ReviewPhilosophical transactions of the Royal Society of London. Series B, Biological sciences2020
How can microbial population genomics inform community ecology?
Review in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Article
- Population Ecology of Glacier Bacteria from the View of Gene Flow inMicroorganisms · 2026Article
- Concurrent ecological and evolutionary processes contribute to mutualism breakdown between legumes and rhizobia.The ISME journal · 2026Article
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy.Nature communications · 2025Article
- Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes.mSystems · 2025Article
- Building microbial synthetic communities: get inspired by the design of synthetic plant communities.The New phytologist · 2025Article
- Microdiversity and fine-scale niche differentiation support persistence and coexistence of acidophiles in acid mine drainage.Frontiers in microbiology · 2025Article
- Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts.PLoS genetics · 2024Article
- Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group.The ISME journal · 2024Article
- Recurring seasonality exposes dominant species and niche partitioning strategies of open ocean picoeukaryotic algae.Communications earth & environment · 2024Article
- The active free-living bathypelagic microbiome is largely dominated by rare surface taxa.ISME communications · 2024Article
- Russian Biodiversity Collections: A Professional Opinion Survey.Animals : an open access journal from MDPI · 2023Article
- Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives.Microbial genomics · 2023Article
- Gene flow and introgression are pervasive forces shaping the evolution of bacterial species.Genome biology · 2022Article
- Genome Evolution of a Symbiont Population for Pathogen Defense in Honeybees.Genome biology and evolution · 2022Article
- Relevance of prokaryotic subspecies in the age of genomics.New microbes and new infections · 2022Article
- Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters.Frontiers in microbiology · 2022Article
- Microcoleus (Cyanobacteria) form watershed-wide populations without strong gradients in population structure.Molecular ecology · 2022Article
- Seasonal niche differentiation among closely related marine bacteria.The ISME journal · 2022Article
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4 authors.
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Abstract
Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identify clearly delineated populations among collections of closely related genomes. Such structure can arise from preferential gene flow caused by coexistence and genetic similarity, defining populations based on biological mechanisms. We show that such gene flow units are sufficiently genetically isolated for specific adaptations to spread, making them also ecological units that are differentially adapted compared to their closest relatives. We discuss the implications of these observations for measuring bacterial and archaeal diversity in the environment. We show that operational taxonomic units defined by 16S rRNA gene sequencing have woefully poor resolution for ecologically defined populations and propose monophyletic clusters of nearly identical ribosomal protein genes as an alternative measure for population mapping in community ecological studies employing metagenomics. These population-based approaches have the potential to provide much-needed clarity in interpreting the vast microbial diversity in human and environmental microbiomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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