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Negotiating mutualism: a locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts

Citation

Wendlandt, Camille et al. (2022), Negotiating mutualism: a locus for exploitation by rhizobia has a broad effect size distribution and context-dependent effects on legume hosts, Dryad, Dataset, https://doi.org/10.5061/dryad.bk3j9kdf9

Abstract

In mutualisms, variation at genes determining partner fitness provides the raw material upon which coevolutionary selection acts, setting the dynamics and pace of coevolution. However, we know little about variation in the effects of genes that underlie symbiotic fitness in natural mutualist populations. In some species of legumes that form root nodule symbioses with nitrogen-fixing rhizobial bacteria, hosts secrete nodule-specific cysteine-rich (NCR) peptides that cause rhizobia to differentiate in the nodule environment. However, rhizobia can cleave NCR peptides through the expression of genes like the plasmid-borne Host range restriction peptidase (hrrP), whose product degrades target NCR peptides. Although hrrP activity can confer host exploitation by depressing host fitness and enhancing symbiont fitness, the effects of hrrP on symbiosis phenotypes depend strongly on the genotypes of the interacting partners. However, the effects of hrrP have yet to be characterized in a natural population context, so its contribution to variation in wild mutualist populations is unknown. To understand the distribution of effects of hrrP in wild rhizobia, we measured mutualism phenotypes conferred by hrrP in 12 wild Ensifer medicae strains. To evaluate context dependency of hrrP effects, we compared hrrP effects across two Medicago polymorpha host genotypes and across two experimental years for five E. medicae strains. We show for the first time in a natural population context that hrrP has a wide distribution of effect sizes for many mutualism traits, ranging from strongly positive to strongly negative. Furthermore, we show that hrrP effect size varies across both host genotype and experiment year, suggesting that researchers should be cautious about extrapolating the role of genes in natural populations from controlled laboratory studies of single genetic variants.

Methods

We genetically disrupted the hrrP locus in 12 wild Mesorhizobium strains and inoculated the wildtype (hrrP+) and knockout mutant (hrrP-) strains onto a single genotype of Medicago polymorpha plants in greenhouse conditions. We collected data on the reproductive fitness of the wildtype and knockout mutant strains in nodules (2018_knockout_CFU_data.csv) and on plant response traits such as shoot mass and nodule count (2018_knockout_greenhouse_data.csv). In a second year, we used a subset of 5 wildtype and knockout mutant strains and inoculated them onto two genotypes of M. polymorpha in greenhouse conditions. We measured reproductive fitness of rhizobia in nodules (2019_GxG_knockout_CFU_data_330plants.csv) and plant response traits (2019_GxG_knockout_CFU_data_330plants.csv).

Usage Notes

We provide four datasets as csv files and one R code file that contains code for analyzing the data in these files. See the "README" file for metadata for each dataset. The contents of each file are as follows:

* 2018_knockout_CFU_data.csv contains nodule culturing data (counts of colony forming units) from the 2018 Knockout Experiment

* 2018_knockout_greenhouse_data.csv contains plant harvest data from the 2018 Knockout Experiment

* 2019_GxG_knockout_CFU_data_330plants.csv contains nodule culturing data (counts of colony forming units) from the 2019 GxG Knockout Experiment

* 2019_GxG_knockout_greenhouse_data_330plants.csv contains plant harvest data from the 2019 GxG Knockout Experiment

* Wendlandt_et_al_2022_JEvolBiol_code.R contains R code for importing, processing, and analyzing data from the above four datasets. It also contains code for producing figures from these data.

Funding

National Science Foundation, Award: DEB-1355216

National Science Foundation, Award: IOS-1755454

National Science Foundation, Award: DEB-1943239