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Nutrient losses via subsurface tile cause environmental degradation of aquatic ecosystems. Various management practices are primarily aimed at reduction of nitrate leaching in tile discharge; however, studies on leaching of other nutrients are limited. A replicated plot experiment was initiated in 2016 as part of the Long-Term Agroecosystem Research (LTAR) network Croplands Common Experiment to quantify the effectiveness of management practices on leaching of NO 3 -N, total P, K, and S from drained soils. Corn (Zea mays L.) and soybean (Glycine max L. Merr.) were grown under five different treatments: (1) BP: basic practice with fall chisel plow; (2) NT: no-till crop production; (3) RC: no-till with a winter rye (Secale cereale L.) cover crop; (4) DW: no-till with woodchip denitrification walls parallel to both sides of the tile; and (5) ZN: zero N; no-till without N fertilization. Compared to BP, both RC and DW treatments reduced NO 3 -N load by 63% and 47%, respectively; 15.5, 5.8, and 8.2 kg N ha -1  year -1 , while omitting N fertilization did not impact N loads (12 kg N ha -1  year -1 ). The DW resulted in greater K loss compared to BP, presumably due to decomposing woodchips. No-till practices increased drainage flow and K and P loads compared to conventionally tilled BP plots but had no impact on other nutrients. The BP produced the highest corn yield, whereas soybean yields were not affected by treatments. These findings indicate that while some conservation practices are effective in reducing nutrient leaching, others are likely to increase their loss and reduce crop yields., (Published 2024. This article is a U.S. Government work and is in the public domain in the USA.)

Vaccines that cross-protect across serovars of Salmonella enterica ( Salmonella ) would be a beneficial intervention against emerging and persistent Salmonella isolates of concern for the turkey industry. The 2017-2019 foodborne outbreak of Salmonella enterica serovar Reading ( S . Reading) revealed the need for effective control of this serovar in turkey production. This study evaluated two live-attenuated Salmonella vaccines, an internally developed cross-protective vaccine and a commercially available vaccine, against an outbreak-associated strain of S . Reading in turkeys. At 1 day and 3 weeks of age, male turkey poults were either mock-vaccinated with phosphate buffered saline (PBS) or given one of the vaccines by oral gavage (primary and booster) or aerosol spray (primary) then drinking water (booster). At 7 weeks of age, poults were challenged with 10 9 colony forming units (CFU) of S . Reading; a mock-vaccinated group was mock-challenged with PBS. Colonization of the cecal contents and cecal tonsil was 1.5-3 log 10 CFU/g lower in vaccinated birds than mock-vaccinated birds at 7 and/or 14 days post-inoculation (DPI). Salmonella dissemination to the spleen was significantly reduced by both vaccines. Gene expression of intestinal transporters (such as SCNN1B and SLC10A2 ) and tight junction proteins was significantly decreased in the turkey cecal tonsil transcriptome at 2 DPI with S . Reading. Vaccination with either vaccine mitigated most cecal tonsil gene expression responses to S . Reading challenge. Therefore, both the internally developed vaccine and commercial vaccine were cross-protective against colonization and dissemination, and both were able to limit transcriptional changes from challenge in intestinal health-related genes in the cecal tonsil, thereby providing vaccination efficacy and impact data against S . Reading in turkeys., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Monson, Gurung, Bearson, Whelan, Trachsel, Looft, Sylte and Bearson.)

Two trials were conducted to determine interactive effects between lipid source (palm oil, PO versus soybean oil, SO) and emulsifier addition (none versus glycerol monolaurate-GML) on apparent total tract digestibility (ATTD) of gross energy (GE) in broilers and growth performance in poults. In trial 1, 0.05 % GML addition had no impact on the ATTD of GE of SO but improved the ATTD of PO from 77.11 % to 88.21 % (interaction, P=0.03). Without GML addition, PO had a lower ATTD of GE (77.11 %) compared to SO (96.48 %) resulting in an AME of 7,259 versus 9,092 kcal/kg for PO and SO, respectively. In trial 2, the addition of 0.10 % GML reduced ADFI in poults fed diets containing 5 % PO compared to poults fed 0 or 0.05 % GML, while the addition of either 0.05 or 0.10 % GML reduced ADFI in poults fed diets containing 5 % SO compared to poults fed no GML (P=0.01). There was a similar response with ADG (P=0.01) where the addition of either 0.05 or 0.10 % GML reduced ADG in poults fed diets containing SO compared to poults fed no GML, while the addition of GML was largely without effect in poults fed diets containing PO. There was no interaction between lipid source and emulsifier addition on feed efficiency (P>0.10). Poults fed diets containing PO had a poorer feed efficiency compared to birds fed diets containing SO (P=0.01). The main effect of emulsifier was inconsistent in that poults fed the diets containing 0.10 % GML had the greatest feed efficiency compared to poults fed the diets containing 0.05 % GML, with poults fed diets containing no emulsifier being intermediate (P=0.10). In conclusion, addition of GML improved the ATTD of GE for PO but had no effect on the ATTD of GE for SO. This improvement in energy digestibility, did not however, translate to an improvement in poult performance. Broilers and poults fed diets containing SO had a greater feed efficiency compared to birds fed diets containing PO., Competing Interests: Declaration of competing interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Inc.)

The evolution and spread of antibiotic resistance are problems with important consequences for bacterial disease treatment. Antibiotic use in animal production and the subsequent export of antibiotic resistance elements in animal manure to soil is a concern. Recent reports suggest that exposure of pathogenic bacteria to glyphosate increases antibiotic resistance. We review these reports and identify soil processes likely to affect the persistence of glyphosate, antibiotic resistance elements, and their interactions. The herbicide molecular target of glyphosate is not shared by antibiotics, indicating that target-site cross-resistance cannot account for increased antibiotic resistance. The mechanisms of bacterial resistance to glyphosate and antibiotics differ, and bacterial tolerance or resistance to glyphosate does not coincide with increased resistance to antibiotics. Glyphosate in the presence of antibiotics can increase the activity of efflux pumps, which confer tolerance to glyphosate, allowing for an increased frequency of mutation for antibiotic resistance. Such effects are not unique to glyphosate, as other herbicides and chemical pollutants can have the same effect, although glyphosate is used in much larger quantities on agricultural soils than most other chemicals. Most evidence indicates that glyphosate is not mutagenic in bacteria. Some studies suggest that glyphosate enhances genetic exchange of antibiotic-resistance elements through effects on membrane permeability. Glyphosate and antibiotics are often present together in manure-treated soil for at least part of the crop-growing season, and initial studies indicate that glyphosate may increase abundance of antibiotic resistance genes in soil, but longer term investigations under realistic field conditions are needed. Although there are demonstratable interactions among glyphosate, bacteria, and antibiotic resistance, there is limited evidence that normal use of glyphosate poses a substantial risk for increased occurrence of antibiotic-resistant, bacterial pathogens. Longer term field studies using environmentally relevant concentrations of glyphosate and antibiotics are needed., (© 2024 The Author(s). Journal of Environmental Quality published by Wiley Periodicals LLC on behalf of American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.)

The Southern Plains (SP) is one of 18 Long-Term Agroecosystem Research network sites that combine strategic research projects with common measurements across multiple agroecosystems. Projects at the SP site focus on the use of indicator measurements to aid in assessment of land and nutrient management's impact on soil health, water quality, carbon and water balances, and forage biomass-quality in diversified, adaptive crop-livestock systems designed to overcome shifts in natural resources and climate. The prevailing treatment is tilled winter wheat (Triticum aestivum L.) that is grazed, hayed, harvested for grain, or grazed and harvested for grain. The alternative treatment is year-round annual cover crop forage mixes for cattle (Bos taurus) production planted in fall and spring under conservation tillage management. The area is subject to variable weather and climatic shifts that reduce the potential to diversify forage crops and limit grazing in southern tall grass prairies and small grain systems. Incorporation of fertilized, rain-fed, annual cool and warm season mixtures of cover crops could fill forage gaps. The presence of year-round ground cover reduces sediment and nutrient loading to surface waters while enhancing soil health and water holding capacity. Tools to aid agricultural producers and land and water resource managers have been developed and implemented to determine how climate, topography, and varying conservation management practices alter hydrological structures, greenhouse gas emissions, water usage, and soil resources., (Published 2024. This article is a U.S. Government work and is in the public domain in the USA.)

Agricultural systems evolve from the interactions of climate, crops, soils, management practices (e.g., tillage, cover crops, nutrient management), and economic risks and rewards. Alternatives to the corn (Zea mays L.)-soybean [Glycine max (L.) Merr.] (C-S) cropping systems that dominate in the US Midwest may provide more sustainable use of resources, reduce the documented environmental impacts of current C-S systems, and improve production efficiency and ecosystem services. Innovative management practices are needed to offer producers options to increase farm resilience to variable weather conditions and offset negative environmental impacts. In response to this need, the Upper Mississippi River Basin Long-Term Agroecosystem Research network site at Ames, IA, established a cropland experiment in 2016 to investigate an alternative crop management system that includes reduced tillage, cover crops, and right source, right rate, right time, and right place (4R) nitrogen (N) management. The experimental site is located on the Iowa State University Kelley Research Farm in Boone County, IA. Crop, soil, air, and tile drainage water measurements are made throughout the year using published methods for each agronomic and environmental metric. Our goal is to provide quantitative information to farmers, consultants, agribusiness partners, and state and federal agencies to help guide decisions on the effective use of alternative management practices. Future changes in experimental treatments will adopt a knowledge co-production approach whereby researchers and stakeholders will work collaboratively to identify problems, implement research protocols, and interpret results., (Published 2024. This article is a U.S. Government work and is in the public domain in the USA. Journal of Environmental Quality published by Wiley Periodicals LLC on behalf of American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.)

Long-term research is essential for guiding the development of agroecosystems to meet escalating production demands in a manner that is environmentally sound and socially acceptable. Research must integrate biophysical and socioeconomic factors to provide geographically scalable knowledge that involves stakeholders across the research-education-extension-policy spectrum. In response to this need, the Long-Term Agroecosystem Research (LTAR) network developed a "Common Experiment," which seeks to develop and disseminate multi-region, science-based information to enable implementation of visionary agricultural innovations while simultaneously promoting food security, well-being, environmental quality, and climate adaptation and mitigation. The core design of the Common Experiment contrasts prevailing and alternative/aspirational production systems, with the latter including novel innovations hypothesized to advance sustainable intensification in locally appropriate ways. Treatments in the Common Experiment represent a diversity of production systems under cropland, grazing land, and integrated crop/grazing land management. Where possible, treatments are evaluated at multiple spatial scales (e.g., from plot to enterprise) and are designed to evolve over the course of the experiment with stakeholder input. A common assessment framework guides data collection for the experiment and is complemented by metric-specific protocols and an emerging data management infrastructure. Currently, there are large differences among sites in the application of the experimental framework and degree of stakeholder engagement; differences largely grounded in pragmatic issues related to land access, site expertise, and resource availability. The full potential of the LTAR Common Experiment may be realized with strategic investments in network capacity., (© 2024 The Author(s). Journal of Environmental Quality published by Wiley Periodicals LLC on behalf of American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

The Upper Mississippi River Basin (UMRB) Long-Term Agroecosystem Research (LTAR) watershed is hydrologically complex, with a notable temperature and precipitation gradient across four locations: Ames, IA; Platteville, WI; Morris, MN; and St. Paul, MN. Each location established LTAR Croplands Common Experiment (CCE) scenarios to fit local climatic and cultural practices. This paper describes the UMRB-Morris location, which was established in 2016 and is the most northern of the sites and contributes to the major watersheds of the UMRB and the Red River of the North. Both on-farm and plot-scale studies are included. The prevailing system is a corn (Zea mays L.)-soybean (Glycine max L.) rotation with annual deep ripping tillage. The signature alternative system is alternative 1, which is a shallow strip-till in a corn-soybean rotation. A second alternative system includes shallow tillage/rotational no-tillage in a corn-soybean-wheat (Triticum aestivum L.) with winter oilseed and cover crops, and it is considered a test ground for future alternative systems. On-farm fields are equipped with eddy covariance towers and include 16 geo-referenced soil core sampling sites for incremental samplings. Each field is sampled annually for crop yield and management data are recorded. Plot-scale versions of the treatments are managed at the Swan Lake Research Farm. On-farm and plot-scale fields are instrumented with Phenocams to capture continuous photographic records. The CCE at UMRB-Morris aims to integrate soil, crop, weather data, and image classification to assess benefits and challenges across different management strategies., (© 2024 The Author(s). Journal of Environmental Quality © 2024 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Alternative agronomic practices are needed to address the various climatic, agronomic, edaphic, and water quality related challenges faced by the dairy farmers of the Driftless Area (DA) in the Upper Mississippi River Basin (UMRB). These practices should be innovative in nature, inclusive of regional stakeholders, and sustainable to meet the future food and climate related challenges of Wisconsin agriculture. Here, we outline our Integrated (grazing and cropland) Long-Term Agroecosystem Research Common Experiment at the University of Wisconsin-Platteville Pioneer Farm (UW-P PF) in the UMRB and describe our collaboration in this USDA network. In this field-scale experiment, we are comparing the conventional dairy production system common to this region (i.e., corn-on-corn [Zea mays L.] for 4 years, followed by alfalfa [Medicago sativa L.] for 3 years, with no cover crops) with two alternative dairy production systems-(1) soil health management with no-till, cover crops, and application of a novel manure-based nutrient-rich stable product, and (2) management intensive grazing-and rotational grazing on pastures established with diverse forage-legume mix. Meteorological, edaphic, hydrologic, and agronomic data are collected and analyzed at regular frequencies. Going forward, the experiment will continue as a form of stakeholder-driven adaptive research and receive evaluation on a regular basis to determine whether any changes are required to address the "real-world" challenges faced by the farmers in the Midwest., (© 2024 The Author(s). Journal of Environmental Quality © 2024 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.)

Amino acids (AA) are an expensive nutritional components of poultry diets. Distillers dried grains with solubles (DDGS) is the primary co-product produced by the dry grind bioethanol industry, although new technologies are being implemented to produce high protein distillers dried grains (HP-DDG) and corn fermented protein (CFP), but data on their nutritive value in poultry are lacking. Two experiments (EXP) were conducted to determine the energy and AA digestibility of DDGS, HP-DDG, and CFP in poults in addition to a feeding trial to evaluate increasing dietary levels of HP-DDG and CFP on growth performance and intestinal characteristics. In EXP 1, 6 different DDGS sources were evaluated using poults to determine their nitrogen-corrected apparent metabolizable energy (AME n ) concentrations, and cecectomized roosters were used to determine their standardized ileal (SID) AA digestibility (SID-AA). In EXP 2, AME n and SID-AA for HP-DDG and CFP were determined in young poults, and a feeding trial was conducted to evaluate growth performance and intestinal morphology and permeability of poults fed diets containing 7.5 and 15% HP-DDG or CFP from 1 to 32 d of age. In EXP 1, the AME n concentration among the DDGS samples ranged from 2,530 to 3,573 kcal/kg DM but was not different (P = 0.57) among the samples, with an average SID for LYS of 66.6%. In EXP 2, different (P = 0.001) AME n concentrations for HP-DDG and CFP were observed (3,114 and 3,760 kcal/kg DM, respectively), with the SID for LYS being 66.55 and 77.00% for HP-DDG and CFP, respectively. Including HP-DDG or CFP into the diet at 7.5 and 15% had no effect (P > 0.05) on growth, feed intake, or feed conversion. Neither co-product nor its inclusion rate affected intestinal morphology and permeability (P > 0.05). Overall, DDGS, HP-DDG, and CFP are excellent sources of AME n and digestible AA, with dietary inclusion rates of up to 15% of HP-DDG or CFP having no impact on growth or intestinal characteristics., Competing Interests: DISCLOSURES The authors declare that a portion of this manuscript was funded by The Anderson Inc. who donated the HP-DDG and CFP used in Experiment 2 in this manuscript and provided financial assistance to support a portion of manuscript. The financial support supported the first authors in their graduate program, farm costs associated with the trial, and assay costs. This declaration is provided in the manuscript under the disclosure section. Mention of a trade name, proprietary product, or specific equipment does not constitute a guarantee or warranty by the USDA, University of Minnesota, or Iowa State University and does not imply approval to the exclusion of other products that may be suitable. The USDA is an equal opportunity provider and employer., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Legacies can become intertwined, none more so than the body of work of Dr. Andrew Sharpley examining agricultural nutrient delivery to waterbodies and the phosphorus (P) accumulation in agricultural soils, or "legacy P." Although Sharpley's work focused on the anthropogenic influence on soil P, our study suggests soils of the Lower Mississippi Alluvial Plain (MAP) represent a natural legacy with moderate levels of available P resulting from minimal anthropogenic input. In 2019, we collected surface (0-5 cm) soil samples from four regionally dominant soil series in either cropland or forested land uses, spanning 76 locations within the MAP. Soil chemical and physical properties were measured utilizing a suite of extractions and texture analysis to correlate properties with soil P values. Total soil P did not vary between land uses. Mehlich-3 extractable P was slightly higher in cropland soils due to higher concentrations in Forestdale and Sharkey soils. Dundee, Forestdale, and Sharkey cropland soils showed significant associations between Mehlich-3-extractable iron (Fe) and P. Ratios of total carbon (TC) to total nitrogen (C:N) and TC to P (C:P) were consistent across all sampled soil series but differed between forest and cropland soils. These ratios are critical for establishing baseline soil nutrient values in simulation models and can be used to improve water quality model simulations that help guide P management in the MAP. As Sharpley routinely demonstrated, understanding sources of P is critical for developing an appropriate management strategy. This study provides critical knowledge on soil P dynamics in the MAP region., (Published 2024. This article is a U.S. Government work and is in the public domain in the USA.)

Antibiotic resistance is increasingly recognized as a critical challenge affecting human, animal, and environmental health. Yet, environmental dynamics and transport of antibiotic resistance genes (ARGs) and microbial communities in karst and non-karst leachate following poultry litter land applications are not well understood. This study investigates impacts of broiler poultry litter application on the proliferation of ARGs (tetW, qnrS, ermB, sulI, and bla CTX-M-32 ), class 1 integron (intI1 i), and alterations in microbial communities (16S rRNA) within karst derived soils, which are crucial and under-researched systems in the global hydrological cycle, and non-karst landscapes. Using large, intact soil columns (45 cm diam. × 100 cm depth) from karst and non-karst landscapes, the role of preferential flow and ARG transport in leachate was enumerated following surface application of poultry litter and simulated rain events. This research demonstrated that in poultry litter amended karst soils, ARG (i.e., ermB and tetW) abundance in leachate increased 1.5 times compared to non-karst systems (p < 0.05), highlighting the influence of geological factors on ARG proliferation. Notably, microbial communities in karst soil leachate exhibited increased diversity and abundance, suggesting a potential linkage between microbial composition and ARG presence. Further, our correlation and network analyses identified relationships between leachate ARGs, microbial taxa, and physicochemical properties, underscoring the complex interplay in these environmentally sensitive areas. These findings illuminate the critical role of karst systems in shaping ARG abundance and pollutant dispersal and microbial community dynamics, thus emphasizing the need for landscape-specific approaches in managing ARG dissemination to the environment. This study provides a deeper understanding of hydrogeological ARG dynamics but also lays the groundwork for future research and strategies to mitigate ARG dissemination through targeted manure applications across agricultural landscapes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier B.V.)

Pit recharge systems (PRS) control odor by managing organic solids in swine manure. However, there needs to be more understanding of PRS's effect on the microbiome composition and its impact on odor formation. A study was conducted to understand how recharge intervals used in PRS impact manure microbiome and odor formation. Bioreactors dynamically loaded simulated recharge intervals of 14, 10, and 4 days by diluting swine manure with lagoon effluent at varying ratios. Treatment ratios tested included 10:0 (control), 7:3 (typical Korean PRS), 5:5 (enhanced PRS #1), and 2:8 (enhanced PRS #2). Manure microbial membership, chemical concentrations, and odorant concentrations were used to identify the interactions between microbiota, manure, and odor. The initial microbial community structure was controlled by dilution ratio and manure barn source material. Firmicutes and Proteobacteria were the dominant microbial phyla in manure and lagoon effluent, respectively, and significantly decreased or increased with dilution. Key microbial species were Clostridium saudiense in manure and Pseudomonas caeni in lagoon effluent. Percentages of these species declined by 8.9% or increased by 17.6%, respectively, with each unit dilution. Microbial community composition was controlled by both treatment (i.e., manure dilution ratio and barn source material) and environmental factors (i.e., solids and pH). Microbiome composition was correlated with manure odor formation profiles, but this effect was inseparable from environmental factors, which explained over 75% of the variance in odor profiles. Consequently, monitoring solids and pH in recharge waters will significantly impact odor control in PRS., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier Ltd.)

Winter cover crop performance metrics (i.e., vegetative biomass quantity and quality) affect ecosystem services provisions, but they vary widely due to differences in agronomic practices, soil properties, and climate. Cereal rye (Secale cereale) is the most common winter cover crop in the United States due to its winter hardiness, low seed cost, and high biomass production. We compiled data on cereal rye winter cover crop performance metrics, agronomic practices, and soil properties across the eastern half of the United States. The dataset includes a total of 5,695 cereal rye biomass observations across 208 site-years between 2001-2022 and encompasses a wide range of agronomic, soils, and climate conditions. Cereal rye biomass values had a mean of 3,428 kg ha -1 , a median of 2,458 kg ha -1 , and a standard deviation of 3,163 kg ha -1 . The data can be used for empirical analyses, to calibrate, validate, and evaluate process-based models, and to develop decision support tools for management and policy decisions., (© 2024. The Author(s).)

Human foodborne outbreaks with antibiotic-resistant Salmonella enterica associated with contaminated poultry products have recently involved serogroup C serovars Infantis and Hadar. The current study evaluated a commercially available Salmonella vaccine for cross-protection against Infantis and Hadar serovars in turkeys. The live, attenuated S. Typhimurium (serogroup B) vaccine significantly reduced colonization of intestinal tissues (cecum, cecal tonsils, and cloaca) by serovars Infantis (C1) and Hadar (C2) and significantly limited systemic dissemination to the spleen. S. Infantis, but not S. Hadar, disseminated to bone marrow in non-vaccinated turkeys, but vaccination prevented S. Infantis dissemination to the bone marrow. The S. Infantis challenge strain contained the pESI megaplasmid, and virulence mechanism(s) residing on this plasmid may support dissemination and/or colonization of systemic niches such as myeloid tissue. Collectively, the data indicate that vaccinating turkeys with the serogroup B S. Typhimurium vaccine limited intestinal colonization and systemic dissemination by serogroup C serovars Infantis and Hadar., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Shawn Bearson reports financial support was provided by USDA Food Safety and Inspection Service., (Copyright © 2023. Published by Elsevier Ltd.)

Salmonella is a global bacterial foodborne pathogen associated with a variety of contaminated food products. Poultry products are a common source of Salmonella -associated foodborne illness, and an estimated 7% of human illnesses in the United States are attributed to turkey products. From November 2017 to March 2019, the Centers for Disease Control and Prevention reported a turkey-associated outbreak of multidrug-resistant (MDR; resistant to ≥3 antimicrobial classes) Salmonella enterica serovar Reading ( S . Reading) linked to 358 human infections in 42 US states and Canada. Since S . Reading was seldom linked to human illness prior to this outbreak, the current study compared genomic sequences of S . Reading isolates prior to the outbreak (pre-outbreak) to isolates identified during the outbreak period, focusing on genes that were different between the two groups but common within a group. Following whole-genome sequence analysis of five pre-outbreak and five outbreak-associated turkey/turkey product isolates of S . Reading, 37 genes located within two distinct chromosomal regions were identified only in the pre-outbreak isolates: (1) an ~5 kb region containing four protein-coding genes including uidA which encodes beta-glucuronidase, pgdA encoding peptidoglycan deacetylase, and two hypothetical proteins and (2) an ~28 kb region comprised of 32 phage-like genes and the xerC gene, which encodes tyrosine recombinase (frequently associated with phage genes). The five outbreak isolates also had a deletional event within the cirA gene, introducing a translational frame shift and premature stop codon. The cirA gene encodes a protein with dual receptor functions: a siderophore receptor for transport of dihydroxybenzoylserine as well as a colicin Ia/b receptor. Significant differences for the identified genetic variations were also detected in 75 S . Reading human isolates. Of the 41 S . Reading isolates collected before or in 2017, 81 and 90% of the isolates contained the uidA and pgdA genes, respectively, but only 24% of the isolates collected after 2017 harbored the uidA and pgdA genes. The truncation event within the cirA gene was also significantly higher in isolates collected after 2017 (74%) compared to before or in 2017 (5%). Phenotypic analysis of the S . Reading isolates for colicin and cefiderocol sensitivities (CirA) and β-methyl-D-glucuronic acid utilization (UidA and accessory proteins) supported the genomic data. Overall, a similar genome reduction pattern was generally observed in both the turkey and human isolates of S . Reading during the outbreak period, and the genetic differences were present in genes that could potentially promote pathogen dissemination due to variation in Salmonella colonization, fitness, and/or virulence., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Sivasankaran, Bearson, Trachsel, Nielsen, Looft and Bearson.)

Isoacids are branched ketoacids which when fed to ruminants have been shown to enhance the growth of fiber-digesting organisms. Ninety finishing gilts were individually fed dietary treatments consisting of diet type: corn-soybean meal (CSBM), a diet containing 40% distillers dried grains with solubles (DDGS), or a diet containing 40% sugar beet pulp (SBP); in combination with either no feed additive (CNT), the addition of 0.50% isobutyrate (IB), or the addition of a 0.88% mix of isobutyrate, isovalerate, and 2-methylbutyrate (MX). Gilts consumed an average of 2.171 kg/d over the 28-d trial. On d 26, fresh fecal samples were collected for determination of apparent total tract digestibility (ATTD) of gross energy (GE) and nitrogen (N), determination of fecal volatile fatty acids (VFA), and evaluation of microbial ecology. There was no interaction between diet type and isoacid addition, and no main effect of isoacid or diet type on alpha or Shannon microbial diversity measures (P > 0.05). There was no interaction between isoacid addition and diet type, and no main effect of isoacid addition on microbial beta diversity (P > 0.05), but differences were observed in microbial beta diversity due to diet type (P ≤ 0.05). There was no interaction between diet type and isoacid addition observed in fecal VFA concentrations (P > 0.05), with only minor differences in fecal VFA concentrations noted due to isoacid addition (P ≤ 0.05). The interaction between diet type and isoacid addition on ATTD of dietary GE and N (P ≤ 0.01) was large because the addition of IB did not affect the ATTD of GE or N in pigs fed the CSBM diet, but increased ATTD of GE and N in pigs fed diets containing DDGS and decreased the ATTD of GE and N in pigs fed diets containing SBP. In contrast, adding a blend of isoacids (i.e., MX) reduced the ATTD of GE and N, regardless of diet type. There was no interaction between diet type and isoacid addition, and no effect of isoacid addition was observed on pig performance (P > 0.05). Diet type did not affect average daily gain (P > 0.05), but pigs fed diets containing DDGS or SBP consumed less feed (P = 0.01) and exhibited greater GF ratios compared to pigs fed the low-fiber CSBM diet (P ≤ 0.05). In conclusion, there was little to no effect of isoacid addition on microbial ecology, fecal VFA concentrations, ATTD of GE or N, or pig performance, but the improvement in ATTD of GE and N in pigs fed diets containing DDGS when IB was added warrants further investigation., (Published by Oxford University Press on behalf of the American Society of Animal Science 2024.)

High crude protein (CP; 21% to 26%) diets fed during the first 21 to 28 d postweaning are viewed negatively because of a perceived increase in the incidence rates of diarrhea due to increased intestinal protein fermentation and/or augmented enteric pathogen burden. This is thought to antagonize nursery pig health and growth performance. Therefore, our objective was to evaluate the impact of low vs. high dietary CP on 21-day postweaned pig intestinal function. Analyzed parameters included ex vivo intestinal barrier integrity (ileum and colon), ileal nutrient transport, tissue inflammation, and fecal DM. One hundred and twenty gilts and barrows (average body weight) were randomly assigned to one of two diets postweaning. Diets were fed for 21 d, in two phases. Phase 1 diets: low CP (17%) with a 1.4% standardized ileal digestible (SID) Lys (LCP), or high CP (24%) with a 1.4% SID Lysine (HCP). Phase 2: LCP (17%) and a 1.35% SID lysine, or HCP (24%) formulated to a 1.35% SID lysine. Pig growth rates, feed intakes, and fecal consistency did not differ (P > 0.05) due to dietary treatment. Six animals per treatment were euthanized for additional analyses. There were no differences in colonic epithelial barrier function as measured by transepithelial electrical resistance (TER) and fluorescein isothiocyanate (FITC)-dextran transport between treatments (P > 0.05). Interleukins (IL)-1α, IL-1β, IL-1ra, IL-2 IL-4, IL-6, and IL-12 were not different between treatments (P > 0.05). However, IL-8 and IL-18 were higher in HCP- vs. LCP-fed pigs (P < 0.05). There were no differences in fecal dry matter (DM; P > 0.05) between treatments. In the ileum, there was a tendency (P = 0.06) for TER to be higher in HCP-fed pigs, suggesting a more robust barrier. Interestingly, glucose and glutamine transport were decreased in HCP- vs. LCP-fed pigs (P < 0.05). FITC-dextran transport was not different between treatments (P > 0.05). There were also no differences in ileal cytokine concentrations between diets (P > 0.05). Taken together, the data show that low CP does not negatively impact colonic barrier function, fecal DM, or inflammation. In contrast, ileal barrier function and nutrient transport were altered, suggesting a regional effect of diet on overall intestinal function., (Published by Oxford University Press on behalf of the American Society of Animal Science 2024.)

Agriculture is a major source of nitrous oxide (N 2 O) emissions into the atmosphere. However, assessing the impacts of agricultural conservation practices, land use change, and climate adaptation measures on N 2 O emissions at a large scale is a challenge for process-based model applications. Here, we integrated six N 2 O emission algorithms for the nitrification processes and seven N 2 O emission algorithms for the denitrification process into the Soil and Water Assessment Tool-Carbon (SWAT-C). We evaluated the different combinations of methods in simulating N 2 O emissions under corn (Zea mays L.) production systems with various conservation practices, including fertilization, tillage, and crop rotation (represented by 14 experimental treatments and 83 treatment-years) at five experimental sites across the U.S. Midwest. The SWAT-C model exhibited wide variability in simulating daily average N 2 O emissions across treatment-years with different method configurations, as indicated by the ranges of R 2 , NSE, and BIAS (0.04-0.68, -1.78-0.60, and -0.94-0.001, respectively). Our results indicate that the denitrification process has a stronger impact on N 2 O emissions than the nitrification process. The best performing N 2 O emission algorithms are those rooted in the CENTURY model, which considers soil pH and respiration effects that were overlooked by other algorithms. The optimal N 2 O emission algorithm explained about 63% of the variability of annual average N 2 O emissions, with NSE and BIAS of 0.60 and -0.033, respectively. The model can reasonably represent the impacts of agricultural conservation practices on N 2 O emissions. We anticipate that the improved SWAT-C model, with its flexible configurations and robust modeling and assessment capabilities, will provide a valuable tool for studying and managing N 2 O emissions from agroecosystems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier Ltd.)

To monitor and meet water quality objectives, it is necessary to understand and quantify the contribution of nonpoint sources to total phosphorus (P) loading to surface waters. However, the contribution of streambank erosion to surface water P loads remains unclear and is typically unaccounted for in many nutrient loading assessments and policies. As a result, agricultural contributions of P are overestimated, and a potentially manageable nonpoint source of P is missed in strategies to reduce loads. In this perspective, we review and synthesize the results of a special symposium at the 2022 ASA-CSSA-SSSA annual meeting in Baltimore, MD, that focused on streambank erosion and its contributions to P loading of surface waters. Based on discussions among researchers and policy experts, we overview the knowns and unknowns, propose next steps to understand streambank erosion contribution to P export budgets, and discuss implications of the science of streambank erosion for policy and nutrient loss reduction strategies., (© 2023 The Authors. Journal of Environmental Quality © 2023 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.)

Management and design affect systems' ability to deliver ecosystem services and meet sustainable intensification needs for a growing population. Soil-plant-animal health evaluations at the systems level for conventional and silvopastoral environments are lacking and challenge adoption across temperate regions. Impacts of silvopasture on soil quality, microclimate, cattle heat stress, forage quality and yield, and cattle weight gain were compared to a conventional pasture in the mid-southern US. Here, we illustrate silvopastures have greater soil organic carbon, water content, and overall quality, with lower temperatures (soil and cattle) than conventional pastures. Forage production and cattle weight gains were similar across systems; yet, conventional pasture systems would need approximately four times more land area to yield equivalent net productivity (tree, nuts, forage, and animal weight) of one ha of silvopasture. Temperate silvopastures enhanced delivery of ecosystem services by improving soil quality and promoting animal welfare without productivity losses, thus allowing sustainable production under a changing climate., (© 2023. The Author(s).)

With the increased global interest in sequestering carbon in soil, it is necessary to understand the composition of different pools of soil organic matter (SOM) that cycle over suitably short timeframes. To explore in detail the chemical composition of agroecologically relevant yet distinct fractions of SOM, the light fraction of SOM (LFOM), the 53-μm particulate organic matter (POM), and the mobile humic acid (MHA) fractions were sequentially extracted from agricultural soils and characterized using both 13 C cross polarization magic angle spinning nuclear magnetic resonance (CPMAS NMR) spectroscopy and also Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The NMR results showed a decrease in the O-alkyl C region assigned to carbohydrates (51-110 ppm) and an increase in the aromatic region (111-161 ppm) proceeding from the LFOM to the POM and then to the MHA fraction. Similarly, based on the thousands of molecular formulae assigned to the peaks detected by FT-ICR-MS, condensed hydrocarbons were dominant only in the MHA, while aliphatic formulae were abundant in the POM and LFOM fractions. The molecular formulae of the LFOM and POM were mainly grouped in the high H/C lipid-like and aliphatic space, whereas a portion of the MHA compounds showed an extremely high (17-33, average of 25) double bond equivalent (DBE) values, corresponding to low H/C values of 0.3-0.6, representative of condensed hydrocarbons. The labile components appeared most pronounced in the POM (93% of formulae have H/C ≥ 1.5) similar to the LFOM (89% of formulae have H/C ≥ 1.5) but in contrast to the MHA (74% of formulae have H/C ≥ 1.5). The presence of both labile and recalcitrant components in the MHA fraction suggests that the stability and persistence of soil organic matter is influenced by a complex interaction of physical, chemical, and biological factors in soil. Understanding the composition and distribution of different SOM fractions can provide valuable insights into the processes that govern carbon cycling in soils, which can help inform strategies for sustainable land management and climate change mitigation., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Phosphorus (P) budgets can be useful tools for understanding nutrient cycling and quantifying the effectiveness of nutrient management planning and policies; however, uncertainties in agricultural nutrient budgets are not often quantitatively assessed. The objective of this study was to evaluate uncertainty in P fluxes (fertilizer/manure application, atmospheric deposition, irrigation, crop removal, surface runoff, and leachate) and the propagation of these uncertainties to annual P budgets. Data from 56 cropping systems in the P-FLUX database, which spans diverse rotations and landscapes across the United States and Canada, were evaluated. Results showed that across cropping systems, average annual P budget was 22.4 kg P ha -1 (range = -32.7 to 340.6 kg P ha -1 ), with an average uncertainty of 13.1 kg P ha -1 (range = 1.0-87.1 kg P ha -1 ). Fertilizer/manure application and crop removal were the largest P fluxes across cropping systems and, as a result, accounted for the largest fraction of uncertainty in annual budgets (61% and 37%, respectively). Remaining fluxes individually accounted for <2% of the budget uncertainty. Uncertainties were large enough that determining whether P was increasing, decreasing, or not changing was inconclusive in 39% of the budgets evaluated. Findings indicate that more careful and/or direct measurements of inputs, outputs, and stocks are needed. Recommendations for minimizing uncertainty in P budgets based on the results of the study were developed. Quantifying, communicating, and constraining uncertainty in budgets among production systems and multiple geographies is critical for engaging stakeholders, developing local and national strategies for P reduction, and informing policy., (Published 2023. This article is a U.S. Government work and is in the public domain in the USA.)

Large sample datasets of in situ evapotranspiration (ET) measurements with well documented data provenance and quality assurance are critical for water management and many fields of earth science research. We present a post-processed ET oriented dataset at daily and monthly timesteps, from 161 stations, including 148 eddy covariance flux towers, that were chosen based on their data quality from nearly 350 stations across the contiguous United States. In addition to ET, the data includes energy and heat fluxes, meteorological measurements, and reference ET downloaded from gridMET for each flux station. Data processing techniques were conducted in a reproducible manner using open-source software. Most data initially came from the public AmeriFlux network, however, several different networks (e.g., the USDA-Agricultural Research Service) and university partners provided data that was not yet public. Initial half-hourly energy balance data were gap-filled and aggregated to daily frequency, and turbulent fluxes were corrected for energy balance closure error using the FLUXNET2015/ONEFlux energy balance ratio approach. Metadata, diagnostics of energy balance, and interactive graphs of time series data are included for each station. Although the dataset was developed primarily to benchmark satellite-based remote sensing ET models of the OpenET initiative, there are many other potential uses, such as validation for a range of regional hydrologic and atmospheric models., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

A study was conducted to determine the effectiveness of supplementing swine manure with Bacillus subtilis (BS) to improve digestion of manure solids and lower odor emission. Large bioreactors (400 L) with manure (100 L) were treated with commercially available BS at a rate of 1% manure volume by either directly pouring or surface spraying the manure with inoculum. Manure physicochemical properties, gas emissions, and microbiome were monitored. Manures treated multiple times with BS or surface sprayed had significantly (P < 0.05) lower electrical conductivity, volatile solids, and chemical oxygen demand, by 3-5% compared to non-treated control manures. Volatile sulfur compound emissions (VSCs) were reduced by 20-30% in both experiments, while ammonia and volatile organic compounds were reduced by 40% and 15%, respectively, in surface spray experiment only. The manure indigenous microbiome remained relatively stable following treatment and BS were never detected in the raw or treated manure following multiple treatments. The reduction in manure organic carbon and VSCs emissions were a result of physical mixing during manure treatment and biological material in the microbial inoculum stimulating microbial activity and not growth of BS., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier Ltd.)

Storm events are the primary mechanisms of delivering fluvial organic carbon (OC) in both dissolved (DOC) and particulate (POC) forms but their sources and flow pathways can vary with seasonal land use and weather. Within the low relief and poorly drained landscapes of a predominantly agricultural watershed in Eastern Iowa, six storm events were monitored for DOC and POC concentrations over a two hydrological year period in order to investigate the export mechanisms, landscape connectivity, and hydro-climatological controls of fluvial OC under representative events and associated management practices. Event-driven dynamics favored POC over DOC, where POC accounted for 54-94 % of total OC export during events, highlighting a sampling-driven bias against POC in the absence of event monitoring. The disparity between POC and DOC export exhibited a seasonal effect, where the POC:DOC export ratio was low (1.3-1.7) for October events while June/July events yielded a much higher value (up to a value of 14.7). The relationships between event DOC and POC export, Normalized Difference Vegetation Index of landscapes, and antecedent wetness conditions suggest a strong interaction or competing influences between vegetation coverage and runoff-generation threshold. While we recognize the low statistical power of the limited data set (n = 6), the storm events could be binned into two clusters: a "bare soil" period and a crop "rapid growth" period. Specifically, intra-storm variations in OC concentration and concentration-discharge (C-Q) hysteresis patterns demonstrated a seasonally-dependent access to contributing OC sources, which can be viewed as the rapid liberation of DOC during the "bare soil" period, and a progressive leaching of terrestrial DOC during the "rapid growth" period. Although high resolution event monitoring of fluvial carbon is rare this work highlights the importance of such efforts to predict C sourcing and transformation in inland water systems under variable land use and across seasons., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier B.V.)

Background: The 2017 Veterinary Feed Directive eliminated the use of medically important antibiotics for growth promotion of food animals; thus, alternative growth promoters are highly desirable by food animal producers to enhance animal health and reduce pathogen colonization, including the human foodborne pathogen Salmonella. β(1-3)(1-6)-D-glucan (β-glucan) is a soluble fiber with prebiotic characteristics; it has been shown to modulate immune and intestinal functions that strengthen swine resistance to health challenges such as bacterial infections when supplemented in the diets of growing pigs. The current study evaluated the effects of a β-glucan product on gut microbial community structure as well as Salmonella shedding and intestinal colonization., Results: Five-week-old pigs were fed a β-glucan amended diet at 500 g/ton (n = 13) or a non-amended control diet (n = 14) for three weeks, followed by inoculation of the 27 pigs with 1 × 10 9 colony forming units of Salmonella enterica serovar Typhimurium strain UK1. While remaining on the respective diets, fecal samples collected at 2, 4, 7, and 16 days post-inoculation (dpi) were similar for Salmonella shedding counts between the two diets. At 16 dpi, Salmonella counts were significantly lower in the cecal contents of the β-glucan-fed pigs (P = 0.0339) and a trend towards a reduction was observed in the Peyer's patches region of the ileum (P = 0.0790) compared to the control pigs. Pigs fed β-glucan for three weeks exhibited an increase in members of the Clostridia class in their fecal microbial communities, and after inoculation with Salmonella, several potentially beneficial microorganisms were enriched in the microbiota of β-glucan-fed pigs (Lactobacillus, Ruminococcaceae, Prevotellaceae, Veillonellaceae, Bifidobacterium and Olsenella)., Conclusion: Administration of β-glucan altered the swine gut microbiome and reduced Salmonella colonization in the cecal contents., (© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Agronomic benefits of humic product application to crops are receiving increasing attention, though underlying biochemical changes remain unexplored, especially in field settings. In this study, maize (Zea mays L.) concentrations of 11 phenol and five carbohydrate monomers were determined in whole plant stover (four growing seasons) and roots (two growing seasons) at physiological maturity for two rainfed fields in Iowa (USA) having humic product applications. Stover and root tissues tended toward greater phenol concentrations in a drier upland transect but greater carbohydrate concentrations in a wetter lowland transect. Two humic treatments further accentuated these trends in upland roots. Their phenol content increased significantly with humic application in the droughtier season of root sampling (2013). Phenol increases above the unamended control averaged 20% for each monomer. Total phenols increased above the control by 12% and 19% for the two humic treatments. Five carbohydrate monomers in the upland roots did not respond to humic application. In the second year of root sampling (2014), which had abundant rainfall, upland root phenols did not respond substantively to humic application, but root carbohydrates increased on average by 11 or 20% for the two humic treatments compared to the control, reaching significance (P< 0.10) in 7 of 10 cases. Upland stover phenol concentrations responded differently to humic product application in each of four years, ranging from numeric increases in the droughtiest year (2012) to significant decreases with abundant rainfall (2014). In the lowland transect, root phenols and carbohydrates and stover phenols responded inconsistently to humic application in four years. Stover carbohydrates did not respond consistently to humic application in either transect. The phenols that were more responsive to humic application or to droughtier conditions included p-coumaric acid and syringaldehyde, which are heavily involved in late-season maize lignification. In summary, humic product application further promoted root lignification, a natural response to drought. Yet under non-drought conditions it promoted root carbohydrate production. Carbohydrate production might be the intrinsic plant response to humic product application in stress-free conditions. These results indicate complex interactions in field conditions between plant biochemistry, environmental signals, and the humic product., Competing Interests: JS and JD were employed by the company Minerals Technologies, Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The authors declare that this study received funding from both USDA-ARS and Mineral Technologies, Inc. through USDA-ARS Trust Fund Cooperative Agreement Nr. 58-3625-2-573. Mineral Technologies, Inc. agreed to the publication of this manuscript but was not involved in sample collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication., (Copyright © 2023 Olk, Dinnes, Hatfield, Scoresby and Darlington.)

Two experiments (EXP) determined the susceptibility of spray-dried egg white (SDEW) to oxidation (heating at 100 °C for 72 h; thermally processed, TP) and whether feeding TP-SDEW, 15-acetyldeoxynivalenol (15-ADON), or peroxidized soybean oil (PSO), singularly or in combination, would affect pig performance, intestinal morphology, digestibility, and markers of oxidative stress in nursery pigs. In EXP 1, 32 pigs (7.14 kg body weight, BW) were placed individually into pens and fed diets containing either 12% SDEW, 6% TP-SDEW plus 6% SDEW, or 12% TP-SDEW. Performance was measured at the end of the 24-d feeding period with biological samples harvested following euthanasia. In EXP 2, 64 pigs (10.6 kg BW) were placed individually into pens and fed diets containing 7.5% soybean oil or PSO, 10% SDEW or TP-SDEW, and diets without or with 3 mg 15-ADON/kg diet in a 2 × 2 × 2 factorial arrangement. Performance was measured at the end of the 28-d feeding period with biological samples harvested following euthanasia. In EXP 1, dietary treatment did not affect pig performance, apparent ileal digestibility of amino acids (AAs), apparent total tract digestibility (ATTD) of gross energy (GE) or nitrogen (N), ileal crypt depth, or villi height:crypt depth ratio (P > 0.05). The effects of feeding TP-SDEW on protein damage in the plasma and liver (P < 0.05) were variable. In EXP 2, there were no three-way interactions and only one two-way interactions among dietary treatments on parameters evaluated. There was no effect of feeding TP-SDEW on ATTD of GE or N, intestinal morphology, or on oxidative markers in the plasma, liver, or ileum (P > 0.05). There was no effect of feeding diets containing added 15-ADON on ATTD of GE, ileal AA digestibility, intestinal morphology, oxidative markers in the plasma, liver, or ileum, or pig performance (P > 0.05). Feeding pigs diets containing PSO resulted in reduced ATTD of GE and N, plasma vitamin E concentration, and pig performance (P < 0.01) but did not affect intestinal morphology or oxidative markers in the liver or ileum (P > 0.05). In conclusion, it was difficult to induce protein oxidation in SDEW and when achieved there were limited effects on performance, digestibility, intestinal morphology, and oxidative status. Furthermore, singly adding 15-A-DON to a diet had no effect on the animal. At last, adding PSO reduces animal performance, but has limited effect on digestibility, intestinal morphology, and oxidative status in nursery pigs., (Published by Oxford University Press on behalf of the American Society of Animal Science 2023.)

An experiment was conducted to determine how feeding calcium (Ca)-deficient diet would affect gastrointestinal pH and volatile fatty acids (VFAs), Ca digestibility, bone mineral density (BMD), and performance in nursery pigs; and if supplementation of nondigestible oligosaccharides would affect these same parameters. In total, 240 weaned pigs (BW = 7.1 kg) were placed into 80 pens with 3 pigs/pen. The eight dietary treatments consisted of: 1) positive control (PC, 0.83% total Ca), 2) negative control (NC, 0.50% total Ca), 3 and 4) NC + 5% or 7.5% soluble corn fiber (SCF), 5 and 6) NC + 5% or 7.5% resistant corn starch (rCS), 7 and 8) NC + 0.25% or 0.50% fat-protected butyrate (pBRT). Pigs were ad libitum fed the dietary treatments for 21 d to determine average daily gain (ADG), average daily feed intake (ADFI) and gain:feed ratio (GF) with a fecal sample collected from each pen to determine Ca digestibility using acid insoluble ash as the dietary marker, with 1 pig/pen euthanized on d 21 for collection of ileal and colon contents and the left humerus. Pigs fed the NC diet had a lower colonic pH compared with pigs fed the PC (P = 0.06) but no effect on total VFA was observed (P > 0.10). Pigs fed diets containing SCF and rCS had lower colonic pH and total VFA compared to pigs fed the NC diet (P ≤ 0.05). Pigs fed diets containing pBRT had greater colonic total VFA compared to pigs fed the NC diet (P ≤ 0.07), but no difference in colonic pH was observed (P > 0.10). Pigs fed the NC diet had a greater Ca digestibility compared to pigs fed the PC (P ≤ 0.01), with no treatment to the NC having any effect on Ca digestibility compared to pigs fed the NC (P > 0.10). There was no effect of dietary Ca level on BMD and no overall addition of feeding SCF, rCS, or pBRT on BMD compared to pigs fed the NC (P > 0.10). There was no impact on pig ADG, ADFI, or GF by reducing dietary Ca by 40% (i.e., pigs fed the NC) compared to pigs fed the PC (P > 0.10). Relative to pigs fed the NC, there was no overall effect of SCF, rCS, or pBRT on ADG, ADFI, or GF (P > 0.10). In conclusion, feeding young pigs a Ca-deficient diet reduced colonic pH, increased digestibility of Ca, but had no impact on bone mineralization or overall pig performance. Supplementation of nondigestible oligosaccharides pr protected butyrate had either no effect or an inconsistent effect on colonic pH, Ca, or PHOS digestibility, bone mineralization, or overall pig performance., (Published by Oxford University Press on behalf of the American Society of Animal Science 2023.)

Evaluating potential environmental and clinical impacts of industrial antibiotic use is critical in mitigating the spread of antimicrobial resistance. Using soil columns to simulate field application of swine or cattle manure and subsequent rain events, and a targeted qPCR-based approach, we tracked resistance genes from source manures and identified important differences in antimicrobial resistance gene transport and enrichment over time in the soil and water of artificially drained cropland. The source manures had distinct microbial community and resistance gene profiles, and these differences were also reflected in the soil columns after manure application. Antibiotic resistance genes (ARGs) were only significantly enriched in effluent samples following the first rain event (day 11) for both soil types compared to the control columns, illustrating the high background level of resistance present in the control soils chosen. For swine, the genes tetQ , tet(36) , tet44 , tetM , sul2 and ant(6)-ib persisted in the soil columns, whereas tetO , strB and sul1 persisted in effluent samples. Conversely, for cattle manure sul2 and strB persisted in both soil and effluent. The distinct temporal dynamics of ARG distribution between soil and effluent water for each manure type can be used to inform potential mitigation strategies in the future.

Twenty-four gilts (PIC 337 × 1050, PIC Genus, Hendersonville, TN) with an initial body weight (BW) of 33.09 ± 1.33 kg were used to investigate the effects of benzoic acid (BA) and a Bacillus-based direct-fed microbial (DFM) on the nutrient metabolism and manure gas emissions of growing pigs. Pigs were blocked by BW, placed into metabolism stalls, and randomly assigned to one of four dietary treatments: basal control (PC), low nitrogen (NC), PC plus 0.3% BA (PC+BA; VevoVitall, DSM Nutritional Products), and PC plus 0.3% BA and 0.025% DFM (PC+BA+DFM; PureGro, DSM Nutritional Products). Pigs were fed a common diet from day 0 to 14, and the experimental diets were fed in two phases (day 14 to 28 and day 28 to 53). The experiment consisted of four collection periods, with each period subdivided into two subperiods to collect samples for gas emissions and nutrient balance. Firstly, manure samples were collected for 72 h. Twice daily, urine and feces were weighed, and urine pH was measured. After each period, manure was subsampled and taken to the lab to measure gas emissions. Secondly, urine and feces were quantitatively collected for 96 h to allow for measurement of nutrient digestibility (ATTD) and retention. Data were analyzed as repeated measures in SAS 9.4 (SAS Inst., Cary, NC) with fixed effects of treatment, collection period, and block. Pig was the experimental unit, and results were considered significant at P ≤ 0.05 and a tendency at 0.05 < P ≤ 0.10. Pigs fed PC+BA had the greatest ADG compared to pigs fed NC (P = 0.016), with intermediate ADG for pigs fed PC or PC+BA+DFM (P ≥ 0.148). The ATTD of dry matter, gross energy, P, and N did not differ between treatments (P ≥ 0.093). However, the ATTD of Ca was reduced in pigs fed PC+BA+DFM compared to pigs fed PC+BA (P = 0.012). Pigs fed PC+BA or NC excreted less urinary N compared to PC and PC+BA+DFM (P ≤ 0.034), which contributed to greater nitrogen retention in PC+BA compared to PC (P = 0.016). Furthermore, decreased manure pH from pigs fed PC+BA or NC resulted in lower ammonia (NH3) emissions compared to pigs fed PC+BA+DFM or PC. There was no effect of dietary treatment on manure hydrogen sulfide, methane, or carbon dioxide emissions. In conclusion, supplementing 0.3% BA improved N retention and reduced manure pH and NH3 emissions, similar to feeding pigs low N, but improved the ADG of pigs when compared to feeding a low N diet., (© The Author(s) 2022. Published by Oxford University Press on behalf of the American Society of Animal Science.)

Three experiments (EXP) were conducted to determine the effect of feed additives on performance, intestinal integrity, gastrointestinal volatile fatty acids (VFA), and energy and nutrient digestion in nonchallenged nursery pigs. In EXP 1, 480 pigs (6.36-kg body weight, BW) were placed into 96 pens with 5 pigs/pen, and allotted to 1 of 10 dietary treatments: 1) negative control containing no feed additive (NC), 2) NC + 44 mg chlortetracycline and 38.5 mg tiamulin/kg diet (CTsb), 3) NC + 5% resistant potato starch (RSpo), 4) NC + 5% soluble corn fiber (SCF), 5) NC + 5% sugar beet pulp (SBP), 6) NC + 0.30% fatty acid mix (FAM), 7) NC + 0.10% phytogenic blend of essential oils and flavoring compounds (PHY), 8) NC + 50 mg Cu and 1,600 mg zinc oxide/kg diet (CuZn), 9) NC + 5% resistant corn starch (RScn), and 10) NC + 0.05% β-glucan (BG) for 28 d. There was no impact of dietary treatment on BW gain or feed intake (P ≥ 0.22). Pigs fed diets containing SCF, CTsb, and RSpo resulted in microbial community differences compared to pigs fed the NC (P < 0.05). In EXP 2, 48 barrows (12.8 kg BW) were selected at the end of EXP 1 and fed the same dietary treatments they had previously received: 1) NC, 2) NC + 5% RScn, 3) NC + 5% SCF, and 4) NC + FAM for 8 d. There was no effect of feeding diets containing RScn, SCF, or FAM on in vivo intestinal permeability (P ≤ 0.21). Ileal or colon pH, concentrations of VFA did not differ due to dietary treatment (P ≥ 0.36), but pigs fed diets containing FAM resulted in a greater butyric acid concentration in the cecum compared to pigs fed the NC (P ≤ 0.05). In EXP 3, 156 pigs (6.11 kg BW) were placed into 52 pens with 3 pigs/pen and allotted to 1 of 4 dietary treatments arranged in a factorial manner: 1) NC, 2) NC + 5% RSpo, 3) NC + 0.30% FAM, and 4) NC + 5% RSpo + 0.30% FAM for 24 d. Feeding pigs diets containing RSpo did not affect BW gain (P = 0.91) while pigs fed diets containing FAM grew improved BW gain (P = 0.09). Colonic butyric acid concentrations were greater in pigs fed diets containing RSpo (P = 0.03), while pigs fed diets containing FAM exhibited reduced total VFA concentrations (P = 0.11). The results indicate that supplementing diets with digestively resistant but fermentable fibers, short- and medium-chain fatty acids, or antibiotics do not have a consistent effect, positive or negative, on markers of intestinal integrity or barrier function, intestinal VFA patterns, ATTD of energy and nutrients, or on pig performance., (Published by Oxford University Press on behalf of the American Society of Animal Science 2022.)

The objectives were to determine how high levels (> 2.5 mg/kg diet) of deoxynivalenol (DON), in conjunction with other naturally occurring mycotoxins (MTX) would impact growth, intestinal integrity, and oxidative status, with or without a mitigation strategy, in nursery pigs. One-hundred and five pigs (5.5 ± 0.52 kg) were randomly allotted to 35 pens and fed dietary treatments for 45 d. Treatments were factorially arranged with the inclusion of MTX being low (L-MTX; < 1 mg/kg diet) or high (H-MTX; > 2.5 mg/kg diet) in combination with no mitigation strategy or the inclusion of a mitigation strategy (Biofix ® Plus, BPL; 1.5 mg/kg diet). There was no interaction between MTX level and BPL inclusion on average daily gain (ADG) or gain to feed ratio (GF), ( P > 0.10). Compared to pigs fed diets containing L-MTX, feeding pigs diets containing H-MTX decreased ADG and GF ( P < 0.05). The addition of BPL had no effect on ADG ( P > 0.10), but improved GF ( P = 0.09). There was an interaction between MTX and BPL on average daily feed intake (ADFI), where the addition of BPL had no effect on ADFI of pigs fed L-MTX diets but improved ADFI of pigs fed H-MTX diets ( P = 0.09). An interaction was detected between MTX and BPL on protein oxidation as measured by plasma protein carbonyls (PC, P = 0.01), where the inclusion of BPL decreased plasma PC in pigs fed H-MTX diets to a greater extent than pigs fed the L-MTX diets. There was no interaction between MTX and BPL, or an effect of MTX or BPL on DNA damage as measured by 8-hydroxy-2'dexoxyguanosine ( P > 0.10). There was no interaction between MTX and BPL, or a BPL effect on lipid damage as measured by thiobarbituic acid reactive substances (TBARS, P > 0.10), but pigs fed diets containing H-MTX exhibited lower concentrations of plasma TBARS ( P = 0.07) compared to pigs fed L-MTX diets. There was no interaction between MTX and BPL, or an effect of MTX or BPL on plasma lactulose and mannitol ratio as a measure of intestinal permeability ( P > 0.10). In conclusion, feeding H-MTX decreased ADG and GF, decreased plasma TBARS, but did not affect plasma 8-hydroxy-2'dexoxyguanosine or plasma LM ratio. The inclusion of a mitigation strategy improved ADFI when pigs were fed H-MTX diets and improved GF regardless of MTX level. Addition of a mitigation strategy also reduced plasma protein damage but did not affect indicators of DNA or lipid damage or affect gastrointestinal integrity., (Published by Oxford University Press for the American Society of Animal Science 2022.)

Agroecosystems in the upper Mississippi River Basin are highly productive but often contribute to deterioration of water quality and greenhouse gas emissions. Cover cropping and no-till are conservation strategies implemented to reduce the environmental impact of these agroecosystems. However, using multiple strategies can lead to systemwide interactions that are not fully understood. These interactions can affect not only environmental quality metrics, such as subsurface drainage nitrate losses or nitrous oxide (N 2 O) emissions, but also may influence crop production potential. A field trial was initiated comparing nitrate losses, N 2 O emissions, and crop production under systems with fall chisel plow tillage, fall chisel plow tillage with an oat (Avena sativa L.) cover crop (CP-oat), no-till (NT), no-till with a rye (Secale cereale L.) cover crop (NT-rye), and NT with zero N fertilizer. Pathways for nitrate losses and N 2 O emissions did not appear linked and were not tied to cover crop or tillage practices. Nitrate losses were linked with drainage volumes, and cover crops and tillage had limited effect on cumulative drainage volumes. Notably, NT-rye altered the relationship between drainage volume and nitrate losses by reducing nitrate concentrations, lowering nitrate losses by 59 ±9% compared with CP-oat and 67 ± 9% compared with NT. Neither cover crop nor tillage consistently affected N 2 O emissions or crop yield. Rather, N 2 O emissions were closely tied with fertilizer N application and seasonal weather patterns. These findings indicate that nitrate leaching and N 2 O emissions are regulated by separate mechanisms, so conservation management may require stacking multiple practices to be effective., (Published 2022. This article is a U.S. Government work and is in the public domain in the USA.)

Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen of concern because many isolates are multidrug-resistant (resistant to ≥3 antimicrobial classes) and metal tolerant. In this study, three in-feed additives were individually tested for their ability to reduce Salmonella I 4,[5],12:i:- shedding in swine: resistant potato starch (RPS), high amylose corn starch, and a fatty acid blend, compared with a standard control diet over 21 days. Only RPS-fed pigs exhibited a reduction in Salmonella fecal shedding, different bacterial community compositions, and different cecal short chain fatty acid (SCFA) profiles relative to control animals. Within the RPS treatment group, pigs shedding the least Salmonella tended to have greater cecal concentrations of butyrate, valerate, caproate, and succinate. Additionally, among RPS-fed pigs, several bacterial taxa ( Prevotella &#95;7, Olsenella , and Bifidobacterium, and others) exhibited negative relationships between their abundances of and the amount of Salmonella in the feces of their hosts. Many of these same taxa also had significant positive associations with cecal concentrations of butyrate, valerate, caproate, even though they are not known to produce these SCFAs. Together, these data suggest the RPS-associated reduction in Salmonella shedding may be dependent on the establishment of bacterial cross feeding interactions that result in the production of certain SCFAs. However, directly feeding a fatty acid mix did not replicate the effect. RPS supplementation could be an effective means to reduce multidrug-resistant (MDR) S. enterica serovar I 4,[5],12:i:- in swine, provided appropriate bacterial communities are present in the gut. IMPORTANCE Prebiotics, such as resistant potato starch (RPS), are types of food that help to support beneficial bacteria and their activities in the intestines. Salmonella enterica serovar I 4,[5],12:i:- is a foodborne pathogen that commonly resides in the intestines of pigs without disease, but can make humans sick if unintentionally consumed. Here we show that in Salmonella inoculated pigs, feeding them a diet containing RPS altered the colonization and activity of certain beneficial bacteria in a way that reduced the amount of Salmonella in their feces. Additionally, within those fed RPS, swine with higher abundance of these types of beneficial bacteria had less Salmonella I 4,[5],12:i:- in their feces. This work illustrates likely synergy between the prebiotic RPS and the presence of certain gut microorganisms to reduce the amount of Salmonella in the feces of pigs and therefore reduce the risk that humans will become ill with MDR Salmonella serovar I 4,[5],12:i:-.

Swine growers seeking to lower costs and environmental impact have turned to alternative carbohydrate feed sources. A feeding trial was conducted to determine the effect carbohydrate sources have on manure composition and gas emissions. A total of 48 gilts averaging 138 kg BW were fed diets consisting of (a) low fiber (LF) grain, or (b) high fiber (HF) aro-industrial co-product (AICP). The LF diets included corn and soybean meal (CSBM) and barley soybean meal (BSBM). The HF AICP diets were CSBM based and supplemented with one of the following materials: beet pulp; corn distillers dried grains with solubles; soybean hulls; or wheat bran. Diets were fed for 42 d with an average daily feed intake of 2.71 kg d -1 . Feces and urine were collected twice daily and added to manure storage containers in which manure slurries were monitored for gas emissions and chemical properties. Manures of animals fed HF diets had significantly (P < 0.05) more excretion of solids, C, N, and organic N, but less total S compared to pigs fed the LF diets. Animals feed HF diets had significantly (P < 0.05) higher levels of ammonia, sulfide, volatile fatty acids, and phenols in manure compared to pigs fed the LF diets. Manure of animals fed HF diets had 30% (P < 0.05) lower NH 3 and 17% lower hydrogen sulfide emissions; however, fiber had no impact on odor emissions. Based on the partitioning of nutrients, animals fed HF fiber diets had increased manure retention for C and N but decreased levels of N gas emissions and manure S. There were little differences in manure and gas emissions for animals fed LF diets, but the source of HF AICP diets had a significant impact on manure composition and gas emissions., Competing Interests: Declaration of competing interest The authors wish to confirm that there are no known conflicts of interest associated with this publication and there has been no significant financial support for this work that could have influenced its outcome., (Published by Elsevier B.V.)

For maize (Zea mays L.), nitrogen (N) fertilizer use is often summarized from field to global scales using average N use efficiency (NUE). But expressing NUE as averages is misleading because grain increase to added N diminishes near optimal yield. Thus, environmental risks increase as economic benefits decrease. Here, we use empirical datasets obtained in North America of maize grain yield response to N fertilizer (n = 189) to create and interpret incremental NUE (iNUE), or the change in NUE with change in N fertilization. We show for those last units of N applied to reach economic optimal N rate (EONR) iNUE for N removed with the grain is only about 6%. Conversely stated, for those last units of N applied over 90% is either lost to the environment during the growing season, remains as inorganic soil N that too may be lost after the growing season, or has been captured within maize stover and roots or soil organic matter pools. Results also showed iNUE decrease averaged 0.63% for medium-textured soils and 0.37% for fine-textured soils, attributable to fine-textured soils being more predisposed to denitrification and/or lower mineralization. Further analysis demonstrated the critical nature growing season water amount and distribution has on iNUE. Conditions with too much rainfall and/or uneven rainfall produced low iNUE. Producers realize this from experience, and it is uncertain weather that largely drives insurance fertilizer additions. Nitrogen fertilization creating low iNUE is environmentally problematic. Our results show that with modest sub-EONR fertilization and minor forgone profit, average NUE improvements of ~10% can be realized. Further, examining iNUE creates unique perspective and ideas for how to improve N fertilizer management tools, educational programs, and public policies and regulations., Competing Interests: The authors have declared that no competing interests exist.

The host-microbe interaction is critical for intestinal homeostasis. By-products from microbial metabolism of unabsorbed dietary components have been studied increasingly as potential contributors to health and disease. In vitro fermentation systems provide a way to simulate microbial activity and by-product production of the colon using human fecal samples. Objectives of the study were to determine how clarified supernatants from two different fermentation conditions affect markers of cell proliferation, differentiation, barrier function, and immune function in a human-induced pluripotent (iPSC) colon organoid model. SCFA and BCFA's of the supernatants were analyzed and were similar to known in vivo concentrations. Molecular results showed 25% of the clarified supernatant from batch fermentation led to a more physiological intestinal phenotype including increased markers of differentiation, including alkaline phosphatase, chromogranin A, SCFA transport monocarboxylate transporter-1, (6.2-fold, 2.1-fold, and 1.8-fold, respectively; p  < 0.05). Mucin production (mucin-2, mucin-4) was increased in cells treated with 25% supernatant, as observed by confocal microscopy. In addition, increased tight junction expression (claudin-3) was noted by immunofluorescence in 25% supernatant- treated cells. A dose-response increase in barrier function was observed over the 72-h time course, with a twofold increase in transepithelial electrical resistance (TER) in the 25% group compared to the control group ( p  < 0.05). To further investigate host effects, clarified supernatants from a continuous multistage fermentation representing the ascending (AC), transverse (TC), and descending (DC) colonic domains were utilized and some regional differences were observed including increased markers of inflammation (IL-1β, 6.15 pg/ml; IL-6, 27.58 pg/ml; TNFα, 4.49 pg/ml; p  < 0.05) in DC-treated samples only. Overall, clarified supernatants represent a valuable model to examine effects of microbial by-products on host intestinal development and function and future efforts will be designed to further understand microbial communities and metabolites, along with additional host response measures., Competing Interests: N/A, (©2022 The Authors FASEB BioAdvances published by The Federation of American Societies for Experimental Biology.)

Background: Of the > 2600 Salmonella serovars, Salmonella enterica serovar I 4,[5],12:i:- (serovar I 4,[5],12:i:-) has emerged as one of the most common causes of human salmonellosis and the most frequent multidrug-resistant (MDR; resistance to ≥3 antimicrobial classes) nontyphoidal Salmonella serovar in the U.S. Serovar I 4,[5],12:i:- isolates have been described globally with resistance to ampicillin, streptomycin, sulfisoxazole, and tetracycline (R-type ASSuT) and an integrative and conjugative element with multi-metal tolerance named Salmonella Genomic Island 4 (SGI-4)., Results: We analyzed 13,612 serovar I 4,[5],12:i:- strain sequences available in the NCBI Pathogen Detection database to determine global distribution, animal sources, presence of SGI-4, occurrence of R-type ASSuT, frequency of antimicrobial resistance (AMR), and potential transmission clusters. Genome sequences for serovar I 4,[5],12:i:- strains represented 30 countries from 5 continents (North America, Europe, Asia, Oceania, and South America), but sequences from the United States (59%) and the United Kingdom (28%) were dominant. The metal tolerance island SGI-4 and the R-type ASSuT were present in 71 and 55% of serovar I 4,[5],12:i:- strain sequences, respectively. Sixty-five percent of strain sequences were MDR which correlates to serovar I 4,[5],12:i:- being the most frequent MDR serovar. The distribution of serovar I 4,[5],12:i:- strain sequences in the NCBI Pathogen Detection database suggests that swine-associated strain sequences were the most frequent food-animal source and were significantly more likely to contain the metal tolerance island SGI-4 and genes for MDR compared to all other animal-associated isolate sequences., Conclusions: Our study illustrates how analysis of genomic sequences from the NCBI Pathogen Detection database can be utilized to identify the prevalence of genetic features such as antimicrobial resistance, metal tolerance, and virulence genes that may be responsible for the successful emergence of bacterial foodborne pathogens., (© 2022. The Author(s).)

Systems-level studies aimed at determining how soil properties are linked to plant production and ultimately animal response spatially are lacking. This study aims to identify if grazing pressure is linked to soil properties, terrain attributes, and above-ground plant accumulation and nutritive value in a silvopastoral (or integrated tree-livestock) system. Overall, cattle prefer grazing native grasses (2.81 vs. 1.24 h ha -1 AU -1 ) and udic (dry) landscape positions compared to aquic (wet) areas (2.07 vs. 1.60 h ha -1 AU -1 ). Greater grazing frequency occurs in udic soils with greater phosphorus and potassium contents and with accumulated forage with less lignin (P ≤ 0.05), which correspond to reduced elevation and greater tree height and diameter (shade) during summer mob grazing. Combining spatial monitoring technologies (both soil and animal) with forage allowance can optimize grazing systems management and sustainability spatially and temporally., (© 2022. The Author(s).)

Poultry litter is a valuable nutrient resource for agricultural production but is also a potential source for introducing antibiotic resistance genes (ARGs) and litter-associated bacteria (LAB) to the environment. Prairie strips have been demonstrated as an effective conservation practice to improve environmental quality in agroecosystems. This research aims to assess prairie strips' potential for reducing the transport of LAB and ARGs in runoff after litter application. Plot-scale rainfall simulations were performed using a replicated block design, with soil and surface runoff samples taken during the rainfall event. Microbial taxa and ARGs were characterized in the litter, soil, and water samples. In plots with litter application, LAB and ARGs were mainly detected in runoff, with very low detection in soils. Detection of ARGs in runoff, irrespective of strip installations, is consistent with previous observations of litter as a source of antimicrobial resistance (AMR) risks. The effectiveness of prairie strips to remove LAB and ARGs varied. In two of the three prairie strip plots, fewer AMR indicators were detected relative to control plots, suggesting that the prairie strips can potentially reduce these risks. In one plot, which was also associated with increased flow rate, we observed increased AMR indicators despite the installation of a prairie strip. Our observations highlight the need to prioritize understanding of soil properties even within the same site. Although we show that prairie strips can potentially reduce AMR risks, further research is needed to better understand the influence of rainfall timing, soil, and litter characteristics., (© 2022 The Authors. Journal of Environmental Quality published by Wiley Periodicals LLC on behalf of American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.)

Denitrification in woodchip bioreactors is a microbial process, but the effects of variations in bioreactors operation on microbial community structure are not well understood. Here, our goals were to understand hydraulic retention time (HRT) as a factor that influences woodchip bioreactor microbial community variation and structure in replicated field bioreactors and to evaluate relationships between microbial community membership and marker genes for denitrification. We used a combination of quantitative polymerase chain reaction of nirS, nirK, nosZI, and nosZII and 16S rRNA amplicon sequencing to characterize the microbial communities of nine pilot-scale woodchip bioreactors located at Iowa State University. Our results showed dynamic microbial communities but with persistent taxa between two sampling years and three HRTs. Similarities between functional gene copy numbers across sampling year and HRT indicate that the potential for denitrification is conserved despite differences in the microbial communities. These results are evidence that there are specific and persistent taxa within replicated bioreactors. Woodchip bioreactor microbial community membership is recommended to be the focus of future studies to better understand the relationship between microbial community functions and bioreactor management., (© 2021 The Authors. Journal of Environmental Quality © 2021 American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.)