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.

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.

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.

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.

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.

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.

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.

Quantification of bacterial indicators and zoonotic pathogens in dairy wastewater ponds.

Zoonotic pathogens in land-applied dairy wastewaters are a potential health risk. The occurrence and abundance of 10 pathogens and 3 fecal indicators were determined by quantitative real-time PCR (qPCR) in samples from 30 dairy wastewaters from southern Idaho. Samples tested positive for Campylobacter jejuni, stx(1)- and eaeA-positive Escherichia coli, Listeria monocytogenes, Mycobacterium avium subsp. paratuberculosis, and Salmonella enterica, with mean recoveries of genomic DNA corresponding to 10(2) to 10(4) cells ml(-1) wastewater. The most predominant organisms were C. jejuni and M. avium, being detected in samples from up to 21 and 29 of 30 wastewater ponds, respectively. The qPCR detection limits for the putative pathogens in the wastewaters ranged from 16 cells ml(-1) for M. avium to 1,689 oocysts ml(-1) for Cryptosporidium. Cryptosporidium and Giardia spp., Yersinia pseudotuberculosis, and pathogenic Leptospira spp. were not detected by qPCR.

Analysis of total metals in waste molding and core sands from ferrous and non-ferrous foundries.

Waste molding and core sands from the foundry industry are successfully being used around the world in geotechnical and soil-related applications. Although waste foundry sands (WFSs) are generally not hazardous in nature, relevant data is currently not available in Argentina. This study aimed to quantify metals in waste molding and core sands from foundries using a variety of metal-binder combinations. Metal concentrations in WFSs were compared to those in virgin silica sands (VSSs), surface soils and soil guidance levels. A total analysis for Ag, Al, Ba, Be, Cd, Co, Cr, Cu, Fe, Mg, Mn, Mo, Ni, Pb, Sb, Te, Tl, V, and Zn was conducted on 96 WFSs and 14 VSSs collected from 17 small and medium-sized foundries. The majority of WFSs analyzed, regardless of metal cast and binder type, contained metal concentrations similar to those found in VSSs and native soils. In several cases where alkyd urethane binder was used, Co and Pb concentrations were elevated in the waste sands. Elevated Cr, Mo, Ni, and Tl concentrations associated with VSSs should not be an issue since these metals are bound within the silica sand matrix. Because of the naturally low metal concentrations found in most WFSs examined in this study, they should not be considered hazardous waste, thus making them available for encapsulated and unencapsulated beneficial use applications.

Ambient endotoxin concentrations and assessment of offsite transport at open-lot and open-freestall dairies.

Endotoxins are derived from gram-negative bacteria and are a potent inducer of inflammatory reactions in the respiratory tract when inhaled. To assess daily fluctuations of airborne endotoxin and their potential for transport from dairies, endotoxin concentrations were monitored over an 8-h period at upwind (background) and downwind (5 m from edge of dairy) locations on three separate days at two dairies. The dairies consisted of an open-lot or an open-freestall production system, both of which were stocked with 10,000 milking cows. Upwind concentrations were stable throughout the sampling period, averaging between 1.2 and 36.8 endotoxin units (EU) m(-3), whereas downwind concentration averages ranged from 179 to 989 EU(-3). Downwind endotoxin concentrations increased with wind speed, animal activity, and lot management practices, resulting in concentrations up to 136-fold hi gher than upwind concentrations. An area-source model was used to predict downwind ground-level endotoxin concentrations at distances up to 2000 m from the production facilities. Predicted concentrations decreased with distance and reached background levels within 500 to 2000 m, depending on the source emision rate and meteorological conditions.

Emissions of ammonia, methane, carbon dioxide, and nitrous oxide from dairy cattle housing and manure management systems.

Concentrated animal feeding operations emit trace gases such as ammonia (NH3), methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O). The implementation of air quality regulations in livestock-producing states increases the need for accurate on-farm determination of emission rates. The objective of this study was to determine the emission rates of NH3, CH4, CO2, and N2O from three source areas (open lots, wastewater pond, compost) on a commercial dairy located in southern Idaho. Gas concentrations and wind statistics were measured each month and used with an inverse dispersion model to calculate emission rates. Average emissions per cow per day from the open lots were 0.13 kg NH3, 0.49 kg CH4, 28.1 kg CO2, and 0.01 kg N2O. Average emissions from the wastewater pond (g m(-2) d(-1)) were 2.0 g NH3, 103 g CH4, 637 g CO2, and 0.49 g N2O. Average emissions from the compost facility (g m(-2) d(-1)) were 1.6 g NH3, 13.5 g CH4, 516 g CO2, and 0.90 g N2O. The combined emissions of NH3, CH4, CO2, and N2O from the lots, wastewater pond and compost averaged 0.15, 1.4, 30.0, and 0.02 kg cow(-1) d(-1), respectively. The open lot areas generated the greatest emissions of NH3, CO2, and N2O, contributing 78, 80, and 57%, respectively, to total farm emissions. Methane emissions were greatest from the lots in the spring (74% of total), after which the wastewater pond became the largest source of emissions (55% of total) for the remainder of the year. Data from this study can be used to develop trace gas emissions factors from open-lot dairies in southern Idaho and potentially other open-lot production systems in similar climatic regions.

Airborne endotoxin from indoor and outdoor environments: effect of sample dilution on the kinetic Limulus amebocyte lysate (LAL) assay.

Airborne endotoxins in occupational environments are a potential respiratory hazard to individuals. In this study, airborne endotoxins were collected using open-face and button aerosol samplers from inside animal housing units and downwind from agricultural production sites and a wastewater treatment plant. Filter extracts were then diluted to examine the effect of interfering substances on the kinetic Limulus amebocyte lysate (LAL) assay. In most cases, the overall endotoxin concentration was shown to decrease with increasing dilution up to 1000-fold, suggesting the presence of enhancing substances in the filter extracts. This dilution-dependent effect was most prominent in the open-face endotoxin samples, while button samples displayed little effect. Using a joinpoint regression model, it was determined that a dilution factor of 50 to 100 was generally sufficient to eliminate the presence of enhancing substances. After screening the data for dilution dependent effects, the airborne endotoxin concentrations were determined. The highest endotoxin concentrations, ranging from 2841 to 49,066 endotoxin units m(-3) of air, were found inside swine farrowing and finishing barns. Airborne endotoxin concentrations were 10- to 100-fold lower inside a dairy barn and downwind of other agricultural production sites and the wastewater treatment plant. Examination of dilution-dependent effects should be considered essential when utilizing the LAL assay, especially if values are to be used for regulatory purposes.

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.

Transport and fate of methyl iodide and its pest control in soils.

For fumigants, information on transport and fate as well as pest control is needed to develop management practices with the fewest negative environmental effects while offering sufficient pest control efficacy. For this purpose, a 2-D soil chamber with a surface-mounted flux chamber was designed to determine volatilization, real-time soil gas-phase concentration, degradation, and organism survivability after methyl iodide (MeI) fumigation. Three types of pests were used to give a broad spectrum of pest control information. An infected sandy loam soil with a volumetric water content of 10.6% was packed carefully into the 2-D chamber to a bulk density of 1.34 g cm(-3). After MeI fumigation at a rate of 56.4 kg ha(-1) for 24 h, about 28.9% of MeI was emitted into air, 6.8% remained in the soil, and 43.6% degraded in the soil (based on the residual iodide concentration). The uncertainty in the measured MeI degradation using iodide concentration was thought to mainly contribute to the unrecovered MeI (about 20%). The citrus nematodes [Tylenchulus semipenetrans] were effectively eliminated even at low concentration-time (CT) values (<30 microg h mL(-1)), but all Fusarium oxysporum survived. The response of barnyardgrass seeds [Echinochloa crus-galli] spatially varied with the CT values in the chamber. To fully control barnyardgrass seeds, CT of greater than 300 microg h mL(-1) was required. Using this experimental approach, different fumigant emission reduction strategies can be tested, and mathematical models can be verified to determine which strategies produce the least emission to the atmosphere while maintaining sufficient pest control efficacy.

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.

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.