Multiscale responses of microbial life to spatial distance and environmental heterogeneity in a patchy ecosystem

Spatial distance (SD) and environmental heterogeneity (EH) are currently thought to represent major factors shaping genetic variation and population abundance, but their relative importance is still poorly understood. Because EH varies at multiple spatial scales, so too are microbial variables expected to vary. The determination of SD x EH interactions at multiple scales is, however, not a trivial exercise, especially when one examines their effects on microbial abundance and genomic similarities. Here we assessed those interactions at all scales perceptible in a patchy environment composed of known plant species and of heterogeneous soil physical and chemical parameters. For free-living, soil-borne Burkholderia ambifaria, genomic similarities responded to most of the spatial scales that the experimental sampling scheme could reveal, despite limited dispersal of the individuals. Species abundance and community composition were, however, responding to much smaller scales more consistent with local responses to EH. Our results suggest that whole-genome similarities may reflect the simultaneous effects of both SD and EH in microbial populations, but the pure effects of each factor only contributed to < 2% of the total genetic variation. The large amount of unexplained variation that remains after considering most environmental, spatial, and biological interactions is then posited to be the result of noise introduced by unmeasured environmental and spatial variability, sampling effects, and neutral ecological drift.