Data from: The evolutionary genomics of adaptation to stress in wild rhizobium bacteria

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 symbiotic with plants however,
horizontal gene transfer allows for adaptation via gene gain and loss,
which could generate fundamentally different evolutionary dynamics. We use
comparative genomics and genetics to elucidate the evolutionary mechanisms
of adaptation to physiologically stressful serpentine soils in rhizobial
bacteria in western North American grasslands. In vitro experiments
demonstrate that the presence of a locus of major effect, the nre operon,
is necessary and sufficient to confer adaptation to nickel, a heavy metal
enriched to toxic levels in serpentine soil, and a major axis of
environmental soil chemistry variation. We find discordance between
inferred evolutionary histories of the core genome and nreAXY genes, which
often reside in putative genomic islands. This suggests that the
evolutionary history of this adaptive variant is marked by frequent
losses, and/or gains via horizontal acquisition across divergent rhizobium
clades. However, different nre alleles confer distinct levels of nickel
resistance, suggesting allelic substitution could also 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 understanding adaptive diversity
in microbes and improving stress-adapted microbial inocula for human use.