Genomic signatures of microbial lifestyles

Background/Question/Methods

Although the benefits of applying trait-based theory to microbial communities has been discussed, it has rarely been meaningfully implemented in microbial ecology. The appeal of a trait-based approach is the ability to link species’ physiology and morphology to their environmental responses and contributions to ecosystem function. Often these traits are considered in the context of trade-offs amongst a set of traits. These tradeoffs can highlight life history strategies or generalizable lifestyles amongst a group of organisms. Using a suite of comparative genomics tools, we sought to answer the question: can consistent bacterial lifestyles be identified across diverse ecosystems and phylogenetic groups?  

Results/Conclusions

A survey of >300 bacterial genomes from human gut, marine, freshwater, and soil environments reveals contrasting bacterial lifestyles that consistently occur across the ecosystems. Cross-validation of two genomic models for growth capacity highlight a strong dichotomy for potential growth of bacteria. Organisms with the capacity to grow rapidly tend to possess the ability to respond to their environment, use diverse substrate, and are subject to greater predation, thus fitting the classic definition of a copiotroph or r-selected. A second population of bacteria can be classified as oligotrophic or K-selected as they are predicted to grow slowly, are passive, and grow efficiently. The presence of this lifestyle dichotomy across diverse ecosystems suggests bacteria face similar adaptive challenges in all environments and consistent tradeoffs have emerged.