Ecosystem biomonitoring with eDNA: Metabarcoding across the tree of life in a tropical marine environment
Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosys...
| Main Authors: | , , , , , , , |
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| Format: | Journal Article |
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Nature Publishing Group
2017
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| Online Access: | http://purl.org/au-research/grants/arc/LP160100839 http://hdl.handle.net/20.500.11937/58923 |
| _version_ | 1848760377192480768 |
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| author | Stat, Michael Huggett, M. Bernasconi, R. Di Battista, Joseph Berry, Tina Newman, Stephen Harvey, Euan Bunce, Michael |
| author_facet | Stat, Michael Huggett, M. Bernasconi, R. Di Battista, Joseph Berry, Tina Newman, Stephen Harvey, Euan Bunce, Michael |
| author_sort | Stat, Michael |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using 'tree of life' (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing 'universal' PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs. © 2017 The Author(s). |
| first_indexed | 2025-11-14T10:14:48Z |
| format | Journal Article |
| id | curtin-20.500.11937-58923 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-14T10:14:48Z |
| publishDate | 2017 |
| publisher | Nature Publishing Group |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-589232022-11-23T05:56:14Z Ecosystem biomonitoring with eDNA: Metabarcoding across the tree of life in a tropical marine environment Stat, Michael Huggett, M. Bernasconi, R. Di Battista, Joseph Berry, Tina Newman, Stephen Harvey, Euan Bunce, Michael Effective marine management requires comprehensive data on the status of marine biodiversity. However, efficient methods that can document biodiversity in our oceans are currently lacking. Environmental DNA (eDNA) sourced from seawater offers a new avenue for investigating the biota in marine ecosystems. Here, we investigated the potential of eDNA to inform on the breadth of biodiversity present in a tropical marine environment. Directly sequencing eDNA from seawater using a shotgun approach resulted in only 0.34% of 22.3 million reads assigning to eukaryotes, highlighting the inefficiency of this method for assessing eukaryotic diversity. In contrast, using 'tree of life' (ToL) metabarcoding and 20-fold fewer sequencing reads, we could detect 287 families across the major divisions of eukaryotes. Our data also show that the best performing 'universal' PCR assay recovered only 44% of the eukaryotes identified across all assays, highlighting the need for multiple metabarcoding assays to catalogue biodiversity. Lastly, focusing on the fish genus Lethrinus, we recovered intra- and inter-specific haplotypes from seawater samples, illustrating that eDNA can be used to explore diversity beyond taxon identifications. Given the sensitivity and low cost of eDNA metabarcoding we advocate this approach be rapidly integrated into biomonitoring programs. © 2017 The Author(s). 2017 Journal Article http://hdl.handle.net/20.500.11937/58923 10.1038/s41598-017-12501-5 http://purl.org/au-research/grants/arc/LP160100839 http://creativecommons.org/licenses/by/4.0/ Nature Publishing Group fulltext |
| spellingShingle | Stat, Michael Huggett, M. Bernasconi, R. Di Battista, Joseph Berry, Tina Newman, Stephen Harvey, Euan Bunce, Michael Ecosystem biomonitoring with eDNA: Metabarcoding across the tree of life in a tropical marine environment |
| title | Ecosystem biomonitoring with eDNA: Metabarcoding across the tree of life in a tropical marine environment |
| title_full | Ecosystem biomonitoring with eDNA: Metabarcoding across the tree of life in a tropical marine environment |
| title_fullStr | Ecosystem biomonitoring with eDNA: Metabarcoding across the tree of life in a tropical marine environment |
| title_full_unstemmed | Ecosystem biomonitoring with eDNA: Metabarcoding across the tree of life in a tropical marine environment |
| title_short | Ecosystem biomonitoring with eDNA: Metabarcoding across the tree of life in a tropical marine environment |
| title_sort | ecosystem biomonitoring with edna: metabarcoding across the tree of life in a tropical marine environment |
| url | http://purl.org/au-research/grants/arc/LP160100839 http://hdl.handle.net/20.500.11937/58923 |