chase lab
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For centuries, biologists have investigated the relative contributions of ecological and evolutionary processes on community dynamics. Yet, it is had only been within the last two decades that these patterns have become evident for the most diverse and ubiquitous organisms, microorganisms. However, if we wish to understand microbial community dynamics, in the soil or the human microbiome, it is imperative to start considering a finer scale of diversity than is currently assessed. Typically, microbial community studies are restricted to a coarse depiction of the community by identifying the response of broad taxonomic groups. These limitations partly stem from the common practice of characterizing microbial communities using conserved marker genes, such as the 16S rRNA region, which mask ecologically-relevant genetic and phenotypic variation. For example, most microbial studies that target the 16S rRNA region, cluster similar sequences into operational taxonomic units (OTUs) that represents 50-150 million years of evolutionary history. This would be roughly equivalent to lumping all birds into a single taxon.
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But just as there are many differences in the traits among bird species, there are important trait differences among bacteria within these OTUs. Thus, there is a need to characterize the degree of trait variation that contribute to the geographic distribution and the ecological role of a bacterium. This often requires designating bacterial ecotypes (what might be considered a species) and delineate populations within those ecotypes. To address this, our work has utilized a combination of bioinformatics (i.e. genomics and metagenomics), physiological assays, and creative field experiments to apply a trait-based framework to the biogeographic distribution of environmental bacteria. Overall, we have focused on identifying the traits responsible for contributing to environmental niche partitioning and diversification within relevant bacterial taxa to link genotypic variation to ecological roles. Recent work has investigated how biotic interactions via the production of specialized metabolites contribute to microbial diversification and community assembly.
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