Soil bacterial populations are shaped by recombination and gene-specific selection across a meadow

Abstract

Soil microbial diversity is often studied from the perspective of community 12 composition, but less is known about genetic heterogeneity within species and how population 13 structures are affected by dispersal, recombination, and selection. Genomic inferences about 14 population structure can be made using the millions of sequencing reads that are assembled de 15 novo into consensus genomes from metagenomes, as each read pair describes a short genomic 16 sequence from a cell in the population. Here we track genome-wide population genetic variation 17 for 19 highly abundant bacterial species sampled from across a grassland meadow. Genomic 18 nucleotide identity of assembled genomes was significantly associated with local geography for 19 half of the populations studied, and for a majority of populations within-sample nucleotide 20 diversity could often be as high as meadow-wide nucleotide diversity. Genes involved in specialized 21 metabolite biosynthesis and extracellular transport were characterized by elevated genetic diversity 22 in multiple species. Microbial populations displayed varying degrees of homologous recombination 23 and recombinant variants were often detected at 7-36% of loci genome-wide. Within multiple 24 populations we identified genes with unusually high site-specific differentiation of alleles, fewer 25 recombinant events, and lower nucleotide diversity, suggesting recent selective sweeps for gene 26 variants. Taken together, these results indicate that recombination and gene-specific selection 27 commonly shape local soil bacterial genetic variation. 28 29 31

Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment

“…It is even possible that nearly all of the mutations that we observed are simply passenger mutations that are hitchhiking alongside the true causative variants. The situation could potentially be improved by combining our read mapping approach with de novo genome assembly, similar to previous studies (44,55,56), particularly if linked reads are used during the assembly step (24). However, given the high levels of genetic linkage we inferred, it would be difficult to pinpoint individual selection pressures even with an exhaustive list of mutations, since one can only observe the net effects of selection across entire haplotypes.…”

The Tempo and Mode of Adaptation in a Complex Natural Population: the Microbiome

“…Microbiomes across a wide range of environments, including oceans ( 21 ), rivers ( 22 ), soil ( 23 ), and the human gut ( 24 ), display complex spatial structure. This spatial structure has been associated with a number of critical functions, including the bioremediation of soils, carbon and nitrogen cycling, and responding to changes in diet and drugs.…”

How can microbial population genomics inform community ecology?

“…Although even for these, some structure can be masked because of rapid speciation, these genes can serve nonetheless as a much more accurate proxy for population structure. Whether this observation holds more broadly across many taxa will have to be explored in larger datasets [56], but importantly, identical ribosomal proteins can be extracted from metagenomic datasets and their dynamics thus easily analysed [57]. We, therefore, recommend targeting ribosomal proteins when species and population dynamics are of interest in metagenomic samples.…”