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Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems.
Clarke LJ
,
Suter L
,
Deagle BE
,
Polanowski AM
,
Terauds A
,
Johnstone GJ
,
Stark JS
.
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Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.
Figure 1. Map of nearshore benthic sampling sites in the Vestfold Hills, East Antarctica.Base map produced by the Australian Antarctic Data Centre, and adapted for this study by Helen Achurch (AAD). Sites are coloured as per the ordinations in Figs. 5 and 7.
Figure 2. Number of sequencing reads from the COI marker classified as “metazoan”, “non-metazoan” and “not classified” for sediment and water environmental DNA (eDNA) and samples.
Figure 3. Number of metazoan species detected per sample by sample type and sediment core section at sites where both sample types were collected, based on 1000 metazoan reads per sample.The inset shows sample-size based rarefaction curves for all samples. Core samples are classified by core section (1: 0–2 cm, 2: 2–4 cm, 3: 4–6 (or 4–7) cm, 4: 6–8 (7–9) cm, 5: 8–10 (9–11) cm). Cores that were not sectioned are grouped with 0–2 cm sections.
Figure 4. Number of species per metazoan phylum detected exclusively with water eDNA, sediment, or with both methods.
Figure 5. Sediment and water eDNA samples yield distinct benthic metazoan communities.Non-metric multidimensional scaling (nMDS) plots based on binary Jaccard distances for metazoan communities from sediment and water eDNA samples based on either (A) all samples, or (B) the uppermost sediment sample and water eDNA for locations where both were collected (marked with an asterisk in the legend). Data ellipses drawn based on a multivariate normal distribution with a confidence level of 0.95.
Figure 6. Mean taxon relative abundance per sample for sediment and water eDNA samples with more than 1,000 reads (n = 66).Taxa with greater than 1% mean relative abundance in either sample type (representing 96% of metazoan reads) are shown. Taxa that were significantly more abundant in the paired water eDNA or sediment samples based on Linear Discriminant Analysis (LDA) Effect Size (LEfSe) are indicated with an asterisk.
Figure 7. Non-metric multidimensional scaling (nMDS) plots based on binary Jaccard distances for metazoan communities from water eDNA samples.Vectors show correlations with environmental variables, with vector length proportional to the strength of the correlation.
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