Variation in Sphingomonas traits across habitats and phylogenetic clades - PubMed (original) (raw)

Variation in Sphingomonas traits across habitats and phylogenetic clades

Bahareh Sorouri et al. Front Microbiol. 2023.

Abstract

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.

Keywords: Sphingomonas; habitats; pangenome; phylogenetics; traits.

Copyright © 2023 Sorouri, Rodriguez, Gaut and Allison.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1

FIGURE 1

Genome-based trait groupings into the Y-A-S life history strategy framework developed by Malik et al. (2020).

FIGURE 2

FIGURE 2

Pangenome analysis of 252 Sphingomonas genomes and the Rhodospirillum centenum SW outgroup. (A) Gene presence-absence heatmap where vertical blue lines represent presence of a gene within rows corresponding to the Sphingomonas genome, and white reflects gene absence. The line graph underneath indicates the percentage of strains possessing the corresponding gene. (B) Close-up of the gene patterns within a clade shows how clades contain similar gene clusters.

FIGURE 3

FIGURE 3

Sphingomonas (A) habitat and (B) phylogenetic tree constructed with 252 Sphingomonas genomes and 404 core genes, separated into 12 clades. The closely related Rhodospirillum centenum SW was used as the outgroup to identify the core gene alignment and construct the tree. Significant (p < 0.05) ANOSIM results indicate that Sphingomonas habitat preferences vary across clades.

FIGURE 4

FIGURE 4

Heatmap depicting the enrichment of genome-based traits by habitat. Each heatmap box was calculated by taking the natural log of the average number of genes within a habitat for a specific trait and dividing it by the natural log of the total gene average in all habitats for the same trait. Traits are grouped together based on their Y-A-S classification: top green rows are growth traits, the middle blue CAZymes row is a resource acquisition trait, and the bottom, red rows are stress tolerance traits. Traits with stars indicate significant (Kruskal–Wallis, p < 0.05) differences of natural log transformed gene counts between habitats.

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