ArticleThe ISME journal2020
Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow.
Article in The ISME journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils.Nature microbiology · 2026Article
- High-resolution metagenome assembly for modern long reads with myloasm.Nature biotechnology · 2026Article
- Types and characteristics of shared microbiota within families of ethnic minorities in Inner Mongolia.Microbiology spectrum · 2026Article
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- Multi-scale ecological drivers shape the genome flexibility of soil-dwellingISME communications · 2026Article
- Community coalescence reveals strong selection and coexistence within species in complex microbial communities.bioRxiv : the preprint server for biology · 2025Article
- High-resolution metagenome assembly for modern long reads with myloasm.bioRxiv : the preprint server for biology · 2025Article
- The physical biogeography ofmBio · 2025Article
- zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters.Nucleic acids research · 2025Article
- High strain-level diversity of Bradyrhizobium across Australian soils.The ISME journal · 2025Article
- Soil bacterial community diversity, composition, and species specificity across different geographical landscapes in the Mu Us Sandy Land.Frontiers in microbiology · 2025Article
- Geographic Distribution Pattern Determines Soil Microbial Community Assembly Process inMicroorganisms · 2024Article
- Selenium alters the gene content but not the taxonomic composition of the soil microbiome.Environmental microbiome · 2024Article
- Microplastic diversity increases the abundance of antibiotic resistance genes in soil.Nature communications · 2024Article
- zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters.bioRxiv : the preprint server for biology · 2024Article
- Comparative genomics reveal a novel phylotaxonomic order in the genus Fusobacterium.Communications biology · 2024Article
- The Response of Rhizosphere Microbial C and N-Cycling Gene Abundance of Sand-Fixing Shrub to Stand Age Following Desert Restoration.Microorganisms · 2024Article
- A hotspot of diversity: novelInternational journal of systematic and evolutionary microbiology · 2024Article
- Homologous recombination and gene-specific selection co-shape the vertical nucleotide diversity of mangrove sediment microbial populations.Ecology and evolution · 2024Article
- The evolutionary genomics of adaptation to stress in wild rhizobium bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
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5 authors.
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Abstract
Soil microbial diversity is often studied from the perspective of community composition, but less is known about genetic heterogeneity within species. The relative impacts of clonal interference, gene-specific selection, and recombination in many abundant but rarely cultivated soil microbes remain unknown. Here we track genome-wide population genetic variation for 19 highly abundant bacterial species sampled from across a grassland meadow. Genomic inferences about population structure are made using the millions of sequencing reads that are assembled de novo into consensus genomes from metagenomes, as each read pair describes a short genomic sequence from a cell in each population. Genomic nucleotide identity of assembled genomes was significantly associated with local geography for over half of the populations studied, and for a majority of populations within-sample nucleotide diversity could often be as high as meadow-wide nucleotide diversity. Genes involved in metabolite biosynthesis and extracellular transport were characterized by elevated nucleotide diversity in multiple species. Microbial populations displayed varying degrees of homologous recombination and recombinant variants were often detected at 7-36% of loci genome-wide. Within multiple populations we identified genes with unusually high spatial differentiation of alleles, fewer recombinant events, elevated ratios of nonsynonymous to synonymous variants, and lower nucleotide diversity, suggesting recent selective sweeps for gene variants. Taken together, these results indicate that recombination and gene-specific selection commonly shape genetic variation in several understudied soil bacterial lineages.
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