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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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Autores principales: Sorouri, Bahareh, Rodriguez, Cynthia I., Gaut, Brandon S., Allison, Steven D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10150699/
https://www.ncbi.nlm.nih.gov/pubmed/37138640
http://dx.doi.org/10.3389/fmicb.2023.1146165
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author Sorouri, Bahareh
Rodriguez, Cynthia I.
Gaut, Brandon S.
Allison, Steven D.
author_facet Sorouri, Bahareh
Rodriguez, Cynthia I.
Gaut, Brandon S.
Allison, Steven D.
author_sort Sorouri, Bahareh
collection PubMed
description 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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spelling pubmed-101506992023-05-02 Variation in Sphingomonas traits across habitats and phylogenetic clades Sorouri, Bahareh Rodriguez, Cynthia I. Gaut, Brandon S. Allison, Steven D. Front Microbiol Microbiology 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. Frontiers Media S.A. 2023-04-17 /pmc/articles/PMC10150699/ /pubmed/37138640 http://dx.doi.org/10.3389/fmicb.2023.1146165 Text en Copyright © 2023 Sorouri, Rodriguez, Gaut and Allison. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Sorouri, Bahareh
Rodriguez, Cynthia I.
Gaut, Brandon S.
Allison, Steven D.
Variation in Sphingomonas traits across habitats and phylogenetic clades
title Variation in Sphingomonas traits across habitats and phylogenetic clades
title_full Variation in Sphingomonas traits across habitats and phylogenetic clades
title_fullStr Variation in Sphingomonas traits across habitats and phylogenetic clades
title_full_unstemmed Variation in Sphingomonas traits across habitats and phylogenetic clades
title_short Variation in Sphingomonas traits across habitats and phylogenetic clades
title_sort variation in sphingomonas traits across habitats and phylogenetic clades
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10150699/
https://www.ncbi.nlm.nih.gov/pubmed/37138640
http://dx.doi.org/10.3389/fmicb.2023.1146165
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