eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem
Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or i...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
| Language: | English |
| Published: |
WILEY
2020
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| Subjects: | |
| Online Access: | https://onlinelibrary.wiley.com/doi/am-pdf/10.1111/mec.15382 http://hdl.handle.net/20.500.11937/90905 |
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| author | West, K.M. Stat, Michael Harvey, Euan Skepper, C.L. Di Battista, Joey Richards, Zoe Travers, M.J. Newman, Stephen Bunce, Michael |
| author_facet | West, K.M. Stat, Michael Harvey, Euan Skepper, C.L. Di Battista, Joey Richards, Zoe Travers, M.J. Newman, Stephen Bunce, Michael |
| author_sort | West, K.M. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate-related threats and as such there is a pressing need for cost-effective whole-ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high-resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)—a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management. |
| first_indexed | 2025-11-14T11:35:33Z |
| format | Journal Article |
| id | curtin-20.500.11937-90905 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-14T11:35:33Z |
| publishDate | 2020 |
| publisher | WILEY |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-909052024-02-06T03:22:29Z eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem West, K.M. Stat, Michael Harvey, Euan Skepper, C.L. Di Battista, Joey Richards, Zoe Travers, M.J. Newman, Stephen Bunce, Michael Science & Technology Life Sciences & Biomedicine Biochemistry & Molecular Biology Ecology Evolutionary Biology Environmental Sciences & Ecology biodiversity environmental DNA island reef monitoring multitrophic whole-ecosystem COCOS KEELING ISLANDS ENVIRONMENTAL DNA CHRISTMAS ISLAND FISH KILL BIODIVERSITY CRUSTACEA BRACHYURA RECORDS biodiversity environmental DNA island reef monitoring multitrophic whole-ecosystem Animals Australia Biota Coral Reefs DNA Barcoding, Taxonomic DNA, Environmental Environmental Monitoring Seawater Animals Seawater Environmental Monitoring Australia Coral Reefs Biota DNA Barcoding, Taxonomic DNA, Environmental Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate-related threats and as such there is a pressing need for cost-effective whole-ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high-resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)—a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management. 2020 Journal Article http://hdl.handle.net/20.500.11937/90905 10.1111/mec.15382 English https://onlinelibrary.wiley.com/doi/am-pdf/10.1111/mec.15382 http://purl.org/au-research/grants/arc/LP160100839 WILEY fulltext |
| spellingShingle | Science & Technology Life Sciences & Biomedicine Biochemistry & Molecular Biology Ecology Evolutionary Biology Environmental Sciences & Ecology biodiversity environmental DNA island reef monitoring multitrophic whole-ecosystem COCOS KEELING ISLANDS ENVIRONMENTAL DNA CHRISTMAS ISLAND FISH KILL BIODIVERSITY CRUSTACEA BRACHYURA RECORDS biodiversity environmental DNA island reef monitoring multitrophic whole-ecosystem Animals Australia Biota Coral Reefs DNA Barcoding, Taxonomic DNA, Environmental Environmental Monitoring Seawater Animals Seawater Environmental Monitoring Australia Coral Reefs Biota DNA Barcoding, Taxonomic DNA, Environmental West, K.M. Stat, Michael Harvey, Euan Skepper, C.L. Di Battista, Joey Richards, Zoe Travers, M.J. Newman, Stephen Bunce, Michael eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem |
| title | eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem |
| title_full | eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem |
| title_fullStr | eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem |
| title_full_unstemmed | eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem |
| title_short | eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem |
| title_sort | edna metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem |
| topic | Science & Technology Life Sciences & Biomedicine Biochemistry & Molecular Biology Ecology Evolutionary Biology Environmental Sciences & Ecology biodiversity environmental DNA island reef monitoring multitrophic whole-ecosystem COCOS KEELING ISLANDS ENVIRONMENTAL DNA CHRISTMAS ISLAND FISH KILL BIODIVERSITY CRUSTACEA BRACHYURA RECORDS biodiversity environmental DNA island reef monitoring multitrophic whole-ecosystem Animals Australia Biota Coral Reefs DNA Barcoding, Taxonomic DNA, Environmental Environmental Monitoring Seawater Animals Seawater Environmental Monitoring Australia Coral Reefs Biota DNA Barcoding, Taxonomic DNA, Environmental |
| url | https://onlinelibrary.wiley.com/doi/am-pdf/10.1111/mec.15382 https://onlinelibrary.wiley.com/doi/am-pdf/10.1111/mec.15382 http://hdl.handle.net/20.500.11937/90905 |