Metabarcoding marine sediments: Preparation of amplicon libraries

Abstract

The accurate assessment of community composition and ultimately species identifi cation is of utmost importance in any ecological and evolutionary study. Advances in sequencing technologies have allowed the unraveling of levels of biodiversity never imagined before when applied to large-scale environmental DNA studies (also termed metabarcoding/metagenetics/metasystematics/environmental barcoding). Here, we describe a detailed protocol to assess eukaryotic biodiversity in marine sediments, identifying key steps that should not be neglected when preparing Next-Generation Sequencing (NGS) amplicon libraries: DNA extraction, multiple PCR amplifi cation of DNA barcode markers with index/tag-primers, and fi nal Illumina MiSeq sequencing library preparation.