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dc.contributor.authorDiBattista, Joseph
dc.contributor.authorReimer, J.D.
dc.contributor.authorStat, Michael
dc.contributor.authorMasucci, G.D.
dc.contributor.authorBiondi, P.
dc.contributor.authorDe Brauwer, M.
dc.contributor.authorBunce, Michael
dc.date.accessioned2023-03-14T04:42:12Z
dc.date.available2023-03-14T04:42:12Z
dc.date.issued2019
dc.identifier.citationDiBattista, J.D. and Reimer, J.D. and Stat, M. and Masucci, G.D. and Biondi, P. and De Brauwer, M. and Bunce, M. 2019. Digging for DNA at depth: Rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient. PeerJ. 2019 (2): ARTN e6379.
dc.identifier.urihttp://hdl.handle.net/20.500.11937/90906
dc.identifier.doi10.7717/peerj.6379
dc.description.abstract

Background: Effective biodiversity monitoring is fundamental in tracking changes in ecosystems as it relates to commercial, recreational, and conservation interests. Current approaches to survey coral reef ecosystems center on the use of indicator species and repeat surveying at specific sites. However, such approaches are often limited by the narrow snapshot of total marine biodiversity that they describe and are thus hindered in their ability to contribute to holistic ecosystem-based monitoring. In tandem, environmental DNA (eDNA) and next-generation sequencing metabarcoding methods provide a new opportunity to rapidly assess the presence of a broad spectrum of eukaryotic organisms within our oceans, ranging from microbes to macrofauna. Methods: We here investigate the potential for rapid universal metabarcoding surveys (RUMS) of eDNA in sediment samples to provide snapshots of eukaryotic subtropical biodiversity along a depth gradient at two coral reefs in Okinawa, Japan based on 18S rRNA. Results: Using 18S rRNA metabarcoding, we found that there were significant separations in eukaryotic community assemblages (at the family level) detected in sediments when compared across different depths ranging from 10 to 40 m (p = 0.001). Significant depth zonation was observed across operational taxonomic units assigned to the class Demospongiae (sponges), the most diverse class (contributing 81% of species) within the phylum Porifera; the oldest metazoan phylum on the planet. However, zonation was not observed across the class Anthozoa (i.e., anemones, stony corals, soft corals, and octocorals), suggesting that the former may serve as a better source of indicator species based on sampling over fine spatial scales and using this universal assay. Furthermore, despite their abundance on the examined coral reefs, we did not detect any octocoral DNA, which may be due to low cellular shedding rates, assay sensitivities, or primer biases. Discussion: Overall, our pilot study demonstrates the importance of exploring depth effects in eDNA and suggest that RUMS may be applied to provide a baseline of information on eukaryotic marine taxa at coastal sites of economic and conservation importance.

dc.languageEnglish
dc.publisherPEERJ INC
dc.relation.sponsoredbyhttp://purl.org/au-research/grants/arc/LP160100839
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectScience & Technology
dc.subjectMultidisciplinary Sciences
dc.subjectScience & Technology - Other Topics
dc.subject18S rRNA
dc.subjectCommunity structure
dc.subjectDemospongiae
dc.subjectAnthozoa
dc.subjectPorifera
dc.subjectEnvironmental DNA
dc.subjectEukaryote
dc.subjectSponge loop
dc.subjectMARINE BIODIVERSITY
dc.subjectSEQUENCE EVOLUTION
dc.subjectVERTICAL ZONATION
dc.subjectFISH ASSEMBLAGES
dc.subjectGLOBAL PATTERNS
dc.subjectOKINAWA
dc.subjectECOSYSTEMS
dc.subjectDIVERSITY
dc.subjectSEARCH
dc.subject18S rRNA
dc.subjectAnthozoa
dc.subjectCommunity structure
dc.subjectDemospongiae
dc.subjectEnvironmental DNA
dc.subjectEukaryote
dc.subjectPorifera
dc.subjectSponge loop
dc.titleDigging for DNA at depth: Rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient
dc.typeJournal Article
dcterms.source.volume2019
dcterms.source.number2
dcterms.source.issn2167-8359
dcterms.source.titlePeerJ
dc.date.updated2023-03-14T04:42:12Z
curtin.departmentSchool of Molecular and Life Sciences (MLS)
curtin.accessStatusOpen access
curtin.facultyFaculty of Science and Engineering
curtin.contributor.orcidDiBattista, Joseph [0000-0002-5696-7574]
curtin.contributor.orcidBunce, Michael [0000-0002-0302-4206]
curtin.contributor.researcheridStat, Michael [K-5290-2012]
curtin.contributor.researcheridDiBattista, Joseph [O-2074-2014]
curtin.identifier.article-numberARTN e6379
dcterms.source.eissn2167-8359
curtin.contributor.scopusauthoridStat, Michael [14326104400]
curtin.contributor.scopusauthoridDiBattista, Joseph [23388559600] [57198360321]
curtin.contributor.scopusauthoridBunce, Michael [55160482300]
curtin.repositoryagreementV3


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