Scholarly Work - Research Centers
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Item Compositional profiling of the rhizosphere microbiome of Canada thistle reveals consistent patterns across the United States northern Great Plains(Springer Science and Business Media LLC, 2024-08) Eberly, Jed O.; Hurd, Asa; Oli, Dipiza; Dyer, Alan T.; Seipel, Tim F.; Carr, Patrick M.Canada thistle is a pervasive perennial weed, causing challenges to agricultural and natural ecosystems globally. Although research has focused on the phenology, genetics, and control of Canada thistle, little is known about the rhizosphere microbiome and the role plant–microbe interactions play in invasion success. This study investigated the rhizosphere microbiome of Canada thistle across diverse climates, soils, and crops in the U.S. northern Great Plains. Soil and rhizosphere samples were collected and bacterial 16S and fungal ITS2 sequencing were performed to characterize the core microbiome and identify potential factors contributing to invasion success. Amplicon sequencing revealed a stable core microbiome that was detected in the Canada thistle rhizosphere across all locations. The core microbiome was dominated by the bacterial phyla Actinobacteriota and Proteobacteria and fungal phyla Ascomycota and Basidiomycota. Differential abundance analysis showed rhizosphere fungal communities were enriched in pathogen-containing genera with a 1.7-fold greater abundance of Fusaria and a 2.6-fold greater abundance of Gibberella compared to bulk soil. Predictive functional profiling showed rhizosphere communities were enriched (p < 0.05, FDR corrected) in plant pathogen fungal guilds which represented 19% of the fungal community. The rhizosphere microbiome was similar in composition across environments, highlighting the stable association between Canada thistle and specific microbial taxa. This study characterized the core microbiome of Canada thistle, and the findings highlight plant–microbe interactions shaping invasive behavior. These findings are important for understanding the ecological impacts of plant invasion and soil-microbe ecological processes.Item Long‐term soil change in the US Great Plains: An evaluation of the Haas Soil Archive(Wiley, 2024-06) Liebig, Mark A.; Calderon, Francisco J.; Clemensen, Andrea K.; Durso, Lisa; Duttenhefner, Jessica L.; Eberly, Jed O.; Halvorson, Jonathan J.; Jin, Virginia L.; Mankin, Kyle; Margenot, Andrew J.; Stewart, Catherine E.; Van Pelt, Scott; Vigil, Merle F.Diverse patterns of climate and edaphic factors challenge detection of soil property change in the US Great Plains. Because detectable soil change can take decades, insights into the trajectory of soil properties frequently require long-term site monitoring and, where available, associated soil archives to enable comparisons with initial or baseline states. Unfortunately, few multi-decadal soil change investigations have been conducted in this region. Here, we document effects of dryland cropping on a suite of soil properties by comparing matched historic (1947) and contemporary (2018) soil samples from the Haas Soil Archive at three sites in the US Great Plains: Moccasin, MT, Akron, CO, and Big Spring, TX. Current analytical methods were used to provide insight into changes in soil texture, pH, carbon, and micronutrients at 0- to 15.2-cm and 15.2- to 30.5-cm depths. Changes in direction and magnitude of soil properties over 71 years were site specific. Changes in textural class occurred at all sites, with Moccasin and Akron transitioning from loam to clay loam and Big Spring from sandy clay loam to sandy loam. The soil pH reaction class changed from slightly alkaline to moderately acid at Akron and slightly alkaline to moderately alkaline at Big Spring. At 0–15.2 cm, soil organic carbon decreased by 15% and 36% at Moccasin and Big Spring, respectively, but increased by 15% at Akron. Soil micronutrients generally declined at all sites. Weather-related variables derived from air temperature and precipitation records were not correlated with soil change. Inferred factors contributing to soil change included on-site management, inherent soil features, weather metrics not evaluated, or a combination thereof.Item Compositional profiling of the rhizosphere microbiome of Canada thistle reveals consistent patterns across the United States northern Great Plains(Springer Science and Business Media LLC, 2024) Eberly, Jed O.; Hurd, Asa; Oli, Dipiza; Dyer, Alan T.; Seipel, Tim F.; Carr, Patrick M.Canada thistle is a pervasive perennial weed, causing challenges to agricultural and natural ecosystems globally. Although research has focused on the phenology, genetics, and control of Canada thistle, little is known about the rhizosphere microbiome and the role plant–microbe interactions play in invasion success. This study investigated the rhizosphere microbiome of Canada thistle across diverse climates, soils, and crops in the U.S. northern Great Plains. Soil and rhizosphere samples were collected and bacterial 16S and fungal ITS2 sequencing were performed to characterize the core microbiome and identify potential factors contributing to invasion success. Amplicon sequencing revealed a stable core microbiome that was detected in the Canada thistle rhizosphere across all locations. The core microbiome was dominated by the bacterial phyla Actinobacteriota and Proteobacteria and fungal phyla Ascomycota and Basidiomycota. Differential abundance analysis showed rhizosphere fungal communities were enriched in pathogen-containing genera with a 1.7-fold greater abundance of Fusaria and a 2.6-fold greater abundance of Gibberella compared to bulk soil. Predictive functional profiling showed rhizosphere communities were enriched (p < 0.05, FDR corrected) in plant pathogen fungal guilds which represented 19% of the fungal community. The rhizosphere microbiome was similar in composition across environments, highlighting the stable association between Canada thistle and specific microbial taxa. This study characterized the core microbiome of Canada thistle, and the findings highlight plant–microbe interactions shaping invasive behavior. These findings are important for understanding the ecological impacts of plant invasion and soil-microbe ecological processes.Item Changes in Biological Soil Health Properties in Response to Increased Crop Diversity in a Dryland Wheat-Based Cropping System(Informa UK Limited, 2024-08) Eberly, Jed O.; Hammontree, Jenni W.; Fordyce, Simion I.; Jones, Clain A.; Carr, Patrick M.Diversifying wheat (Triticum aestivum L.)-based cropping systems is important for the sustainability of dryland agriculture. Research has focused on the agronomic benefits of increased crop diversity in semi-arid environments, but less is known about the impacts of increased crop diversity on the soil microbial community. This work compared soil health parameters between a continuous wheat crop sequence to a diverse sequence that included pea (Pisum sativum L.), proso millet (Panicum miliaceum L.), safflower (Carthamus tinctorius, L.), and spring wheat. Respiration was higher (p < .005) in the diverse sequence while activity of N-acetyl-β-d-glucosaminidase was lower (p < .05) with a mean rate of 26.3 and 16.3 mg ρ-nitrophenol kg−1 soil h−1 for the continuous wheat and diverse sequences, respectively. The mean net nitrogen mineralized during the growing season was 33.2 ± 2.5 kg ha−1 and was not different between treatments (p > .05). No difference was observed in bacterial alpha diversity, while fungal community diversity was 52% lower in the diverse rotation. The results of this work suggest that specific crops in a rotation may impact microbial processes related to nitrogen mineralization and that the soil fungal community may be more sensitive to changes in crop sequence than the soil bacterial community.Item Sentinel-2-based predictions of soil depth to inform water and nutrient retention strategies in dryland wheat(Elsevier BV, 2023-11) Fordyce, Simon I.; Carr, Patrick M.; Jones, Clain; Eberly, Jed O.; Sigler, W. Adam; Ewing, Stephanie; Powell, Scott L.The thickness or depth of fine-textured soil (zf) dominates water storage capacity and exerts a control on nutrient leaching in semi-arid agroecosystems. At small pixel sizes (< 1 m; ‘fine resolution’), the normalized difference vegetation index (NDVI) of cereal crops during senescence (Zadoks Growth Stages [ZGS] 90–93) offers a promising alternative to destructive sampling of zf using soil pits. However, it is unclear whether correlations between zf and NDVI exist (a) at larger pixel sizes (1–10 m; ‘intermediate resolution’) and (b) across field boundaries. The relationship of zf to NDVI of wheat (Triticum aestivum L.) was tested using images from a combination of multispectral sensors and fields in central Montana. NDVI was derived for one field using sensors of fine and intermediate spatial resolution and for three fields using intermediate resolution sensors only. Among images acquired during crop senescence, zf was correlated with NDVI (p < 0.05) independent of sensor (p = 0.22) and field (p = 0.94). The zf relationship to NDVI was highly dependent on acquisition day (p < 0.05), but only when pre-senescence (ZGS ≤ 89) images were included in the analysis. Results indicate that cereal crop NDVI of intermediate resolution can be used to characterize zf across field boundaries if image acquisition occurs during crop senescence. Based on these findings, an empirical index was derived from multi-temporal Sentinel-2 imagery to estimate zf on fields in and beyond the study area.Item Rumen microbiome response to sustained release mineral bolus supplement with low- and high-quality forages(Frontiers Media SA, 2023-06) Eberly, Jed O.; Wyffels, Samuel A.; Carlisle, Tanner J.; DelCurto, TimothyIntroduction: Limited forage quantity and quality are challenges faced in livestock production systems in semi-arid rangelands of the western United States, particularly when livestock face stressors such as cold weather or have increased nutritional requirements such as during pregnancy and lactation. To meet livestock nutrient requirements, producers frequently provide supplemental nutrition, however there is limited knowledge regarding the effects of these practices on the rumen microbiome in these environments. Methods: A study was conducted to evaluate changes in the rumen microbiome in response to high- and low- quality forage with sustained release mineral boluses. The study consisted of 16 ruminally-cannulated 2–3-year-old black angus cows fed high quality grass alfalfa hay or low-quality grass hay with a 90 or 180 day sustained release mineral bolus. Rumen samples were collected pre-feeding and 8 hours post feeding and bacterial 16S rRNA gene amplicons were sequenced from the rumen fluid. Results: Alpha diversity as measured by Shannon’s diversity index decreased significantly over time (p<0.01) and averaged 5.6 pre-feeding and 5.4 post- feeding and was not significantly different between high- and low-quality forages or between mineral bolus types (p>0.05). Principal coordinates analysis (PCoA) of the Bray-Curtis dissimilarity matrix showed distinct grouping by feed quality and time but not by mineral bolus type. Bacteroidetes and Firmicutes were the dominant phyla in all treatments and significant increases (p<0.05) in the relative abundance of the family Lachnospiraceae and the genus Prevotella were observed in high quality forage diets. Rumen VFA and NH3-N concentrations were also strongly associated with the high-quality forage diet. Predictive functional profiling indicated that functions associated with methanogenesis were negatively correlated with feed quality. Discussion: The results of this study suggest that mineral bolus type is unlikely to affect rumen bacterial community structure or function while forage quality can significantly alter community structure and predicted functions associated with methanogenesis and VFA production.Item Rumen microbiome response to sustained release mineral bolus supplement with low- and high-quality forages(Frontiers Media SA, 2023-06) Eberly, Jed O.; Wyffels, Samuel A.; Carlisle, Tanner J.; DelCurto, TimothyIntroduction: Limited forage quantity and quality are challenges faced in livestock production systems in semi-arid rangelands of the western United States, particularly when livestock face stressors such as cold weather or have increased nutritional requirements such as during pregnancy and lactation. To meet livestock nutrient requirements, producers frequently provide supplemental nutrition, however there is limited knowledge regarding the effects of these practices on the rumen microbiome in these environments. Methods: A study was conducted to evaluate changes in the rumen microbiome in response to high- and low- quality forage with sustained release mineral boluses. The study consisted of 16 ruminally-cannulated 2–3-year-old black angus cows fed high quality grass alfalfa hay or low-quality grass hay with a 90 or 180 day sustained release mineral bolus. Rumen samples were collected pre-feeding and 8 hours post feeding and bacterial 16S rRNA gene amplicons were sequenced from the rumen fluid. Results: Alpha diversity as measured by Shannon’s diversity index decreased significantly over time (p<0.01) and averaged 5.6 pre-feeding and 5.4 post- feeding and was not significantly different between high- and low-quality forages or between mineral bolus types (p>0.05). Principal coordinates analysis (PCoA) of the Bray-Curtis dissimilarity matrix showed distinct grouping by feed quality and time but not by mineral bolus type. Bacteroidetes and Firmicutes were the dominant phyla in all treatments and significant increases (p<0.05) in the relative abundance of the family Lachnospiraceae and the genus Prevotella were observed in high quality forage diets. Rumen VFA and NH3-N concentrations were also strongly associated with the high-quality forage diet. Predictive functional profiling indicated that functions associated with methanogenesis were negatively correlated with feed quality. Discussion: The results of this study suggest that mineral bolus type is unlikely to affect rumen bacterial community structure or function while forage quality can significantly alter community structure and predicted functions associated with methanogenesis and VFA production.Item Soil bacterial community response to cover crop introduction in a wheat-based dryland cropping system(Frontiers Media SA, 2022-11) Eberly, Jed O.; Bourgault, Maryse; Dafo, Julia M.; Yeoman, Carl J.; Wyffels, Samuel A.; Lamb, Peggy F.; Boss, Darrin L.The incorporation of cover crops into cropping systems is important for enhancing soil health in agricultural systems. Soil microbes contribute to soil health by supplying key nutrients and providing protection against plant pests, diseases, and abiotic stress. While research has demonstrated the connection between cover crops and the soil microbiology, less is known regarding the impact of cover crops on the soil microbial community in semi-arid regions of the Northern Great Plains. Our objectives were to evaluate changes in the soil bacterial community composition and community networks in wheat grown after multi-species cover crops. Cover crops were compared to continuous cropping and crop/fallow systems and the effects of cover crop termination methods were also evaluated. Cover crops consisted of a cool season multispecies mix, mid-season multispecies mix, and a warm season multispecies mix, which were grown in rotation with winter wheat. A continuous cropping (wheat/barley) and wheat/fallow system were also included along with cover crop termination by grazing, herbicide application, and haying. Cover crop treatments and termination methods had no significant impact on microbial community alpha diversity. Cover crop termination methods also had no significant impact on microbial community beta diversity. Families belonging to the phyla Actinobacteria, Bacterioidota, and Proteobacteria were more abundant in the cool season cover crop treatment compared to the warm season cover crop treatment. Co-occurrence network analysis indicated that incorporation of cool season cover crops or mid-season mixes in a wheat-based cropping system led to greater complexity and connectivity within these microbial networks compared to the other treatments which suggests these communities may be more resilient to environmental disturbances.Item Modeling a synthetic aptamer-based riboswitch biosensor sensitive to low hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) concentrations(Public Library of Science, 2020-11) Mayo, Michael L.; Eberly, Jed O.; Crocker, Fiona H.; Indest, Karl J.RNA aptamers are relatively short nucleic acid sequences that bind targets with high affinity, and when combined with a riboswitch that initiates translation of a fluorescent reporter protein, can be used as a biosensor for chemical detection in various types of media. These processes span target binding at the molecular scale to fluorescence detection at the macroscale, which involves a number of intermediate rate-limiting physical (e.g., molecular conformation change) and biochemical changes (e.g., reaction velocity), which together complicate assay design. Here we describe a mathematical model developed to aid environmental detection of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) using the DsRed fluorescent reporter protein, but is general enough to potentially predict fluorescence from a broad range of water-soluble chemicals given the values of just a few kinetic rate constants as input. If we expose a riboswitch test population of Escherichia coli bacteria to a chemical dissolved in media, then the model predicts an empirically distinct, power-law relationship between the exposure concentration and the elapsed time of exposure. This relationship can be used to deduce an exposure time that meets or exceeds the optical threshold of a fluorescence detection device and inform new biosensor designs.