Refining the root-associated microbial consortia for enhanced biocontrol of the root-rot pathogen of corn

Authors: KAKI, PRANAYA - University Of Minnesota; Schlatter, Daniel; KHOKHANI, DEVANSHI - University Of Minnesota

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/26/2026
Publication Date: 4/10/2026
Citation: Kaki, P., Schlatter, D.C., Khokhani, D. 2026. Refining the root-associated microbial consortia for enhanced biocontrol of the root-rot pathogen of corn. Frontiers in Microbiology. 17. Article 1714069. https://doi.org/10.3389/fmicb.2026.1714069.
DOI: https://doi.org/10.3389/fmicb.2026.1714069

Interpretive Summary: Biological control via rhizosphere microbiota may provide an environmentally friendly alternative to fungicides to effectively control soilborne diseases, but efficacy can be highly variable due to the complexity of microbial interactions in soil environments. Synthetic communities of taxa with known interactions, rather than single strain inoculants, allow for a more realistic yet tractable means to provide more consistent biocontrol. ARS and university scientists modified a consortium of core corn-associated microbes to provide enhanced disease control, characterized their dynamics over time, and designed a highly effective, reduced consortium that controls corn root disease and promotes plant growth. This work indicates that simplified consortia that provide key functions, rather than highly complex communities, can be designed to provide robust and consistent biocontrol solutions to soilborne diseases.

Technical Abstract: Microbial consortia play a crucial role in plant protection by suppressing soil-borne pathogens. A previously studied root-associated microbial consortium consisting of seven bacterial strains (C7) demonstrated biocontrol activity against the seedling blight disease in corn caused by Fusarium verticillioides. To enhance its biocontrol potential, we incorporated a free-living bacterial strain (S8) exhibiting biocontrol activity, forming a modified community (C8). We evaluated the biocontrol efficacy of S8, C7, and C8 against four major corn pathogens: Pythium torulosum, Fusarium graminearum, Fusarium subglutinans, and Rhizoctonia solani. Plate assays revealed that S8 and C8 exhibited the highest inhibition against P. torulosum (>65% growth inhibition) but were less effective against Fusarium species (25–30%), while none of the communities restricted R. solani growth. In pot assays, under growth chamber conditions, S8 alone exhibited superior pathogen suppression compared to C7 and C8.; Hhowever, integrating S8 into C7 did not enhance overall biocontrol efficacy. Community analysis via 16S amplicon sequencing revealed no significant shifts in C7 community strain abundance upon S8 introduction, suggesting a lack of establishment of S8 into the C7 community. Given that some individual strains exhibited stronger pathogen suppression than C7 and had variable effects on root biomass and plant height, we designed three sub-communities (SC1, SC2, SC3) based on the highest inhibitory activity. Pot assays revealed that inoculation with SC1 and SC2 restored the plant height and root biomass, suggesting biocontrol efficacy is driven by specific strain combinations within the entire broader synthetic community.