Is everything everywhere? Population metagenomics of the "pink berries" microbial communities from Woods Hole salt marshes

How are bacterial populations structured in marine ecosystems? This is a critical question if one wants to understand how biotic interactions can influence the evolution of marine bacteria. Yet the spatial and temporal scales at which new bacterial populations or species emerge in environments with potentially high connectivity remains largely unexplored. This lack of knowledge is mainly due to the challenges of following planktonic bacterial populations through time and space, and sequencing complex metagenomes deeply enough to reveal strain-level variation. Here we used the bacterial aggregates known as "pink berries" as a tractable model system to overcome these issues. These spherical, mm-sized multispecies biofilms are found at the sediment-water interface in ponds of the salt marshes around Woods Hole, MA. They are dominated by two bacterial species living in a mutualistic, sulfur cycling symbiosis, a purple sulfur bacterium and a sulfate reducer. We sampled aggregates from 19 sites located in 3 different marshes to cover a wide variety of spatial distances between samples. The long-read metagenomic sequencing of these aggregates revealed the genetic population structure of the two main species in the "pink berries" and showed how recombination between intraspecific populations is affected by geographic distance. We then used these data to assess the extent of coevolution between the two partners. Finally, we combined the analysis of CRISPR-Cas regions and viral reads present in the metagenomes to examine virus-host interactions and their effect on the diversification of bacterial populations. These results bring invaluable insights to inform bacterial population genetic theories, in particular by examining the role of spatial scales in microbial speciation.