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Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta

Published on by M Tragin
High Throughput Sequencing (HTS) approaches are getting more and more used to investigate the diversity and community structure of microbial eukaryotes in marine waters. Partial 18S rRNA gene regions (V4 and V9 regions) are commonly used as genetic barcodes. Selecting between the V4 and V9 regions remains a matter of debate. Here, we compared the composition of communities estimated using these two genetic markers at 27 sites sampled during Ocean Sampling Day 2014, with a focus on photosynthetic groups and, more specifically, Chlorophyta. Globally, the V4 and V9 regions of the 18S rRNA gene provided similar images of alpha diversity and ecological patterns. However, the V9 dataset provided 20% more OTUs built at 97% identity than the V4 dataset and 39% and 56% of the genera were found only in one dataset, respectively V4 and V9. For photosynthetic groups, the V4 and V9 regions also performed equally well to describe global communities at different taxonomic levels from the division to the genus and provided similar Chlorophyta distribution patterns. However, at lower taxonomic level, the V9 dataset failed for example to describe the diversity of Dolichomastigales (Chlorophyta, Mamiellophyceae) unveiling the lack of V9 sequences for this group and the importance of the reference database in the metabarcoding process. We conclude that, to address specific questions, regarding specific groups (e.g. a given genus), it is necessary to choose the marker based not only on the genetic divergence within this group but also on the existence of reference sequences in databases.

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Funding

Université Pierre et Marie Curie, the Région Bretagne and the european project Ocean Sampling Day

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