Single-cell genomics of a bloom-forming phytoplankton species reveals population genetic structure across continents

Abstract

The study of microbial diversity over time and space is fundamental to the understanding of their ecology and evolution. The underlying processes driving these patterns are not fully resolved but can be studied using population genetic approaches. Here we investigated the population genetic structure of Gonyostomum semen, a bloom-forming phytoplankton species, across two continents. The species appears to be expanding in Europe, whereas similar trends are not observed in the United States. Our aim was to investigate if populations of G. semen in Europe and in the United States are genetically differentiated, if there is population genetic structure within the continents, and what the potential drivers of differentiation are. To this end, we used a novel method based on Single Amplified Genomes (SAGs) combined with RADseq (SAG-RAD), that allows de novo genotyping of natural single cell isolates without the need for culturing. We amplified over 900 single-cell genomes from 25 lake populations across Europe and the United States and identified two distinct population clusters, one in Europe and another in the United States. Low genetic diversity in European populations supports the hypothesized recent expansion of G. semen on this continent. Geographic population structure within each continent was associated with differences in environmental variables which may have led to ecological divergence of population clusters. Overall, our results show that SAG-RAD can be used to analyze microalgal population structure and differentiation based on single-cell isolates from natural, uncultured samples.