Environmental DNA analysis at multiple taxonomic levels highlights geographic variation in subtropical coastal marine communities
Abstract In this study, environmental DNA was used to assess marine diversity across the southern part of Okinawa Island, Japan, located in the subtropics. Diversity analysis was performed for prokaryotes and eukaryotes. Differences in diversity were detected between the west side of Okinawa (an are...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-07-01
|
| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-025-05106-w |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849335038090412032 |
|---|---|
| author | Kodai Gibu Kohei Hamamoto Keita Koeda Miyuki Nishijima Hiroki Kise Masaru Mizuyama Atsushi Suzuki Nobuyuki Aoki Nina Yasuda Akira Iguchi |
| author_facet | Kodai Gibu Kohei Hamamoto Keita Koeda Miyuki Nishijima Hiroki Kise Masaru Mizuyama Atsushi Suzuki Nobuyuki Aoki Nina Yasuda Akira Iguchi |
| author_sort | Kodai Gibu |
| collection | DOAJ |
| description | Abstract In this study, environmental DNA was used to assess marine diversity across the southern part of Okinawa Island, Japan, located in the subtropics. Diversity analysis was performed for prokaryotes and eukaryotes. Differences in diversity were detected between the west side of Okinawa (an area exposed to groundwater influenced by land-derived loads) and the east side (an area where coral reefs, beaches, and seagrass beds coexist). In particular, the community composition of prokaryotes, for which 16S rRNA metabarcoding analysis was performed, differed markedly between the east and west sides of the island. Differences in the composition of eukaryotic communities between the east and west coasts are relatively unclear, likely due to the fact that 18S rRNA metabarcoding targets a wide range of species (including almost all eukaryotic taxonomic groups), making it difficult to identify differences. On the other hand, MiFish analysis indicated that distributions of various fish species differed markedly between the east and west coasts of the island, suggesting a close relationship between differences in the coastal environment and the habitat selection by fish. We show that prokaryotic communities can be evaluated using eDNA analysis in order to monitor extensive geographic environments via water cycles. This can then be used to promote understanding of geographic variations of marine community structures of eukaryotes, including fish. |
| format | Article |
| id | doaj-art-d7099ea1b7e94763abf5482bf7c8a7d0 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-d7099ea1b7e94763abf5482bf7c8a7d02025-08-20T03:45:24ZengNature PortfolioScientific Reports2045-23222025-07-0115111010.1038/s41598-025-05106-wEnvironmental DNA analysis at multiple taxonomic levels highlights geographic variation in subtropical coastal marine communitiesKodai Gibu0Kohei Hamamoto1Keita Koeda2Miyuki Nishijima3Hiroki Kise4Masaru Mizuyama5Atsushi Suzuki6Nobuyuki Aoki7Nina Yasuda8Akira Iguchi9RNAGeological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST)Center for Marine Environmental Studies (CMES), Ehime University, Ehime UniversityFaculty of Science, University of the RyukyusRNAGeological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST)RNAGeological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST)Faculty of Human Health Sciences, Meio UniversityRNAGeological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST)Integrated Research Center for Nature Positive Technology, National Institute of Advanced Industrial Science and Technology (AIST)Graduate School of Agricultural and Life Sciences, The University of TokyoRNAGeological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST)Abstract In this study, environmental DNA was used to assess marine diversity across the southern part of Okinawa Island, Japan, located in the subtropics. Diversity analysis was performed for prokaryotes and eukaryotes. Differences in diversity were detected between the west side of Okinawa (an area exposed to groundwater influenced by land-derived loads) and the east side (an area where coral reefs, beaches, and seagrass beds coexist). In particular, the community composition of prokaryotes, for which 16S rRNA metabarcoding analysis was performed, differed markedly between the east and west sides of the island. Differences in the composition of eukaryotic communities between the east and west coasts are relatively unclear, likely due to the fact that 18S rRNA metabarcoding targets a wide range of species (including almost all eukaryotic taxonomic groups), making it difficult to identify differences. On the other hand, MiFish analysis indicated that distributions of various fish species differed markedly between the east and west coasts of the island, suggesting a close relationship between differences in the coastal environment and the habitat selection by fish. We show that prokaryotic communities can be evaluated using eDNA analysis in order to monitor extensive geographic environments via water cycles. This can then be used to promote understanding of geographic variations of marine community structures of eukaryotes, including fish.https://doi.org/10.1038/s41598-025-05106-w |
| spellingShingle | Kodai Gibu Kohei Hamamoto Keita Koeda Miyuki Nishijima Hiroki Kise Masaru Mizuyama Atsushi Suzuki Nobuyuki Aoki Nina Yasuda Akira Iguchi Environmental DNA analysis at multiple taxonomic levels highlights geographic variation in subtropical coastal marine communities Scientific Reports |
| title | Environmental DNA analysis at multiple taxonomic levels highlights geographic variation in subtropical coastal marine communities |
| title_full | Environmental DNA analysis at multiple taxonomic levels highlights geographic variation in subtropical coastal marine communities |
| title_fullStr | Environmental DNA analysis at multiple taxonomic levels highlights geographic variation in subtropical coastal marine communities |
| title_full_unstemmed | Environmental DNA analysis at multiple taxonomic levels highlights geographic variation in subtropical coastal marine communities |
| title_short | Environmental DNA analysis at multiple taxonomic levels highlights geographic variation in subtropical coastal marine communities |
| title_sort | environmental dna analysis at multiple taxonomic levels highlights geographic variation in subtropical coastal marine communities |
| url | https://doi.org/10.1038/s41598-025-05106-w |
| work_keys_str_mv | AT kodaigibu environmentaldnaanalysisatmultipletaxonomiclevelshighlightsgeographicvariationinsubtropicalcoastalmarinecommunities AT koheihamamoto environmentaldnaanalysisatmultipletaxonomiclevelshighlightsgeographicvariationinsubtropicalcoastalmarinecommunities AT keitakoeda environmentaldnaanalysisatmultipletaxonomiclevelshighlightsgeographicvariationinsubtropicalcoastalmarinecommunities AT miyukinishijima environmentaldnaanalysisatmultipletaxonomiclevelshighlightsgeographicvariationinsubtropicalcoastalmarinecommunities AT hirokikise environmentaldnaanalysisatmultipletaxonomiclevelshighlightsgeographicvariationinsubtropicalcoastalmarinecommunities AT masarumizuyama environmentaldnaanalysisatmultipletaxonomiclevelshighlightsgeographicvariationinsubtropicalcoastalmarinecommunities AT atsushisuzuki environmentaldnaanalysisatmultipletaxonomiclevelshighlightsgeographicvariationinsubtropicalcoastalmarinecommunities AT nobuyukiaoki environmentaldnaanalysisatmultipletaxonomiclevelshighlightsgeographicvariationinsubtropicalcoastalmarinecommunities AT ninayasuda environmentaldnaanalysisatmultipletaxonomiclevelshighlightsgeographicvariationinsubtropicalcoastalmarinecommunities AT akiraiguchi environmentaldnaanalysisatmultipletaxonomiclevelshighlightsgeographicvariationinsubtropicalcoastalmarinecommunities |