Tomohiro Kuwae

Updated on 4 September 2018

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Tomohiro Kuwae, Ph.D

Tomohiro Kuwae, Ph.D

Group Head, Coastal and Estuarine Environment Research Group
Port and Airport Research Institute (PARI)
3-1-1, Nagase, Yokosuka 239-0826, Japan
Phone: +81-46-844-5046
Facsimile: +81-46-844-1274
E-mail: kuwae (at)


Professional Experience

Research Interests

  1. Biogeochemical cycling in shallow coastal waters
    Nutrient and oxygen fluxes across the sediment-water interface, Nutrient and oxygen dynamics in sediments, Analysis of food-webs using carbon and nitrogen stable isotope ratios, CO2 sequestration and carbon storage by shallow coastal ecosystems
  2. Intertidal flat ecology
    Feeding ecology and foraging behaviour of shorebirds, Dynamics of benthic bacteria and microphytobenthos
  3. Conservation, restoration, and creation of intertidal flat ecosystems
    Intertidal flat experimental ecosystems, Mesocosm experiments, Development stage of created intertidal flat ecosystems, Dynamics of benthic microbes, macroinvertebrates, and shorebirds in created intertidal flat ecosystems, Response of created intertidal flat ecosystems to varying environmental conditions

Research Approach

  1. Well-balanced multidisciplinary approach to environmental sciences: synthesis of biology, chemistry, physics, and engineering
  2. Dealing with various organisms within trophic levels, from bacteria to birds
  3. Focusing on coastal ecosystems
  4. Seeking for new techniques and methodologies contributing to accurate measurement and data analysis
  5. Application- and practice-oriented fundamental research

Technical Experience


  1. Sampling and counting of phytoplankton and bacterioplankton
  2. Sampling and counting of microphytobenthos, benthic bacteria, macrofauna (bivalves, polychaetes, gastropods, crustaceans) in sediments
  3. Observation of shorebirds in intertidal flats Go to Shorebird Photo Gallery


  1. Analyses of nitrogen, phosphorus, and carbon concentrations in seawaters, sediments, and organisms
  2. Analysis of chlorophyll concentration in seawaters and sediments
  3. Analyses of carbon and nitrogen stable isotope ratios in seawaters, sediments, and organisms


  1. Analyses of grain size, porosity, and water content in sediments
  2. Mesocosm experiment using the Intertidal Flat Experimental Facility in PARI
  3. Oxygen flux measurement using the eddy-correlation technique

Selected Publications


  • Kuwae, T. and Hori, M. (eds) (2018) Blue Carbon in Shallow Coastal Ecosystems: Carbon Dynamics, Polocy, and Implementation, Springer Nature. (Front matter) (Link)


  • Tokoro, T., and Kuwae, T. (2018) Improved post-processing of eddy-covariance data to quantify atmosphere-aquatic ecosystem CO2 exchanges. Frontiers in Marine Science, in press (PDF)
  • Nakayama, K., Maruya, K., Matsumoto, K., Komai, K., and Kuwae, T. (2018) Nitrogen fluxes between the ocean and a river basin using stable isotope analysis. Estuarine, Costal and Shelf Science, 212: 286-393 (PDF)
  • Tanaya, T., Watanabe, K., Yamamoto, S., Hongo, C., Kayanne, H., and Kuwae, T. (2018) Contributions of the direct supply of belowground seagrass detritus and trapping of suspended organic matter to the sedimentary organic carbon stock in seagrass meadows. Biogeosciences, 15: 4033-4045 (PDF)
  • Sohma, A., Shibuki, H., Nakajima, F., Kubo, A., and Kuwae, T. (2018) Modeling a coastal ecosystem to estimate climate change mitigation and model demonstration in Tokyo Bay. Ecological Modelling, 384: 261-289. (PDF)
  • Takai, N., Kawabe, K., Togura, K., Kawasaki, K., and Kuwae, T. (2018) The seasonal trophic link between Great Cormorant Phalacrocorax carbo and ayu Plecoglossus altivelis altivelis reared for mass release. Ecological Research,10.1007/s11284-018-1610-4 (PDF
  • Morita, A., Touyama, S., Kuwae, T., Nishimura, O., and Sakamaki, T. (2017) Effects of watershed land-cover on the biogeochemical properties of estuarine tidal flat sediments: a test in a densely-populated subtropical island. Estuarine, Coastal and Shelf Science, 184: 207-213 (Link)
  • Akhand, A., Chanda, A., Manna, S., Das, S., Hazra, S., Roy, R., Choudhury, S. B., Rao, K. H., Dadhwal, V. K., Chakraborty, K., Mostofa, K. M. G., Tokoro, T., Kuwae, T., Wanninkhof, R. (2016) A comparison of CO2 dynamics and air-fluxes in a river-dominated estuary and a mangrove-dominated marine estuary. Geophysical Research Letters, 43: 11726-11735 (Link)
  • Watanuki, Y., Yamashita, A., Ishizuka, M., Ikenaka, Y., Nakayama, S. M. M., Ishii, C., Yamamoto, T., Ito, M., Kuwae, T., and Trathan, P. N. (2016) Feather mercury concentration in streaked shearwaters wintering in seperate areas of southeast Asia. Marine Ecology Progress Series, 546: 263-269 (Link)
  • Kuwae, T., Kanda, J., Kubo, A., Nakajima, F., Ogawa, H., Sohma, A., and Suzumura, M. (2016) Blue carbon in human-dominated estuarine and shallow coastal systems. Ambio, 45: 290-301 (PDF)
  • Watanabe, K., and Kuwae, T. (2015) Radiocarbon isotopic evidence for assimilation of atmospheric CO2 by the seagrass Zostera marina. Biogeosciences, 12: 6251-6258 (PDF)
  • Watanabe, K., and Kuwae, T. (2015) How organic carbon derived from multiple sources contributes to carbon sequestration processes in a shallow coastal system? Global Change Biology, 21, 2612-2623 (PDF)
  • Jardine, C.B., Bond, A. L., Davidson, P. J. A.,Butler, R. W., and Kuwae, T. (2015) Biofilm consumption and variable diet composition of Western Sandpipers (Calidris mauri) during migratory stopover. PLoS ONE, 10: e0124164 (PDF)
  • Takahashi, A., Ito, M., Suzuki, Y., Watanuki, Y., Thiebot, J. P., Yamamoto, T., Iida, T., Trathan, P., Niizuma, Y., and Kuwae, T. (2015) Migratory movements of rhinoceros auklets in the northwestern Pacific: connecting seasonal productivities. Marine Ecology Progress Series, 525: 229-243 (PDF)
  • Hosokawa, S., Nakaoka, M., Miyoshi, E., and Kuwae, T. (2015) Seed dispersal in the seagrass Zostera marina is mostly within the parent bed in a protected bay. Marine Ecology Progress Series, 523: 41-56 (PDF)
  • Yamamoto, S., Kayanne, H., Tokoro, T., Kuwae, T., and Watanabe, A. (2015) Total alkalinity flux in coral reefs estimated from eddy covariance and sediment pore-water profiles. Limnology and Oceanography, 60: 229-241 (PDF)
  • Tokoro, T., Hosokawa, S., Miyoshi, E., Tada, K., Watanabe, K., Montani, S., Kayanne, H., and Kuwae, T.(2014): Net uptake of atmospheric CO2 by coastal submerged aquatic vegetation. Global Change Biology, 20: 1873-1884. (PDF)

       (for details)

  • Sassa, S., Watabe, Y., Yang, S., and Kuwae, T. (2013) Ecological geotechnics: Role of waterfront geoenvironment as habitats in the activities of crabs, bivalves, and birds for biodiversity restoration. Soils and Foundations, 53: 246-258. (PDF)
  • Tokoro, T., Hosokawa, S., Miyoshi, E., Montani, S., Kayanne, H., and Kuwae, T. (2013): Field measurements and analyses of coastal Blue Carbon and atmospheric CO2 sequestration. Report of Port and Airport Research Institute 52(1): 3-49.(PDF)   
  • Kuwae, T., Miyoshi, E., Hosokawa, S., Ichimi, K., Hosoya, J., Amano, T., Moriya, T., Kondoh, M., Ydenberg, R. C., and Elner, R. W. (2012): Variable and complex food web structures revealed by exploring missing trophic links between birds and biofilm. Ecology Letters 15:347-356. (PDF)  

      Selected by the Faculty of 1000!  

Lafferty K: " The idea that some shorebirds are scum-sucking members of food webs might not have an intuitive appeal, but it does change the way that we view their ecological roles and needs. This paper does a very nice job of quantifying several aspects of this issue. I was impressed that the authors combined observations, isotope analysis, and morphological analysis to evaluate the importance of scum sucking

Lawler S: "Kuwae et al. surprised ecologists and ornithologists in 2008 by showing that intertidal biofilm is..."

      Highlighted in the journal's cover photo!


           (for details)

  • Sassa. S., Watabe, Y., Yang, S., and Kuwae, T. (2011): Burrowing criteria and burrowing mode adjustment in bivalves to varying geoenvironmental conditions in intertidal flats and beaches. PLoS ONE 6: e25041 (PDF)
  • Kuwae, T., Miyoshi, E., Sassa, S., and Watabe, Y. (2010): Foraging mode shift in varying environmental conditions by dunlin Calidris alpina. Marine Ecology Progress Series 406:281-289. (PDF)
  • Takai, N., Takatsu, E., Sawairi, Y., Kuwae, T., and Yoshihara, K. (2010): Transport and deposition of macrophytes to the dysphotic bottom of coastal waters. Aquatic Botany 92:289-293. (Link)
  • Hosokawa, S., Nakamura, Y., and Kuwae, T. (2009): Increasing temperature induces shorter leaf life span in an aquatic plant. Oikos 118:1158-1163 (PDF)
  • Kuwae, T., Beninger, P. G., Decottignies, P., Mathot, K. J., Lund, D. R., and Elner, R. W. (2008): Biofilm grazing in a higher vertebrate: the Western Sandpiper Calidris mauri. Ecology 89:599-606. (PDF)
    Selected as a "Featured Article" in Ecology, the articles of the Bulletin of the Ecological Society of America (Link), the Berkeley Daily Planet (Link), and the Times Colonist (Link). Video clips of biofilm feeding (Normal, Slow-motion)
  • Kuwae, T. (2008): Food source of sandpipers feeding on intertidal flats: biofilm as a major dietary component. In: Tomonaga, O., and Takai, N. (eds) Discoveries in Aquatic Animal Ecology Presented by Stable Isotope Scope - Bivalve to Whale, Koseisha Koseikaku Co., Ltd. Tokyo, pp. 85-96 (in Japanese).
  • Kuwae, T., Nakagawa, Y., and Miyoshi, E. (2008): Oxygen consumption flux across the sediment-water interface: in situ measurements by the eddy-correlation technique. Annual Journal of Coastal Engineering JSCE 55:1001-1005 (in Japanese). (PDF)
  • Sohma, A., Sekiguchi, Y., Kuwae, T., and Nakamura, Y. (2008): A benthic-pelagic coupled ecosystem model to estimate the hypxic estuary including tidal flat ? model description and validation of seasonal/daily dynamics. Ecological Modelling 215:10-39. (Link).
  • Kuwae, T. (2007): Diurnal and nocturnal feeding rate in Kentish plovers Charadrius alexandrinus on an intertidal flat as recorded by telescope video systems. Marine Biology 151:663-673. (PDF)
  • Takai, N., Ishida, S., Okazaki, Y., Hoshika, A., Kuwae, T., and Yoshihara, K. (2007): Carbon source and trophic position of pelagic fish in the coastal waters of the southeastern Izu Peninsula, Japan, identified by stable isotope analyses. Fisheries Science 73:593-608. (Link)
  • Kuwae, T., Kamio, K., Inoue, T., Miyoshi, E., and Uchiyama, Y. (2006): Oxygen exchange flux between sediment and water in an intertidal sandflat, measured in situ by the eddy-correlation method. Marine Ecology Progress Series 307:59-68.(PDF)
  • Kuwae, T. (2005): Development and self-stabilization of restored and created intertidal flat ecosystems. JSCE Journal of Environmental Systems and Engineering 790-VII-35:25-34 (in Japanese). (PDF)
  • Kuwae, T. (2005): Intertidal flats. In: Kameyama, A., Kuramoto, T., and Hioki, Y. (eds) Nature Restoration and Rehabilitation: Using Ecotechnological Approach, Soft Science Inc. Tokyo, pp. 223-230 (in Japanese).
  • Kuwae, T., Miyoshi, E., Konuma, S. Inoue T., and Nakamura, Y. (2004): Feasibility of the restoration and creation of intertidal flat ecosystems--long-term experiments using Intertidal Flat Experimental Facility--. Report of Port and Airport Research Institute 43(1):21-48 (in Japanese). (PDF)
  • Kuwae, T., Kibe, E., and Nakamura, Y. (2003): Effect of emersion and immersion on the porewater nutrient dynamics of an intertidal sandflat in Tokyo Bay. Estuarine, Coastal and Shelf Science 57:929-940. (PDF)
  • Kuwae, T., Kawai, T., Akaishi, M., and Yamaguchi, Y. (2003): Role of shorebirds in ecological functions for several intertidal flats in Mikawa Bay. Proceedings of Coastal Engineering JSCE 50:1256-1260 (in Japanese). (PDF)
  • Kuwae, T. (2002) Factors affecting nutrient cycling in intertidal sandflats. Report of Port and Airport Research Institute 41(1):91-134. (PDF)
  • Kuwae, T., and Hosokawa, Y. (2000): Mesocosm experiments for the restoration and creation of intertidal flat ecosystems. Environmental Sciences 7:129-137. (PDF)
  • Kuwae, T., and Hosokawa, Y. (1999): Determination of abundance and biovolume of bacteria in sediments by dual staining with 4',6-diamidino-2-phenylindole and acridine orange: relationship to dispersion treatment and sediment characteristics. Applied and Environmental Microbiology 65:3407-3412. (PDF)
  • Kuwae, T., Hosokawa, Y., and Eguchi, N. (1998): Dissolved inorganic nitrogen cycling in Banzu intertidal sand-flat, Japan. Mangroves and Salt Marshes 2:167-175. (PDF)
  • Kuwae, T., Hosokawa, Y., Furukawa, K., Miyoshi, E., Kibe, E., and Eguchi, N. (1997): Mesocosm experiments on the effects of physical disturbance and water exchange on benthic communities. Report of Port and Harbour Research Institute 36(3):3-35 (in Japanese). (PDF)
  • Yoshida, Y., Nakahara, H., and Kuwae, T. (1996): Mechanisms on the occurrence of Microcystis bloom at harbors in the north basin of Lake Biwa. Nippon Suisan Gakkaishi 62:230-235 (in Japanese). (PDF)

Reviewed journals

Journal of Ecology, Geophysical Research Letters, Limnology and Oceanography, Biogeosciences, Scientific Reports, Biology Letters, Oikos, Marine Ecology Progress Series, Frontiers in Marine Science, Environmental Science and Pollution Research, Estuarine Coastal and Shelf Science, Estuaries and Coasts, Journal of Sea Research, Environmental Monitoring and Assessment, Ecological Modelling, Limnology and Oceanography: Methods, Journal of the Marine Biological Association of the United Kingdom, Canadian Journal of Zoology, Journal of Ornithology, AUK, Journal of Water and Health, Ecological Research, Journal of Oceanography, Limnology, Journal of Ethology, Journal of Field Ornithology, Waterbirds, Coastal Engineering Journal, Wetland Ecology and Management, Fisheries Science, Ornithological Science, PLoS ONE, PeerJ, La mer, Japanese Journal of Ornithology, Bulletin on Coastal Oceanography, Bulletin of the Japanese Society of Fisheries Oceanography, Japanese Journal of Conservation Ecology, Journal of Advanced Marine Science and Technology Society, JSCE Journal of Environmental Systems and Engineering, JSCE Journal of Environmental Engineering, JSCE Journal of Hydraulic, Coastal and Environmental Engineering, JSCE Journal of Hydroscience and Hydraulic Engineering, Journal of Japan Society on Water Environment, JSCE Journal of Environmental Systems Research, JSCE Journal of Global Environment Engineering, JSCE Annual Journal of Civil Engineering in the Ocean 

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