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

Kevin K Beentjes1,2, Arjen G C L Speksnijder1, Menno Schilthuizen1,2

  • 1Naturalis Biodiversity Center, Leiden, The Netherlands.

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|August 8, 2019
PubMed
Summary

Temporal variation in environmental DNA (eDNA) significantly impacts community composition, even weekly. Spatial sampling alone may miss diversity, and temporal factors are crucial for bio-indicator assessments.

Keywords:
Environmental DNAFreshwaterHigh-throughput sequencingMetabarcodingReplicatesSampling strategySpatiotemporal variation

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Area of Science:

  • Environmental DNA (eDNA) research
  • Aquatic ecology
  • Molecular ecology

Background:

  • Environmental DNA (eDNA) heterogeneity affects species detection and community composition estimates.
  • Studies often focus on large-scale spatial distribution, with fewer examining within-water body spatial or temporal variation.
  • Temporal eDNA studies typically focus on seasonality over long periods and limited taxa like fish and amphibians.

Purpose of the Study:

  • To analyze and compare small-scale spatial and temporal variation in eDNA.
  • To assess the impact of sampling intervals on community composition estimates.
  • To evaluate the reliability of eDNA for bio-indicator species, particularly plankton.

Main Methods:

  • Sampling eDNA from two isolated dune lakes over 20 consecutive weeks.
  • Performing metabarcoding using generic COI primers.
  • Utilizing molecular operational taxonomic units (MOTUs) to assess sample dissimilarities.

Main Results:

  • Significant differences observed between spatial and temporal eDNA samples, even weekly.
  • Between-site dissimilarities correlated linearly with time frame, inflating differences over time.
  • PCR replicate strategies affected richness but not overall dissimilarity patterns.

Conclusions:

  • Weekly eDNA temporal dissimilarity is comparable to spatial dissimilarity.
  • Population turnover can exceed community heterogeneity over longer time intervals.
  • Temporal variation is critical for eDNA bio-indicators, especially plankton, due to rapid community shifts.