Japan Society for the Promotion of Science: Core-to-Core Program

Research and Education Network on coastal ecosystems in SouthEast Asia (RENSEA)


Office Manager:  Shuhei Nishida

  1. Species diversity and food-web in meso-    and batypelagic ecosystem

  2. Vertical structure of pelagic ecosystem
    Ecology and morphology of copepods

  3. Taxonomy, distribution, and phylogeny of  copepods

  4. Feeding habits of micronekton

  5. Biology of rock lobsters during planktonic  and pre-settlement stages

  My present research focuses on the evolution of pelagic communities with particular reference to the species diversity of zooplankton in the mesopelagic zone.  While a large body of knowledge has accumulated on the structure of pelagic communities, and the elevated species diversity in the physically-stable and homogenous mesopelagic zone, relative to the coastal and epipelagic habitats, has widely been accepted, there remains much to be explained for this phenomenon, referred to as one of "the paradox of the plankton". This is due largely to the lack of information on the life of organisms in situ. I am dealing with this problem by examining several distinct, but closely-related topics: (1) ecology of gelatinous plankton, (2) distribution and characteristics of marine snow, (3) food-web structure, (4) parasitism/symbiosis in pelagic communities, (5) deep-sea bioluminescence, and (6) functional morphology of pelagic copepods. In addition to conventional methods such as samplings with nets and bottles, variety of research- and analytical techniques has been applied, e.g., deep-sea submersible dives, electron and epifluorescent microscopy, microspectrophotometry, stable-isotope-ratio analysis, immunochemistry, and video-record analysis of zooplankton behavior. Major results in the past several years include: the first comprehensive description of midwater fauna of gelatinous plankton from the western Pacific by using a submersible; development of sampling gears for use on submersibles; discovery of species-specific, light-dependent reverse diel vertical migration in a group of iridescent copepods; description of specialized chemoreceptors in the copepods feeding on marine snow; discovery of venomous-predatory structure and its evolution in pelagic copepods; and observations on a possible use of bacterial luminescence in food detection by deep-sea copepods. Through these studies it has become progressively more evident that marine-snow feeding, carnivory, and association with gelatinous organisms are essential in elucidating the species diversity in mesopelagic communities, that major copepod groups in this habitat have evolved unique feeding strategies which are different from those of the epipelagic copepods, and that multiple approaches, e.g., combining distributional data with the results of feeding ecology and functional morphology, are powerful in mesopelagic research. Analyses of mesopelagic food web by stable-isotope analysis and immunochemical method, and of evolutionary history in mesopelagic copepods by using molecular genetics are now in progress.

- Publications - by September 2015)

1. Original paper( from 2000, numbered serially)

37) Matsuura, H. and S. Nishida 2000. Fine structure of the "button setae" in the deep-sea pelagic copepods of the genus Euaugaptilus (Calanoida: Augaptilidae). Marine Biology 137: 339-345.

38) Nishikawa, J., S. Nishida, M. Moku, K. Hidaka, and K. Kawaguchi 2001. Biomass, abundance, and vertical distribution of micronekton and large gelatinous zooplankton in the subarctic Pacific and the Bering Sea during the summer of 1997. Journal of Oceanography 57: 361-375.

39) Ohtsuka, S., S. Nishida and K. Nakaguchi 2002. Three new species of the genus Macandrewella (Copepoda: Calanoida: Scolecitrichidae) from the Pacific Ocean, with notes on distribution and feeding habits. Journal of Natural History 36: 531-564.

40) Nishida, S., S. Ohtsuka and A.R. Parker 2002. Functional morphology and food habits of deep-sea copepods of the genus Cephalophanes (Calanoida: Phaennidae): perception of bioluminescence as a strategy for food detection. Marine Ecology Progress Series 227: 157-171.

41) Itoh, H. and S. Nishida (2002). A new species of Hemicyclops (Copepoda: Poecilostomatoida) from burrows of the mud shrimp Upogebia major in an estuarine mud-flat in Tokyo Bay, Japan. Hydrobiologia 474: 139-146.

42) Booth, J.D., J. Kittaka, S. Nishida, Y. Hayakawa and W.R. Webber (2002). Cooperative research between Japan and New Zealand advances understanding of early life history of spiny lobsters.Fisheries Science 68 (Suppliment II): 1956-1959.

43) Hayakawa, Y. and S. Nishida (2002). Diel behavior of the puerulus and the first instar of the red rock lobster, Jasus edwardsii. Fisheries Science 68 (Suppliment I): 393-396.

44) Machida, J. R., M. M. Miya, M. Nishida and S. Nishida (2002). Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda). Marine Biotechnology, 4: 406-417.

45) Machida, J. R., M. U. Miya, M. Nishida and S. Nishida (2004). Large-scale rearrangements in the mitochondrial genomes of two calanoid copepods Eucalanus bungii and Neocalanus cristatus (Crustacea) with notes on new versatile primers for the srRNA and COI genes. Gene 332: 71-78.

46) Machida J. R., M. U. Miya, M. M. yamauchi, M. Nishida, and S. Nishida (2004). Organization of the mitochondrial genome of Antarctic krill, Euphausia superba (Crustacea: Malacostraca). Marine Biotechnology 6: 238-250.

47) Rezai, H., F.Md. Yusoff, A. Arshad, A. Kawamura, S. Nishida and B.H.R. Othman (2004). Spatial and temporal distribution of copepods in the Straits of Malacca. Zoological Studies 43: 486-497.

48) Chae J. and S. Nishida (2004). Swimming behaviour and photoresponses of the iridescent copepods, Sapphirina gastrica and Sapphirina opalina (Copepoda : Poecilostomatoida). Journal of the Marine Biological Association of the United Kingdom 84: 727-731.

49) Nishida, S. and I.F.M. Rumengan (2005). A new species of Pseudodiaptomus (Copepoda: Calanoida: Pseudodiaptomidae) from the coastal waters of Sulawesi, Indonesia. Plankton Biology and Ecology 52: 27-32.

50) Nishida, S. and N. Cho (2005). A new species of Tortanus (Atortus) (Copepoda: Calanoida: Tortanidae) from the coastal waters of Nha Trang, Vietnam. Crustaceana 78 (2): 223-235.

51) Ohtsuka, S., S. Nishida and R. J. Machida (2005). Systematics and zoogeography of the deep-sea hyperbenthic family Arietellidae (Copepoda: Calanoida) collected from the Sulu Sea. Journal of Natural History 39 (27): 2483-2514.

52) Miyake, H., D.J. Lindsay, M. Kitamura and S. Nishida (2005). Occurrence of the Scyphozmedusa Parumbrosa polylobata Kishinouye, 1910 in Suruga Bay, Japan. Plankton Biology and Ecology 52: 58-66.

53) Nishikawa, J., Y. Suzuki and S. Nishida (2005). Immunochemical recognition of gelatinous zooplankton: an application to identify the origin of "barrel" made by the pelagic amphipod, Phronima sedentaria. Journal of Marine Biological Association of the United Kingdom 85: 635-639.

54) Inagaki, T., J. Hiromi, K. Ara, J. Nishikawa and S. Nishida (2005). Acoustic observation of jellyfish Aurelia aurita in Tokyo Bay. Bulletin of The Plankton Society of Japan 52 (2): 73-76. (In Japanese with English abstract.)

55) Machida, R. J., M. U. Miya, M. Nishida and S. Nishida (2006). Molecular phylogeny and evolution of the pelagic copepod genus Neocalanus (Crustacea: Copepoda). Marine Biology 148: 1071-1079.

56) Kuriyama, M. and S. Nishida (2006). Species diversity and niche-partitioning in the pelagic copepods of the family Scolecitrichidae (Calanoida). Crustaceana 79 (3): 293-317.

57) Ramu, K., N. Kajiwara, H. Mochizuki, H. Miyasaka, K.A. Asante, S. Takahashi, S. Ota, H.-M. Yeh, S. Nishida and S. Tanabe (2006). Occurrence of organochlorine pesticides, polychlorinated biphenyls and plolybrominated diphenyl ethers in deep-sea fishes from the Sulu Sea. Marine Pollution Bulletin 52: 1827-1832.

58) Nishida, S. and T. Gamo (2007). Biogeochemistry and biodiversity in the Sulu Sea. Deep-Sea Research Part II 54: 1-3.

59) Nishikawa, J., H. Matsuura, L.V. Castillo. W.L. Campos and S. Nishida (2007). Biomass, vertical distribution and community structure of mesozooplankton in the Sulu Sea and its adjacent waters. Deep-Sea Research Part II 54: 114-130.

60) Toyoshima, S., S. Takahashi, T. Ikemoto, T. Agusa, H. Miyasaka, K. Omori, S. Nishida and S. Tanabe (2007). Evaluation of accumulation properties of trace elements in a deep-sea ecosystem of Sagami Bay, Japan by using stable isotope ratios (15N and 13C), Chemical Pollution and Environmental Changes (Proceedings of the International Symposium: Pioneering Studies of Young Scientists on Chemical Pollution and Environmental Changes, November 17-19, 2006), Universal Academy Press, 225-228.

61) Itoh, H. and S. Nishida (2007). Life history of the copepod Hemicyclops gomsoensis (Poecilostomatoida, Clausidiidae) associated with decapod burrows in the Tama-River estuary, central Japan. Plankton and Benthos Research 2 (3): 134-146.

62) Nonomura, T., R.J. Machida and S. Nishida (2008). Stage-V copepodites of Calanus sinicus and C. jashnovi (Copepoda: Calanoida) in mesopelagic zone of Sagami Bay as identified with genetic markers, with special reference to their vertical distribution. Progress in Oceanograhy 77 (1): 45-55.

2. Review paper

4) 西田周平 2000. 親潮域におけるネット動物プランクトンの生物量 ― 鉛直構造と成立要因. 日本プランクトン学会報 47: 125-128.

5) Nishida, S. (2002). Sensory, feeding, and digestive systems in the phyllosoma and puerulus of palinuid lobsters. Fisheries Science 68 (Suppliment I): 297-400.]

6) Bucklin, A., S. Nishida, S. Schnack-Schiel, P.H. Wiebe, D. Lindsay, R.J. Machida, and N.J. Copley (2010) A Census of Zooplankton of the Global Ocean, Chapter 13, In: Life in the World's Oceans: Diversity, Distribution, and Abundance. Alasdair D. McIntyre (Ed.), Blackwell Publishing Ltd. (Oxford).  Pp. 247-265.

7) ノブレザダ メアリー マー・宮本洋臣・西田周平 (2012) 南シナ海およびその周辺海域における浮遊性ヤムシ類の動物相と分布生態に関するレビュー.日本プランクトン学会報 59 (2): 113-116.

8) Noblezada, M. M. P., H. Miyamoto, and S. Nishida (2012) Review on the fauna and distribution ecology of pelagic chaetognaths in the South China Sea and its adjacent seas. Bulletin Plankton Society of Japan, 59(2): 113-116.

18) 岩崎 望・武田正倫・西田周平・村野正昭・キャロル ヴァレー・岩井雅夫 (2001). 室戸沖南海トラフ海底地震総合観測システム周辺の動物相 2.甲殻類.海洋科学技術センターJAMSTEC深海研究、第18号: 217-224.

19) Nishida, S, J. Chae and R. Kimura (2001). Jewels in the sea. Journal of Visualization, 4: 6.

20) 大塚攻・西田周平 (2001). 海産浮遊性カイアシ類の進化:生殖や摂餌にどのような変化がおこったか?月刊海洋 号外 No. 27: 116-124.

21) 西田周平 (2001). 無脊椎動物の多様性と系統(書評).日本プランクトン学会報、48: 138-139.

22) 西田周平 (2002). 動物プランクトン--生物多様性に関する研究.海の研究、 11: 62-64.

23) 西田周平 (2002). 生物採集・計測法.海の研究、11: 96-97.

24) 西田周平 (2003). 「プランクトンて何?」、「プランクトンの調べ方」、「イセエビもプランクトン?」、「隠れ家のない海でどう暮らす?」、「海の宝石、サフィリナはなぜ光 る?」. 海の生き物100不思議(東京書籍), 東京大学海洋研究所編, p 18-19, 20-21, 36-37, 38-39, 68-69.

24) Bucklin, A., S. Nishida and S. Schiel (2005). Census of Marine Zooplankton: a new global survey of marine biodiversity. IGBP Newsletter No. 60, 4.

25) 西田周平 (2006). 深海に暮らす生物の悲鳴?汚染物質による深海生物の危機.海の環境100の危機(東京書籍)、東京大学海洋研究所編、p 116-117.

26) Nishida, S. and T. Gamo (eds) (2007). Biogeochemistry and Biodiversity in the Sulu Sea. Deep-Sea Research, Part II 54 (1-2), Elsevier Ltd., 176 pp.

27) 西田周平 (2009) 深海生態系:動物プランクトンの多様性と食物網.Pp. 338-363:(塚本編)海と生命-「海の生命観」を求めて、東海大出版、520 pp.

28) Nishida, S., M.D. Fortes and N. Miyazaki (eds) (2011) Coastal Marine Science in Southeast Asia – Synthesis Report of the Core University Program of the Japan Society for the Promotion of Science: Coastal Marine Science (2001-2010). TERRAPUB, Tokyo, 315 pp.

29) Nishida, S., N. Miyazaki and M.D Fortes (2011) Chapter 1. Project overview. In Coastal Marine Science in Southeast Asia – Synthesis Report of the Core University Program of the Japan Society for the Promotion of Science: Coastal Marine Science (2001-2010). Nishida, S., M.D. Fortes and N. Miyazaki (eds), pp. 3-10, TERRAPUB, Tokyo.

30) Nishida, S. (2011) Chapter 5. Biodiversity of marine zooplankton in Southeast Asia (Project-3: Plankton Group). In Coastal Marine Science in Southeast Asia – Synthesis Report of the Core University Program of the Japan Society for the Promotion of Science: Coastal Marine Science (2001-2010). Nishida, S., M.D. Fortes and N. Miyazaki (eds), pp. 59-71, TERRAPUB, Tokyo.

31) Nishida, S. and J. Nishikawa (2011) Chapter 12. Biodiversity of zooplankton: Activities in Project-3. In Coastal Marine Science in Southeast Asia – Synthesis Report of the Core University Program of the Japan Society for the Promotion of Science: Coastal Marine Science (2001-2010). Nishida, S., M.D. Fortes and N. Miyazaki (eds), pp. 117-123, TERRAPUB, Tokyo.

32) Nishida, S., N. Miyazaki and M.D. Fortes (2011) Chapter 21. Synthesis, challenges and future prospects. In Coastal Marine Science in Southeast Asia – Synthesis Report of the Core University Program of the Japan Society for the Promotion of Science: Coastal Marine Science (2001-2010). Nishida, S., M.D. Fortes and N. Miyazaki (eds), pp. 213-216s, TERRAPUB, Tokyo.

33) Nishida, S. (Ed.) (2012) Proceedings of the Horiba International Conference "New Direction of Ocean Research in the Western Pacific"-Past, Present and Future of UNESCO/IOC/WESTPAC Activity for 50 years and the JSPS Project "Coastal Marine Science". International Coastal Research Center, The University of Tokyo (Coastal Marine Science Vol. 35: 1-254).

34) 西田周平 (2012) イセエビ科幼生の生活とさまざまな器官のはたらき.Pp. 263-281:(橘高二郎監修、早川康博編)ミナミイセエビ-驚くべき生態と増養殖への挑戦、生物研究社、372 pp.

35) 西田周平 (2012) 深海生態系の生物多様性と食物網.Blue Earth, Special Issue, 2012.

36) 西田周平 (2013) 地獄一転至福の航海.Ocean Breeze

37) 西田周平 (2013) 新青丸の建造.Ocean Breeze、No. 13、2–4.

38) 西田周平・長井敏・町田龍二(編) (2015) 遺伝子解析とプランクトン研究(日本プランクトン学会2014年度春季シンポジウム論文集).日本プランクトン学会報、62: 8–82.

3. Others

- Outline of my research -

- Main subjects -

63) Itoh, H. and S. Nishida (2008). Life history of the copepod Hemicyclops spinulosus (Poecilostomatoida, Clausidiidae) associated with crab burrows with notes on male polymorphism and precopulatory mate guarding. Plankton and Benthos Research 3 (4): 189-201.

64) Machida, R.J., Y. Hashiguchi, M. Nishida, and S. Nishida (2009) Zooplankton diversity analysis through single-gene sequencing of a community sample. BMC Genomics 10: 438 doi: 10.1186/1471-2164-10-438.

65) Miyamoto, H., R. J. Machida, and S. Nishida (2010) Complete mitochondrial genome sequences of the three pelagic chaetognaths Sagitta nagae, Sagitta decipiens and Sagitta enflata. Comparative Biochemistry and Physiology, Part D 5: 65-72.

66) Fujikura, K., D. Lindsay, H. Kitazato, S. Nishida and Y. Shirayama (2010) Marine biodiversity in Japanese waters. PLoS ONE 5 (8): e11836. Doi: 10.1371/journal.pone.0011836.

67) Wiebe, P.H., S.B. Schnack-Schiel and S. Nishida (2010) Introduction to specie diversity of marine zooplankton. Deep-Sea Research Part II 57: 2061-2063.

68) Matsuura, H., S. Nishida and J. Nishikawa (2010) Species diversity and vertical distribution of the deep-sea copepods of the genus Euaugaptilus in the Sulu and Celebes Seas. Deep-Sea Research Part II 57: 2098-2109.

69) Miyamoto, H., R.J. Machida and S. Nishida (2010) Genetic diversity and cryptic speciation of the deep sea chaetognath Caecosagitta macrocephala (Fowler, 1904). Deep-Sea Research Part II 57: 2211-2219.

70) Machida, R.J. and S. Nishida (2010) Amplified fragment length polymorphism analysis of the mesopelagic copepod Disseta palumbii in the equatorial western Pacific and adjacent waters: Role of marginal seas in the genetic isolation of mesopelagic animals. Deep-Sea Research Part II 57: 2130-2134.

71) Asante, K.A., T. Agusa, R. Kubota, H. Mochizuki, K. Ramu, S. Nishida, S. Ohta, H. Yeh, A. Subramanian and S. Tamabe (2010) Trace elements and stable isotope ratios (δ13C and δ15N) in fish from deep-waters of the Sulu Sea and the Celebes Sea. Marine Pollution Bulletin 60: 1560-1570.

72) Nishida, S. and T. Nonomura (2011) Structure of novel exocrine glands in Calanus species with notes on their possible function. J. Mar. Biol. Assoc. U.K. 91: 801-805.

73) Miyamoto, H. and S. Nishida (2011) A new deep-sea benthopelagic chaetognath of the genus Bathyspadella (Chaetognatha) with ecological and molecular phylogenetic remarks. Journal of Natural History 45: 2785-2794.

74) Nonomura, T., S. Nishida, A. Tsuda and I. Yasuda (2011) Morphological characters for practical identification of the copepodite stages of three sympatric Calanus species in the western North Pacific. Journal of Plankton Research 33: 1496-1509. 

75) Temnykh, A. and S. Nishida (2012) New record of the planktonic copepod Oithona davisae Ferrari and Orsi in the Black Sea with notes on the identity of “Oithona brevicornis”. Aquatic Invasions 7: 425-431.

76) Miyamoto, H., S. Nishida, K. Kuroda and Y. Tanaka (2012) Vertical distribution and seasonal variation of pelagic chaetognaths in Sagami Bay, central Japan. Plankton and Benthos Research 7: 41-54.

77) Miyamoto, H., R.J. Machida and S. Nishida (2012) Global phylogeography of the deep-sea pelagic chaetognath Eukrohnia hamata. Progress in Oceanography 104: 99-109.

78) Nishida, S., M. Sano and Y. Hayakawa (2013) Fine structure of cincinnuli on the appendices internae of puerulus larvae in the rock lobster Jasus edwardsii (Hutton, 1875) (Decapoda, Palinuridae). Crustaceana 86: 372-376.

79) Sano, M., K. Maki, Y. Nishibe, T. Nagata and S. Nishida (2013) Feeding habits of mesopelagic copepods in Sagami Bay: Insights from integrative analysis. Progress in Oceanography 110: 11-26.

80) Kawabata, T., D. J. Lindsay, M. Kitamura, S. Konishi, J. Nishikawa, S. Nishida, M. Kamio and H. Nagai (2013) Evaluation of the bioactivities of water-soluble extracts from twelve deep-sea jellyfish species. Fisheries Science 79: 487-494. (DOI 10.1007/s12562-013-0612-y)

81) Itoh, H. and S. Nishida (2013) Burrow association of Hemicyclops (Copepoda: Poecilostomatoida) as a possible strategy for predator avoidance. Plankton and Benthos Research 8: 141–149. ?

82) Srinui, K., S. Nishida, and S. Ohtsuka (2013) A new species of Pseudodiaptomus (Crustacea, Copepoda, Calanoida, Pseudodiaptomidae) from the Prasae River Estuary, Gulf of Thailand. ZooKeys 338: 39–54 (doi: 10.3897/zookeys.338.5531)?

83) Miyamoto, H., M. Kotori, H. Itoh and S. Nishida (2014) Species diversity of pelagic chaetognaths in the Indo-Pacific region. J. Plankton Res. doi: 10.1093/plankt/fbu001 (First published online: January 31, 2014) 36 (3): 816–830 May/June 2014

84) Kondo, Y., S. Ohtsuka, J. Nishikawa, E. Metillo, H. Pagliawan, S. Sawamoto, M. Moriya, S. Nishida and M. Urata (2014) Associations of fish juveniles with rhizostome jellyfishes in the Philippines, with taxonomic remarks on a commercially harvested  species in Carigara Bay, Leyte Island. Plankton and Benthos Research 9: 1–6.

85) Metillo, E.B., C.S. Acabado, W.L. Campos, and S. Nishida (2014) Distribution of Rhincalanus nasutus Giesbrecht 1888 (Calanoida, Copepoda) during the eastern Sulu Sea coastal upwelling season. Philippine J. Sci., 143 (1): 9–19.

86) Nishikawa, J., S. Ohtsuka, Mulyadi, N. Mujiono, D. J. Lindsay, H. Miyamoto & S. Nishida (2014) A new species of the commercially harvested jellyfish Crambionella (Scyphozoa) from central Java, Indonesia with remarks on the fisheries. J. Mar. Biol. Ass. U.K. DOI: http://dx.doi.org/10.1017/S002531541400157X (About DOI), 11 pages. Published online: 17 November 2014.

87) Nishida, S., I. Anandavelu & G. Padmavati (2015) Two new species of Tortanus (Atortus) (Copepoda, Calanoida, Tortanidae) from the Andaman Islands. Crustaceana, 88 (2): 216–230.

88) Sano, M., Y. Nishibe, Y. Tanaka & S. Nishida (2015) Temporally sustained dietary niche partitioning in two mesopelagic copepod species and their mouthpart morphology. Mar. Ecol. Prog. Ser., 518: 51–67.

89) Itoh, H. & S. Nishida (2015) Spatiotemporal distribution of planktonic copepod communities in Tokyo Bay where Oithona davisae Ferrari and Orsi dominated in mid-1980s. Journal of Natural History (in press) DOI: 10.1080/00222933.2015.1022617

90) Takehisa Yamakita, Hiroyuki Yamamoto, Hiroya Yamano, Katsunori Fujikura, Kiyotaka Hidaka, Yuichi Hirota, Tadafumi Ichikawa, Shigeho Kakehi, Takahiko Kameda, Satoshi Kitajima, Kazuhiro Kogure, Teruhisa Komatsu, Naoki H. Kumagai, Hiroomi Miyamoto, Kazushi Miyashita, Haruyuki Morimoto, Ryota Nakajima, Shuhei Nishida, Kou Nishiuchi, Shingo Sakamoto, Masayoshi Sano, Kenji Sudo, Hiroya Sugisaki, Kazuaki Tadokoro, Katsuhiko Tanaka, Yoshie Jintsu-Uchifune, Kentaro Watanabe, Hiromi Watanabe,Yumiko Yara, Norishige Yotsukura, Yoshihisa Shirayama (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 (Jan 2015)