Variation in bacterial traits across phylogenetic clades and environments

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 whether Sphingomonas genomes exhibit a phylogenetic signal for habitat preference, and whether key, genome-based habitat preference traits demonstrate phylogenetic clustering and correlate with habitat preference. We hypothesized that Sphingomonas strains from different isolation sources would cluster together in shallow, recently diverged clades. Furthermore, key traits that improve fitness in specific environments should correlate with the isolation source. Although there were some exceptions, Sphingomonas genomes did not cluster in clades by their isolation source. However, phylogenetic generalized least squares analyses revealed that genomes from some isolation sources (e.g., plants and contaminated sites) showed a strong correlation (p < 0.05) with specific carbohydrate-active enzyme gene frequencies. Additionally, there was a strong, positive correlation (p < 0.05) between carbohydrate-active enzyme genes and genome size. This knowledge of how environment and host relate to phylogeny may also help with future functional predictions. Because of their bioremediation potential, understanding the genetics and distributions of Sphingomonas traits could help rehabilitate natural habitats.