FY2011 Annual Report

Marine Biophysics Unit

Professor Satoshi Mitarai



Marine Biophysics Unit will develop forecasting system for the coastal ocean circulation processes around Okinawa and implement a validated connectivity assessment tool, coupling available modeling and observation techniques. This modeling tool will

  • Help marine biologists and geneticists estimate rates of gene flow among sites,
  • Enable public agencies to build and evaluate marine protected areas based on population connectivity, and
  • Provide marine ecologists with a modeling system for predicting the global and long-term dynamics of the marine ecosystem.

Marine Biophysics Unit was established on Sep 1, 2009 when Satoshi Mitarai joined OIST.

1. Staff


  • Masako Nakamura (March 2010–)
  • Daisuke Hasegawa (October 2011–)


  • Taichiro Sakagami (February 2010–)
  • Yukiko Murabayashi (July 2011–)
  • Shohei Nakada (August 2011–)

Research administrator

  • Chihiro Arasaki (July 2012–)

Short-term Students

  • Emile Trimoreau (September 2010–February 2011)
  • Flora Vincent (July 2011–December 2011)
  • Hirohito Yamazaki (August 2011–September 2011)
  • Fiona Francis (May 2012–August 2012)

2. Collaborations

Theme: Larval dispersal of coral reef species

  • Type of collaboration: Joint research
  • Researchers: K. Sakai (University of the Ryukyus)*, D. Siegel, R. Warner, J. Caselle (University of California, Santa Barbara), P. Barbar (University of California, Los Angeles),

Theme: Larval dispersal of hydrothermal vent species

  • Type of collaboration: Joint research
  • Researchers: T. Maruyama, Y. Fujiwara, Y. Furushima and H. Watanabe (Japan Agency for Marine-Earth Science and Technology)*, S. Beaulieu, D. McGillicuddy, J. Ledwell, L. Mullineaux, S. Mills (Woods Hole Oceanographic Institution)

Theme: Regional ocean circulation modeling

  • Type of collaboration: Joint research
  • Researchers: J. McWilliams, J. Molemaker (University of California, Los Angeles), Y. Uchiyama (Kobe University)*, E. Gross (Stanford University)

Theme: Okinawa coastal ocean observing system

  • Type of collaboration: Joint research
  • Researchers: K. Hirate (Okinawa Prefectural Fisheries and Ocean Research Center)*, K. Muneda, T. Kimura (11th Regional Coast Guard Headquarters)*, S. Gallager (Woods Hole Oceanographic Institution), M. Toda (Okinawa Churaumi Aquarium).

* indicates that a joint research agreement has been established.

3. Activities and Findings

Coastal ocean circulation modeling

Taichiro Sakagami

We have been developing high-resolution ocean circulation simulation for Okinawa by using the Regional Ocean Modeling System, a collaboration with Prof. Jim McWilliam’s group (University of California, Los Angeles) and Prof. Uchiyama (Kobe University). We plan to build three-level nested grids for Okinawa region. We finished two grids (12.5 km horizontal resolution and 4 km resolution) and have been evaluating the simulation outputs and available observation data. We will assess larval dispersal patterns with the particle tracking simulation for Okinawa islands and Okinawa trough.

Coastal ocean observation

Daisuke Hasegawa

We made an observation along the Kuroshio current with an Argo float deployed near the Kuroshio axis. The float successfully traveled from the west of Kume Island to the south of Tanega-shima (~800 km) while taking 190 vertical profiles of temperature and salinity from the surface to 1000-m deep. The results show how the water properties change from the upstream to the downstream when the Kuroshio across the shallow Tokara Islands region, which may be associated with the vertical mixing due to the bottom friction. High-resolution data of Kuroshio is hard to obtain. We will investigate the result furthermore.

Larval recruitment of benthos in coral reefs and hydrothermal vents

Masako Nakamura

We investigated the coral settlement and community structure in the Central Ryukyu Islands; Okinawa Island, Kerama Islands and Kume Island, using artificial settlement plates (upper photo) and video transect survey methods in collaboration with Prof. Sakai (University of the Ryukuys). The amount of settled coral spats varied among areas. The settlement pattern was not associated with adult coral distribution. It could be due to transport by ocean currents. We will continue to observe settlement pattern of the area to reveal annual variability in the coral settlement. We set the artificial settlement plates at several hydrothermal vents in Okinawa Trough to quantify the new recruits of benthic animals in hydrothermal vents. These plates will be retrieved in 2012. We are also conducting population structure and reproductive trait of deep-sea limpets in Okinawa trough to reveal the breeding season and subsequent larval dispersal periods.

4. Publications

4.1 Journals

Fiscal year 2009
  1. Mitarai, S., Siegel, D., Watson, J., Dong, C., and McWilliams, J. Quantifying connectivity in the coastal ocean with application to the Southern California Bight. Journal of Geophysical Research-Oceans, 114, C10026, October 2009. (25)
  2. Berkley, H., Kendall, B., Mitarai, S., and Siegel, D. Turbulent dispersal promotes species coexistence. Ecology Letters, 13, 360–371, March 2010. (12)
  3. Watson, J., Mitarai, S., Siegel, D., Caselle, J., Dong, C., and McWilliams, J. Realized and potential larval connectivity in the Southern California Bight. Marine Ecology–Progress Series, 401, 31–48, February 2010. (20)
Fiscal year 2010
  1. Selkoe, K., Watson, J., White, C., Ben Horin, T., Iacchei, M., Mitarai, S., Siegel, D., Gaines, S., and Toonen, R. Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef species. Molecular Ecology, 19, 3708–3726, September 2010 (20).
  2. Ohlmann, J., and Mitarai, S. Lagrangian assessment of simulated surface current dispersion in the coastal ocean. Geophysical Research Letters, 37, L17602, September 2010. (7)
  3. Nakamura, M., Ohki, S., Suzuki, A., and Sakai, K. Coral larvae under ocean acidification: survival, metabolism, and metamorphosis, PLoS One 6, e14521, January 2011. (7).
Fiscal year 2011
  1. Alberto, F., Raimondi, P., Reed, D., Watson, J., Siegel, D., Mitarai, S., Coelho, N., and Serrao, E. Isolation by oceanographic distance explains genetic structure for Macrocystis pyrifera in the Santa Barbara Channel, Molecular Ecology, 20, 2543-2554 , May 2011. (0)
  2. Watson, J., Hays, C., Raimondi, P., Mitarai, S., Dong, C., McWilliams, J., Blanchette, C., Caselle, J. and Siegel, D., Currents connecting communities: nearshore community similarity and ocean circulation, Ecology, 92, 1193–1200, June 2011. (4)
  3. Watson, J., Siegel, D., Kendall, B., Mitarai, S., Rassweiller, A., and Gaines, S. Identifying critical regions in small-world marine metapopulations, Proceedings of the National Academy of Sciences of the United States of America, 108, E907–913, October 2011 (1)
  4. Nakamura, M., Morita, M., Kurihara, H. and Mitarai, S. Expression of hsp 70, hsp 90, hsf1 in the reef coral Acropora digitifera under prospective acidified conditions over the next several decades, Biology Open, 1, 75–81, November 2011. (N/A)

4.2 Books and other one-time publications

  • Mitarai, S., “Okinawa Marine Eco-system Research Project: OIST’s efforts to create world-class center for research”, Ryukyu Simpo (local newspaper), February 2, 2011.
  • Trimoreau, E., “Internship at the Okinawa Institute of Science and Technology Promotion Corporation”, Ryukyu Simpo (local newspaper), September 11, 2011.

4.3 Oral and Poster Presentations

Fiscal year 2009
  1. Mitarai, S., Ohlmann, J., Dong, C., Siegel, D. and McWilliams, J., "An Empirical Examination of Simulated Connectivity, with Application to the Southern California Bight,"  2010 Ocean Sciences Meeting, Portland, Oregon, USA, February 22–26, 2010.
  2. Mitarai, S., "Larval Dispersal in the Turbulent Coastal Ocean: Dynamics and Impacts," Life Science Special Seminar, University of California, Los Angeles, USA, December 7, 2009.
Fiscal year 2010
  1. Nakamura, M., Ohki S., Suzuki, A. and Sakai, K., “Metabolism and Metamorphosis of Coral Larvae in Acidified Seawater”, PICES, Sendai, Japan, April 2010.
  2. Nakamura, M. and Sakai, K., “Biological and physical factors affecting recruitment variability of spawning corals at local scale-implications for dispersal”, 9th Larval Biology Symposium, Wellington, New Zealand, August 23–27, 2010.
  3. Nakamura, M., Morita, M., Suzuki, A., Sakai, K. and Mitarai, S., “How do coral larvae respond to change in ocean pH?”, 9th Larval Biology Symposium, Wellington, New Zealand, August 23–27, 2010.
  4. Nakamura, M., Morita, M., Kurihara, H. and Mitarai, S., “Effect of acidified seawater on hsp gene expressions in coral larvae”, Okinawa IPCC OAEM side event, Intergovernmental Panel on Climate Change, Nago, Okinawa, January 16, 2011.
  5. Sakagami, T. and Barber, R., “Seasonal cycle of chlorophyll biomass in Peru coastal upwelling ecosystem”, 2011 ASLO Aquatic Sciences Meeting, American Society for Limnology and Oceanography, San Juan, Puerto Rico, February 13–18, 2011.
  6. Nakamura, M., Morita, M., Kurihara, H. and Mitarai, S.,”Gene expression of hsps in coral larvae under acidified conditions”, 2011 ASLO Aquatic Sciences Meeting, American Society for Limnology and Oceanography, San Juan, Puerto Rico, Feb 13–18, 2011.
Fiscal year 2011
  1. Mitarai, S,, Sakagami, T. and Nakamura, M., “Larval dispersal and metapopulation dynamics of hydrothermal vent species”, Workshop for Larval Dispersal of Hydrothemal vent species, Japan Agency for Earth System Science and Technology, Tokyo, Japan, December 16, 2011.
  2. Nakamura, M., Higa, Y. and Mitarai, S., “Outbreaks of crown-of-thorns starfish Acanthaster planci in the Central Ryukyu Islands; some steps toward supply-side effects”,  Joint Meeting of the 59th Annual Meeting of ESJ and the 5th EAFES International Congress, Shiga, Japan, March 17–21, 2012.
  3. Hasegawa, D., “How small islands induce upwelling in strong geostrophic currents”, 2012 Ocean Sciences Meeting,  Salt Lake City, Utah, USA, Feb 20–24, 2012.
  4. Hasegawa, D., and Sheng, J. “Far-field effects of tidal energy extraction in the Minas Passage on tidal circulation in the Bay of Fundy and Gulf of Maine”, The Oceanographic Society of Japan Spring Meeting 2012, Tsukuba, Japan, March 26–30, 2012.

5. Intellectual Property Rights and Other Specific Achievements

External funding

  • Pursuit of Dream Grant, Canon Foundation, “Larval dispersal and metapopulation dynamics of hydrothermal vent species”, Lead PI: S. Mitarai (OIST), Co-PIs: N. Satoh, H. Kitano, T. Maruyama, Y. Fujiwara, Y. Furushima, H. Watanabe (Japan Agency for Marine-Earth Science and Technology), Amount: 38M Yen, Period: Apr 2011–Mar 2014.   
  • Grants-in-Aid for Scientific Research C, Japan Society for the Promotion of Science, “Quantification of spatio-temporal variability in recruitment at hydrothermal vents”, Lead PI: M. Nakamura (OIST), Co-PIs: H. Watanabe (Japan Agency for Marine-Earth Science and Technology), T. Sasaki (University of Tokyo), Amount: 4.3M Yen, Period: Apr 2012–Mar 2016.
  • Sasagawa Grants for Scientific Research, “ Study on mechanisms of outbreaks of crown-of-thorns starfish Acanthaster planci in the Central Ryukyu Islands – relationship with larval transport by currents”, Lead PI : M. Makamura (OIST), Co-PIs: None, Amount: 500K Yen, Period: Apr 2012–Feb 2013.
  • Strategic Information and Communications R&D Promotion Programme, Ministry of Internal Affairs and Communications, “Development of high-frequency radars for Okinawa coral reefs”, Lead PI: S. Fujii (University of the Ryukyus), Co PI: S. Mitarai, Amount: 19M Yen, Period: July 2012–Mar 2014.

Honors and awards

  • 2011 Annual Award for an Outstanding Published Paper in Ecological Theory, “Turbulent dispersal promotes species coexistence” by H. Berkley, B. Kendall, S. Mitarai, and D. Siegel, Theoretical Ecology Section, Ecological Society of America.

6. Meetings and Events

OIST International Workshop on Computational Ecology

Organizer: Satoshi Mitarai (OIST)
Co-organizer: Dave Robertson (University of Edinburgh)
Dates: Dec 1–3, 2010
Place: OIST Seaside House / OIST campus
Invited Speakers:

  • Robert Warner (University of California, Santa Barbara, USA)
  • Stephen Monismith (Stanford University, USA)
  • Amaztia Genin (Hebrew University of Jerusalem, Israel)
  • Louis Legendre (Laboratoire d'Oceanographie de Villefranche, France)
  • James Mitchell (Flinders University, Australia)
  • Hidekatsu Yamazaki (Tokyo Institute of Marine Science and Technology, Japan)
  • Paul Barber (University of California, Los Angeles, USA)
  • Jennifer Caselle (University of California, Santa Barbara, USA)
  • David Robertson (University of Edinburgh, UK)
  • Malcolm Atkinson (University of Edinburgh, UK)
  • Siu-Wai Leung (University of Macau, China)
  • Fang-Pang Lin (National Center for High Performance Computing, Taiwan)
  • Scott Gallager (Woods Hole Oceanographic Institution, USA)
  • Amber York (Woods Hole Oceanographic Institution, USA)

Partnership for Okinawan Ocean Observation

Organizer: 11th Regional Coast Guard Headquarters
Co-orgnizer: Marine Biophysics Unit, OIST
Dates: Jan 31, 2012
Place: OIST Campus

  • 11th Regional Coast Guard Headquarters, Naha, Okinawa
  • National Institute of Information and Communications Technology, Onna, Okinawa
  • University of the Ryukyus, Nishihara, Okinawa
  • Okinawa Prefectural Fisheries and Ocean Research Center, Itoman Okinawa
  • Seikai National Fisheries Research Institute, Fisheries Agency, Ishigaki, Okinawa
  • Okinawa Meteorological Observatory, Japan Meteorological Agency, Naha, Okinawa

International Study of Connectivity Between Hydrothermal Vents (Mariana Vent Larvae Workshop)

Organizers: Satoshi Mitarai (OIST), Stace Beaulieu (Woods Hole Oceanographic Institution), H. Watanabe (Japan Agency for Marine-Earth Science and Technology)
Dates: May 9–11, 2012
Place: OIST Campus
Funding sources: OIST and National Science Foundation, USA
Invited Spealers:

  • D. Adams (National Instutes of Health),
  • S. Allerano, S. Beaulieu, J. Kellner, J. Ledwell, D. McGuillicuddy, S. Mills, L. Mullineaux, J. Wheeler, W. Zhang (Woods Hole Oceanographic Institution),
  • E. Breuer (National Oceannic and Atmospheric Administration)
  • D. Butterfield (University of Washington)
  • B. Chadwick (Oregon State University)
  • R. Davis (Oregon Health and Science University)
  • J. Huber (Marine Biological Laboratory)
  • J. Ishibashi (Kyushu University)
  • S. Kojima, M. Sunamura, T. Yahagi, M. Seo (University of Tokyo), K. Komaki (Kanso)
  • A. Thurnherr, X. Liang (Lamont-Doherty Earth Laboratory)
  • D. Milton (InterRidge)
  • S. Mino (Hokkaido University)
  • H. Miyake (Kitasato University)
  • C. Moyer (Western Washington University)
  • F. Pradillon (French Research Institute for Exploration of the Sea)
  • S. Seama (Kobe University)
  • H. Watanabe, F. Sinniger (Japan Agency for Marine-Earth Science and Technology)
  • V. Tunnicliffe (University of Victoria)
  • R. Young (Massachusetts Institute of Technology).

7. Other

Media coverage

  • Nihon Keizai Shimbun (Japanese leading economic newspaper), June 7, 2011.
  • Ryukyu Simpo (local newspaper), December 23, 2012.
  • NHK (Japan broadcasting corporation), World Wave Tonight, May 15, 2012.