Diversity of Wadden Sea macrofauna and meiofauna communities highest in DNA from extractions preceded by cell lysis

• Published in: Journal of sea research 2019-10, Vol.152, p.101764, Article 101764
• Main Authors: Klunder, Lise, Duineveld, Gerard C.A., Lavaleye, Marc S.S., van der Veer, Henk W., Palsbøll, Per J., van Bleijswijk, Judith D.L.
• Format: Article
• Language: English
• Subjects: Benthic communities; Benthic fauna; Benthos; Biodiversity; Bioinformatics; Classifiers (sedimentation); Communities; Deoxyribonucleic acid; DNA; DNA extraction; Environmental DNA; Extracellular; Lysis; Macrofauna; Meiobenthos; Meiofauna; Metabarcoding; Pipelines; rRNA 18S; Sediment; Sediments; Species classification; Species composition; Submarine pipelines; Surveys; Taxonomy; Wadden Sea; Zoobenthos
• ISSN: 1385-1101; 1873-1414
• DOI: 10.1016/j.seares.2019.101764

Metabarcoding of genetic material in environmental samples has increasingly been employed as a means to assess biodiversity, also of marine benthic communities. Current protocols employed to extract DNA from benthic samples and subsequent bioinformatics pipelines differ considerably. The present study compares three commonly deployed metabarcoding approaches against a morphological approach to assess benthic biodiversity in an intertidal bay in the Dutch Wadden Sea. Environmental DNA was extracted using three different approaches; extraction of extracellular DNA, extraction preceded by cell lysis of a sieved fraction of the sediment, and extraction of DNA directly from small amounts of sediment. DNA extractions after lysis of sieved sediment fractions best recovered the macrofauna diversity whereas direct DNA extraction of small amounts of sediment best recovered the meiofauna diversity. Extractions of extracellular DNA yielded the lowest number of OTUs per sample and hence an incomplete view of benthic biodiversity. An assessment of different bioinformatic pipelines and parameters was conducted using a mock sample with a known species composition. The RDP classifier performed better than BLAST for taxonomic assignment of the samples in this study. Novel metabarcodes obtained from local specimens were added to the SILVA 18S rRNA database to improve taxonomic assignment. This study provides recommendations for a general metabarcoding protocol for marine benthic surveys in the Wadden Sea. •Metabarcoding is a feasible method to assess benthic fauna in the Dutch Wadden Sea.•Biodiversity outcomes varies with the DNA extraction methods used.•DNA extraction methods including a lysis step were most accurate.•A metabarcoding protocol is proposed to generate reliable and replicable results.•Metabarcoding studies need to incorporate mock samples to acquire reliable results.