Ecological Insights from the Evolutionary History of Microbial Innovations

Abstract

Bacteria and Archaea represent the base of the evolutionary tree of life and contain the vast majority of phylogenetic and functional diversity. Because these organisms and their traits directly impact ecosystems and human health, a focus on functional traits has become increasingly common in microbial ecology. These trait-based approaches have the potential to link microbial communities and their ecological function. But an open question is how, why, and in what order microorganisms acquired the traits we observe in the present day. To address this, we reconstructed the evolutionary history of microbial traits using genomic data to understand the evolution, selective advantage, and similarity of traits in extant organisms and provide insights into the composition of genomes and communities. We used the geological timeline and physiological expectations to provide independent evidence in support of this evolutionary history. Using this reconstructed evolutionary history, we explored hypotheses related to the composition of genomes. We showed that gene transition rates can be used to make predictions about the size and type of genes in a genome: generalist genomes comprise many evolutionarily labile genes while specialist genomes comprise more highly conserved functional genes. These findings suggest that generalist organisms do not build up and hoard an array of functions, but rather tend to experiment with functions related to environmental sensing, transport, and complex resource degradation. Our results provide a framework for understanding the evolutionary history of extant microorganisms, the origin and maintenanceof traits, and linking evolutionary relatedness and ecological function.

Diverse interactions and ecosystem engineering stabilize community assembly

“…For example, engineering has been shown to promote invasion [59], alter primary productivity [60], and change the selective environment over eco-evolutionary timescales [61,62] which can lead to unexpected outcomes such as the fixation of deleterious alleles [63]. On smaller scales, microbiota construct shared metabolitic resources that have a significant influence on microbial communities [64], the dynamics of which may even serve as the missing ingredient stabilizing some complex ecological systems [65].…”

“…In the microbiome, redundant engineering may be very common due to the influence of horizontal gene transfer in structuring metabolite production [68]. In these systems, redundancy in the production of shared metabolitic resources may play a key role in community structure and dynamics [64,65].…”