Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities

Handle URI:
http://hdl.handle.net/10754/623716
Title:
Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities
Authors:
Laroche, Olivier; Wood, Susanna A.; Tremblay, Louis A.; Lear, Gavin; Ellis, Joanne ( 0000-0002-2625-4274 ) ; Pochon, Xavier
Abstract:
Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.
KAUST Department:
Red Sea Research Center (RSRC)
Citation:
Laroche O, Wood SA, Tremblay LA, Lear G, Ellis JI, et al. (2017) Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. PeerJ 5: e3347. Available: http://dx.doi.org/10.7717/peerj.3347.
Publisher:
PeerJ
Journal:
PeerJ
Issue Date:
17-May-2017
DOI:
10.7717/peerj.3347
Type:
Article
ISSN:
2167-8359
Sponsors:
This research was co-funded by the Cawthron Institute Internal Investment Fund (IIF #15955) and the ``Fonds de Recherche du Québec-Natures et Technologies'' as part of a doctoral research scholarship (grant ID#184395). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Additional Links:
https://peerj.com/articles/3347/
Appears in Collections:
Articles; Red Sea Research Center (RSRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorLaroche, Olivieren
dc.contributor.authorWood, Susanna A.en
dc.contributor.authorTremblay, Louis A.en
dc.contributor.authorLear, Gavinen
dc.contributor.authorEllis, Joanneen
dc.contributor.authorPochon, Xavieren
dc.date.accessioned2017-05-25T10:55:14Z-
dc.date.available2017-05-25T10:55:14Z-
dc.date.issued2017-05-17en
dc.identifier.citationLaroche O, Wood SA, Tremblay LA, Lear G, Ellis JI, et al. (2017) Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. PeerJ 5: e3347. Available: http://dx.doi.org/10.7717/peerj.3347.en
dc.identifier.issn2167-8359en
dc.identifier.doi10.7717/peerj.3347en
dc.identifier.urihttp://hdl.handle.net/10754/623716-
dc.description.abstractSequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.en
dc.description.sponsorshipThis research was co-funded by the Cawthron Institute Internal Investment Fund (IIF #15955) and the ``Fonds de Recherche du Québec-Natures et Technologies'' as part of a doctoral research scholarship (grant ID#184395). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.publisherPeerJen
dc.relation.urlhttps://peerj.com/articles/3347/en
dc.rightsArchived with thanks to PeerJ. Distributed under Creative Commons CC-BY 4.0en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectBiomonitoringen
dc.subjectOil and gas activitiesen
dc.subjectBenthic ecologyen
dc.subjectHigh-throughput sequencingen
dc.subjectBacteria (16S)en
dc.subjectEukaryotes (18S)en
dc.subjectMethod testingen
dc.subjecteDNAen
dc.subjecteRNAen
dc.titleMetabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communitiesen
dc.typeArticleen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalPeerJen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionSchool of Biological Sciences, University of Auckland, Auckland, New Zealanden
dc.contributor.institutionEnvironmental Technologies, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealanden
dc.contributor.institutionEnvironmental Research Institute, University of Waikato, Hamilton, New Zealanden
dc.contributor.institutionInstitute of Marine Science, University of Auckland, Auckland, New Zealanden
kaust.authorEllis, Joanneen
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