期刊
出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.2201285119
关键词
Arabidopsis thaliana; genome-wide association study; microbiome; fitness; microbial hubs
资金
- National Health Institute [R01 GM 083068]
- Dropkin Foundation Fellowship
- University of Chicago
- European Union [267196]
- Biological Sciences Division at the University of Chicago
- Institute for Translational Medicine
- CTSA Grant from NIH [UL1 TR000430]
- New York University
- genotoul bioinformatics platform Toulouse Occitanie, France (Bioinfo Genotoul)
- Bordeaux Bioinformatics Center at the University of Bordeaux, France
Host genetic variation has consistent effects on microbial communities, impacting plant fitness. Specific microbial species are preferentially associated with certain genotypes, and the interactions between host genes and microbes significantly affect seed production in plants.
Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200 Arabidopsis thaliana genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial species (operational taxonomic unit [OTUs]). Host genetic effects disproportionately influenced central ecological hubs, with heritability of particular OTUs declining with their distance from the nearest hub within the microbial network. These host effects could reflect either OTUs preferentially associating with specific genotypes or differential microbial success within them. Host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins, and the immune system. Using untargeted metabolomics, we corroborate the consistent association between variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host genetic variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.
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