Stress adaptation of free-living microbes generates novel benefits to plant hosts

Most microbes that live in or on hosts are not obligate symbionts. Instead, they often cycle between host-associated and free-living phases and experience selection in both environments. The benefits that microbes confer to hosts are often assumed to be a product of host-microbe (co)evolution, but microbial benefits to hosts may also evolve independent of the host-microbe interaction, while the microbe is free-living. We investigated this hypothesis by experimentally evolving a beneficial Allorhizobium bacterium we had previously isolated from duckweed (Lemna japonica). We evolved this Allorhizobium strain in the absence of any host at high and low salinity and at high and low nitrogen, and then tested how the evolved strains performed as symbionts when host-associated. Microbial salinity adaptation drove the emergence of novel benefits to host plants in high-salinity environments. However, these locally adaptive benefits emerged only when microbes evolved under low-nitrogen conditions; microbial adaptation to high nitrogen reduced plant growth. Bacterial phenotyping indicated that the same microbial traits that underlie salinity adaptation mediate host benefits. Whole-genome sequencing of the evolved strains revealed significant genomic shifts between selective treatments, including plasmid variation and point mutations associated with osmotic regulation. The emergence of the microbial benefits to hosts, as a byproduct of microbial adaptation, highlights that these benefits do not require targeted host-microbe co-evolution. Rather, predicting the evolutionary trajectory of these symbioses may require understanding both the abiotic and biotic selective agents acting on key microbial traits mediating the host-microbe interaction.