ORCID Profile
0000-0002-5314-7351
Current Organisations
Australian National University
,
Fisheries and Oceans Canada
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Oxford University Press (OUP)
Date: 27-05-2023
Abstract: Marine Protected Areas require comprehensive monitoring to ensure objectives are achieved however, monitoring natural ecosystems at scale is challenged by the bio ersity it aims to measure. Environmental DNA (eDNA) metabarcoding holds promise to address this monitoring challenge. We conducted paired s ling at 54 sites for fish and invertebrate assemblages in the Northwest Atlantic using groundfish trawls and eDNA metabarcoding of benthic seawater using four genetic markers (12S rRNA, 16S rRNA, 18S rRNA, and CO1). Compared to trawling, eDNA detected similar patterns of species turnover, larger estimates of gamma ersity, and smaller estimates of alpha ersity. A total of 63.6% (42/66) of fish species captured by trawling were detected by eDNA, along with an additional 26 species. Of the 24 missed detections by eDNA, 12 were inevitable as they lacked reference sequences. Excluding taxa assigned to higher than species level and those without a species name, 23.6% (17/72) of invertebrate species captured by trawling were detected by CO1, which detected an additional 98 species. We demonstrate that eDNA is capable of detecting patterns of community assemblage and species turnover in an offshore environment, emphasizing its strong potential for a non-invasive, comprehensive, and scalable tool for bio ersity monitoring supporting marine conservation programmes.
Publisher: Wiley
Date: 31-08-2022
Abstract: Advances in high-throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological s les. Research institutions worldwide increasingly employ HTS methods for bio ersity assessments. However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups. An international experiment was conducted to assess the consistency of metabarcoding results derived from identical s les and primer sets using varying laboratory procedures. Homogenized biofouling s les collected from four coastal locations (Australia, Canada, New Zealand and the USA) were distributed to 12 independent laboratories. Participants were asked to follow one of two HTS library preparation workflows. While DNA extraction, primers and bioinformatic analyses were purposefully standardized to allow comparison, many other technical variables were allowed to vary among laboratories ( lification protocols, type of instrument used, etc.). Despite substantial variation observed in raw results, the primary signal in the data was consistent, with the s les grouping strongly by geographical origin for all data sets. Simple post hoc data clean-up by removing low-quality s les gave the best improvement in s le classification for nuclear 18S rRNA gene data, with an overall 92.81% correct group attribution. For mitochondrial COI gene data, the best classification result (95.58%) was achieved after correction for contamination errors. The identified critical methodological factors that introduced the greatest variability (preservation buffer, s le defrosting, template concentration, DNA polymerase, PCR enhancer) should be of great assistance in standardizing future bio ersity studies using metabarcoding.
Publisher: Cold Spring Harbor Laboratory
Date: 12-10-2023
Publisher: Wiley
Date: 13-01-2020
DOI: 10.1002/EDN3.65
Abstract: Environmental DNA (eDNA) methods are providing tools for detecting invasive species in aquatic environments. Targeted qPCR assays applied to eDNA s les promise to overcome limitations of traditional methods, especially for early detection. The European green crab ( Carcinus maenas ) is considered one of the most successful invasive species globally due to the large range it has invaded and negative impacts on native species, marine habitats, and shellfish industries. We developed, laboratory‐validated, and field‐tested a specific qPCR assay for the detection of green crab from eDNA s les. We also show that the assay can detect green crab in bulk DNA extracted from plankton s les. Assay design, optimization, sensitivity, and specificity testing generally followed the validation pathway recommended by the World Organization for Animal Health for assays used to manage global aquatic animal health and infectious disease. Assay specificity was verified in silico and in vitro by laboratory testing 26 nontarget species, none of which showed potential for lification. Assay sensitivity was appropriately high, with the limit of detection approaching two gene copies/μl. The assay was field‐tested on eDNA s les collected from filtered seawater at five sites on the Pacific coast of Canada known to harbor green crab based on historical monitoring data green crab DNA was lified from all sites. We also present early pilot field testing of the assay done on bulk DNA extracted from plankton s les from four sites from Australia, two sites with and two sites without reported records of green crab presence. Green crab was detected at both sites with known green crab records. Significant inhibition was recorded for some plankton s les but not for eDNA s les. This is the first qPCR assay for detection of European green crab, providing researchers and managers with a valuable new tool to aid early detection and ongoing monitoring.
No related grants have been discovered for Cathryn Abbott.