Microbial Responses to Biochar Soil Amendment and Influential Factors: A Three-Level Meta-Analysis.

Biochar is a multifunctional soil conditioner capable of enhancing soil health and crop production while reducing greenhouse gas emissions. Understanding how soil microbes respond to biochar amendment is a vital step toward precision biochar application. Here, we quantitatively synthesized 3899 observations of 24 microbial responses from 61 primary studies worldwide. Biochar significantly boosts microbial abundance [microbial biomass carbon (MBC) > colony-forming unit (CFU)] and C- and N-cycling functions (dehydrogenase > cellulase > urease > invertase > nirS) and increases the potential nitrification rate by 40.8% while reducing cumulative N2O by 12.7%. Biochar derived at lower pyrolysis temperatures can better improve dehydrogenase and acid phosphatase and thus nutrient retention, but it also leads to more cumulative CO2. Biochar derived from lignocellulose or agricultural biomass can better inhibit N2O through modulating denitrification genes nirS and nosZ; repeated biochar amendment may be needed as inhibition is stronger in shorter durations. This study contributes to our understanding of microbial responses to soil biochar amendment and highlights the promise of purpose-driven biochar production and application in sustainable agriculture such that biochar preparation can be tuned to elicit the desired soil microbial responses, and an amendment plan can be optimized to invoke multiple benefits. We also discussed current knowledge gaps and future research needs.

Contrasting Genetic Diversity of Listeria Pathogenicity Islands 3 and 4 Harbored by Nonpathogenic Listeria spp.

Listeria monocytogenes causes the severe foodborne disease listeriosis. Several clonal groups of L. monocytogenes possess the pathogenicity islands Listeria pathogenicity island 3 (LIPI-3) and LIPI-4. Here, we investigated the prevalence and genetic diversity of LIPI-3 and LIPI-4 among 63 strains of seven nonpathogenic Listeria spp. from the natural environment, i.e., wildlife (black bears [Ursus americanus]) and surface water. Analysis of the whole-genome sequence data suggested that both islands were horizontally acquired but differed considerably in their incidence and genetic diversity. LIPI-3 was identified among half of the L. innocua strains in the same genomic location as in L. monocytogenes (guaA hot spot) in a truncated form, with only three strains harboring full-length LIPI-3, and a highly divergent partial LIPI-3 was observed in three Listeria seeligeri strains, outside the guaA hot spot. Premature stop codons (PMSCs) and frameshifts were frequently noted in the LIPI-3 gene encoding listeriolysin S. On the other hand, full-length LIPI-4 without any PMSCs was found in all Listeria innocua strains, in the same genomic location as L. monocytogenes and with ~85% similarity to the L. monocytogenes counterpart. Our study provides intriguing examples of genetic changes that pathogenicity islands may undergo in nonpathogenic bacterial species, potentially in response to environmental pressures that promote either maintenance or degeneration of the islands. Investigations of the roles that LIPI-3 and LIPI-4 play in nonpathogenic Listeria spp. are warranted to further understand the differential evolution of genetic elements in pathogenic versus nonpathogenic hosts of the same genus. IMPORTANCE Listeria monocytogenes is a serious foodborne pathogen that can harbor the pathogenicity islands Listeria pathogenicity island 3 (LIPI-3) and LIPI-4. Intriguingly, these have also been reported in nonpathogenic L. innocua from food and farm environments, though limited information is available for strains from the natural environment. Here, we analyzed whole-genome sequence data of nonpathogenic Listeria spp. from wildlife and surface water to further elucidate the genetic diversity and evolution of LIPI-3 and LIPI-4 in Listeria. While the full-length islands were found only in L. innocua, LIPI-3 was uncommon and exhibited frequent truncation and genetic diversification, while LIPI-4 was remarkable in being ubiquitous, albeit diversified from L. monocytogenes. These contrasting features demonstrate that pathogenicity islands in nonpathogenic hosts can evolve along different trajectories, leading to either degeneration or maintenance, and highlight the need to examine their physiological roles in nonpathogenic hosts.

Diversity of Plasmids and Genes Encoding Resistance to Extended-Spectrum ß-Lactamase in Escherichia coli from Different Animal Sources.

Antimicrobial resistance associated with the spread of plasmid-encoded extended-spectrum ß-lactamase (ESBL) genes conferring resistance to third generation cephalosporins is increasing worldwide. However, data on the population of ESBL producing E. coli in different animal sources and their antimicrobial characteristics are limited. The purpose of this study was to investigate potential reservoirs of ESBL-encoded genes in E. coli isolated from swine, beef, dairy, and poultry collected from different regions of the United States using whole-genome sequencing (WGS). Three hundred isolates were typed into different phylogroups, characterized by BOX AIR-1 PCR and tested for resistance to antimicrobials. Of the 300 isolates, 59.7% were resistant to sulfisoxazole, 49.3% to tetracycline, 32.3% to cephalothin, 22.3% to ampicillin, 20% to streptomycin, 16% to ticarcillin; resistance to the remaining 12 antimicrobials was less than 10%. Phylogroups A and B1 were most prevalent with A (n = 92, 30%) and B1 (87 = 29%). A total of nine E. coli isolates were confirmed as ESBL producers by double-disk synergy testing and multidrug resistant (MDR) to at least three antimicrobial drug classes. Using WGS, significantly higher numbers of ESBL-E. coli were detected in swine and dairy manure than from any other animal sources, suggesting that these may be the primary animal sources for ESBL producing E. coli. These isolates carry plasmids, such as IncFIA(B), IncFII, IncX1, IncX4, IncQ1, CollRNAI, Col440I, and acquired ARGs aph(6)-Id, aph(3″)-Ib, aadA5, aph(3')-Ia, blaCTX-M-15, blaTEM-1B, mphA, ermB, catA1, sul1, sul2, tetB, dfrA17. One of the E. coli isolates from swine with ST 410 was resistant to nine antibiotics and carried more than 28 virulence factors, and this ST has been shown to belong to an international high-risk clone. Our data suggests that ESBL producing E. coli are widely distributed in different animal sources, but swine and dairy cattle may be their main reservoir.

Antimicrobial Resistance in Escherichia coli and Enterococcal Isolates From Irrigation Return Flows in a High-Desert Watershed.

Irrigation return flows (IRFs) collect surface runoff and subsurface drainage, causing them to have elevated contaminant and bacterial levels, and making them a potential source of pollutants. The purpose of this study was to determine antimicrobial susceptibility among Escherichia coli and enterococcal isolates that were collected from IRFs in a south-central Idaho watershed. Environmental isolates can be a potentially important source of antimicrobial resistance (AMR) and IRFs may be one way resistance genes are transported out of agroecosystems. Water samples were collected from nine IRFs and one background site (canal water from Snake River) on a biweekly basis during 2018. Escherichia coli and enterococci were enumerated via a most probable number (MPN) technique, then subsamples were plated on selective media to obtain isolates. Isolates of E. coli (187) or enterococci (185) were tested for antimicrobial susceptibility using Sensititre broth microdilution plates. For E. coli, 13% (25/187) of isolates were resistant to tetracycline, with fewer numbers being resistant to 13 other antimicrobials, with none resistant to gentamicin. While 75% (141/187) of the E. coli isolates were pan-susceptible, 12 multidrug resistance (MDR) patterns with 17 isolates exhibiting resistance to up to seven drug classes (10 antimicrobials). For the enterococcal species, only 9% (16/185) of isolates were pan-susceptible and the single highest resistance was to lincomycin (138/185; 75%) followed by nitrofurantoin (56/185; 30%) and quinupristin/dalfopristin (34/185; 18%). In addition, 13 enterococcal isolates belonging to Enterococcus faecalis, Enterococcus faecium, Enterococcus casseliflavus, and Enterococcus thailandicus, were determined to be MDR to up to six different antimicrobial drug classes. None of the enterococcal isolates were resistant to gentamycin, linezolid, tigecycline, and vancomycin.

A newly developed Escherichia coli isolate panel from a cross section of U.S. animal production systems reveals geographic and commodity-based differences in antibiotic resistance gene carriage.

There are limited numbers of Escherichia coli isolate panels that represent United States food animal production. The majority of existing Escherichia coli isolate panels are typically designed: (i) to optimize genetic and/or phenotypic diversity; or (ii) focus on human isolates. To address this shortfall in agriculturally-related resources, we have assembled a publicly-available isolate panel (AgEc) from the four major animal production commodities in the United States, including beef, dairy, poultry, and swine, as well as isolates from agriculturally-impacted environments, and other commodity groups. Diversity analyses by phylotyping and Pulsed-field Gel Electrophoresis revealed a highly diverse composition, with the 300 isolates clustered into 71 PFGE sub-types based upon an 80% similarity cutoff. To demonstrate the panel's utility, tetracycline and sulfonamide resistance genes were assayed, which identified 131 isolates harboring genes involved in tetracycline resistance, and 41 isolates containing sulfonamide resistance genes. There was strong overlap in the two pools of isolates, 38 of the 41 isolates harboring sulfonamide resistance genes also contained tetracycline resistance genes. Analysis of antimicrobial resistance gene patterns revealed significant differences along commodity and geographical lines. This panel therefore provides the research community an E. coli isolate panel for study of issues pertinent to U.S. food animal production.

Antibiotic resistance genes, class 1 integrons, and IncP-1/IncQ-1 plasmids in irrigation return flows.

Surface waters could be a dominant route by which antibiotic resistance genes (ARGs) are disseminated. In the present study we explored the prevalence and abundance of ARGs [blaCTX-M-1, erm(B), sul1, tet(B), tet(M), and tet(X)], class 1 integron-integrase gene (intI1), and IncP-1 and IncQ-1 plasmids in eight irrigation return flows (IRFs) and a background site (Main Line Canal, MLC) in the Upper Snake Rock watershed in southern Idaho. Grab samples were collected on a monthly basis for a calendar year, which were processed to extract microbial DNA, followed by droplet digital PCR to quantify the gene copies on an absolute (per 100 mL) and relative (per 16S rRNA gene copies) basis. The antibiotic resistance and intI1 genes and IncP-1/IncQ-1 plasmids were recovered at all IRF sampling sites with detections ranging from 55 to 81 out of 81 water sampling events. The blaCTX-M-1 gene was detected the least frequently (68%), while the other genes were detected more frequently (88-100%). All of the genes were also detected at MLC from April to Oct when water was present in the canal. The genes from lowest to greatest relative abundance in the IRFs were: blaCTX-M-1 < erm(B) < tet(B) < IncQ-1 < tet(M) < sul1 < intI1 = IncP-1 < tet(X). When compared to the average annual relative gene abundances in MLC water samples, they were found to be at statistically greater levels (P ≤ 0.008) except that of the IncP-1 and IncQ-1 plasmids (P = 0.8 and 0.08, respectively). The fact that most IRFs contained higher levels than found in the canal water, indicates that IRFs can be a point source of ARGs that ultimately discharge into surface waters.

Survey of selected antibiotic resistance genes in agricultural and non-agricultural soils in south-central Idaho.

Improving our understanding of antibiotic resistance in soils is important for the protection of human, animal and ecological health. In south-central Idaho, antibiotic resistance genes (ARGs) [blaCTX-M-1, erm(B), sul1, tet(B), tet(M) and tet(X)] and a class 1 integron-integrase gene (intI1) were quantified in agricultural and non-agricultural soils (96 total sites) under various land use practices (cropland, forestland, inactive cropland, pastureland, rangeland, recreational, residential). We hypothesized that gene occurrence and abundance would be greater in intensively managed agricultural soils. The ARGs (except blaCTX-M-1) and intI1 gene were detected in many of the soils (15 to 58 out of 96 samples), with sul1 and intI1 being detected the most frequently (60% of samples). All of the genes were detected more frequently in the cropland soils (46 sites) and at statistically greater relative abundances (per 16S rRNA gene) than in soils from the other land use categories. When the cropland gene data was separated by sites that had received dairy manure, dairy wastewater, and/or biosolids (27 sites), it was revealed that the genes [except tet(B)] were found at statistically greater abundances (7- to 22-fold higher on average) than in soils that were not treated. The results from this study provide convincing evidence that manure/biosolids use in Idaho cropland soils increases the expansion of antibiotic resistance-related determinants.

Tracking antibiotic resistance genes in soil irrigated with dairy wastewater.

The application of dairy wastewater to agricultural soils is a widely used practice to irrigate crops and recycle nutrients. In this study, small-scale field plots were irrigated monthly (6 times) with dairy wastewater (100%), wastewater diluted to 50% with irrigation (canal) water, and diluted wastewater spiked with copper sulfate (50 mg Cu L-1), while control plots were irrigated with canal water. In addition, half of all plots were either planted with wheat or were left as bare soil. Biweekly soil samples were collected during this period and processed to determine the occurrence and abundance of antibiotic resistance genes [blaCTX-M-1, erm(B), sul1, tet(B), tet(M), and tet(X)] and a class 1 integron-integrase gene (intI1) via quantitative real-time PCR (qPCR). Only sul1 and tet(X) were detected in soil (3 out of 32 samples) before the wastewater treatments were applied. However, the occurrence and relative abundance (normalized to 16S rRNA gene copies) of most genes [erm(B), intI1, sul1, and tet(M)] increased dramatically after wastewater irrigation and levels were maintained during the entire study period. blaCTX-M-1 was the only gene not detected in wastewater-treated soils, which is likely related to its absence in the dairy wastewater. Relative gene levels in soil were found to be statistically similar among the treatments in most cases, regardless of the wastewater percentage applied and presence or absence of plants. The key result from this study is that dairy wastewater irrigation significantly enlarges the reservoir of ARGs and intI1 in soils, while detection of these genes rarely occurred in soil irrigated only with canal water. In addition, elevated levels of Cu in the wastewater and treated soil did not produce a concomitant increase of the ARG levels.

Occurrence and abundance of antibiotic resistance genes in agricultural soil receiving dairy manure.

Animal manures are commonly used to enhance soil fertility, but there are growing concerns over the impact of this practice on the development and dissemination of antibiotic resistance. The aim of this field study was to determine the effect of annual dairy manure applications on the occurrence and abundance of antibiotic resistance genes (ARGs) in an agricultural soil during four years of crop production. Treatments included (i) control (no fertilizer or manure), (ii) inorganic fertilizer and (iii) dairy manure at three application rates. Quantitative PCR was used to determine absolute (per g dry soil) and relative (per 16S rRNA gene) abundances of ARGs in DNA extracted from soils. Six ARGs and one class 1 integron were targeted. This study found that (i) manure application increases ARG abundances above background soil levels; (ii) the higher the manure application rate, the higher the ARG abundance in soil; (iii) the amount of manure applied is more important than reoccurring annual applications of the same amount of manure; (iv) absolute abundance and occurrence of ARGs decreases with increasing soil depth, but relative abundances remained constant. This study demonstrated that dairy manure applications to soil significantly increase the abundance of clinically relevant ARGs when compared to control and inorganic fertilized plots.

Use of new technologies to evaluate the environmental footprint of feedlot systems.

With increased concern over the effects of livestock production on the environment, a number of new technologies have evolved to help scientists evaluate the environmental footprint of beef cattle. The objective of this review was to provide an overview of some of those techniques. These techniques include methods to measure individual feed intake, enteric methane emissions, ground-level greenhouse gas and ammonia emissions, feedlot and pasture emissions, and identify potential pathogens. The appropriate method to use for measuring emissions will vary depending upon the type of emission, the emission source, and the goals of the research. These methods should also be validated to assure they produce accurate results and achieve the goals of the research project. In addition, we must not forget to properly use existing technologies and methods such as proper feed mixing, feeding management, feed/ingredient sampling, and nutrient analysis.

Occurrence of Antibiotics in an Agricultural Watershed in South-Central Idaho.

The polar organic compound integrative sampler (POCIS) is a tool that has been effectively used to passively sample organic pollutants over long periods in aquatic environments. In this study, POCIS were used to investigate the spatial and temporal occurrence of 21 antibiotics in irrigation return flows and upstream sites of an intensively managed agricultural watershed in south-central Idaho. The antibiotic metabolite, erythromycin-HO, and the antibiotics monensin, oxytetracycline, sulfadimethoxine, sulfamethazine, sulfamethoxazole, trimethoprim, and tylosin were detected at frequencies ranging from 3.1 to 62.5%, with monensin having the highest rate of detection. The fact that monensin was the most frequently detected compound indicates that it is entering return flows in runoff from fields that had received livestock manure or wastewater. Antibiotics (except oxytetracycline, sulfamethazine, and tylosin) were also detected at an upstream site that consisted of diverted Snake River water and is the source of irrigation water for the watershed. Therefore, even cropped soils that are not treated with manure are still receiving low-level antibiotics during irrigation events. This study provides the first set of evidence that surface waters within this agricultural watershed contain antibiotic residues associated with veterinary and human uses.

Nutritional and Environmental Effects on Ammonia Emissions from Dairy Cattle Housing: A Meta-Analysis.

Nitrogen excreted in dairy manure can be potentially transformed and emitted as NH, which can create livestock and human respiratory problems and be an indirect source of NO. The objectives of this study were to: (i) investigate environmental factors influencing NH emissions from dairy housing; and (ii) identify key explanatory variables in the NH emissions prediction from dairy housing using a meta-analytical approach. Data from 25 studies were used for the preliminary analysis, and data from 10 studies reporting 87 treatment means were used for the meta-analysis. Season and flooring type significantly affected NH emissions. For nutritional effect analysis, the between-study variability (heterogeneity) of mean NH emission was estimated using random-effect models and had a significant effect ( < 0.01). Therefore, random-effect models were extended to mixed-effect models to explain heterogeneity regarding the available dietary and animal variables. The final mixed-effect model included milk yield, dietary crude protein, and dry matter intake separately, explaining 45.5% of NH emissions heterogeneity. A unit increase in milk yield (kg d) resulted in a 4.9 g cow d reduction in NH emissions, and a unit increase in dietary crude protein content (%) and dry matter intake (kg d) resulted in 10.2 and 16.3 g cow d increases in NH emissions, respectively, in the scope of this study. These results can be further used to help identify mitigation strategies to reduce NH emissions from dairy housing by developing predictive models that could determine variables with strong association with NH emissions.

Antibiotics in Agroecosystems: Introduction to the Special Section.

The presence of antibiotic drug residues, antibiotic resistant bacteria, and antibiotic resistance genes in agroecosystems has become a significant area of research in recent years and is a growing public health concern. While antibiotics are used in both human medicine and agricultural practices, the majority of their use occurs in animal production where historically they have been used for growth promotion, in addition to the prevention and treatment of disease. The widespread use of antibiotics and the application of animal wastes to agricultural lands play major roles in the introduction of antibiotic-related contamination into the environment. Overt toxicity in organisms directly exposed to antibiotics in agroecosystems is typically not a major concern because environmental concentrations are generally lower than therapeutic doses. However, the impacts of introducing antibiotic contaminants into the environment are unknown, and concerns have been raised about the health of humans, animals, and ecosystems. Despite increased research focused on the occurrence and fate of antibiotics and antibiotic resistance over the past decade, standard methods and practices for analyzing environmental samples are limited and future research needs are becoming evident. To highlight and address these issues in detail, this special collection of papers was developed with a framework of five core review papers that address the (i) overall state of science of antibiotics and antibiotic resistance in agroecosystems using a causal model, (ii) chemical analysis of antibiotics found in the environment, (iii) need for background and baseline data for studies of antibiotic resistance in agroecosystems with a decision-making tool to assist in designing research studies, as well as (iv) culture- and (v) molecular-based methods for analyzing antibiotic resistance in the environment. With a focus on the core review papers, this introduction summarizes the current state of science for analyzing antibiotics and antibiotic resistance in agroecosystems, discusses current knowledge gaps, and develops future research priorities. This introduction also contains a glossary of terms used in the core reivew papers of this special section. The purpose of the glossary is to provide a common terminology that clearly characterizes the concepts shared throughout the narratives of each review paper.

How Should We Be Determining Background and Baseline Antibiotic Resistance Levels in Agroecosystem Research?

Although historically, antibiotic resistance has occurred naturally in environmental bacteria, many questions remain regarding the specifics of how humans and animals contribute to the development and spread of antibiotic resistance in agroecosystems. Additional research is necessary to completely understand the potential risks to human, animal, and ecological health in systems altered by antibiotic-resistance-related contamination. At present, analyzing and interpreting the effects of human and animal inputs on antibiotic resistance in agroecosystems is difficult, since standard research terminology and protocols do not exist for studying background and baseline levels of resistance in the environment. To improve the state of science in antibiotic-resistance-related research in agroecosystems, researchers are encouraged to incorporate baseline data within the study system and background data from outside the study system to normalize the study data and determine the potential impact of antibiotic-resistance-related determinants on a specific agroecosystem. Therefore, the aims of this review were to (i) present standard definitions for commonly used terms in environmental antibiotic resistance research and (ii) illustrate the need for research standards (normalization) within and between studies of antibiotic resistance in agroecosystems. To foster synergy among antibiotic resistance researchers, a new surveillance and decision-making tool is proposed to assist researchers in determining the most relevant and important antibiotic-resistance-related targets to focus on in their given agroecosystems. Incorporation of these components within antibiotic-resistance-related studies should allow for a more comprehensive and accurate picture of the current and future states of antibiotic resistance in the environment.

Detection of Purple Sulfur Bacteria in Purple and Non-purple Dairy Wastewaters.

The presence of purple bacteria in manure storage lagoons is often associated with reduced odors. In this study, our objectives were to determine the occurrence of purple sulfur bacteria (PSB) in seven dairy wastewater lagoons and to identify possible linkages between wastewater properties and purple blooms. Community DNA was extracted from composited wastewater samples, and a conservative 16S rRNA gene sequence within and genes found in both purple sulfur and nonsulfur bacteria was amplified. Analysis of the genes indicated that all of the lagoons contained sequences that were 92 to 97% similar with . Sequences from a few lagoons were also found to be similar with other PSB, such as sp. (97%), (93-100%), and (95-98%). sequences amplified from enrichment and pure cultures were most similar to (93-96%). Carotenoid pigment concentrations, which were used as an indirect measure of purple bacteria levels in the wastewaters, were found to be positively correlated with salinity, nitrogen, total and volatile solids, and chemical oxygen demand; however, salinity could be the dominant factor influencing purple blooms. Due to the detection of PSB sequences in all lagoons, our findings suggest that the non-purple lagoons may have been purple in the past or may have the potential to become purple in the future.

Estimation of infectious risks in residential populations exposed to airborne pathogens during center pivot irrigation of dairy wastewaters.

In the western United States where dairy wastewaters are commonly land applied, there are concerns over individuals being exposed to airborne pathogens. In response, a quantitative microbial risk assessment (QMRA) was performed to estimate infectious risks after inhalation exposure of pathogens aerosolized during center pivot irrigation of diluted dairy wastewaters. The dispersion of pathogens (Campylobacter jejuni, Escherichia coli O157:H7, non-O157 E. coli, Listeria monocytogenes, and Salmonella spp.) was modeled using the atmospheric dispersion model, AERMOD. Pathogen concentrations at downwind receptors were used to calculate infectious risks during one-time (1, 8, and 24 h) and multiday (7 d at 1 h d(-1)) exposure events using a ß-Poisson dose-response model. This assessment considered risk of infection in residential populations that were 1 to 10 km from a center pivot operation. In the simulations, infectious risks were estimated to be the greatest in individuals closest to the center pivot, as a result of a higher pathogen dose. On the basis of the results from this QMRA, it is recommended that wastewaters only be applied during daylight hours when inactivation and dilution of airborne pathogens is highest. Further refinement of the dispersion and dose-response models should be considered to increase the utility of this QMRA.

Livestock GRACEnet: A Workgroup Dedicated to Evaluating and Mitigating Emissions from Livestock Production.

Ammonia, greenhouse gases, and particulate emissions from livestock operations can potentially affect air quality at local, regional, and even global scales. These pollutants, many of which are generated through various anthropogenic activities, are being increasingly scrutinized by regulatory authorities. Regulation of emissions from livestock production systems will ultimately increase on farm costs, which will then be passed onto consumers. Therefore, it is essential that scientifically based emission factors are developed for on-farm emissions of air quality constituents to improve inventories and assign appropriate reduction targets. To generate a larger database of on-farm emissions, the USDA-ARS created the workgroup Livestock GRACEnet (Greenhouse gas Reduction through Agricultural Carbon Enhancement Network). This introduction for the special section of papers highlights some of the research presently being conducted by members of Livestock GRACEnet with the intent of drawing attention to critical information gaps, such as (i) improving emissions measurements; (ii) developing emissions factors; (iii) developing and validating tools for estimating emissions; and (iv) mitigating emissions. We also provide a synthesis of the literature with respect to key research areas related to livestock emissions, including feeding strategies, animal housing, manure management, and manure land application, and discuss future research priorities and directions.

The characterization of microorganisms in dairy wastewater storage ponds.

Dairy wastewaters from storage ponds are commonly land applied to irrigate forage crops. Given that diverse microbial populations are associated with cattle feces, the objective of this study was to use a culture-independent approach to characterize bacteria and archaea in dairy wastewaters. Using domain-specific primers, a region of the 16S rRNA gene was amplified from pooled DNA extracts from 30 dairy wastewaters and subsequently used to create a clone library. A total of 152 bacterial clones were examined and sequence matches were affiliated with the following groups: Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Synergistetes. Firmicutes was identified as the largest phylum, representing up to 69% of the clone sequences. Of 167 clones representing Archaea, seven genera were found to be closely related (91-100% sequence similarity) to isolates obtained from sediments and feces. Most of the putative sequence matches (98%) represented members from the class Methanomicrobia. With respect to the archaeal clones, only one of the putative sequence matches was affiliated with a methanogenic bacterium known to inhabit the rumen.

Greenhouse gas and ammonia emissions from an open-freestall dairy in southern idaho.

Concentrated dairy operations emit trace gases such as ammonia (NH), methane (CH), and nitrous oxide (NO) to the atmosphere. The implementation of air quality regulations in livestock-producing states increases the need for accurate on-farm determination of emission rates. Our objective was to determine the emission rates of NH, CH, and NO from the open-freestall and wastewater pond source areas on a commercial dairy in southern Idaho using a flush system with anaerobic digestion. Gas concentrations and wind statistics were measured and used with an inverse dispersion model to calculate emission rates. Average emissions per cow per day from the open-freestall source area were 0.08 kg NH, 0.41 kg CH, and 0.02 kg NO. Average emissions from the wastewater ponds (g m d) were 6.8 NH, 22 CH, and 0.2 NO. The combined emissions on a per cow per day basis from the open-freestall and wastewater pond areas averaged 0.20 kg NH and 0.75 kg CH. Combined NO emissions were not calculated due to limited available data. The wastewater ponds were the greatest source of total farm NH emissions (67%) in spring and summer. The emissions of CH were approximately equal from the two source areas in spring and summer. During the late fall and winter months, the open-freestall area constituted the greatest source area of NH and CH emissions. Data from this study can be used to develop trace gas emissions factors from open-freestall dairies in southern Idaho and other open-freestall production systems in similar climatic regions.

Use of standardized procedures to evaluate metal leaching from waste foundry sands.

As part of the casting process, foundries create sand molds and cores to hold the molten metal to specific dimensional tolerances. Although most of the waste foundry sands (WFSs) from this process are land filled, there is great interest in diverting them for use in agricultural and geotechnical applications. One potential limitation to their beneficial use is concern that the WFSs will leach high levels of trace metals. The aim of this study was to quantify Ag, Ba, Cd, Cr, Cu, Ni, Pb, and Zn in leaching extracts from 96 waste molding and core sands from ferrous and nonferrous foundries. The procedures used to assess leaching in the WFSs were the Extraction Procedure, the Toxicity Characteristic Leaching Procedure, and the American Society for Testing and Materials water extraction procedure. The metal extract concentrations were compared with those found in virgin silica sands and Argentinean and U.S. hazardous waste laws to determine if the WFSs met toxicity limits. Regardless of metal cast and sand binder type, the majority of the WFS extracts analyzed contained metal concentrations similar to those found in virgin sand extracts and were below levels considered hazardous. However, 4 of 28 sands that used alkyd urethane binder were deemed hazardous because Pb concentrations in these sands were found to exceed regulatory thresholds. Although other regulated metals, such as As, Hg, and Se, were not analyzed in the extracts, this dataset provides additional evidence that many WFSs have a low metal leaching potential.