Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems
Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding...
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| Format: | Journal Article |
| Language: | English |
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NATURE PORTFOLIO
2020
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| Online Access: | http://purl.org/au-research/grants/arc/LP160101508 http://hdl.handle.net/20.500.11937/90913 |
| _version_ | 1848765458919981056 |
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| author | Di Battista, Joey Reimer, J.D. Stat, Michael Masucci, G.D. Biondi, P. De Brauwer, Maarten Wilkinson, S.P. Chariton, A.A. Bunce, Michael |
| author_facet | Di Battista, Joey Reimer, J.D. Stat, Michael Masucci, G.D. Biondi, P. De Brauwer, Maarten Wilkinson, S.P. Chariton, A.A. Bunce, Michael |
| author_sort | Di Battista, Joey |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of ‘snapshots’ across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine learning sequence assignment algorithms and co-occurrence network analyses, we examined how anthropogenic pressures may have impacted marine biodiversity on subtropical coral reefs in Okinawa, Japan. Based on 18 S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification for this marker, as well as proxies for anthropogenic disturbance, we show that eukaryotic richness at the family level significantly increases with medium and high levels of disturbance. This change in richness coincides with compositional changes, a decrease in connectedness among taxa, an increase in fragmentation of taxon co-occurrence networks, and a shift in indicator taxa. Taken together, these findings demonstrate the ability of eDNA to act as a barometer of disturbance and provide an exemplar of how biotic networks and coral reefs may be impacted by anthropogenic activities. |
| first_indexed | 2025-11-14T11:35:35Z |
| format | Journal Article |
| id | curtin-20.500.11937-90913 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-14T11:35:35Z |
| publishDate | 2020 |
| publisher | NATURE PORTFOLIO |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-909132023-05-04T08:45:50Z Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems Di Battista, Joey Reimer, J.D. Stat, Michael Masucci, G.D. Biondi, P. De Brauwer, Maarten Wilkinson, S.P. Chariton, A.A. Bunce, Michael Science & Technology Multidisciplinary Sciences Science & Technology - Other Topics CORAL-REEFS ECOLOGICAL NETWORKS RYUKYU ISLANDS DIVERSITY OKINAWA MARINE COMMUNITIES ASSOCIATIONS ASSEMBLAGES DISCHARGE Biodiversity Biota Coral Reefs DNA Barcoding, Taxonomic DNA, Environmental DNA, Ribosomal Spacer Environmental Monitoring Genetic Markers Oceans and Seas RNA, Ribosomal, 18S Seawater Spatio-Temporal Analysis DNA, Ribosomal Spacer RNA, Ribosomal, 18S Genetic Markers Biodiversity Seawater Environmental Monitoring Oceans and Seas Coral Reefs Biota DNA Barcoding, Taxonomic Spatio-Temporal Analysis DNA, Environmental Loss of biodiversity from lower to upper trophic levels reduces overall productivity and stability of coastal ecosystems in our oceans, but rarely are these changes documented across both time and space. The characterisation of environmental DNA (eDNA) from sediment and seawater using metabarcoding offers a powerful molecular lens to observe marine biota and provides a series of ‘snapshots’ across a broad spectrum of eukaryotic organisms. Using these next-generation tools and downstream analytical innovations including machine learning sequence assignment algorithms and co-occurrence network analyses, we examined how anthropogenic pressures may have impacted marine biodiversity on subtropical coral reefs in Okinawa, Japan. Based on 18 S ribosomal RNA, but not ITS2 sequence data due to inconsistent amplification for this marker, as well as proxies for anthropogenic disturbance, we show that eukaryotic richness at the family level significantly increases with medium and high levels of disturbance. This change in richness coincides with compositional changes, a decrease in connectedness among taxa, an increase in fragmentation of taxon co-occurrence networks, and a shift in indicator taxa. Taken together, these findings demonstrate the ability of eDNA to act as a barometer of disturbance and provide an exemplar of how biotic networks and coral reefs may be impacted by anthropogenic activities. 2020 Journal Article http://hdl.handle.net/20.500.11937/90913 10.1038/s41598-020-64858-9 English http://purl.org/au-research/grants/arc/LP160101508 http://purl.org/au-research/grants/arc/LP160100839 http://creativecommons.org/licenses/by/4.0/ NATURE PORTFOLIO fulltext |
| spellingShingle | Science & Technology Multidisciplinary Sciences Science & Technology - Other Topics CORAL-REEFS ECOLOGICAL NETWORKS RYUKYU ISLANDS DIVERSITY OKINAWA MARINE COMMUNITIES ASSOCIATIONS ASSEMBLAGES DISCHARGE Biodiversity Biota Coral Reefs DNA Barcoding, Taxonomic DNA, Environmental DNA, Ribosomal Spacer Environmental Monitoring Genetic Markers Oceans and Seas RNA, Ribosomal, 18S Seawater Spatio-Temporal Analysis DNA, Ribosomal Spacer RNA, Ribosomal, 18S Genetic Markers Biodiversity Seawater Environmental Monitoring Oceans and Seas Coral Reefs Biota DNA Barcoding, Taxonomic Spatio-Temporal Analysis DNA, Environmental Di Battista, Joey Reimer, J.D. Stat, Michael Masucci, G.D. Biondi, P. De Brauwer, Maarten Wilkinson, S.P. Chariton, A.A. Bunce, Michael Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems |
| title | Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems |
| title_full | Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems |
| title_fullStr | Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems |
| title_full_unstemmed | Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems |
| title_short | Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems |
| title_sort | environmental dna can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems |
| topic | Science & Technology Multidisciplinary Sciences Science & Technology - Other Topics CORAL-REEFS ECOLOGICAL NETWORKS RYUKYU ISLANDS DIVERSITY OKINAWA MARINE COMMUNITIES ASSOCIATIONS ASSEMBLAGES DISCHARGE Biodiversity Biota Coral Reefs DNA Barcoding, Taxonomic DNA, Environmental DNA, Ribosomal Spacer Environmental Monitoring Genetic Markers Oceans and Seas RNA, Ribosomal, 18S Seawater Spatio-Temporal Analysis DNA, Ribosomal Spacer RNA, Ribosomal, 18S Genetic Markers Biodiversity Seawater Environmental Monitoring Oceans and Seas Coral Reefs Biota DNA Barcoding, Taxonomic Spatio-Temporal Analysis DNA, Environmental |
| url | http://purl.org/au-research/grants/arc/LP160101508 http://purl.org/au-research/grants/arc/LP160101508 http://hdl.handle.net/20.500.11937/90913 |