About

Mallory Choudoir is an Assistant Professor and Extension Specialist in Microbiology at North Carolina State University. Her research focuses on agroecosystems, specifically on microbial communities within soils and their links to food systems. Her group investigates the ecological and evolutionary processes that drive plant-soil-microbe interactions in North Carolina agroecosystems, supporting the NC State Extension mission. Her work addresses the impacts of climate change, intensive agriculture practices, and increasing food system demands on soil microbiome biodiversity and ecosystem functions. Additionally, her research aims to identify microbial solutions to agronomic challenges to promote sustainability, soil microbiome resilience, and crop productivity.

Research topics

• Political Science
• Sociology
• Biology
• Social Science
• Ecology
• Organic chemistry
• Environmental science
• Environmental chemistry
• Engineering
• Environmental ethics
• Soil science
• Chemistry
• Business
• Genetics

Selected publications

• High-quality draft genome sequences of seven <i>Ralstonia</i> spp. isolated from temperate forest soils

  Microbiology Resource Announcements · 2025-04-14

  articleOpen access

  ABSTRACT We report seven highquality draft genomes of Ralstonia spp. isolated from the Harvard Forest Long-Term Warming Experimental plots: four de novo hybrid assemblies and three de novo long-read assemblies. The genomes have a minimum estimated completeness of 92.6% and an average GC content of 63.45%.

  PublisherDOI

• Draft genomes of six <i>Streptomyces</i> species from a United States biogeography survey

  Microbiology Resource Announcements · 2025-12-08

  articleOpen access

  ABSTRACT Streptomyces bacteria play key ecological and functional roles in terrestrial ecosystems. We surveyed soil samples across the continental United States, identifying six novel Streptomyces species. Here, we report the whole genome sequences of these strains and their predicted biosynthetic products, providing additional information for studying biological and chemical diversity in this ubiquitous species.

  PublisherDOI

• Pangenomes suggest ecological-evolutionary responses to experimental soil warming

  mSphere · 2025-03-19 · 2 citations

  articleOpen access1st authorCorresponding

  ABSTRACT Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing in situ soil warming experiment where, for over three decades, temperate forest soils are continuously heated at 5°C above ambient. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing dominant taxa sensitive to warming, including lineages of Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. We investigated genomic attributes and functional gene content to identify signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation, with few functional annotations explicitly associated with long-term warming. Trends in functional gene patterns suggest genomes from heated plots were relatively enriched in central carbohydrate and nitrogen metabolism pathways, while genomes from control plots were relatively enriched in amino acid and fatty acid metabolism pathways. We observed that genomes from heated plots had less codon bias, suggesting potential adaptive traits related to growth or growth efficiency. Codon usage bias varied for organisms with similar 16S rrn operon copy number, suggesting that these organisms experience different selective pressures on growth efficiency. Our work suggests the emergence of lineage-specific trends as well as common ecological-evolutionary microbial responses to climate change. IMPORTANCE Anthropogenic climate change threatens soil ecosystem health in part by altering below-ground carbon cycling carried out by microbes. Microbial evolutionary responses are often overshadowed by community-level ecological responses, but adaptive responses represent potential changes in traits and functional potential that may alter ecosystem function. We predict that microbes are adapting to climate change stressors like soil warming. To test this, we analyzed the genomes of bacteria from a soil warming experiment where soil plots have been experimentally heated 5°C above ambient for over 30 years. While genomic attributes were unchanged by long-term warming, we observed trends in functional gene content related to carbon and nitrogen usage and genomic indicators of growth efficiency. These responses may represent new parameters in how soil ecosystems feedback to the climate system.

  PublisherDOI

• Investigating GERMs: How Genotype, Environment, and Rhizosphere Microbiome interactions underlie heat response in maize and sorghum

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-10

  preprintOpen access

  Plant resistance to heat stress can be modelled by variation attributable to the genotype, environment, the rhizosphere microbiome, and their interactions. Using this Genotype × Environment × Rhizosphere Microbiome (GERMs) model, we studied three cereal genotypes: two inbred maize lines with contrasting heat sensitivity, and a sorghum inbred that displayed moderate heat tolerance. Plants were grown under optimal and heat stressed conditions across two soil treatments. We developed a systems-level metatranscriptomics approach to examine both plant and microbial transcriptomic profiles and integrated them with microbiome compositional data and plant phenotypes. We compared our strategy to amplicon profiling and found that our metatranscriptomic strategy offers greater functional and taxonomic resolution, allowing us to characterize active microbial pathways and analyze them jointly with plant gene expression profiles within a single system. We show that the microbiome functional profile is driven by host genotype and environmental factors and can enhance plant resilience. Our analyses identified plant genes and microbial pathways consistently associated with heat tolerance and key host-microbe interactions. Specifically, we identified D-amino acid metabolism as a plausible mechanism underlying a synergistic response to heat stress. These results demonstrate that the rhizosphere microbiome is not a passive component but an active participant in plant responses to abiotic stress. This work offers a new perspective on cereal adaptation to high temperatures and underscores the utility of the GERMs framework for dissecting functional relationships among plant genotype, environment, and the rhizosphere microbiome.

  PublisherDOI

• The case for microbiome stewardship: what it is and how to get there

  mSystems · 2025-04-16 · 4 citations

  articleOpen access1st authorCorresponding

  Microbiomes are essential for human, animal, plant, and ecosystem health. Despite widespread recognition of the importance of microbiomes, there is little attention paid to monitoring and safeguarding microbial ecologies on policy levels. We observe that microbiomes are deteriorating owing to practices at societal levels such as pesticide use in agriculture, air and water pollution, and overuse of antibiotics. Potential policy on these issues would cross multiple domains such as public health, environmental protection, and agriculture. We propose microbiome stewardship as a foundational concept that can act across policy domains to facilitate healthy microbiomes for human and ecosystem health. We examine challenges to be addressed and steps to take toward developing meaningful microbiome stewardship.

  PublisherDOI

• High-quality draft genome sequence of <i>Paenibacillus</i> sp. RC80, a candidate for biofuel production

  Microbiology Resource Announcements · 2024-06-07

  articleOpen access

  sp. RC80 was isolated from temperate deciduous forest soil in New England. The assembled genome is a single contig with 5,977,337 bp and 97.15% estimated completion. RC80 contains features for 2,3-butanediol dehydrogenase production and pathways involved in ethanol production.

  PublisherDOI

• Seasonal effects of long-term warming on ecosystem function and bacterial diversity

  PLoS ONE · 2024-10-24 · 4 citations

  articleOpen access

  Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained within ecosystems under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5°C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having a higher intercept than summer samples in our model, suggesting a higher overall baseline of ecosystem function in the fall. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial evenness in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community evenness.

  PublisherDOI

• Seasonal effects of long-term warming on ecosystem function and bacterial diversity

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-08-15

  preprintOpen access

  1 Abstract Across biomes, soil biodiversity promotes ecosystem functions. However, whether this relationship will be maintained under climate change is uncertain. Here, using two long-term soil warming experiments, we investigated how warming affects the relationship between ecosystem functions and bacterial diversity across seasons, soil horizons, and warming duration. Soils were sampled from these warming experiments located at the Harvard Forest Long-Term Ecological Research (LTER) site, where soils had been heated +5 °C above ambient for 13 or 28 years at the time of sampling. We assessed seven measurements representative of different ecosystem functions and nutrient pools. We also surveyed bacterial community diversity. We found that ecosystem function was significantly affected by season, with autumn samples having higher function than summer samples. The effect of warming on bacterial diversity was similarly affected by season, where warming in the summer was associated with decreased bacterial evenness in the organic horizon. Despite the decreased bacterial diversity in the warmed plots, we found that the relationship between ecosystem function and bacterial diversity was unaffected by warming or warming duration. Our findings highlight that season is a consistent driver of ecosystem function as well as a modulator of climate change effects on bacterial community diversity.

  PublisherOA PDFDOI

• Draft genome sequence of <i>Paenibacillus</i> sp. strain RC67, an isolate from a long-term forest soil warming experiment in Petersham, Massachusetts

  Microbiology Resource Announcements · 2023-10-12

  articleOpen access

  sp. strain RC67 was isolated from the Harvard Forest long-term soil warming experiment. The assembled genome is a single contig with 7,963,753 bp and 99.4% completion. Genome annotation suggests that the isolate is of a novel bacterial species.

  PublisherDOI

• Complete genome sequence of <i>Bacillus thuringiensis</i> strain RC340, isolated from a temperate forest soil sample in New England

  Microbiology Resource Announcements · 2023-10-31

  articleOpen access

  ABSTRACT The complete genome sequence of Bacillus thuringiensis strain RC340, isolated from an environmental microbiology experiment soil sample is presented here. B. thuringiensis strain RC340 sequenced by GridION consists of a single genome consisting of 5.86 million bases, 8,152 predicted genes, and 0.23% contamination.

  PublisherDOI

Frequent coauthors

• Kristen M. DeAngelis

  University of Massachusetts Amherst

  17 shared

• Noah Fierer

  16 shared

• Luiz A. Domeignoz‐Horta

  Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

  14 shared

• Sam Rossabi

  Google (United States)

  12 shared

• Daniel H. Buckley

  11 shared

• Rachel Simoes

  University of Massachusetts Amherst

  10 shared

• Detlev Helmig

  NOAA Air Resources Laboratory

  8 shared

• Nipuni Dayarathne

  University of Massachusetts Amherst

  8 shared

Education

• Ph.D., Plant Pathology

  University of North Carolina at Chapel Hill

  2010

• M.S., Plant Pathology

  University of North Carolina at Chapel Hill

  2006

• B.S., Botany

  University of North Carolina at Chapel Hill

  2004