Metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom

Summary Most studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. We tested whether DNA-metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. We found significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a three-month period in spring. Patterns followed the same trend as plankton estimates using traditional microscopic methods. We characterized the bloom of a conditionally rare bacterial taxon belonging to Arcicella , which rapidly came to dominate the whole lake ecosystem and would have remained unnoticed without metabarcoding. Our data demonstrate the potential of universal DNA-metabarcoding applied to unfractionated samples for providing a more holistic view of plankton communities.