Metabarcoding the marine environment: from single species to biogeographic patterns

Extending deep-sea benthic biodiversity inventories with environmental DNA metabarcodingExtending deep-sea benthic biodiversity inventories with environmental DNA metabarcoding

“…As expected there was little overlap between the eDNA survey and the known biodiversity of the area sampled, including from specimens identi ed from the same sampling opportunity. The lack of barcodes (see for example Gaither et al 2022; von der Heyden 2022), hampered species identi cation and we reiterate the call for concerted foundational barcoding efforts of marine life, particularly of biodiversity beyond coastal areas. Overall, our results show that metabarcoding of sediment eDNA is a promising complimentary tool for capturing the biodiversity of areas that are logistically challenging to survey, but that there also exists a need to extend several aspects of the eDNA work ow in southern Africa to ensure that this methodology becomes rmly embedded in biodiversity monitoring of the unique diversity of the regions deep-sea systems.…”

“…Some reasons for the lack in congruence include a) that the eDNA concentration of the species at the site was too low to be detected at the time of sampling; b) if their eDNA was present in su ciently high concentrations, the resulting sequences may not have been identi ed or present in reference databases, c) eDNA may have been present but was not captured by the sampling methods used or d) methodological issues arose, such as primer mismatches (Deagle et al 2014;Deiner et al 2017;Cowart et al,2018). In addition, the effectiveness of eDNA metabarcoding as a biodiversity assessment tool is limited by the fact that many genetic reference databases lack adequate representation of many taxa, including those from the deep-sea (Gaither et al 2022). Further, within an African context, environmental DNA surveys from marine systems are rare, although more generally, the African continent is currently under-represented in studies utilising eDNA for biodiversity surveys (von der Heyden 2022).…”

MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences

“…Furthermore, some studies have demonstrated important features of nuclear markers: They are more abundant relative to mitochondrial markers (Jo et al, 2020;Moushomi et al, 2019) and allow the detection and identification of environmentally sensitive taxa that would otherwise have been missed with mitochondrial markers (bioindicator taxa; Seymour et al, 2020). Nonetheless, highly variable mitochondrial genes are becoming increasing popular markers for understanding trophic interactions and biogeographic patterns, and in studies that employ eDNA sequencing for biodiversity monitoring, in part because of the availability of an increasing number of effective primer sets (Gaither et al, 2022). Recent research showed that broad-range primers designed to amplify metazoan mitochondrial sequences also recover a diversity of mitochondrial sequences belonging to unicellular eukaryotes and fungi, particularly when samples contain traces of target metazoan DNA (Collins et al, 2019;Nguyen et al, 2020).…”

Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience

“…Environmental DNA (eDNA) methods focus on the detection and monitoring of sequenced nucleic acid data extracted from environmental samples and can be classed as a form of environmental genomics. They have been successfully used to survey fish biodiversity [ 22 ], invasive species [ 23 ], detect signature bacteria associated with contaminants [ 24 ], assess environmental health and status using indicator organisms [ 25 , 26 ], for species monitoring [ 23 ], exploring trophic interactions [ 27 ] through to investigating broad biogeographic patterns [ 28 ].…”