Abstract
Specific members of complex microbiota can influence host phenotypes, depending on both the abiotic environment and the presence of other microorganisms. Therefore, it is challenging to define bacterial combinations that have predictable host phenotypic outputs. We demonstrate that plant–bacterium binary-association assays inform the design of small synthetic communities with predictable phenotypes in the host. Specifically, we constructed synthetic communities that modified phosphate accumulation in the shoot and induced phosphate starvation–responsive genes in a predictable fashion. We found that bacterial colonization of the plant is not a predictor of the plant phenotypes we analyzed. Finally, we demonstrated that characterizing a subset of all possible bacterial synthetic communities is sufficient to predict the outcome of untested bacterial consortia. Our results demonstrate that it is possible to infer causal relationships between microbiota membership and host phenotypes and to use these inferences to rationally design novel communities.
Highlights
The composition of plant-associated microbial communities influences plant health and development [1][2]
We demonstrated that our Pi transitions were sufficient to induce a reconfiguration of plant exudate primary metabolic profiles (S1C and S1D Fig, and S1 Table). We tested whether these exudates modified the in vitro growth capacity of a collection of 440 bacterial strains isolated from the roots of Brassicaceae grown in soil that is not overtly Pi deficient ([28], S1B Fig, and Materials and methods 1c)
We identified a range of bacterial growth behaviors (Materials and methods 1f, 1g) and found that the bacterial growth differences between phosphate conditions are much weaker than the differences between strains (S2 Fig)
Summary
The composition of plant-associated microbial communities influences plant health and development [1][2]. A number of in vitro screening strategies are commonly applied to identify candidate plant-interacting microbes; none of the traits typically screened are correlated with a plant-beneficial outcome [5] Another common prescreening strategy involves performing plant–bacterium binary-association assays [6], but only a few have been successfully translated into agricultural settings [7][8][9], suggesting that these assays fail to capture critical aspects of nature’s complexity. We systematically evaluated the performance of a large collection of root bacterial isolates using in vitro screening and binary plant–bacterium association assays as predictors for the effect of derived bacterial consortia on plant phenotypes in response to phosphate starvation. Our results provide a useful road map from binary host–microbe assays to the design and testing of useful small consortia to predictably alter host phenotypes
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