ScholarWorks

ScholarWorks is an open access repository for the capture of the intellectual work of Montana State University (MSU) in support of its teaching, research and service missions. MSU ScholarWorks is a central point of discovery for accessing, collecting, sharing, preserving, and distributing knowledge to the Montana State University community and the world.

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Seismic shifts in the geochemical and microbial composition of a Yellowstone aquifer
(Oxford University Press, 2025-10)
Boyd, Eric S.
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Colman, Daniel R.
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Menchaca, Ana
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Spietz, Rachel L.
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Shoemaker, Anna
Seismic energy, like that released by earthquakes, can fracture rock and thereby alter subsurface fluid flow paths, release substrates from inclusions, and expose fresh mineral surfaces capable of reacting with water. However, it is unclear how such seismic-induced changes influence microbial communities. Volcanically active areas experience frequent seismic activity and thus represent ideal locations to examine the influence of seismic-induced geochemical change on subsurface microbial communities. Here, we demonstrate that energy released in an earthquake swarm in 2021 correlated with extensive temporal change in the geochemical and microbial composition of aquifer fluids sampled from ∼100 m depth in a borehole in Yellowstone National Park. Increased energy absorbed at the borehole over time was correlated with increased concentrations of hydrogen, dissolved organic carbon, and sulfide and was associated with depletion of δ13C in dissolved organic carbon, increased concentrations of cells, and increased abundances of chemolithotrophic, putative hydrogen-oxidizing Dethiobacteraceae and Desulfotomaculum bacteria. Dissipation of the earthquake swarm was associated with decreased concentrations of hydrogen, sulfide, and cells. These results suggest the subsurface biosphere dynamically responds to seismic-induced geochemical change at the level of activity and growth. Laboratory mechanical comminution of rhyolite, the primary bedrock in Yellowstone, released organic carbon and hydrogen and generated hydrogen when exposed to water. This indicates the presence of a large subsurface reservoir of organic carbon and hydrogen that can be released or generated by seismic induced bedrock fracturing. Taken together, these data indicate seismic-induced generation of chemical disequilibria can support the persistence of complex subsurface microbiomes.
GacA uses two distinct regulatory mechanisms to control the biosynthesis of 2,4-diacetylphloroglucinol in Pseudomonas protegens Pf-5
(American Society for Microbiology, 2025-11)
Purnamasari, Maria
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Ritu, Marjana
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Wu, Xiaogang
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Tripet, Brian
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Yan, Qing
Antibiotic 2,4-diacetylphloroglucinol (DAPG) is produced by many plant-associated beneficial bacteria of the Pseudomonas genus and plays an important role in plant disease control due to its broad antimicrobial activity against different pathogens. DAPG biosynthesis is activated by the conserved GacA/GacS two-component regulatory system. Here, we report that a ΔgacA mutant of Pseudomonas protegens Pf-5, lacking both DAPG production and pathogen inhibition in culture, controlled pea Aphanomyces root rot in a DAPG-dependent manner in the greenhouse. DAPG production of the ΔgacA mutant could be restored by exogenous phloroglucinol (PG), the first intermediate in DAPG biosynthesis, by culturing the ΔgacA mutant with either PG or PG-producing bacteria. We identified a new Gac-dependent promoter of phlD. Gene expression assays demonstrated that GacA is required to activate the phlD promoter. In vitro binding assays showed that the RNA-binding protein RsmE bound directly to the leader mRNA of phlA, another DAPG biosynthetic gene converting PG into DAPG, indicating that GacA regulates phlA expression post-transcriptionally. No detectable binding activity was observed between RsmE and the phlD leader mRNA. These results show that GacA regulates DAPG biosynthesis at multiple steps via different mechanisms and elucidate a novel layer of Gac-Rsm regulation in secondary metabolism. Targeted PG supplementation and/or partner microbe interactions may help to enhance the disease control efficacy and stability of the DAPG-producing bacteria.
Decomposable Neural Symbolic Regression
(TMLR, 2026)
Morales, Giorgio
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Sheppard, John W.
Symbolic regression (SR) models complex systems by discovering mathematical expressions that capture underlying relationships in observed data. However, most SR methods prioritize minimizing prediction error over identifying the governing equations, often producing overly complex or inaccurate expressions. To address this, we present a decomposable SR method that generates interpretable multivariate expressions leveraging transformer models, genetic algorithms (GAs), and genetic programming (GP). In particular, our explainable SR method distills a trained "opaque'' regression model into mathematical expressions that serve as explanations of its computed function. Our method employs a Multi-Set Transformer to generate multiple univariate symbolic skeletons that characterize how each variable influences the opaque model's response. We then evaluate the generated skeletons' performance using a GA-based approach to select a subset of high-quality candidates before incrementally merging them via a GP-based cascade procedure that preserves their original skeleton structure. The final multivariate skeletons undergo coefficient optimization via a GA. We evaluated our method on problems with controlled and varying degrees of noise, demonstrating lower or comparable interpolation and extrapolation errors compared to two GP-based methods, three neural SR methods, and a hybrid approach. Unlike these methods, our approach consistently learned expressions that matched the original mathematical structure. Similarly, our method achieved both a high symbolic solution recovery rate and competitive predictive performance relative to benchmark methods on the Feynman dataset.
Rural Active Living: A Call to Action 2.0, 10-Year Review and Recommendations to Advance the Field
(Lippincott Williams & Wilkins, 2025-11)
Umstattd Meyer, M. Renée
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Wende, Marilyn E.
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Stroope, Jessica
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Kellstedt, Debra K.
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Johnson, Ashleigh M.
Context & Objective: Written a decade ago, the 2015 Rural Active Living: A Call to Action (published in 2016) described rural-specific efforts in the fields of active living and physical activity (PA) and identified 8 recommendations to guide rural active living research and practice. Given that rural populations continue to experience a higher burden of PA-related chronic health conditions, the objective of this review was to revisit the 8 Rural Active Living Calls to Action, reassess the evidence base, summarize advances in each area, and identify emerging areas that warrant examination or further study. Methods: We leveraged expertise from researchers and practitioners within the CDC-funded Physical Activity Policy Research and Evaluation Network Rural Active Living Workgroup and reviewed literature published since the original call to action. Teams were formed for each of the original 8 calls to action. Each team reviewed the literature, synthesized findings, and developed recommendations for future research. Results: Academic and practice-based progress was evident across multiple of the original calls to action. Despite these findings, the need persists for rural-specific national surveillance data scaled to small geographies (census tract and block group) that accounts for differences within and across rural communities, various forms of rural governance, and how these factors interplay with active living opportunities. Six emerging areas of research (best practices, social issues, COVID-19 effects, collaboration, implementation science, and implications of rural health-related funding changes) are discussed and warrant further study. Conclusions: In summarizing progress since the original Call to Action, we recommend strategies to continue advancing rural active living and identify emerging focus areas.
Nature’s Kidneys: The Role of Wetland Reserve Easements in Restoring Water Quality
(University of Chicago Press, 2025-10)
Karwowski, Nicole
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Skidmore, Marin
Billions of dollars have been dedicated to mitigating nonpoint source pollution from US agriculture. Wetlands provide an ex post natural solution by filtering sediments and excess nutrients from the landscape. Quantifying the impact of wetland easements in the Wetland Reserve Program (WRP) and Agricultural Conservation Easement Program (ACEP) on water quality is critical for optimal fund allocation for nonpoint source pollution abatement. We causally identify whether newly restored wetlands reduce nitrogen and phosphorus loads at the subwatershed level in the Mississippi River Basin. Results show that wetland easements reduce ammonia and total Kjeldahl nitrogen concentrations in the local subwatershed as well as downstream. A short-term increase in local phosphorus immediately following restoration likely reflects soil disturbance. While wetlands have no significant long-term impact on local phosphorus levels, downstream reductions are observed. We estimate that this federal investment in natural infrastructure leads to lower treatment costs for local water systems.