Linking genomic traits and phenotypic traits in microbial ecology
Functional traits permit microbes to adapt to abiotic and biotic conditions. At the community level, traits mediate the intricate relationships between species composition and ecosystem-level processes. However, measuring microbial traits is a challenging task given that most taxa remain poorly described. With the ever accumulating amount of genomic data, it is now possible to mine the literature for phenotypic traits of interest and identify genomic attributes or specific gene categories associated with them.
We mined The International Journal of Systematic and Evolutionary Microbiology (IJSEM) for phenotypic (cell size, cell shape, motility, spore production), ecophysiological characteristics (general metabolism, carbon substrate use), and environmental preferences (habitat, pH, temperature, salt, oxygen) of bacterial cultured strains. The majority of strains belonged to the phyla Proteobacteria, Actinobacteria, Firmicutes, and Bacteroides/Chlorobi. We explored the relationships among evolutionary history, genomic content, physiological and phenotypic traits, and environmental preferences.