Measuring selection acting on microbial populations in natural or even seminatural environments is challenging because many microbial populations experience variable selection. The majority of rhizobial bacteria are found in the soil. However, they also live symbiotically inside nodules of legume hosts and each nodule can release thousands of daughter cells back into the soil. We tested how past selection (i.e., legacies) by two plant genotypes and by the soil alone affected selection and genetic diversity within a population of 101 strains of Ensifer meliloti. We also identified allelic variants most strongly associated with soil- and host-dependent fitness. In addition to imposing direct selection on rhizobia populations, soil and host environments had lasting effects across host generations. Host presence and genotype during the legacy period explained 22% and 12% of the variance in the strain composition of nodule communities in the second cohort, respectively. Although strains with high host fitness in the legacy cohort tended to be enriched in the second cohort, the diversity of the strain community was greater when the second cohort was preceded by host rather than soil legacies. Our results indicate the potential importance of soil selection driving the evolution of these plant-associated microbes.
Bibliographical noteFunding Information:
LTB and PT designed and conducted the experiment, BE and LTB analyzed the data, LTB took the lead in writing the manuscript, and PT and BE provided extensive input on content and writing throughout. We thank Matt Nelson for creating the synthetic communities, Joseph Guhlin for bioinformatic assistance, Margaret Taylor for leading the plant benefit experiment, and the Minnesota Supercomputing Institute for facilitating analyses. This work was supported by the National Science Foundation under Grant Numbers IOS-1237993 and IOS-1724993, and USDA-HATCH Award MIN-71-030. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Illumina short read sequences are available on NCBI (pools: accession nos. SRR6029825? SRR6029912, individual strains: accession nos. under accession numbers SRR6055493 to SRR6055593 (https://www.ncbi.nlm.nih.gov/sra) under BioProject PRJNA401434. Phenotypic data, strain frequencies, and all major scripts used to analyze the data and generate figures are available via Dryad (https://doi.org/10.5061/dryad.qf36gd4).
© 2019 The Author(s). Evolution © 2019 The Society for the Study of Evolution.
- Ensifer (Sinorhizobium) meliloti
- Medicago truncatula
- facultative mutualism
- fitness correlations
- microbial evolution
- selective legacy