Mallory Choudoir
Asst Professor
and Extension Specialist
Plant and Microbial Biology
Thomas Hall 4550A
[email protected]Bio
Agroecosystems harbor microbial communities with immense diversity, and these microbiomes link soils to food systems. Our group focuses on the ecological and evolutionary processes driving plant-soil-microbe interactions in North Carolina agroecosystems, and our work supports the NC State Extension mission.
Climate change, intensive agriculture practices, and the increasing demands of food systems threaten soil microbiome biodiversity and their important ecosystem functions. At the same time, microbial solutions to agronomic challenges can support sustainability goals! Our research impacts decisions about land management, cropping systems, and nutrient inputs to prioritize soil microbiome resilience and stability and to maximize crop productivity.
Education
Ph.D. Microbiology Cornell University
B.S. Microbiology University of Wisconsin-Madison
Area(s) of Expertise
- Microbial ecology & evolution
- Soil ecology
- Plant-soil-microbe interactions
- Agroecosystems
Global change biology
- Biogeography, genomics, environmental & social justice
Publications
-
Investigating
GERMs : how genotype, environment, and rhizosphere microbiome interactions underlie heat response in maize and sorghum , New Phytologist (2026) - Microbiome stewardship: definition and guiding principles for implementation , Sustainable Microbiology (2026)
- Draft genomes of six Streptomyces species from a United States biogeography survey , Microbiology Resource Announcements (2025)
- High-quality draft genome sequences of seven Ralstonia spp. isolated from temperate forest soils , Microbiology Resource Announcements (2025)
- Investigating GERMs: How Genotype, Environment, and Rhizosphere Microbiome interactions underlie heat response in maize and sorghum , bioRxiv (Cold Spring Harbor Laboratory) (2025)
- Pangenomes suggest ecological-evolutionary responses to experimental soil warming , mSphere (2025)
- The case for microbiome stewardship: what it is and how to get there , mSystems (2025)
- High-quality draft genome sequence of Paenibacillus sp. RC80, a candidate for biofuel production , Microbiology Resource Announcements (2024)
- Seasonal effects of long-term warming on ecosystem function and bacterial diversity , PLoS ONE (2024)
- Complete genome sequence of Bacillus thuringiensis strain RC340, isolated from a temperate forest soil sample in New England , Microbiology Resource Announcements (2023)
Grants
Commercial microbial inoculants capitalize on the beneficial relationships between crops and their microbiomes (i.e. diverse microbial communities living on and inside plant tissues). While agricultural microbiome engineering is a promising strategy for maximizing crop productivity, efficacy data for determining profitability is highly variable or missing. Without relevant, high-quality, and unbiased field efficacy evaluations, North Carolina soybean producers face challenging production decisions while navigating the commercial market of microbial inoculants. This project will support the installation of replicated small plot efficacy trials at multiple sites in the Coastal Plains and the Piedmont. We also lack robust mechanistic data describing how these microbial inoculants drive crop yield metrics in field conditions, or how these mechanisms may differ across yield environments and cropping varieties. This project will also support a microbiome evaluation to increase our mechanistic understanding of microbial inoculants. We will compare soybean microbiomes across inoculant treatments and field sites to quantify the relationships between agricultural microbiomes and yield metrics. We will extend efficacy results and microbiome analyses to North Carolina soybean producers, Extension Agents, and agricultural industry partners. Together, efficacy and a mechanistic activity data will support North Carolina soybean producers in production decisions to maximize profitability.