Mallory Choudoir

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. 

Find more information on our lab webpage.

View publications on Google Scholar.

Area(s) of Expertise

Microbial ecology & evolution, soil ecology, plant-soil-microbe interactions, agroecosystems, global change biology, biogeography, genomics, environmental & social justice

Publications

• High-quality draft genome sequences of seven Ralstonia spp. isolated from temperate forest soils , MICROBIOLOGY RESOURCE ANNOUNCEMENTS (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)
• Draft genome sequence of Paenibacillus sp. strain RC67, an isolate from a long-term forest soil warming experiment in Petersham, Massachusetts , MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2023)
• High-quality genomes of Paenibacillus spp. RC334 and RC343, isolated from a long-term forest soil warming experiment , MICROBIOLOGY RESOURCE ANNOUNCEMENTS (2023)
• Pangenomes reveal genomic signatures of microbial adaptation to experimental soil warming , (2023)
• A framework for integrating microbial dispersal modes into soil ecosystem ecology , iScience (2022)