United States dairy operations use antibiotics (primarily β-lactams and tetracyclines) to manage bacterial diseases in dairy cattle. Antibiotic residues, antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARG) can be found in dairy manure and may contribute to the spread of antibiotic resistance (AR). Although β-lactam residues are rarely detected in dairy manure, tetracycline residues are common and perhaps persistent. Generally, <15% of bacterial pathogen dairy manure isolates are ARB, although resistance to some antibiotics (e.g., tetracycline) can be higher. Based on available data, the prevalence of medically important ARB on dairy operations is generally static or may be declining for antibiotic-resistant Staphylococcus spp. Over 60 ARG can be found in dairy manure (including β-lactam and tetracycline resistance genes), although correlations with antibiotic usage, residues, and ARB have been inconsistent, possibly because of sampling and analytical limitations. Manure treatment systems have not been specifically designed to mitigate AR, though certain treatments have some capacity to do so. Generally, well-managed aerobic compost treatments reaching higher peak temperatures (>60°C) are more effective at mitigating antibiotic residues than static stockpiles, although this depends on the antibiotic residue and their interactions. Similarly, thermophilic anaerobic digesters operating under steady-state conditions may be more effective at mitigating antibiotic residues than mesophilic or irregularly operated digesters or anaerobic lagoons. The number of ARB may decline during composting and digestion or be enriched as the bacterial communities in these systems shift, affecting relative ARG abundance or acquire ARG during treatment. Antibiotic resistance genes often persist through these systems, although optimal management and higher operating temperature may facilitate their mitigation. Less is known about other manure treatments, although separation technologies may be unique in their ability to partition antibiotic residues based on sorption and solubility properties. Needed areas of study include determining natural levels of AR in dairy systems, standardizing and optimizing analytical techniques, and more studies of operating on-farm systems, so that treatment system performance and actual human health risks associated with levels of antibiotic residues, ARB, and ARG found in dairy manure can be accurately assessed.

The use of antimicrobials by the livestock industry can lead to the release of unmetabolized antimicrobials and antimicrobial resistance genes (ARG) into the environment. However, the relationship between antimicrobial use, residual antimicrobials, and ARG prevalence within manure is not well understood, specifically across temporal and locationbased scales. The current study determined ARG abundance in untreated manure blend pits and long-term storage systems from 11 conventional and one antimicrobial-free dairy farms in the Northeastern U.S. at six times over one-year. Thirteen ARGs corresponding to resistance mechanisms for tetracyclines, macrolides-lincosamides, sulfonamides, aminoglycosides, and β-lactams were quantified using a Custom qPCR Array or targeted qPCR. ARG abundance differed between locations, suggesting farm specific microbial resistomes. ARG abundance also varied temporally. Manure collected during the winter contained lower ARG abundances. Overall, normalized ARG concentrations did not correlate to average antimicrobial usage or tetracycline concentrations across farms and collection dates. Of the 13 ARGs analyzed, only four genes showed a higher abundance in samples from conventional farms and eight ARGs exhibited similar normalized concentrations in the conventional and antimicrobial-free farm samples. No clear trends were observed in ARG abundance between dairy manure obtained from blend pits and long-term storage collected during two drawdown periods (fall and spring), although higher ARG abundances were generally observed in spring compared to fall. This comprehensive study informs future studies needed to determine the contributions of ARGs from dairy manure to the environment.

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Methane (CH) is a powerful greenhouse gas emitted from natural and anthropogenic sources, and its emission rates vary among sources as a function of environment, microbial respiration, and feedbacks. Biological CH flux from natural and engineered systems is typically represented simply as generation of CH by methanogens minus oxidation by methanotrophs. In many cases, however, CH flux is modulated by transport and solubility mechanisms that occur before oxidation or other chemical transformation. The ability of fungi to directly oxidize CH remains unclear; however, their hydrophobic growths extending above microbial biofilms can improve surface area and sorption of hydrophobic gases. This can improve overall oxidation rates in a biofilm simply by improving phase transfer dynamics and bioavailability to bacterial or archaeal associates. This indirect facilitation is not necessarily intuitive, but there has been a recent emerging interest in harnessing these fungal abilities in engineering bioreactors and filtration systems designed to capture and oxidize CH. These dynamics may be playing a similar facilitative role in natural CH oxidation, where fungi may indirectly influence carbon mineralization and methanogen/methanotroph communities, and/or directly oxidize and dissolve gaseous CH. This review highlights these unique roles for fungi in determining net CH oxidation rates, and it summarizes the potential to harness fungi to mitigate CH emissions.

Abstract. The performance of manure management systems, on a component-by-component basis, at 11 Northeastern U.S. dairy farm concentrated animal feeding operations (CAFO) was quantified by semi-continuous monitoring for 15 months. Each collaborating farm (CF) had one or more of the following: solid-liquid separation (SLS), separated solids(SS) treatment by lime, rotary drum processing and windrow composting, anaerobic treatment by anaerobic digestion (AD), lagoons, and long-term storage(s). Operational and performance metrics included: temperature, pH, total solids (TS), volatile solids (VS), loading rates, and biogas production. Generally, most CFs had functional and well-operating systems based on expected and optimal operating conditions and sample constituent changes, although, sampling and monitoring limitations restricted complete performance assessments. Despite the limitations, differences in treatment effectiveness were noted, which were often related to influent conditions. Higher SLS solids capture efficiencies (typ. &gt; 40%), and biogas production rates (= 3.8 m3 d-1 lactating cow equivalents (LCE)-1), were associated with more concentrated manure slurry influents [TS &gt; 0.050 g g-1 wet basis (w.b.)]. Anaerobic digester configuration and the use of co-substrates also influenced anaerobic treatments. Generally, intensively managed ADs outperformed passively managed lagoons, and co-digestion enhanced biogas production (= 4.3 m3 d-1 LCE-1) and VS reductions (up to 48% w.b.), though co-digestion sometimes hampered process stability. The effectiveness of SS processing was also treatment dependent, with well-managed windrows yielding the greatest increases in TS concentrations (up to 0.600 g g-1 w.b.). Long-term storage of manure slurry had modest, non-significant, impacts on TS and VS concentrations, and pH. This work illustrated a range of manure management systems used on NE dairy farm CAFOs, parameterized their treatment of manure slurries and SS, and established a baseline for additional studies aimed at the capacity of these systems to mitigate emerging contaminant like antibiotic residues. Keywords: Anaerobic digestion, Antimicrobial resistance, Biogas, Compost, Lime treatment, Long-term storage, Solid-liquid separation.