Soil microbiome disruption reveals specific and general plant-bacterial relationships in three agroecosystem soils

Authors: DILEGGE, MICHAEL - Colorado State University; Manter, Daniel; VIVANCO, JORGE - Colorado State University

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/28/2022
Publication Date: 11/16/2022
Citation: DiLegge, M.J., Manter, D.K., Vivanco, J.M. 2022. Soil microbiome disruption reveals specific and general plant-bacterial relationships in three agroecosystem soils. PLOS ONE. 17(11). Article e0277529. https://doi.org/10.1371/journal.pone.0277529.
DOI: https://doi.org/10.1371/journal.pone.0277529

Interpretive Summary: Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, which often results in increase crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members within the soil microbiome. Here, we applied soil microbiome disruption, in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abundances of Pseudomonas and Sporocytophaga, regardless of the disrupted soil in which it was grown. Whereas the promotion of Bosea, Dyadobacter and Luteoliobacter was shared by all crops grown in all disrupted soils. In summary, soil disruption followed by crop introduction amplified plant-mediated selection of plant benefiting bacterial genera. This information is critical to our understanding of the controls on soil microbial communities including the degree and time required for plant-mediated shifts to occur.

Technical Abstract: Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, which often results in increase crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members within the soil microbiome. Here, we applied soil microbiome disruption, in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abundances of Pseudomonas and Sporocytophaga, regardless of the disrupted soil in which it was grown. Whereas the promotion of Bosea, Dyadobacter and Luteoliobacter was shared by all crops grown in all disrupted soils. In summary, soil disruption followed by crop introduction amplified plant-mediated selection of plant benefiting bacterial genera.