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Grab what you can-an evaluation of spatial replication to decrease heterogeneity in sediment eDNA metabarcoding.

Jon T Hestetun1, Anders Lanzén2,3, Thomas G Dahlgren1,4

  • 1NORCE Environment, Bergen, Vestland, Norway.

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Summary
This summary is machine-generated.

Environmental DNA (eDNA) metabarcoding shows potential for marine benthic community assessment. Combining sediment samples and replicates improves diversity assessment, with 18S rRNA offering better consistency than COI for eukaryotic and metazoan communities, respectively.

Keywords:
BenthosCommunity EcologyDNA ExtractionMetabarcodingEnvironmental DNAEnvironmental impactMarine biology

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Area of Science:

  • Marine Ecology
  • Molecular Ecology
  • Environmental DNA (eDNA) Analysis

Background:

  • Morphology-based methods are standard for benthic community assessment.
  • Environmental DNA (eDNA) metabarcoding offers a potential alternative or complement.
  • Concerns exist regarding eDNA sampling volume and potential biases in marine sediment studies.

Purpose of the Study:

  • To investigate the impact of sampling bias and spatial heterogeneity on metabarcoding data in marine sediment.
  • To compare the consistency of 18S rRNA (eukaryotes) and COI (metazoans) metabarcoding.
  • To assess the representativeness of diversity metrics based on varying sampling strategies.

Main Methods:

  • Collected North Sea sediment samples using three grab parallels, with five subsamples per grab.
  • Performed five DNA extraction replicates from each sediment sample.
  • Amplified DNA targeting 18S SSU rRNA (total eukaryotes) and COI (metazoans) genes.

Main Results:

  • Extract replicates from the same sediment sample were more similar than samples from different locations.
  • 18S rRNA data showed higher similarity within grabs than between grabs, unlike COI data.
  • 18S metabarcoding effectively represented eukaryotic diversity with manageable replicates; COI biotic indices were more consistent than alpha diversity measures.

Conclusions:

  • Combining multiple sediment subsamples per grab and using several grab replicates enhances alpha diversity coverage and dilutes dominance effects.
  • 18S rRNA metabarcoding provides a consistent method for assessing total eukaryotic benthic diversity.
  • While COI metabarcoding showed lower consistency, derived macrofaunal biotic indices were reliable indicators of environmental status.