Dataset Information

The effects of spatial and temporal replicate sampling on eDNA metabarcoding.

ABSTRACT: Background:The heterogeneous nature of environmental DNA (eDNA) and its effects on species detection and community composition estimates has been highlighted in several studies in the past decades. Mostly in the context of spatial distribution over large areas, in fewer occasions looking at spatial distribution within a single body of water. Temporal variation of eDNA, similarly, has mostly been studied as seasonality, observing changes over large periods of time, and often only for small groups of organisms such as fish and amphibians. Methods:We analyzed and compared small-scale spatial and temporal variation by sampling eDNA from two small, isolated dune lakes for 20 consecutive weeks. Metabarcoding was performed on the samples using generic COI primers. Molecular operational taxonomic unit (MOTUs) were used to assess dissimilarities between spatial and temporal replicates. Results:Our results show large differences between samples taken within one lake at one point in time, but also expose the large differences between temporal replicates, even those taken only 1 week apart. Furthermore, between-site dissimilarities showed a linear correlation with time frame, indicating that between-site differences will be inflated when samples are taken over a period of time. We also assessed the effects of PCR replicates and processing strategies on general patterns of dissimilarity between samples. While more inclusive PCR replicate strategies lead to higher richness estimations, dissimilarity patterns between samples did not significantly change. Conclusions:We conclude that the dissimilarity of temporal replicates at a 1 week interval is comparable to that of spatial replicate samples. It increases, however, for larger time intervals, which suggests that population turnover effects can be stronger than community heterogeneity. Spatial replicates alone may not be enough for optimal recovery of taxonomic diversity, and cross-comparisons of different locations are susceptible to inflated dissimilarities when performed over larger time intervals. Many of the observed MOTUs could be classified as either phyto- or zooplankton, two groups that have gained traction in recent years as potential novel bio-indicator species. Our results, however, indicate that these groups might be susceptible to large community shifts in relatively short periods of time, highlighting the need to take temporal variations into consideration when assessing their usability as water quality indicators.

SUBMITTER: Beentjes KK

PROVIDER: S-EPMC6662575 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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The effects of spatial and temporal replicate sampling on eDNA metabarcoding.

Beentjes Kevin K KK Speksnijder Arjen G C L AGCL Schilthuizen Menno M Hoogeveen Marten M van der Hoorn Berry B BB

PeerJ 20190726

<h4>Background</h4>The heterogeneous nature of environmental DNA (eDNA) and its effects on species detection and community composition estimates has been highlighted in several studies in the past decades. Mostly in the context of spatial distribution over large areas, in fewer occasions looking at spatial distribution within a single body of water. Temporal variation of eDNA, similarly, has mostly been studied as seasonality, observing changes over large periods of time, and often only for smal ...[more]

PMID: 31388472

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Project description:Environmental DNA methods such as metabarcoding have been suggested as possible alternatives or complements to the current practice of morphology-based diversity assessment for characterizing benthic communities in marine sediment. However, the source volume used in sediment eDNA studies is several magnitudes lower than that used in morphological identification. Here, we used data from a North Sea benthic sampling station to investigate to what extent metabarcoding data is affected by sampling bias and spatial heterogeneity. Using three grab parallels, we sampled five separate sediment samples from each grab. We then made five DNA extraction replicates from each sediment sample. Each extract was amplified targeting both the 18S SSU rRNA V1-V2 region for total eukaryotic composition, and the cytochrome c oxidase subunit I (COI) gene for metazoans only. In both datasets, extract replicates from the same sediment sample were significantly more similar than different samples from the same grab. Further, samples from different grabs were less similar than those from the same grab for 18S. Interestingly, this was not true for COI metabarcoding, where the differences within the same grab were similar to the differences between grabs. We also investigated how much of the total identified richness could be covered by extract replicates, individual sediment samples and all sediment samples from a single grab, as well as the variability of Shannon diversity and, for COI, macrofaunal biotic indices indicating environmental status. These results were largely consistent with the beta diversity findings, and show that total eukaryotic diversity can be well represented using 18S metabarcoding with a manageable number of biological replicates. Based on these results, we strongly recommend the combination of different parts of the surface of single grabs for eDNA extraction as well as several grab replicates, or alternatively box cores or similar. This will dilute the effects of dominating species and increase the coverage of alpha diversity. COI-based metabarcoding consistency was found to be lower compared to 18S, but COI macrofauna-based indices were more consistent than direct COI alpha diversity measures.

Dataset Information

The effects of spatial and temporal replicate sampling on eDNA metabarcoding.

Publications

The effects of spatial and temporal replicate sampling on eDNA metabarcoding.

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