Variation in bacterial traits across habitats and phylogenetic clades

Background/Question/Methods

Microbes are instrumental for nutrient cycling and the functioning of host organisms. To answer why specific bacteria are present in certain environments and climates, but not others, it is necessary to determine how microbial traits vary with phylogeny. Sphingomonas is an ideal bacterial clade in which to investigate the distribution of traits, such as habitat preference, since these bacteria inhabit a wide variety of environments and hosts. Furthermore, with appropriate management and manipulation, Sphingomonas can be useful in remediating polluted environments.In this study, we downloaded publicly available Sphingomonas genomes, curated them based on their isolation source, analyzed their gene content, and assessed their phylogenetic relationships. We aimed to test 1) if Sphingomonas genomes exhibit a phylogenetic signal for habitat preference, and 2) whether key genome-based habitat preference traits demonstrate phylogenetic clustering and correlate with habitat preference. We hypothesized that Sphingomonas strains from the same habitat would cluster together in shallow, recently diverged clades. Furthermore, we expected that key traits that improve fitness in specific environments would correlate with the isolation habitat.

Results/Conclusions

After careful curation and outgroup selection, we selected 252 high quality genomes and constructed a phylogenetic tree from a core gene alignment of 404 genes. The tree contained 12 well-defined clades that were confirmed with significant ANOSIM tests (p < 0.05). Additionally, a significant ANOSIM test (p < 0.05) reflected that Sphingomonas strains from the same habitat (e.g., plants and contaminated sites) loosely clustered together within the same clades. Moreover, strains within the same clade share similar clusters of accessory genes. Furthermore, through ANOVA tests with a phylogenetic generalized least squares model we found significant differences (p < 0.05) between habitats and frequencies of genome-based traits (e.g., carbohydrate-active enzymes, chaperones and folding catalysts, lipid biosynthesis proteins). Moreover, the frequencies of genome-based traits also significantly varied (ANOVA, p < 0.05) across phylogenetic clades. Together, these results suggest that local adaptation to the environment is reflected in the genomic content of the Sphingomonas genus. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions. Due to their bioremediation potential, understanding the genetics and distributions of Sphingomonas traits could help rehabilitate natural habitats.