DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments

PLoS One. 2017 Jun 16;12(6):e0179443. doi: 10.1371/journal.pone.0179443. eCollection 2017.

Abstract

Human impact on marine benthic communities has traditionally been assessed using visible morphological traits and has focused on the macrobenthos, whereas the ecologically important organisms of the meio- and microbenthos have received less attention. DNA metabarcoding offers an alternative to this approach and enables a larger fraction of the biodiversity in marine sediments to be monitored in a cost-efficient manner. Although this methodology remains poorly standardised and challenged by biases inherent to rRNA copy number variation, DNA extraction, PCR, and limitations related to taxonomic identification, it has been shown to be semi-quantitative and useful for comparing taxon abundances between samples. Here, we evaluate the effect of replicating genomic DNA extraction in order to counteract small scale spatial heterogeneity and improve diversity and community structure estimates in metabarcoding-based monitoring. For this purpose, we used ten technical replicates from three different marine sediment samples. The effect of sequence depth was also assessed, and in silico pooling of DNA extraction replicates carried out in order to maintain the number of reads constant. Our analyses demonstrated that both sequencing depth and DNA extraction replicates could improve diversity estimates as well as the ability to separate samples with different characteristics. We could not identify a "sufficient" replicate number or sequence depth, where further improvements had a less significant effect. Based on these results, we consider replication an attractive alternative to directly increasing the amount of sample used for DNA extraction and strongly recommend it for future metabarcoding studies and routine assessments of sediment biodiversity.

MeSH terms

  • Aquatic Organisms* / chemistry
  • Aquatic Organisms* / genetics
  • Biodiversity*
  • DNA Barcoding, Taxonomic / methods*
  • DNA, Ribosomal* / chemistry
  • DNA, Ribosomal* / genetics
  • DNA, Ribosomal* / isolation & purification
  • Eukaryota* / chemistry
  • Eukaryota* / genetics
  • RNA, Ribosomal / genetics*

Substances

  • DNA, Ribosomal
  • RNA, Ribosomal

Grant support

This work was supported by the Research Council of Norway (NFR, http://www.forskningsradet.no/en, grant no. 190265/S40), Statoil (http://www.statoil.com) and the Norwegian Deepwater Program (NDP; https://epim.no/ndp/). Statoil contributed to the financing of a PhD stipend related to the project funded by NFR, which was in no way contingent on, or linked to, specific research outcomes. Statoil or other funders had no involvement in or influence of study design, data collection and analysis, or preparation of the manuscript.