Assessing the diversity of plankton-associated prokaryotes along a size-fraction gradient: A methodological evaluation

Marine free-living (FL) and plankton-associated prokaryotes (plankton-microbiota) are at the basis of trophic webs and play crucial roles in the transfer and cycling of nutrients, organic matter, and contaminants. Different ecological niches exist along the plankton size fraction gradient. Despite its relevant ecological role, the plankton-microbiota has rarely been investigated with a sufficient level of size-fraction resolution, and it can be challenging to study because of overwhelming eukaryotic DNA. Here we compared the prokaryotic diversity obtained by 16S rRNA gene sequencing from six plankton size fractions (from FL to mesoplankton), through three DNA recovery methods: direct extraction, desorption pretreatment, enrichment post-treatment. The plankton microbiota differed strongly according to the plankton size-fraction and methodological approach. Prokaryotic taxa specific to each size fraction, and methodology used, were identified. Vibrionaceae were over-represented by cell desorption pretreatment, while prokaryotic DNA enrichment had taxon-specific effects, indicating that direct DNA extraction was the most appropriate method.