Location: Plant Science Research
Project Number: 5062-21500-001-039-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Sep 1, 2026
End Date: Aug 31, 2027
Objective:
(1) Analyze data from the cooperator (LTARN) study to identify microbial taxa and community signatures of alfalfa versus alternative rotation crops on corn-associated microbiomes; (2) use shotgun metagenomic sequencing on a prioritized subset of rhizosphere samples to identify functional pathways and metagenome-assembled genomes (MAGs) associated with crop rotations; and (3) cultivate and test alfalfa-driven microbial taxa for beneficial functions as members of existing and novel synthetic communities (SynComs).
Approach:
Initial amplicon data has been collected from the LTARN study from early-season corn (~2 weeks post-emergence) plots following alfalfa, wheat, and soybean. These data will be analyzed using existing or further improved bioinformatic pipelines to table of amplicon sequence variants (ASVs). Cutting-edge statistical approaches will be used to test for differences in microbial community composition, diversity, and differentially abundant taxa associated with different rotation crops. Based on these results, additional metagenomic sequencing will be performed on a target subset of rhizosphere samples and processed using existing tools to identify metagenome features and MAG signatures of different rotations. Finally, rhizosphere and root-associated bacteria will be cultivated from corn seedlings following alfalfa using standard or high-throughput cultivation approaches and prioritized based on enrichment following alfalfa in metagenomic analyses. Target taxa will be characterized and integrated into existing beneficial SynComs and evaluated for their impacts on plant nutrient uptake and disease suppression.
The cooperator has a consortium of seven bacterial strains isolated from corn roots that confers numerous plant health benefits. Additional strains from the above experiments from corn seedlings, following alfalfa rotation, could enhance disease suppression or other beneficial traits related to nutrient uptake. We will use the refined community to test against other corn pathogens, such as Rhizoctonia solani, Fusarium graminearum, and Fusarium subglutinans, as well as other oomycete pathogens that cause root rot in corn.