ArticleApplied and environmental microbiology2014
Genomic heterogeneity and ecological speciation within one subspecies of Bacillus subtilis.
Article in Applied and environmental microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Life in sediments fosters 'sexual' speciation in the Shewanella baltica complex.PLoS genetics · 2026Article
- Isolation and Identification ofPlants (Basel, Switzerland) · 2023Article
- Target and Enhance Ethanol and Butyrate Production from Anaerobic Fermentation via the pH and Organic Loading Rate Combined Strategy.Applied biochemistry and biotechnology · 2022Article
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- Evidence of episodic positive selection inPeerJ · 2022Article
- Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution ofFrontiers in plant science · 2022Article
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- Complex Interaction Networks Among Cyanolichens of a Tropical Biodiversity Hotspot.Frontiers in microbiology · 2021Article
- Diversity within species: interpreting strains in microbiomes.Nature reviews. Microbiology · 2020Review
- Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium.Genome biology and evolution · 2017Article
- Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla.Microbiology spectrum · 2017Article
- Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool.Applied and environmental microbiology · 2017Article
- Comparative Genomics of cpn60-Defined Enterococcus hirae Ecotypes and Relationship of Gene Content Differences to Competitive Fitness.Microbial ecology · 2016Article
- Article
- SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli.BMC microbiology · 2016Article
- Ecological genomics of mutualism decline in nitrogen-fixing bacteria.Proceedings. Biological sciences · 2016Article
- Kin discrimination between sympatric Bacillus subtilis isolates.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Exploring ComQXPA quorum-sensing diversity and biocontrol potential of Bacillus spp. isolates from tomato rhizoplane.Microbial biotechnology · 2015Article
- Ecological genomics in Xanthomonas: the nature of genetic adaptation with homologous recombination and host shifts.BMC genomics · 2015Article
- Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat.Frontiers in microbiology · 2015Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Closely related bacterial genomes usually differ in gene content, suggesting that nearly every strain in nature may be ecologically unique. We have tested this hypothesis by sequencing the genomes of extremely close relatives within a recognized taxon and analyzing the genomes for evidence of ecological distinctness. We compared the genomes of four Death Valley isolates plus the laboratory strain W23, all previously classified as Bacillus subtilis subsp. spizizenii and hypothesized through multilocus analysis to be members of the same ecotype (an ecologically homogeneous population), named putative ecotype 15 (PE15). These strains showed a history of positive selection on amino acid sequences in 38 genes. Each of the strains was under a different regimen of positive selection, suggesting that each strain is ecologically unique and represents a distinct ecological speciation event. The rate of speciation appears to be much faster than can be resolved with multilocus sequencing. Each PE15 strain contained unique genes known to confer a function for bacteria. Remarkably, no unique gene conferred a metabolic system or subsystem function that was not already present in all the PE15 strains sampled. Thus, the origin of ecotypes within this clade shows no evidence of qualitative divergence in the set of resources utilized. Ecotype formation within this clade is consistent with the nanoniche model of bacterial speciation, in which ecotypes use the same set of resources but in different proportions, and genetic cohesion extends beyond a single ecotype to the set of ecotypes utilizing the same resources.
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