Variation in Sphingomonas traits across habitats and phylogenetic clades
Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous. Sphingomonas is an ideal bacterial clade in which to investigate h...
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Veröffentlicht in: | Frontiers in microbiology 2023-04, Vol.14 |
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Sprache: | eng |
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Zusammenfassung: | Whether microbes show habitat preferences is a fundamental question in microbial ecology. If different microbial lineages have distinct traits, those lineages may occur more frequently in habitats where their traits are advantageous.
Sphingomonas
is an ideal bacterial clade in which to investigate how habitat preference relates to traits because these bacteria inhabit diverse environments and hosts. Here we downloaded 440 publicly available
Sphingomonas
genomes, assigned them to habitats based on isolation source, and examined their phylogenetic relationships. We sought to address whether: (1) there is a relationship between
Sphingomonas
habitat and phylogeny, and (2) whether there is a phylogenetic correlation between key, genome-based traits and habitat preference. We hypothesized that
Sphingomonas
strains from similar habitats would cluster together in phylogenetic clades, and key traits that improve fitness in specific environments should correlate with habitat. Genome-based traits were categorized into the Y-A-S trait-based framework for high growth yield, resource acquisition, and stress tolerance. We selected 252 high quality genomes and constructed a phylogenetic tree with 12 well-defined clades based on an alignment of 404 core genes.
Sphingomonas
strains from the same habitat clustered together within the same clades, and strains within clades shared similar clusters of accessory genes. Additionally, key genome-based trait frequencies varied across habitats. We conclude that
Sphingomonas
gene content reflects habitat preference. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions about
Sphingomonas
and facilitate applications in bioremediation. |
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ISSN: | 1664-302X 1664-302X |