Large-scale environmental DNA survey reveals niche axes of a regional coastal fish community

The concept of the ecological niche, defined as the basic habitat requirements for a species, is central to understanding species geographic distributions and predicting their responses to environmental change. However, identifying the essential niche for large regional communities remains a challenge because niche axes can be "hidden" by the complexity of the underlying ecological processes. Here, applying advanced species distribution modelling to nationwide environmental DNA survey data, we identified hidden niche axes of the Japanese coastal fish community and investigated the response diversity to these axes. Our survey detected 1,220 coastal fish species. The hidden niche axes collectively explained most of the variation in fish biodiversity and revealed five biogeographic boundaries for the regional community. These niches of the Japanese fish community may primarily relate to several processes due to ocean currents, such as environmental filters, transport from source areas and dispersal barriers. We also found that the response diversity to niche axes was positively correlated with species richness, although local communities with particularly high response diversity were geographically biased. A better understanding of the niche axes of the regional ecological community should help to mitigate the loss of biodiversity and ecosystem services caused by ongoing environmental change.

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Publication Details

Journal
Scientific Reports
Published
2026-02-16
DOI
https://doi.org/10.1038/s41598-025-31307-4
Primary Topic
Environmental DNA in Biodiversity Studies
Type
article
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article

Large-scale environmental DNA survey reveals niche axes of a regional coastal fish community

Yumi Kobayashi, Hiroki Yamanaka, Ryo O. Gotoh, Hiroaki Murakami et al.
Scientific Reports
Environmental DNA in Biodiversity Studies
article

Large-scale environmental DNA survey reveals niche axes of a regional coastal fish community

Yumi Kobayashi, Hiroki Yamanaka, Ryo O. Gotoh, Hiroaki Murakami, Kenji Nohara, Masaki Miya, Hiroki Mizumoto, Teruhiko Takahara, Keiichi Fukaya, Midori Iida, Koichi Shibukawa, Takashi Kanbe, Tetsuya Sado, Mitsuhiro Aizu-Hirano, Kōji Takayama, Takehiko Fukuchi, Shinichiro Oka, Hisashi Yamakawa, Hitoshi Araki, Tomoki Sunobe, Tadashi Kajita, Akihide Kasai, Katsuhiko Tanaka, Tomohito Imaizumi, Hiroshi Senou, Tanaka Kenta, Reiji Masuda, Satoshi Yamamoto, Satoru Yokoyama, Seokjin Yoon, Tomohiko Matsuura, Michio Kondoh, Masakazu Hori, Hiroshi Takahashi, Satoquo Seino, Toshifumi Minamoto, Yutaka Osada, Hiroyuki Motomura, Hideyuki Doi
article en

Abstract

The concept of the ecological niche, defined as the basic habitat requirements for a species, is central to understanding species geographic distributions and predicting their responses to environmental change. However, identifying the essential niche for large regional communities remains a challenge because niche axes can be "hidden" by the complexity of the underlying ecological processes. Here, applying advanced species distribution modelling to nationwide environmental DNA survey data, we identified hidden niche axes of the Japanese coastal fish community and investigated the response diversity to these axes. Our survey detected 1,220 coastal fish species. The hidden niche axes collectively explained most of the variation in fish biodiversity and revealed five biogeographic boundaries for the regional community. These niches of the Japanese fish community may primarily relate to several processes due to ocean currents, such as environmental filters, transport from source areas and dispersal barriers. We also found that the response diversity to niche axes was positively correlated with species richness, although local communities with particularly high response diversity were geographically biased. A better understanding of the niche axes of the regional ecological community should help to mitigate the loss of biodiversity and ecosystem services caused by ongoing environmental change.

Scientific ReportsVol. 16(1)
Ryukoku University (JP), Kagoshima University (JP), Nagano University (JP), Ministry of Agriculture, Forestry and Fisheries (JP), Tokai University (JP), Kyushu University (JP), Shimane University (JP), National Institute for Environmental Studies (JP), Tohoku University (JP), Hokkaido University (JP), Kyoto University (JP), Shimizu (Japan) (JP), Hakodate University (JP), Fukuoka University (JP), University of the Ryukyus (JP), Okinawa Churashima Foundation (JP), National Institute of Technology, Maizuru College (JP), Advanced Institute of Materials Science (JP), Kanagawa Prefectural Museum of Natural History (JP), National Institute for Agro-Environmental Sciences (JP), Japan Fisheries Research and Education Agency (JP), National Institute of Fisheries Science (KR), Tateyama Elementary School (JP), Museum of Natural and Environmental History, Shizuoka (JP), The Institute of Statistical Mathematics (JP), Environmental Research Institute (GB), National Fisheries University (JP), Kazusa DNA Research Institute (JP), Natural History Museum and Institute (JP), Kobe University (JP), Tokyo Metropolitan University (JP), Niigata University (JP)
Life below water
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Environmental DNA in Biodiversity Studies
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