A reproducible and tunable synthetic soil microbial community provides new insights into microbial ecology

Abstract

AbstractMicrobial soil communities form commensal relationships with plants to promote the growth of both parties. Optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model community of 17 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for use with fabricated ecosystem devices (EcoFABs). EcoFABs allow reproducible research in model plant systems, with precise control of environmental conditions and easy measurement of plant-microbe metrics. The model soil community grows reproducibly in vitro between replicates and experiments, with high community α-diversity achieved through growth in low-nutrient media and adjustment of starting composition ratios for the growth of individual organisms. The community additionally grows in EcoFAB devices and regrows with a similar composition to unfrozen communities following cryopreservation with glycerol, allowing for dissemination of the model community. Our results demonstrate the generation of a stable microbial community that can be used with EcoFAB devices and shared between research groups for maximum reproducibility.ImportanceMicrobes associate with plants in distinct soil communities, to the benefit of both the soil microbes and the plant. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 17 soil bacteria has been developed to further reproducible study of plant-soil microbe interactions. Preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through optimization of a robust, reproducible model community.