific isotope ratios as natural tracers of marine organismal growth, migration, and diet histories. The overall goal is to contribute to a better understanding of mechanisms by which marine ecosystems respond to regional and global environmental changes. See PROJECT for more details.

 

Professional Activities

Associate Editor, Frontiers in Marine Science (2015- )
Contributing Editor, Marine Ecology Progress Series (2012- )
Section Editor, Fundamental and Applied Limnology (2011-2020)
Review Editor, Aquatic Microbial Ecology (2003 – )
Editorial Board, Microbial Ecology (2002 – )
Contributing Editor, Aquatic Biology (2007 – )
Associate Editor, Microbes and Environments (2010 – 2015)
Editor-in-Chief, Limnology (2001 – 2003)
Editorial Board, Limnology (2000 – 2001)
Editorial Board, Ecological Research (1998 – 1999)
Editorial Board, Microbes and Environments (1996 – 2000)

Awards

Okada Award, Oceanographic Society of Japan (1994)

Hidaka Outstanding Publication Award, Oceanographic Society of Japan (2003)

The JOS prize, Oceanographic Society of Japan (2018)

Publications

  1. Nagata, T. and Watanabe, Y. (1983) Observations on the colonial pattern of periphytic bacteria in a river. Physiology and Ecology Japan 20: 71-79.
  2. Nagata, T. (1984) Bacterioplankton in Lake Biwa; Annual fluctuations of bacterial numbers and their possible relationship with environmental variables. The Japanese Journal of Limnology 45: 126-133.
  3. Nagata, T. (1985) Filter mesh-sizes of Daphnia longispina and its filtering rates on natural bacteria. Memoirs of the Faculty of Science, Kyoto University, Series of Biology 10: 109-114.
  4. Nagata, T. (1986) Carbon and nitrogen content of natural planktonic bacteria. Applied and Environmental Microbiology 52: 28-32.
  5. Nagata, T. (1986) The seasonal abundance and vertical distribution of the <3-µm phytoplankton in the north basin of Lake Biwa. Ecological Research 1: 207-221. DOI:10.1007/BF02347022
  6. Nagata, T. (1987) Production rate of planktonic bacteria in the north basin of Lake Biwa Japan. Applied and Environmental Microbiology 53: 2872-2882.pdf
  7. Nagata, T. (1988) Seasonal abundance, grazing impacts on bacteria, and vertical distribution of heterotrophic microflagellates in the south basin of Lake Biwa. The Japanese Journal of Limnology 49: 167-174.
  8. Nagata, T. (1988) The microflagellate-picoplankton food linkage in the water column of Lake Biwa. Limnology and Oceanography 33: 504-517. DOI: 10.4319/lo.1988.33.4.0504. Open Access
  9. Nagata, T. and Okamoto, K. (1988) Filtering rates on natural bacteria by Daphnia longispina and Eodiaptomus japonicus in Lake Biwa. Journal of Plankton Research 10: 835-850. DOI:10.1093/plankt/10.4.835
  10. Nagata, T. (1988) Contribution of planktonic bacteria to the carbon cycling in lake environments. Topics in Prokaryotes Biology 1: 16-23.
  11. Nagata, T., Someya, T., Konda, T., Yamamoto, M., Morikawa, K., Fukui, M., Kuroda, N., Takahashi, K., Oh, S., Mori, M., Araki, S. and Kato, K. (1989) Intercalibration of the acridine orange direct count method of aquatic
    bacteria. Bulletin of Japanese Society of Microbial Ecology 4: 89-99. Open Access
  12. Nagata, T. and Kirchman, D. L. (1990) Filtration-induced release of dissolved free amino acids: application to cultures of marine protozoa. Marine Ecology Progress Series 68: 1-5. Open Access
  13. Nagata, T. and Watanabe, Y. (1990) Carbon- and nitrogen-to-volume ratios of bacterioplankton grown under different nutritional conditions. Applied and Environmental Microbiology 56: 1303-1309.
  14. Nagata, T. (1990) Contribution of picoplankton to the grazer food chain of Lake Biwa. In: Large Lakes – Ecological Structure and Function (eds. by M. M. Tilzer and C. Serruya) pp. 526-539. Springer-Verlag Berlin. DOI: 10.1007/978-3-642-84077-7_28
  15. Nagata, T. and Kirchman, D. L. (1991) Release of dissolved free and combined amino acids by bacterivorous marine flagellates. Limnology and Oceanography 36: 433-443. DOI: 10.4319/lo.1991.36.3.0433. Open Access
  16. Nagata, T. and Kirchman, D. L. (1992) Release of dissolved organic matter by heterotrophic protozoa: Implications for microbial food webs. Archiv fur Hydrobiologie, Beiheft Ergebnisse der Limnologie 35: 99-109.
  17. Nagata, T. and Kirchman, D. L. (1992) Release of macromolecular organic complexes by heterotrophic marine flagellates. Marine Ecology Progress Series 83: 233-240. DOI: 10.3354/meps083233
  18. Nagata, T., Takai, K., Kawanobe, K., Kim, D-S., Nakazato, R., Guselnikova, N., Bondarenko, N., Mologawaya, O., Kostronova, T., Drucker, V., Satoh, Y. and Watanabe, Y. (1994) Autotrophic picoplankton in southern Lake Baikal: abundance, growth, and grazing mortality during summer. Journal of Plankton Research 16: 945-959. DOI: 10.1093/plankt/16.8.945
  19. Haga, H., Nagata, T. and Sakamoto, M. (1995) Size-fractionated NH4+ regeneration in the pelagic environments of two mesotrophic lakes. Limnology and Oceanography 40: 1091-1099. DOI: 10.4319/lo.1995.40.6.1091
  20. Nagata, T. and Koike, I. (1995) Marine colloids: Their roles in food webs and biogeochemical fluxes. In: Biogeochemical Processes and Ocean Flux in the Western Pacific (eds. by Sakai, H. and Nozaki, Y.) pp. 275-292. Terra Scientific Publishers Co., Tokyo.
  21. Nagata, T. and Kirchman, D. L. (1996) Bacterial degradation of protein adsorbed to model submicron particles in seawater. Marine Ecology Progress Series 132: 241-248. DOI:10.3354/meps132241
  22. Nagata, T., Takai, K., Kawabata, K., Nakanishi, M. and Urabe, J. (1996) The trophic transfer via a picoplankton-flagellate-copepod food chain during a picocyanobacterial bloom in Lake Biwa. Archiv fur Hydrobiologie 137: 145-160.
  23. Frenette, J-J., Vincent, W.F., Legendre, L. and Nagata, T. (1996) Size-dependent phytoplankton responses to atmospheric forcing in Lake Biwa. Journal of Plankton Research 18: 371-391. DOI: 10.1046/j.1365-2427
  24. Frenette, J-J., Vincent, W.F., Legendre, L. and Nagata, T. (1996) Size-dependent changes in phytoplankton C and N uptake in the dynamic mixed layer of Lake Biwa. Freshwater Biology 36: 221-236. DOI: 10.1046/j.1365-2427. Open Access
  25. Haga, H., Nagata, T. and Sakamoto, M. (1996) NH4+ regeneration and uptake in mesotrophic lakes: Diurnal and seasonal variations. The Japanese Journal of Limnology 57: 213-223. DOI:10.3739/rikusui.57.213
  26. Frenette, J-J., Vincent, W.F., Legendre, L., Nagata, T., Kawabata, K. and Kumagai, M. (1996) Biological responses to typhoon-induced mixing in two morphologically distinct basins of Lake Biwa. The Japanese Journal of Limnology 57: 501-510. DOI:10.3739/rikusui.57.501
  27. Nagata, T., Ogawa, T., Frenette, J-J., Legendre, L. and Vincent, W. F. (1996) Uncoupled responses of bacterial and algal production to storm-induced mixing in Lake Biwa. The Japanese Journal of Limnology 57: 533-543. DOI:10.3739/rikusui.57.533
  28. Ogawa, T. and Nagata, T. (1996) Effects of strom disturbance on bacterial utilization of dissolved amino acids in the shallow, eutrophic South Basin of Lake Biwa. The Japanese Journal of Limnology 57: 523-531. DOI:10.3739/rikusui.57.523
  29. Kumagai, M., Shimoda, C., Vincent, W.F. and Nagata, T. (1996) Fine scale profiling at core stations. In: Lake Biwa Study Monographs. pp. 91-114. Lake Biwa Research Institute.
  30. Koike, I. and Nagata, T. (1997) High potential activity of extracellular alkaline phosphatase in deep waters of the central Pacific. Deep-Sea Research II 44: 2283-2294. DOI:10.1016/S0967-0645(97)00025-8
  31. Nagata, T. and Kirchman, D. L. (1997) Roles of submicron particles and colloids in microbial food webs and biogeochemical cycles within marine environments. Advances in Microbial Ecology 15: 81-103. DOI:10.1007/978-1-4757-9074-0_3
  32. Nagata, T., Fukuda, R., Koike, I., Kogure, K. and Kirchman, D.L. (1998) Degradation by bacteria of membrane and soluble protein in seawater. Aquatic Microbial Ecology 14: 29-37. DOI: 10.3354/ame014029
  33. Yamasaki, A., Fukuda, H., Fukuda, R., Miyajima, T., Nagata, T., Ogawa, H. and Koike, I. (1998) Submicrometer particles in northwest Pacific coastal environments: Abundance, size distribution and biological origins. Limnology and Oceanography 43: 536-542. DOI: 10.4319/lo.1998.43.3.0536. Open Access
  34. Fukuda, R., Ogawa, H., Nagata, T. and Koike, I. (1998) Direct determination of carbon and nitrogen content of natural bacterial assemblages in marine environments. Applied and Environmental Microbiology 64: 3352-3358.
  35. Nagata, T., Fukuda, H., Fukuda, R. and Koike, I. (2000) Bacterioplankton distribution and production in deep Pacific waters: Large-scale geographic variations and possible coupling with sinking particle fluxes. Limnology and Oceanography 45: 426-435. DOI:10.4319/lo.2000.45.2.0426
  36. Fukuda, R., Sohrin, Y., Saotome, N., Fukuda, H., Nagata, T. and Koike, I. (2000) East-west gradient in ectoenzyme activities in the subarctic Pacific: Possible regulation by zinc. Limnology and Oceanography 45: 930-939. DOI:10.4319/lo.2000.45.4.0930
  37. Nagata, T. (2000) Production mechanisms of dissolved organic matter. In: Microbial Ecology of the Oceans (ed. by Kirchman, D.L.) pp. 121-152. John Wiley & Sons, New York.
  38. Nagata, T. and Kirchman, D.L. (2000) Bacterial mortality: A pathway for the formation of refractory DOM? In: Microbial Biosystems: New Frontiers – Proceedings of the 8th International Symposium on Microbial Ecology (eds. by Bell, C. R., Brylinsky, M, and Johnson-Green, P.) pp. 153-158. Atlantic Canada Society for Microbial Ecology.
  39. Nagata, T. (2000) “Picopellets” produced by phagotrophic nanoflagellates: Role in the material cycling within marine environments. In: Dynamics and Characterization of Marine Organic Matter (eds. by Handa, N., Tanoue, E. and Hama, T.) pp. 241-256. Terra Scientific Publication Tokyo. DOI:10.1007/978-94-017-1319-1_12
  40. Koike, I., Ogawa, H., Nagata, T., Fukuda, R. and Fukuda, H. (2001) Silicate to nitrate ratio of the upper sub-arctic Pacific and the Bering Sea basin in summer: Its implication for phytoplankton dynamics. Journal of Oceanography 57(3): 253-260. DOI:10.1023/A:1012474327158
  41. Nagata, T., Fukuda, R. Fukuda, H. and Koike, I. (2001) Basin-scale geographic patterns of bacterioplankton biomass and production in the subarctic Pacific, July-September 1997. Journal of Oceanography 57(3): 301-313. DOI:10.1023/A:1012482528975
  42. Aranami, K., Watanabe, S., Tsunogai, S., Hayashi, M., Furuya, K. and Nagata, T. (2001) Biogeochemical variation in dimethylsulfide, phytoplankton pigments and heterotrophic bacterial production in the subarctic North Pacific during summer. Journal of Oceanography 57(3): 315-322. DOI:10.1023/A:1012434613046
  43. Haga, T., Nagata, T. and Sakamoto, M. (2001) Ammonium regeneration within the euphotic zone. In: Lake Kizaki. Limnology and Ecology of a Japanese Lake (eds. by Saijo, Y. and Hayashi, H.) pp. 207-215. Backhuys, Leiden.
  44. Nagata, T., Meon, B. and Kirchman, D. L. (2003) Microbial degradation of peptidoglycan in seawater. Limnology and Oceanography 48: 745-754. DOI:10.4319/lo.2003.48.2.0745. Open Access
  45. Yoshida, T., Sekino, T., Genkai-Kato, M., Logachva, N.P., Bondarenko, N.A., Kawabata, Z., Khodzher, T.V., Melnik, N.G., Hino, S., Nozaki, K., Nishimura, Y., Nagata, T., Higashi, M. and Nakanishi, M. (2003) Seasonal dynamics of primary production in the pelagic zone of southern Lake Baikal. Limnology. 4:53-62. DOI:10.1007/s10201-002-0089-3
  46. Yokokawa, T., Nagata, T., Cottrell, M.T. and Kirchman, D.L. (2004) Growth rate of the major phylogenetic bacterial groups in the Delaware estuary. Limnology and Oceanography 49:1620-1629.
  47. Nishimura, Y., Kim, C. and Nagata, T. (2005) Vertical and seasonal variations of bacterioplankton subgroups with different nucleic acid content: Possible regulation by phosphorus. Applied and Environmental Microbiology 71:5828-5836. DOI: 10.4319/lo.2004.49.5.1620
  48. Yokokawa, T. and Nagata, T. (2005) Growth and grazing mortality rates of phylogenetic groups of bacterioplankton in coastal marine environments. Applied and Environmental Microbiology 71:6799-6807 . DOI:10.1128/AEM.71.11.6799-6807.2005
  49. Kim, C., Nishimura, Y. and Nagata, T. (2006) Role of dissolved organic matter in hypolimnetic mineralization of carbon and nitrogen in a large, monomictic lake. Limnology and Oceanography 51(1):70-78. DOI:10.4319/lo.2006.51.1.0070
  50. Fukuda, H., Sohrin, R., Nagata, T. and Koike, I. (2007) Size distribution and biomass of nanoflagellates in meso- and bathypelagic layers of the subarctic Pacific. Aquatic Microbial Ecology 46: 203-207. DOI:10.3354/ame046203
  51. Ram, A.S.P., Nagata, T., Tomaru, Y. and Nagasaki, K. (2007) Tungstate compounds as an alternative to uranyl acetate for enumerating viral infected prokaryote cells in aquatic systems. Aquatic Microbial Ecology 47: 209-212. DOI:10.3354/ame047209
  52. Motegi, C. and Nagata, T. (2007) Enhancement of viral production by addition of nitrogen or nitrogen plus carbon in subtropical surface waters of the South Pacific. Aquatic Microbial Ecology 48: 27-34. DOI:10.3354/ame048027. Open Access
  53. Nishimura, Y. and Nagata, T. (2007) Alphaproteobacterial dominance in a large mesotrophic lake (Lake Biwa, Japan). Aquatic Microbial Ecology 48: 231-240. DOI:10.3354/ame048231. Open Access
  54. Kim, C., Nishimura, Y. and Nagata, T. (2007) High potential activity of alkaline phosphatase in the benthic nepheloid layer of a large mesotrophic lake: Implications for phosphorus regeneration in oxygenated hypolimnion. Aquatic Microbial Ecology 49: 303-311. DOI:10.3354/ame01137
  55. Umezawa, Y., Ishitobi, T., Rungsupa, S., Onodera, S., Yamanaka, T., Yoshimizu, C., Tayasu, I., Nagata, T., Wattayakorn, G. and Taniguchi, M. (2007) Evaluation of fresh groundwater contributions to the nutrient dynamics at shallow subtidal areas adjacent to metro-Bangkok. IAHS-AISH Publications 312：169-179.
  56. Miki, T., Nakazawa, T., Yokokawa, T. and Nagata, T. (2008) Functional　consequences　of　viral　impacts　on　bacterial　communities:　a food-web model analysis. Freshwater Biology 53:1142-1153. DOI:10.1111/j.1365-2427.2007.01934.x. Open Access
  57. Kohzu, A., Tayasu, I., Yoshimizu, C., Maruyama, A., Kohmatsu, Y., Hyodo, F., Onoda, Y., Igeta, A., Matsui, K., Nakano, T., Wada, E., Nagata, T. and Takemon, Y. (2009) Nitrogen stable isotopic signatures of basal food items, primary consumers and omnivores in rivers with different levels of human impact. Ecological Research 24:127-136. DOI:10.1007/s11284-008-0489-x
  58. Nagata, T. (2008) Organic Matter -Bacteria Interactions in Seawater. In: Microbial Ecology of the Oceans (2nd edition) (ed. by Kirchman, D.L.) pp. 207-241. John Wiley & Sons, New York
  59. Umezawa, Y., Hosono, T., Onodera, S., Siringan, F., Buapeng, S., Delinom, R., Yoshimizu, C., Tayasu, I., Nagata, T. and Taniguchi, M. (2008) Sources of nitrate and ammonium contamination in groundwater under developing Asian megacities. Science of the Total Environment 404: 361-376. DOI:10.1016/j.scitotenv.2008.04.021
  60. Miki, T., Yokokawa, T., Nagata, T. and Yamamura, N. (2008) Immigration of prokaryotes to local environments enhances remineralization efficiency of sinking particles: a metacommunity model. Marine Ecology Progress Series 366: 1-14. DOI:10.3354/meps07597. Open Access
  61. Kashiyama, Y., Miyashita, H., Ohkubo, S., Ogawa, N. O., Chikaraishi, Y., Takano, Y., Suga, H., Toyofuku, T., Nomaki, H., Kitazato, H., Nagata, T. and Ohkouchi, N. (2008) Evidence of global chlorophyll d. Science 321:658. DOI:10.1126/science.1158761
  62. Kohzu. A., Miyajima, T., Tayasu, I., Yoshimizu, C., Hyodo, F., Matsui, K., Nakano, T., Wada, E., Fujita, N. and Nagata, T. (2008) Use of stable nitrogen isotope signatures of riparian macrophytes as an indicator of anthropogenic N inputs to river ecosystems. Environmental Science and Technology 42: 7837-7841. DOI:10.1007/s11284-008-0489-x
  63. Kobayashi, Y., Kim, C., Yoshimizu, C., Kohzu, A., Tayasu, I. and Nagata, T. (2009) Longitudinal changes in bacterial community composition in river epilithic biofilms: influence of nutrients and organic matter. Aquatic Microbial Ecology 54: 135-152. DOI:10.3354/ame01258
  64. Miki, T., Giuggioli, L., Kobayashi, Y., Nagata, T. and Levin, S.A. (2009) Vertically structured prokaryotic community can control the efficiency of the biological pump in the oceans. Theoretical Ecology 2: 199-216. DOI:10.1007/s12080-009-0042-8
  65. Motegi, C., Nagata, T., Miki, T., Weinbauer, M. G., Legendre, L. and Rassoulzadegan, F. (2009) Viral control of bacterial growth efficiency in marine pelagic environments. Limnology and Oceanography 54: 1901-1910. DOI:10.4319/lo.2009.54.6.1901. Open Access
  66. Miyajima, T., Yoshimizu, C., Tsuboi, Y., Tanaka, Y., Tayasu, I., Nagata, T. and Koike, I. (2009) Longitudinal distribution of nitrate δ15N and δ18O in two contrasting tropical rivers: implications for instream nitrogen cycling. Biogeochemistry　95:243-260. DOI:10.1007/s10533-009-9334-8
  67. Motegi, C. and Nagata, T. (2009) Addition of monomeric and polymeric organic substrates alleviates viral lytic pressure on bacterial communities in coastal seawaters. Aquatic Microbial Ecology 57: 343–350. DOI:10.3354/ame01365. Open Access
  68. Maki, K., Kim, C., Yoshimizu, C., Tayasu, I., Miyajima, T. and Nagata, T. (2010) Autochthonous origin of semi-labile dissolved organic carbon in a large monomictic lake (Lake Biwa): carbon stable isotopic evidence. Limnology. 11: 143-153. DOI:10.1007/s10201-009-0299-z
  69. Yokokawa, T. and Nagata, T. (2010) Linking bacterial community structure to carbon fluxes in marine environments. Journal of Oceanography 66:1-12. DOI:10.1007/s10872-010-0001-4
  70. Pradeep Ram, A.S., Nishimura, Y., Tomaru, Y., Nagasaki, K. and Nagata, T. (2010) Seasonal variation in viral-induced mortality of bacterioplankton in the water column of a large mesotrophic lake (Lake Biwa, Japan). Aquatic Microbial Ecology 58:249-259. DOI:10.3354/ame01381
  71. Yoshimizu, C., Yoshiyama, K., Tayasu, I., Koitabashi, T. and Nagata, T. (2010) Vulnerability of a large monomictic lake (Lake Biwa) to warm winter event. Limnology. 11:233-239 DOI:10.1007/s10201-009-0307-3
  72. Osaka, K., Ohte, N., Koba, K., Yoshimizu, C., Katsuyama, M., Tani, M., Tayasu, I. and Nagata, T. (2010) Hydrological influences on spatiotemporal variations of δ15N and δ18O of nitrate in a forested headwater catchment in central Japan: Denitrification plays a critical role in groundwater. Journal of Geophysical Research – Biogeosciences: DOI:10.1029/2009JG000977. Open Access
  73. Ohte, N., Tayasu, I., Kohzu, A., Yoshimizu, C., Osaka, K., Makabe, A., Koba, K., Yoshida, N. and Nagata, T. (2010) Spatial distribution of nitrate sources of rivers in the Lake Biwa watershed, Japan: Controlling factors revealed by nitrogen and oxygen isotope values. Water Resources Research: DOI: 10.1029/2009WR007871
  74. Karube, Z., Sakai, Y., Takeyama, T., Okuda, N., Kohzu, A., Yoshimizu, C., Nagata, T. and Tayasu, I. (2010) Carbon and nitrogen stable isotope ratios of macroinvertebrates in the littoral zone of Lake Biwa as indicators of anthropogenic activities in the watershed. Ecological Research. DOI 10.1007/s11284-010-0715-1
  75. Nagata, T., Tamburini, C., Arı´stegui, J., Baltar, F., Bochdansky, A., Fonda-Umani, S., Fukuda, H., Gogou, A., Hansell, D.A., Hansman R.L., Herndl G.J., Panagiotopoulos, C., Reinthaler, T., Sohrin, R., Verdugo, P., Yamada, N., Yamashita, Y., Yokokawa, T. and Bartlett, D.H. Emerging concepts on microbial processes in the bathypelagic ocean – ecology, biogeochemistry, and genomics. Deep-Sea Research II. 57(2010)1519-1536. DOI:10.1016/j.dsr2.2010.02.019
  76. Burd, A.B., Hansell, D.A., Steinberg, D.K., Anderson, T.R., Arı´stegui, J., Baltar, F., Beaupre´, S.R., Buesseler, K.O., DeHairs, F., Jackson, G.A., Kadko, D.C., Koppelmann, R., Lampitt, R.S., Nagata, T., Reinthaler, T., Robinson, C., Robison, B.H., Tamburini, C. and Tanaka, T. (2010) Assessing the apparent imbalance between geochemical and biochemicalindicators of meso- and bathypelagic biological activity:　What the @$#! Is wrong with present calculations of carbon budgets? Deep- Sea Research II. 57: 1557-1571. DOI:10.1016/j.dsr2.2010.02.022
  77. Yang, Y., Motegi, C., Yokokawa, T. and Nagata, T. (2010) Large-scale distribution patterns of virioplankton in the upper ocean. Aquatic Microbial Ecology. 60: 233-246. DOI:10.3354/ame01428
  78. Ogawa, N. O., Nagata, T., Kitazato, H. and Ohkouchi, N. (2010) Ultra-sensitive elemental analyzer/isotope ratio mass spectrometer for stable nitrogen and carbon isotope analyses. In: Earth, Life, and Isotopes. (eds. Ohkouchi, N., Tayasu, I., and Koba, K.) pp. 339-353. Kyoto University Press.
  79. Kawasaki, N., Sohrin, R., Ogawa, H., Nagata, T. and Benner, R. (2011) Bacterial carbon content and the living and detrital bacterial contributions to suspended particulate organic carbon in the North Pacific Ocean. Aquatic Microbial Ecology. 62: 165-176. DOI:10.3354/ame01462
  80. Hosono, T., Wang, C-H., Umezawa, Y., Nakano, T., Onodera, S., Nagata, T., Yoshimizu, C., Tayasu, I. and Taniguchi, M. (2011) Multiple isotope (H, O, N, S and Sr) approach elucidates complex pollution causes in the shallow groundwaters of the Taipei urban area. Journal of Hydrology. 397: 23-36. DOI:10.1016/j.jhydrol.2010.11.025
  81. Itoh, M., Takemon, Y., Makabe, T., Yoshimizu, C., Khozu, A., Ohte, N., Tumurskh, D., Tayasu, I., Yoshida, N. and Nagata, T. (2011) Evaluation of wastewater nitrogen transformation in a natural wetland (Ulaanbaatar, Mongolia) using dual-isotope analysis of nitrate. Science of the Total Environment. 409:1530-1538. DOI:10.1016/j.scitotenv.2011.01.019
  82. Kojima, K., Murakami, M., Yoshimizu, C., Tayasu, I., Nagata, T. and Furumai, H. (2011) Evaluation of surface runoff and road dust as sources of nitrogen using nitrate isotopic composition. Chemosphere. 84: 1716-1722. DOI:10.1016/j.chemosphere.2011.04.071
  83. Uchimiya, M., Fukuda, H., Nishino, S., Kikuchi, T., Ogawa, H. and Nagata, T. (2011) Does freshening of surface water enhance heterotrophic prokaryote production in the western Arctic? Empirical evidence from the Canada Basin during September 2009. Journal of Oceanography.67: 589-599. DOI:10.1007/s10872-011-0059-7
  84. Uchimiya, M., Fukuda, H., Nishino, S., Kikuchi, T., Ogawa, H. and Nagata, T. (2013) Vertical distribution of prokaryote production and abundance in the mesopelagic and bathypelagic layers of the Canada Basin, western Arctic: Implications for the mode and extent of organic carbon delivery. Deep-Sea Research I. 71: 103–112. DOI:10.1016/j.dsr.2012.10.001
  85. Yokokawa, T., Yang, Y., Motegi, C. and Nagata, T. (2013) Large-scale geographical variation in prokaryotic abundance and production in meso- and bathypelagic zones of the central Pacific and Southern Ocean. Limnology and Oceanography. 58(1): 61–73. DOI:10.4319/lo.2013.58.1.0061. Open Access
  86. Sakai, Y., Karube, Z., Takeyama, T., Kohzu, A., Yoshimizu, C., Nagata, T., Tayasu, I. and Okuda, N.　(2013) Seasonal and site-specific variability in terrigenous particulate organic carbon concentration in near-shore waters of Lake Biwa, Japan, Limnology. 14:167-177. DOI:10.1007/s10201-012-0394-4
  87. Sano, M., Maki, K., Nishibe, Y., Nagata, T. and Nishida, S. (2013) Feeding habits of mesopelagic copepods in Sagami Bay: Insights from integrative analysis. Progress in Oceanography. 110: 11-26. DOI:10.1016/j.pocean.2013.01.004
  88. Thibodeau, B., Miyajima, T., Tayasu, I., Wyatt, A.S.J., Watanabe, A., Morimoto, M., Yoshimizu, C. and Nagata, T. (2013) Heterogeneous dissolved organic nitrogen supply over a coral reel: first evidence from nitrogen stable isotope ratios. Coral Reefs, DOI:10.1007/s00338-1070-9
  89. Yamada, Y., Fukuda, H., Inoue, K., Kogure, K. and Nagata, T. (2013) Effects of attached bacteria on organic aggregate settling velocity in seawater. Aquatic Microbial Ecology 70: 261-272. DOI:10.3354/ame01658. Open Access
  90. Motegi, C., Nagata, T., Miki, T., Weinbauer, M.G., Legendre, L. and Rassoulzadegan, F. (2013) Interactive effects of viral and bacterial production on marine bacterial diversity. PLoS ONE 8(11): e76800.DOI:10.1371/journal.pone. 0076800
  91. Yang, Y., Yokokawa, T., Motegi, C. and Nagata, T. (2014) Large-scale distribution of viruses in deep waters of the Pacific and Southern Oceans. Aquatic Microbial Ecology, 71: 193-202. DOI:10.3354/ame01677. Open Access
  92. Shiozaki, T., Itoh, S., Takahashi, K., Saito, H., Nagata, T. and Furuya, K. (2014) Regional variability of factors controlling the onset timing and magnitude of spring algal blooms in the northwestern North Pacific. Journal of Geophysical Research: Oceans, 119: DOI:10.1002/2013JC009187. Open Access
  93. Maki, K., Ohkouchi, N., Chikaraishi, Y., Fukuda, H., Miyajima, T. and Nagata, T. (2014) Influence of nitrogen substrates and substrate C:N ratios on the nitrogen isotopic composition of amino acids from the marine bacterium Vibrio harveyi. Geochimica et Cosmochimica Acta, 140: 521-530.　DOI:10.1016/j.gca.2014.05.052
  94. Hasumi, Y. and Nagata, T. (2014) Modelling the global cycle of marine dissolved organic matter and its influence on marine productivity. Ecological Modelling, 288: 9-24. DOI:10.1016/j.ecolmodel.2014.05.009
  95. Fukuda, H., Katayama, R., Yang, Y., Takasu, H., Nishibe, Y., Tsuda, A. and Nagata, T. (2015) Nutrient status of Otsuchi Bay (northeastern Japan) following the 2011 off the Pacific coast of Tohoku Earthquake. Journal of Oceanography. DOI:10.1007/s10872-015-0296-2
  96. Kusuno, H., Matsuzakia, H., Nagata, T., Miyairi, Y., Yokoyama, Y. and Ohkouchi, N. (2015) An approach for measuring the 129I/127I ratio in fish samples. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms DOI:10.1016/j.nimb.2015.04.074
  97. Yamada, Y., Fukuda, H., Uchimiya, M., Motegi, C., Nishino, N., Kikuchi, T. and Nagata, T. (2015) Localized accumulation and a shelf-basin gradient of particles in the Chukchi Sea and Canada Basin, western Arctic. Journal of Geophysical Research: Oceans. 120, DOI:10.1002/2015JC010794. Open Access
  98. Shiozaki, T., Nagata, T., Ijichi, M. and Furuya, K (2015) Nitrogen fixation and the diazotroph community in the temperate coastal region of the northwestern North Pacific. Biogeosciences. 12: 4751-4764, DOI:10.5194/bg-12-4751-2015
  99. Takasu, H. and Nagata T. (2015) High proline content of bacteria-sized particles in the western North Pacific and its potential as a new biogeochemical indicator of organic matter diagenesis Frontiers in Marine Science | doi: 10.3389/fmars.2015.00110
  100. Nishibe Y., Isami, H., Fukuda, H., Nishida, S., Nagata, T., Tachibana, A., Tsuda, A. (2015) Impact of the 2011 Tohoku earthquake tsunami on zooplankton community in Otsuchi Bay, northeastern Japan, Journal of Oceanography, DOI: 10.1007/s10872-015-0339-8
  101. Ohkouchi N., Shibata, H., Chikaraishi, Y., Nomaki, H., Ogawa, N.O., Nagata, T., Goto, T., Fujikura, K., and Kitazato, H. (2016) A monitoring result of polychlorinated biphenyls (PCBs) in deep-sea organisms and sediments off Tohoku during 2012–2014: temporal variation and the relationship with the trophic position, Journal of Oceanography, DOI: 10.1007/s10872-016-0359-z
  102. Yamada Y., Fukuda H., Tada Y., Kogure K. and Nagata T. (2016) Bacterial enhancement of gel particle coagulation in seawater.  Aquatic Microbial Ecology, doi: 10.3354/ame01784
  103. Uchimiya, C. Motegi, S. Nishino, Y. Kawaguchi, J. Inoue, H. Ogawa, and T. Nagata (2016) Coupled response of bacterial production to a wind-induced fall phytoplankton bloom and sediment resuspension in the Chukchi Sea Shelf, Western Arctic Ocean. Frontiers in Marine Science-Marine Biogeochemistry | doi: 10.3389/fmars.2016.00231
  104. Kaneko, R., T. Nagata, S. Suzuki, and K. Hamasaki (2016) Depth‑dependent and seasonal variability in archaeal community structure in the subarctic and subtropical western North Pacific. Journal of Oceanography, 72:427–438 DOI 10.1007/s10872-016-0372-2
  105. Uchimiya, M., Ogawa, H., and Nagata, T. (2016) Effects of temperature elevation and glucose addition on prokaryotic production and respiration in the mesopelagic layer of the western North Pacific. Journal of Oceanography, 72(3): 419-426 10. Doi: 10.1007/s10872-015-0294-4
  106. Honda, M. C., Wakita, M., Matsumoto, K., Fujiki, T., Siswanto, E., Sasaoka, K., Kawakami, H., Min,o Y., Sukigara, C., Kitamura, M., Sasai, Y., Smith, L. S., Hashioka, T., Yoshikawa, C., Kimoto, K., Watanabe, S., Kobari, T., Nagata, T., Hamasaki, K., Kaneko, R., Uchimiya, M., Fukuda, H., Abe, O., and Saino T., (2017) Comparison of carbon cycle between the western Pacific subarctic and subtropical time‑series stations: highlights of the K2S1 project. Journal of Oceanography. DOI: 10.1007/s10872-017-0423-3
  107. Ohkouchi, N., Chikaraishi, Y., Close, H.G., Fry, B., Larsen, T., Madigan, D.J., McCarthy, M.D., McMahon, K.W., Nagata, T., Naito, Y.I., Ogawa, N.O., Popp, B.N., Steffan, S., Takano, Y., Tayasu, I., Wyatt, A.S.J., Yamaguchi, Y.T., and Yokoyama, Y. (2017) Advances in the application of amino acid nitrogen isotopic analysis in ecological and biogeochemical studies. Organic Geochemistry, 113, 150-174. doi:10.1016/j.orggeochem.
  108. Yamada Y, Yokokawa T, Uchimiya M, Nishino S, Fukuda H, Ogawa H, Nagata T (2017) Transparent exopolymer particles (TEP) in the deep ocean: Full-depth distribution patterns and contribution to the organic carbon pool. Marine Ecology Progress Series. 583:81-93. doi.org/10.3354/meps12339
  109. Mario Uchimiya, Hideki Fukuda, Masahide Wakita, Minoru Kitamura, Hajime Kawakami, Makio C. Honda, Hiroshi Ogawa, Toshi Nagata (2018) Balancing organic carbon supply and consumption in the ocean’s interior: Evidence from repeated biogeochemical observations conducted in the subarctic and subtropical western North Pacific. LIMNOLOGY AND OCEANOGRAPHY   63(5) 2015-2027   https://doi.org/10.1002/lno.10821|
  110. Yamada, Y., Tomaru, Y., Fukuda, H. and Nagata T. (2018) Aggregate Formation During the Viral Lysis of a Marine Diatom. Frontiers in Marine Science-Marine Biogeochemistry    https://doi.org/10.3389/fmars.2018.00167
  111. Takuhei Shiozaki, Amane Fujiwara, Minoru Ijichi, Naomi Harada, Shigeto Nishino, Shinro Nishi, Toshi Nagata, Koji Hamasaki (2018) Diazotroph community structure and the role of nitrogen fixation in the nitrogen cycle in the Chukchi Sea (western Arctic Ocean) LIMNOLOGY AND OCEANOGRAPHY   63(5) 2191-2205      https://doi.org/10.1002/lno.10933
  112. Hikaru Endo, Hideki Fukuda, Daisuke Takahashi, Yutaka Okumura, Eri Inomata, Kinuko Ito, Chikage Yoshimizu, Ichiro Tayasu, Toshi Nagata (2018) Influence of isotope fractionation on the nitrogen isotope composition of the brown macroalga Undaria pinnatifida PHYCOLOGICAL RESEARCH   66(4) 262-268  https://doi.org/10.1111/pre.12332
  113. Ishikawa Naoto F., Chikaraishi Yoshito, Takano Yoshinori, Sasaki Yoko, Takizawa Yuko, Tsuchiya Masashi, Tayasu Ichiro, Nagata Toshi, Ohkouchi Naohiko (2018) A new analytical method for determination of the nitrogen isotopic composition of methionine: Its application to aquatic ecosystems with mixed resources LIMNOLOGY AND OCEANOGRAPHY-METHODS, 16(9) 607-620 https://doi.org/10.1002/lom3.10272
  114. Ishikawa Naoto F., Itahashi Yu, Blattmann Thomas M., Takano Yoshinori, Ogawa Nanako O., Yamane Masako, Yokoyama Yusuke, Nagata Toshi, Yoneda Minoru, Haghipour Negar, Eglinton Timothy I, Ohkouchi Naohiko (2018) Improved Method for Isolation and Purification of Underivatized Amino Acids for Radiocarbon Analysis. ANALYTICAL CHEMISTRY, 90(20) 12035-12041.　 DOI: 10.1021/acs.analchem.8b02693
  115. Wyatt, A.S.J., R. Matsumoto, Y. Chikaraishi, Y. Miyairi, Y. Yokoyama, K. Sato, N. Ohkouchi, and T. Nagata (2019) Enhancing insights into foraging specialization in the world’s largest fish using a multi-tissue, multi-isotope approach. Ecological Monographs, DOI: 10.1002/ecm.1339
  116. Satoh, N., H. Fukuda, Y. Miyairi, Y. Yokoyama, and T. Nagata (2019) Position-dependent radiocarbon content of the macroalgae Undaria pinnatifida as an indicator of oceanographic conditions during algal growth. Journal of Oceanography, 　　doi.org/10.1007/s10872-019-00508-7
  117. Wyatt, A.S.J., Leichter, J.J., Toth, L.T., Miyajima, T., Aronson, R.B. and Nagata, T.　(2020) Heat accumulation on coral reefs mitigated by internal waves. Nature Geoscience, 13:28-34 DOI: 10.1038/s41561-019-0486-4 online 2019/11/18
  118. Shiozaki, T., Tada, Y., Fukuda, H., Furuya, K., and Nagata, T. (2020) Primary production and nitrogen assimilation rates from bay to offshore waters in the oyashio-kuroshio-Tsugaru Warm Current interfrontal region of the northwestern north Pacific Ocean. Deep-Sea Research Part 1, https://doi.org/10.1016/j.dsr.2020.103304 online 19 May 2020
  119. MATSUBAYASHI, J., OSADA, Y., TADOKORO, K., ABE, Y., YAMAGUCHI, A., SHIRAI, K., and others (2020) Tracking long-distance migration of marine fishes using compound-specific stable isotope analysis of amino acids. Ecology Letters 23, 881-890
  120. CUI, Y., WONG, S.-K., KANEKO, R., MOURI, A., TADA, Y., NAGAO, I., and others (2020) Distribution of Dimethylsulfoniopropionate Degradation Genes Reflects Strong Water Current Dependencies in the Sanriku Coastal Region in Japan: From Mesocosm to Field Study. Frontiers in Microbiology (Original Research) 11
  121. SHIOZAKI, T., TADA, Y., FUKUDA, H., FURUYA, K. & NAGATA, T. (2020) Primary production and nitrogen assimilation rates from bay to offshore waters in the oyashio-kuroshio-Tsugaru Warm Current interfrontal region of the northwestern north Pacific Ocean. Deep Sea Research Part I: Oceanographic Research Papers 164, 103304
  122.  ISHIKAWA, N. F., OGAWA, N. O., CHIKARAISHI, Y., YAMAGUCHI, M.-O., FUJIKURA, K., MIYAIRI, Y., YOKOYAMA, Y., NAGATA, T. & OHKOUCHI, N. (2021) Influences of Ocean Currents on the Diets of Demersal Fish Communities in the Western North Pacific Revealed by Their Muscle Carbon and Nitrogen Isotopic Compositions. Frontiers in Marine Science (Original Research) 8
  123. NAGATA, T., YAMADA, Y. & FUKUDA, H. (2021) Transparent Exopolymer Particles in Deep Oceans: Synthesis and Future Challenges. Gels 7, 75