ArticleProceedings of the National Academy of Sciences of the United States of America2007
Genome dynamics in a natural archaeal population.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- Genome-resolved metagenomics and evolutionary analysis reveal conserved metabolic adaptations in extremophile communities from a copper mining tailing.Environmental microbiome · 2025Article
- Review
- Shifts in the Microbial Populations of Bioleach Reactors Are Determined by Carbon Sources and Temperature.Biology · 2023Article
- Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution.Science advances · 2023Article
- A method for achieving complete microbial genomes and improving bins from metagenomics data.PLoS computational biology · 2021Article
- The Proposed Molecular Mechanisms Used by Archaea for Fe(III) Reduction and Fe(II) Oxidation.Frontiers in microbiology · 2021Review
- Diversity within species: interpreting strains in microbiomes.Nature reviews. Microbiology · 2020Review
- Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels.Nature microbiology · 2019Article
- Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations.BMC genomics · 2019Article
- In a quest for engineering acidophiles for biomining applications: challenges and opportunities.Genes · 2018Review
- Strain-level genetic diversity ofPeerJ · 2018Article
- Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YScientific reports · 2017Article
- The Ecology of Acidophilic Microorganisms in the Corroding Concrete Sewer Environment.Frontiers in microbiology · 2017Review
- Metatranscriptomic evidence of pervasive and diverse chemolithoautotrophy relevant to C, S, N and Fe cycling in a shallow alluvial aquifer.The ISME journal · 2016Article
- Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations.The ISME journal · 2016Article
- Metagenomic reconstructions of bacterial CRISPR loci constrain population histories.The ISME journal · 2016Article
- Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) from Thermoplasma acidophilum, a thermo-acidophilic archaeon.Nucleic acids research · 2016Article
- Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum".Frontiers in microbiology · 2016Article
- Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia.Applied and environmental microbiology · 2016Article
- Migration and horizontal gene transfer divide microbial genomes into multiple niches.Nature communications · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Evolutionary processes that give rise to, and limit, diversification within strain populations can be deduced from the form and distribution of genomic heterogeneity. The extent of genomic change that distinguishes the acidophilic archaeon Ferroplasma acidarmanus fer1 from an environmental population of the same species from the same site, fer1(env), was determined by comparing the 1.94-megabase (Mb) genome sequence of the isolate with that reconstructed from 8 Mb of environmental sequence data. The fer1(env) composite sequence sampled approximately 92% of the isolate genome. Environmental sequence data were also analyzed to reveal genomic heterogeneity within the coexisting, coevolving fer1(env) population. Analyses revealed that transposase movement and the insertion and loss of blocks of novel genes of probable phage origin occur rapidly enough to give rise to heterogeneity in gene content within the local population. Because the environmental DNA was derived from many closely related individuals, it was possible to quantify gene sequence variability within the population. All but a few gene variants show evidence of strong purifying selection. Based on the small number of distinct sequence types and their distribution, we infer that the population is undergoing frequent genetic recombination, resulting in a mosaic genome pool that is shaped by selection. The larger genetic potential of the population relative to individuals within it and the combinatorial process that results in many closely related genome types may provide the basis for adaptation to environmental fluctuations.
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