Publications (peer-reviewed)


37. Bodenmann A,  Blair T, Nakajima R, Ura T (2017) Methods for quantitative studies of seafloor hydrothermal systems using 3D visual reconstructions. ROBOMECH Journal 4:22

36. Nakajima R, Tanaka Y,  Guillemette R, Kurihara H (2017) Effects of coral-derived organic matter on the growth of bacterioplankton and heterotrophic nanoflagellates. Coral Reefs

35. Nakajima R, Yamazaki H, Lewis LS, Khen A, Smith JE, Nakatomi N, Kurihara H (2017) Planktonic trophic structure in a coral reef ecosystem – grazing versus microbial food webs and the production of mesozooplankton. Progress in Oceanography 156: 104-120.

34. Tsuchiya T, Kuwahara VS, Yoshiki T,  Nakajima R, Shimode S, Kikuchi T, Toda T (2017) Response of phytoplankton and enhanced biogeochemical activity to an episodic typhoon event in the coastal waters of Japan. Estuarine, Coastal and Shelf Science 194: 30-39.

33. Tanaka Y,  Nakajima R (in press) Dissolved organic matter in coral reefs: distribution, production, and bacterial consumption. In: Coral Reef Studies of Japan (Iguchi A and Hongo C, eds). Springer

32. Nakajima R, Rimachi EV, Santos-Silva EN, Calixto LSF, Leite RG, Khen A, Yamane T, Mazeroll AI, Inuma JC, Utumi EYK, Tanaka A (2017) The density and biomass of mesozooplankton and ichthyoplankton in the Negro and the Amazon Rivers during the rainy season: the ecological importance of the confluence boundary. PeerJ 5: e3308.


31. Nakajima R, Nakatomi N, Kurihara H, Fox M, Smith J, Okaji K (2016) Crown-of-thorns starfish larvae can feed on organic matter released from corals. Diversity 8: 18.

30. Thornton B, Bodenmann A, Pizarro O, Williams SB, Friedman A,  Nakajima R, Takai K, Motoki K, Watsuji T, Hirayama H, Matsui Y, Watanabe H, Ura T (2016) Biometric assessment of deep-sea vent megabenthic communities using multi-resolution 3D image reconstructions. Deep Sea Research I 116: 200-219.


29. Tsuchiya T, Kuwahara VS, Hamasaki K, Tada Y, Ichikawa T, Yoshiki T,  Nakajima R, Imai A, Shimode S, Toda T (2015) Thphoon-induced response of phytoplankton and bacteria in temperate coastal waters. Estuarine, Coastal and Shelf Science 167: 458-465.

28. Nakajima R, Yoshida T, Othman BHR, Toda T (2015) Monsoonal changes in the planktonic copepod community structure in a tropical coral reef at Tioman Island, Malaysia. Regional Studies in Marine Science 2: 9-26.

27. Nakajima R, Yamamoto H, Kawagucci S, Takaya Y, Nozaki T, Chen C, Fujikura K, Miwa T, Takai K (2015) Post-drilling change in seabed landscape and megabenthos in a deep-sea hydrothermal system, the Iheya North field, Okinawa Trough. PLoS ONE 10: e0123095.

26. Nakajima R, Tanaka Y, Yoshida T, Fujisawa T, Nakayama A, Fuchinoue Y, Othman BHR, Toda T (2015) High inorganic phosphate concentration in coral mucus and its utilization by heterotrophic bacteria. Marine Ecology, 36: 835-841.

25. Yamakita T, HY, MN, HY, KF, KH, YH, TI, SK, TK, SK, KK, TK, NHK, HM, KM, HM, Nakajima R, SN, KN, SS, MS, KS, HS, KT, KT, YJ-U, KW, HW, YY, NY, Shirayama Y (2015) Identification of important marine areas around the Japanese Archipelago: establishment of a protocol for evaluating a broad area using ecologically and biologically significant areas selection criteria. Marine Policy 51: 136-147.


24. Nakajima R, Komuku T, Yamakita T, Lindsay DJ, Jintsu-Uchifune Y, Watanabe H, Tanaka K, Shirayama Y, Yamamoto H, K Fujikura (2014) A new method for estimating the area of the seafloor from oblique image taken by deep-sea submersible survey platforms. JAMSTEC Report of Research and Development, 19: 59-66.

23. Nakajima R, Tanaka Y (2014) The role of coral mucus in the material cycle in reef ecosystems: biogeochemical and ecological perspectives. Journal of the Japanese Coral Reef Society, 16, 3-27 (in Japanese)

22. Tsuchiya K, Kuwahara VS, Yoshiki T, Nakajima R, Miyaguchi H, Kumekawa N, Kikuchi T, Toda T (in press) Phytoplankton community response and succession in relation to typhoon passages in the coastal waters of Japan. Journal of Plankton Research.

21. Nakajima R, Yamakita T, Watanabe H, Fujikura K, Tanaka K, Yamamoto H, Shirayama Y (2014) Species richness and community structure of benthic macrofauna and megafauna in the deep-sea chemosynthetic ecosystems around the Japanese Archipelago: an attempt to identify priority areas for conservation. Diversity and Distributions, 20, 1160-1172 (open access)

20. Nakajima R, Yoshida T, Othman BHR, Toda T (2014) Biomass and estimated production rates of metazoan zooplankton community in a tropical coral reef of Malaysia. Marine Ecology, 35: 112-131.

19. Nakajima R, Lindsay DJ, Yoshida T, Othman BHR, Toda T (2014) Short-term temporal variation in gelatinous zooplankton populations over 48 hours in a coral-reef at Redang Island, Malaysia. Marine Ecology, 35: 254-260.


18. Nakajima R, Yoshida T, Azman B.A.R, Yamazaki H, Toda T, Othman B. H. R, Zaleha K, Effendy A.W.M. (2013) A preliminary study of small scavenging crustaceans collected by baited traps in a coral reef of Bidong Island, Malaysia. Malaysian Journal of Science. 32(2): 59-66.

17. Nakajima R, Yoshida T, Othman BHR, Toda T (2013) First record of a blue-pigmented Acartiid copepod in the tropical coral reef waters of Malaysia. Galaxea Journal of Coral Reef Studies, 15: 27-28.

16. Bodenmann A, Thornton B, Nakajima R, Yamamoto H, Ura T (2013) Wide area 3D seafloor reconstruction and its application to sea fauna density mapping. Proceedings of the OCEANS 2013 MTS/IEEE. 1-5.

15. Nakajima R, Yoshida T, Fuchinoue Y, Okashita T, Maekawa T, Kushairi MRM, Othman BHR, Toda T (2013) Sedimentation impact on the growth of the scleractinian coral Acropora formosa from fringing reefs of Tioman Island, Malaysia. Sains Malaysiana 42: 1201-1205.

14. Kawagucci S, Miyazaki J, Nakajima R, Nozaki T, Takaya Y, Kato Y, Shibuya T, Konno U, Nakaguchi Y, Hirayama H, Fujikura K, Furushima Y, Yamamoto H, Watsuji T, Ishibashi J, Takai K (2013) Post drilling change in fluid discharge pattern, mineral deposition, and fluid chemistry in the Iheya North hydrothermal field, Okinawa Trough. Geochemistry, Geophysics, Geosystems 14: 4774-4790.

13. Nakajima R, Tsuchiya K, Nakatomi N, Yoshida T, Tada Y, Konno F, Toda T, Kuwahara VS, Hamasaki K, Othman BHR, Segaran TC, Effendy AWM (2013) Enrichment of microbial abundance in the sea-surface microlayer over a coral reef: implications for biogeochemical cycles in reef ecosystems. Marine Ecology Progress Series 490: 11-22. (open access)

12. Tsuchiya K, Yoshiki T, Nakajima R, Miyaguchi H, Kuwahara VS, Taguchi S, Kikuchi T, Toda T (2013) Typhoon-driven variations in primary production and phytoplankton assemblages in Sagami Bay, Japan: A case study of typhoon Mawar (T0511). Plankton & Benthos Research 8: 74-87.




11. Nakajima R, Yoshida T, Shibata A, Othman BHR, Toda T (2011) Quality and quantity of particulate organic carbon in a coral reef at Tioman Island, Malaysia. Sains Malaysiana 40: 1375-1382.


10. Nakajima R, Nakayama A, Yoshida T, Kushairi MRM, Othman BHR, Toda T (2010) An evaluation of photo line-intercept transect (PLIT) method for coral reef monitoring. Galaxea Journal of Coral Reef Studies 12: 37-44. Erratum.pdf

9. Kuwahara VS, Nakajima R, Kushairi MRM, Othman BHR, Toda T (2010) Spatial variability of UVR attenuation and bio-optical factors in shallow coral reef waters of Malaysia. Coral Reefs 29: 693-704.

8. Nakajima R, Yoshida T, Fujita K, Nakayama A, Fuchinoue Y, Othman BHR, Toda T (2010) Release of particulate and dissolved organic carbon by the scleractinian coral Acropora formosa. Bulletin of Marine Science 86: 861-870. ※Selected as ”This month’s feature” in the journal website

7. Nakajima R, Yoshida T, Othman BHR, Toda T (2010) High detritus/phytoplankton content in net-plankton samples from coral reef water: source of over-estimation in zooplankton biomass by measuring seston weight. Plankton & Benthos Research 5: 69-73. Nakajima2010c.pdf


6. Nakajima R, Yoshida T, Azman BAA, Zaleha K, Othman BHR, Toda T (2009) In situ release of coral mucus by Acropora and its influence on the heterotrophic bacteria. Aquatic Ecology 43: 815-823.

5. Nakajima R, Yoshida T, Othman BHR, Toda T (2009) Diel variation of zooplankton in the tropical coral-reef water of Tioman Island, Malaysia. Aquatic Ecology 43: 965-975.


4. Nakajima R, Yoshida T, Othman BHR, Toda T (2008) Diel variation in abundance, biomass and size composition of zooplankton community over a coral-reef in Redang Island, Malaysia. Plankton & Benthos Research 3: 216-226.


3. Toda T, Okashita T, Maekawa T, Kee Alfian BAA, Kushairi MRM, Nakajima R, Chen W, Takahashi KT, Othman BHR, Terazaki M (2007) Community structures of coral reefs around Peninsular Malaysia. Journal of Oceanography 63: 113-123.


2.  Shibata A, Goto Y, Nakajima R (2006) Use of SYBR Gold stain for enumerating bacteria and viruses in seawater samples. Bulletin of The Plankton Society of Japan 53: 64-68.  (in Japanese)

1.  Nakajima R, Yoshida T, Othman BHR, Toda T (2006) Diel variation and trophic structure of coral-reef zooplankton in Peninsular Malaysia. Coastal Marine Science 30: 336-343.

Other publications (non peer-reviewed)

4. Nakajima R (2017) The role of coral mucus in coral reef ecosystems. Sea slug news letter 93, 2-4. (in Japanese)

3. Nakajima R (2014) Deep-sea creature map around Japan. In: Deep sea and Earth’s Encyclopedia (eds: Kato C, Isozaki Y, Kodaira S, Kawano K). Maruzen Press. (in Japanese)

2. Nakajima R, T. Toda, T. Yoshida and B. H. R. Othman (2004) Trophic structure of pelagic ecosystem in tropical coral reef: Which size fraction is the most important? Proceeding of 3rd Annual Seminar on Sustainability Science and Management, 366-370.

1. Nakajima R, T. Yoshida, A. Shibata, B. H. R. Othman and T. Toda (2009) Size composition of particulate organic matter in a coral reef at Tioman Island, Peninsular Malaysia. Proceedings of International Conference on Marine Ecosystem 2009, 209-220.

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