Seasonal population structure and adaptive signatures across long-term marine microbial time series

A study examining the long-term dynamics of ocean microbial populations has revealed how these communities respond to environmental changes. To achieve this, researchers combined 30 PacBio HiFi long-read metagenome-assembled genomes (MAGs) collected from the northwestern Mediterranean Sea with monthly Illumina metagenomes spanning 12 and 7 years. The differentiation among these genomes varied significantly and often differed greatly between sites. However, a subset of genomes exhibited increasing differentiation with time.

Genetic diversity and population structure were frequently influenced by seasonal factors. Populations were associated with either warm or cold waters, while others straddled both thermal regimes. Within these genetic differences, candidate adaptive genes accounted for 1.6-3.0% of the coding sequences. Interestingly, many of these adaptive genes were detected in both time series.

The analysis of these genes' pN/pS trajectories (nucleotide substitutions per site) revealed regular seasonal fluctuations. These fluctuations were likely due to shifts in strain or ecotype contributions. Additionally, the researchers identified irregular temporal patterns in some of the data. The findings of this research demonstrate that integrating long-read MAG references with dense short-read time series can effectively uncover seasonal population structure, site-specific differentiation, and candidate adaptive variation within marine microbial species.

This approach provides a valuable framework for monitoring contemporary population-genomic changes within the ocean.