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Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally-occurring isolates of a model plant symbiont

View ORCID ProfileRebecca T. Batstone, View ORCID ProfileLiana T. Burghardt, View ORCID ProfileKaty D. Heath
doi: https://doi.org/10.1101/2021.07.19.452989
Rebecca T. Batstone
aCarl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801 USA
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  • For correspondence: rtbatstone@gmail.com
Liana T. Burghardt
bDepartment of Plant Science, The Pennsylvania State University, 103 Tyson Building, University Park, PA, 16802 USA
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Katy D. Heath
aCarl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801 USA
cDepartment of Plant Biology, University of Illinois at Urbana-Champaign, 286 Morrill Hall, 505 South Goodwin Avenue, Urbana, IL 61801 USA
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Abstract

Given the need to predict the outcomes of (co)evolution in host-associated microbiomes, whether microbial and host fitnesses tend to trade off, generating conflict, remains a pressing question. Examining the relationships between host and microbe fitness proxies at both the phenotypic and genomic levels can illuminate the mechanisms underlying interspecies cooperation and conflict. We examined naturally-occurring genetic variation in 191 strains of the model microbial symbiont, Ensifer meliloti, paired with each of two host Medicago truncatula genotypes in single- or multi-strain experiments to determine how multiple proxies of microbial and host fitness were related to one another and test key predictions about mutualism evolution at the genomic scale, while also addressing the challenge of measuring microbial fitness. We found little evidence for interspecies fitness conflict; loci tended to have concordant effects on both microbe and host fitnesses, even in environments with multiple co-occurring strains. Our results emphasize the importance of quantifying microbial relative fitness for understanding microbiome evolution and thus harnessing microbiomes to improve host fitness. Additionally, we find that mutualistic coevolution between hosts and microbes acts to maintain, rather than erode, genetic diversity, potentially explaining why variation in mutualism traits persists in nature.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • R.T.B., K.D.H, and L.T.B conceived of the work. R.T.B led the data analysis and drafted the article with guidance from K.D.H. and L.T.B., who also provided critical revisions and approved the final version for submission.

  • The authors declare no competing interests.

  • Feedback from second round of revision incorporated

  • https://github.com/rtbatstone/complex_genetics_of_symbiosis

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 25, 2022.
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Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally-occurring isolates of a model plant symbiont
Rebecca T. Batstone, Liana T. Burghardt, Katy D. Heath
bioRxiv 2021.07.19.452989; doi: https://doi.org/10.1101/2021.07.19.452989
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Phenotypic and genomic signatures of interspecies cooperation and conflict in naturally-occurring isolates of a model plant symbiont
Rebecca T. Batstone, Liana T. Burghardt, Katy D. Heath
bioRxiv 2021.07.19.452989; doi: https://doi.org/10.1101/2021.07.19.452989

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