Below is an overview of example projects from our lab. Detailed results are shared through peer-reviewed publications.
North Dakota Agricultural Microbiome Project
The North Dakota Agricultural Microbiome Project is a statewide effort to better understand the living biological communities that support agricultural soils. Although microbes play essential roles in nutrient cycling, plant health, and ecosystem stability, we still know surprisingly little about how these communities vary across real farms and how they influence crop performance. This project was designed to explore those questions by examining agricultural microbiomes across a wide range of soils, climates, and management practices in North Dakota.
Figure: Spatial patterns of soil bacterial diversity across North Dakota over time (unpublished).
Our lab sampled 201 agricultural fields across the state and collected bulk soil, rhizosphere, and root samples at three key time points of the growing season. In total, the project generated 1,809 samples. Each field was carefully characterized using detailed environmental data, including measurements of 31 soil properties, 14 weather variables, and information on crop management. To understand the biological communities, we use the Illumina NovaSeq 6000 to produce more than 300,000 high-quality ASVs and OTUs of bacteria, archaea, fungi, protists, and arbuscular mycorrhizal fungi. In addition to sequencing, we directly examined plant roots to measure colonization by mycorrhizal fungi using microscopy. This work generated more than 60,000 observations of root colonization, giving us a rare opportunity to link DNA-based microbial data with direct measurements of plant-microbe interactions. This provides a foundation for understanding how microbial communities assemble in farming systems, how they interact with plants and environmental conditions, and how they contribute to the resilience and productivity of agricultural ecosystems.
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Microbial Keystone Taxa and Community Stability
The microbial world is inherently complex, and microbial diversity alone is insufficient to explain the performance of entire communities. Keystone taxa are highly connected organisms that exert a disproportionate influence on microbiome structure and functioning irrespective of their abundance across space and time. These taxa play unique roles within microbial communities, and their removal can lead to dramatic shifts in community structure and functioning. There is growing interest in identifying such taxa and using this knowledge to develop predictive understanding of microbiome dynamics. Network analysis is a powerful statistical tool for identifying putative keystone taxa (see Publications for our recent articles).
While useful for generating hypotheses, predicting keystones solely from observational data and network-based scores must be complemented with empirical evidence demonstrating their impact on microbiome structure and performance. Our work focuses on stressed soils where we previously conducted network analyses to statistically identify candidate keystone taxa. To isolate these organisms, our lab uses high-throughput culturing to build large culture collections and construct synthetic communities (SynComs). We combine these resources with multi-omics and biotechnological tools to experimentally validate how keystone taxa influence microbiome stability.
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Environmental and Anthropogenic Stressors and Microbiome Dynamics
Environmental change and land-use intensification are rapidly reshaping ecosystems across agricultural and managed landscapes. Practices such as grazing, fertilization, pesticide application, and tillage alter soil properties, plant communities, and resource availability. At the same time, environmental stressors associated with global change, including drought and increasing soil salinity, impose additional pressures on plant and soil systems. Together, these anthropogenic and environmental drivers act as strong ecological filters that reshape microbial diversity and community structure in soils. They also influence how microbes are recruited from bulk soil into the rhizosphere and ultimately into roots, altering the composition of plant-associated microbiomes. In many cases, global change stressors can exacerbate the effects of
intensive management practices, further destabilizing plant-microbe interactions that regulate nutrient cycling, plant productivity, and ecosystem stability.
In our research, we investigate how gradients of environmental and anthropogenic stressors regulate plant and soil microbiome dynamics. We examine how management intensity and environmental conditions influence microbial diversity, community structure, and functional potential in soils and the rhizosphere, and how these changes determine which microbes successfully colonize plant roots. By integrating field experiments across environmental and management gradients with multi-omics approaches, we aim to uncover the mechanisms through which environmental change reshapes plant and soil microbiomes and to identify management strategies that sustain resilient ecosystems.
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Plant Invasion and Soil Microbiome Feedback
Biological invasions are a major driver of biodiversity loss and ecosystem transformation across terrestrial ecosystems. Invasive plant species can alter nutrient cycling, restructure plant communities, and modify ecosystem processes at landscape scales. While many invaders are known for their strong aboveground competitive traits, increasing evidence shows that their success is also shaped by interactions with soil microbial communities in the rhizosphere. These belowground interactions can influence nutrient acquisition, plant health, and plant-soil feedback, ultimately affecting the ability of invasive species to establish and dominate in new environments. In our research, we investigate how invasive plants alter soil microbiota during establishment in novel ecosystems, reshaping microbial community composition, diversity, and network structure in the rhizosphere. By integrating field studies, controlled experiments, and multi-omics approaches, we aim to uncover the microbial mechanisms that enable invasive species to establish, persist, and transform ecosystems.
