Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the β-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function.

Microbial communities drive soil ecosystem function but are also susceptible to environmental disturbances. We investigated whether exposure to manure sourced from cattle either administered or not administered antibiotics affected microbially mediated terrestrial ecosystem function. We quantified changes in microbial community composition via amplicon sequencing, and terrestrial elemental cycling via a stable isotope pulse‐chase. Exposure to manure from antibiotic‐treated cattle caused: (i) changes in microbial community structure; and (ii) alterations in elemental cycling throughout the terrestrial system. This exposure caused changes in fungal : bacterial ratios, as well as changes in bacterial community structure. Additionally, exposure to manure from cattle treated with pirlimycin resulted in an approximate two‐fold increase in ecosystem respiration of recently fixed‐carbon, and a greater proportion of recently added nitrogen in plant and soil pools compared to the control manure. Manure from antibiotic‐treated cattle therefore affects terrestrial ecosystem function via the soil microbiome, causing decreased ecosystem carbon use efficiency, and altered nitrogen cycling.

In agroecosystems, application of manure from livestock treated with antibiotics has the potential to spread antibiotic compounds, resistant bacteria, and antibiotic resistance genes (ARGs) to soil. Although environmental transmission of antibiotic resistance is a major human health concern, few studies have looked at long-term effects on soil microbial communities from applying manure from livestock administered antibiotics. We examined the impacts of three years of repeated manure additions from cattle under different antibiotic treatments on microbial community structure and ARG abundances. While manure additions altered both soil bacterial and fungal communities, manure from cattle administered antibiotics further altered soil bacterial communities, but not fungal, compared to manure from antibiotic-free cattle. Furthermore, addition of manure from antibiotic-free cattle resulted in increased abundances of several ARGs compared to soil with no manure inputs, but manure from cattle administered antibiotics did not change overall profiles of ARG abundances compared to manure from antibiotic-free cattle. Finally, although bacterial and fungal community structure and ARG abundances varied among years, manure treatment effects on each were persistent during the full three-year period. Taken together, our results suggest that manure and antibiotic impacts on soil microbial communities can persist for long periods of repeated manure application. Furthermore, soil management strategies for addressing the antibiotic resistance crisis should consider the broader context of manure management. •Manure and antibiotics affected bacterial and fungal communities differently.•Antibiotic-free manure increased antibiotic resistance genes (ARGs) in soil.•Manure from cattle administered antibiotics had little additional effect on ARGs.•Impacts persisted over multiple years with repeated manure application.

Core Ideas The effect of cover crops on soil microbes and biogeochemistry was examined. Cover crops increase microbial biomass and bioavailable soil carbon. Increasing cover crop biomass amplifies belowground effects. Agricultural soils are largely degraded or under threat of degradation. Given a growing human population and the subsequent need to feed this population, agricultural practices must maintain productivity and soil quality. Cover cropping regimes are a management approach that aims to address these dual goals. Although the use of cover crops has been linked to many positive effects on soil quality and crop yields, few studies have examined their effects on soil microbial community structure and function under active farm management. We assessed soil characteristics and microbial community structure and function between agricultural field plots with and without cover crops. We expected microbes would respond in the short‐term to increasing cover crop biomass, with increases in microbial activity and a shift in C acquisition toward substrates indicative of root exudation. In the presence of cover crops, we found active microbial biomass and bioavailable‐C increased by 64 and 37%, respectively, indicating the potential for increased C sequestration. Soil NH 4 + increased by 64%, whereas soil NO 3 ‐ decreased by 30%, indicating a shift toward less mobile N forms and the potential of greater nutrient retention under cover cropping regimes. Additionally, increasing cover crop biomass was related to lower microbial biomass C/N ratios and to decreased utilization of recalcitrant C substrates. These results potentially suggest a shift toward greater microbial utilization of root‐derived compounds with increasing cover crop biomass. Together, these results indicate that, in the short‐term, the presence of cover crops may improve soil quality, as measured by indices of microbial activity, and soil C and nutrients.

Dairy manure often has elevated concentrations of copper (Cu) that when applied to soil may create toxicity risks to seedlings and soil microbes. Manure application also increases dissolved organic matter (DOM) in soil solution. We hypothesize that high rates of dairy manure amendment over several years will cause increased DOM in the soil that complexes Cu, increasing its mobility. To test this hypothesis, this study investigated water soluble Cu concentrations and dissolved organic carbon (DOC) in soil samples from 3 years of manure-amended soils. Samples were collected at two depths over the first 3 years of a long-term manure-amendment field trial. DOC, Cu, Fe, and P concentrations were measured in water extracts from the samples. Ultraviolet/visible (UV/Vis) spectra were used to assess the DOC characteristics. After 3 years of manure application, extractable Cu concentration was approximately four times greater in the surface and two times greater in subsurface samples of manure-amended soils as compared to non-amended control soils and traditional mineral fertilizer-amended soils. The extractable Cu concentration was greatest in plots that had the highest manure amendment rates (35 t ha (super -1) and 52 t ha (super -1) , dry weight). The UV/Vis parameters SUVA (sub 254) and E (sub 2) /E (sub 3) correlated with Cu concentration in the extracts (p < 0.05), suggesting that DOC characteristics are important in Cu-binding. The molecular characteristics of the DOC in the subsurface after 3 years of manure amendment were distinct from the DOC in the control plot, suggesting that manure amendment creates mobile DOC that may facilitate Cu mobilization through soil. The 10-fold increase in extractable Cu concentration after only 3 years of manure application indicates that repeated applications of the dairy manure sources used in this study at rates of 35 t/ha or greater may create risks for Cu toxicity and leaching of Cu into ground and surface waters.

Continuous application of dairy manure to soils can lead to excessive phosphorus (P) accumulation (legacy P), which requires understanding for managing nutrient availability and leaching. This study was conducted in Kimberly, ID, where dairy manure or conventional fertilizer was applied to calcareous soil plots under continuous crop rotations for 8 years (2013–2020), followed by 2 years with no amendment. To understand legacy P behavior in the soils, total P, organic/inorganic P, and plant‐available Olsen bicarbonate P and Truog extraction measurements were made from surface and subsurface samples. Additionally, P in soluble and less soluble calcium phosphate (Ca‐P) minerals was estimated using selective extractions, and P desorption was measured in a flow‐through reactor. Manure amendments resulted in increased total soil P and plant‐available P, particularly in the initial 5 years. In the 0‐ to 30‐cm depth, 54%–65% of the soil P added from manure amendments was readily soluble by the Truog P test. Phosphorus released from the 2022 manure‐amended soil in the desorption experiments was about five times greater than the fertilizer‐amended soil, suggesting high leaching potential. After 8 years of manure amendment, subsurface Olsen‐P levels exceeded the 40 mg kg−1 management threshold, suggesting P adsorption potential of the surface had become saturated, allowing for P leaching. In the manure‐amended surface soils, calcium phosphate minerals increased compared to the controls. Even after 2 years without manure amendment, soluble Ca‐P mineral phases persisted in the soils, which can be a long‐term source of P leaching. Core Ideas Repeated dairy manure application at 52 Mg ha−1 rate led to soil legacy phosphorus (P) buildup in calcareous soils in southern Idaho. Manure‐amended soil P leached downward causing subsurface soil Olsen P levels to exceed the regulatory limit. Manure‐amended soil had about five times greater leachable P than conventional chemical fertilizer‐amended soil. P desorption from manure‐amended surface soil was slower compared to subsurface soil. Slow P release was correlated with poorly crystalline Ca‐P mineral phases in the soils. Plain Language Summary Continuous application of dairy manure to soils leads to excessive phosphorus (P) accumulation (legacy P), which can contribute to nutrient availability and leaching. This study characterized P pools and measured P availability in calcareous soils amended with either dairy manure or conventional fertilizer for 8 years, followed by 2 years with no amendment. Manure amendments resulted in increased total soil P and plant‐available P. In the 0‐ to 30‐cm depth, 54%–65% of the soil P added from manure amendments was readily available. After 8 years of manure amendment and 2 years of no amendment, P was five times more available to the soil solution than in controls with chemical fertilizer treatments, suggesting high plant availability and leaching potential in the manure‐amended soils.

In confined animal feeding operations, such as dairies, manure is amended to soils at high rates leading to increases in P and organic matter in the soils. Phosphorus reacts with soil-Ca to form Ca-P minerals, which controls P availability for leaching and transport through the watershed. In this research, the effects of manure sourced dissolved organic matter (DOM) on P sorption on calcite were measured at different reaction times and concentrations. Reactions were monitored in 1% and 10% manure-to-water extract solutions spiked with P. When manure-DOM was present, a significant reduction in P sorption occurred (2–90% absolute decrease) compared to samples without manure-DOM. The greatest decrease occurred in the samples reacted in the 10% manure solution. XANES spectroscopic analysis showed that at 1% manure solution, a Ca-P phase similar to hydroxyapatite formed. In the calcite samples reacted in the 10% manure solution, K-edge XANES spectroscopy revealed that P occurred as a Ca-Mg-P phase instead of the less soluble hydroxyapatite-like phase. Results from this study suggest that in manure-amended calcareous soils, increased DOM from manure will decrease P sorption capacity and increase the overall P concentration in solution, which will increase the mobility of P and subsequently pose greater risks for impairment of surface water quality. [Display omitted] •Dairy manure added to calcareous soils releases dissolved organic carbon (DOC) and phosphate to the soil solution.•Dairy-manure sourced DOC greatly reduces P sorption.•High DOC levels promote formation of more soluble Ca-Mg-P minerals.•Mg substituted amorphous hydroxyapatite minerals occur on calcite minerals exposed to dairy manure extract.

Growing concerns about the global antimicrobial resistance crisis require a better understanding of how antibiotic resistance persists in soil and how antibiotic exposure impacts soil microbial communities. In agroecosystems, these responses are complex because environmental factors may influence how soil microbial communities respond to manure and antibiotic exposure. The study aimed to determine how soil type and moisture alter responses of microbial communities to additions of manure from cattle treated with antibiotics. Soil microcosms were constructed using two soil types at 15, 30, or 45% moisture. Microcosms received biweekly additions of manure from cattle given cephapirin or pirlimycin, antibiotic-free manure, or no manure. While soil type and moisture had the largest effects on microbiome structure, impacts of manure treatments on community structure and individual ARG abundances were observed across varying soil conditions. Activity was also affected, as respiration increased in the cephapirin treatment but decreased with pirlimycin. Manure from cattle antibiotics also increased NH 4 + and decreased NO 3 − availability in some scenarios, but the effects were heavily influenced by soil type and moisture. Overall, this work demonstrates that environmental conditions can alter how manure from cattle administered antibiotics impact the soil microbiome. A nuanced approach that considers environmental variability may benefit the long-term management of antibiotic resistance in soil systems.

Life cycle assessment (LCA) and techno-economic analysis (TEA) models are developed for a tertiary wastewater treatment system that employs a biochar-integrated reactive filtration (RF) approach. This innovative system incorporates the utilization of biochar (BC) either in conjunction with or independently of iron-ozone catalytic oxidation (CatOx)-resulting in two configurations: Fe-CatOx-BC-RF and BC-RF. The technology demonstrates 90%-99% total phosphorus removals, adsorption of phosphorus to biochar for recovery, and >90% destructive removal of observed micropollutants. In this work, we conduct an ISO-compliant LCA of a 49.2 m /day (9 gpm) field pilot-scale Fe-CatOx-BC-RF system and a 1130 m /day (0.3 MGD) water resource recovery facility (WRRF)-installed RF system, modeled with BC addition at the same rate of 0.45 g/L to quantify their environmental impacts. LCA results indicated that the Fe-CatOx-BC-RF pilot system is a BC dose-dependent carbon-negative technology at -1.21 kg CO e/m , where biochar addition constitutes a -1.53 kg/m CO e beneficial impact to the process. For the WRRF-installed RF system, modeled with the same rate of BC addition, the overall process changed from 0.02 kg CO e/m to a carbon negative -1.41 kg CO e/m , demonstrating potential as a biochar dose-dependent negative emissions technology. Using the C 100-year carbon accounting approach rather than C reduces these CO e metrics for the process by about 25%. A stochastic TEA for the cost of water treatment using this combinatorial P removal/recovery, micropollutant destructive removal, and disinfection advanced technology shows that at scale, the mean cost for treating 1130 m /day (0.3 MGD) WRRF secondary influent water with Fe-CatOx-BC-RF using the C metric is US$0.18 ± US$0.01/m to achieve overall process carbon neutrality. Using the same BC dose in an estimation of a 3780 m /day (1 MGD) Fe-CatOx-BC-RF facility, the carbon neutral cost of treatment is reduced further to US$0.08 ± $0.01 with added BC accounting for US$0.03/m . Overall, the results demonstrate the potential of carbon negativity to become a water treatment performance standard as important and attainable as pollutant and pathogen removal. PRACTITIONER POINTS: Life cycle assessment (LCA) of a pilot scale tertiary biochar water treatment process with or without catalytic ozonation at a WRRF shows a carbon negative global warming potential of -1.21-kg CO2e/m3 while removing 90%-99% TP and >90% of detected micropollutants. Biochar-integrated reactive filtration use can aid in long-term carbon sequestration by reducing the carbon footprint of advanced water treatment in a dose-dependent manner, allowing an overall carbon-neutral or carbon-negative process. A companion paper to this work (Yu et al., 2023) presents the details related to the process operation and mechanism and evaluates the pollutant removal performance of this Fe-CatOx-BC-RF process in engineering laboratory pilot research and field WRRF pilot-scale water resource recovery trials. Techno-economic analysis (TEA) of this biochar catalytic oxidation reactive filtration process using Monte Carlo stochastic modeling shows a forecasted carbon-neutral process cost with low P and micropollutant removal as US$0.11/m3 ± 0.01 for a 3780-m3/day (1 MGD) scale installation with BC cost at US$0.03/m3 of that total. The results demonstrate the potential of carbon negativity to become a water treatmentperformance standard as important and attainable as pollutant and pathogen removal.

Surface broadcast of dairy slurry is a common practice; however, concerns over nuisance odors and nutrient losses have prompted research into alternatives. Manure injection is one practice that addresses these concerns but is not widely adopted. Therefore, two studies were conducted to quantify NH3-N loss by volatilization, impacts on soil N cycling, and microbial response between surface broadcast and subsurface injection of dairy slurry. A constant air flow volatilization chamber system measured NH3-N losses and soil inorganic N, mineralizable carbon, and active microbial biomass. A 40-day static air incubation was performed to study nitrogen transformations over a longer period after application. Statistical significance was evaluated at the α = 0.05 level. In the volatilization study, subsurface injection reduced NH3-N losses by 98% and 87% in a clay loam and sandy loam, respectively, resulting in greater soil inorganic nitrogen compared with surface application. There were no significant differences in active microbial biomass between treatments. Surface application prompted greater microbial respiration in the sandy loam, but there were no significant differences between treatments in the clay loam. In the static incubation study, differences in soil NO3-N became significant on day 28, and by day 40, injection showed increases in soil NO3-N of 13% and 26% in the sandy loam and clay loam, respectively, relative to surface application. While the effect of subsurface injection on soil microbial response was unclear, it remains a tool that can greatly reduce NH3-N losses by volatilization and increase soil plant available nitrogen.