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Contributed Talk

Session: : Evolution: Selection And Adaptation 1

COS 105-6 - The evolutionary genomics of adaptation to stress in wild soil microbiota

Tuesday, August 8, 2023
2:45 PM – 3:00 PM PDT
Location: B116
Abstract: Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes however, horizontal gene transfer allows for adaptation via gene gain and loss which could generate fundamentally different evolutionary dynamics during adaptation. We use comparative genomics and genetics across distinct clades of symbiotic rhizobium bacteria to elucidate the evolutionary genetics of adaptation to physiologically stressful serpentine soils in western North American grasslands. We demonstrate that the presence of a locus of major effect, the nre operon, is necessary and sufficient to confer rhizobium adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major environmental axis of natural soil chemistry variation. Discordance between inferred evolutionary histories of the core genome and the nreAXY genes, which often reside in putative genomic islands, suggests that frequent loss and gain events via horizontal acquisition of nre across divergent rhizobium clades underlies the evolutionary history of this adaptive variant. However, different nre alleles are associated with various levels of nickel resistance, suggesting allelic substitution could play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss, and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for improving stress-adapted microbial inocula for human use and for the generation of microbial diversity.