Manure-amended Soils Research Articles

Determination of N2O reduction to N2 from manure-amended soil based on isotopocule mapping and acetylene inhibition

The quantification of N2O reduction during denitrification is crucial to take measures reducing N2O emissions from arable soils. The analysis of site specific N2O isotopic composition may help to quantify the pathway of N2O reduction to N2 during denitrification process. In manure-amended soil (chicken manure, cow manure and sheep manure), N2O reduction was evaluated by examining the N2O emissions in the presence of acetylene (C2H2) and by analyzing the N2O isotopocule deltas. The results indicated that the three manures had no significant differences for the N2O emission rates and N2O isotopocule deltas. The extent of N2O reduction to N2 was 81–84% using the mapping of Δδ18O(N2O-H2O/N2O-NO3-) (different value of δ18O between the N2O and H2O or NO3−) vs. SP (15N site preference in N2O) and approximately 76% using C2H2 (10% v/v) inhibition method under 60% WFPS (water–filled pore space). Moreover, complete N2O reduction held η18OR and SPR (net isotopocule effect of N2O reduction to N2) values of −13.6‰ and −6.7‰, respectively. It was also found that oxygen exchange between N2O and soil water was approximately 92%. In summary, the mapping of Δδ18O(N2O-H2O/N2O-NO3-) vs. SP was very useful to distinguish the production and consumption pathways of N2O during denitrification. The extent of N2O reduction was underestimated by the C2H2 method. These results provide guidance in correcting the acetylene effect, which is important in evaluating the impact of manure on the N2O reduction.

Morphological effect of dichloromethane on alfalfa (Medicago sativa) cultivated in soil amended with fertilizer manures

In this work, we investigated the morphological effect of dichloromethane (DCM) on alfalfa (Medicago sativa) plant. We studied in vitro the influence of its concentration on alfalfa germination. The plants were placed in pots for 15 weeks, and exposed to increasing concentrations of DCM (50 µg L−1 and 84 mg L−1). In addition, we examined the effect of two manures (cow and sheep), which were applied to a contaminated soil, on alfalfa plant growth. The effect of the presence of dichloromethane is obvious even in plant–soil manure system. In fact, in the event of contamination, the soil–cow manure mixture represents the best setting medium for the Alfalfa plant compared to other environments, regardless of the contamination level. Indeed, the presence of two types of manure does not allow the suppression of the inhibitory effect of dichloromethane on the mass of the dry matter of the aerial part which is 18.38% for the cow manure-amended soil and 13.96% for the sheep manure-amended soil.

Manure as a Potential Hotspot for Antibiotic Resistance Dissemination by Horizontal Gene Transfer Events.

The increasing demand for animal-derived foods has led to intensive and large-scale livestock production with the consequent formation of large amounts of manure. Livestock manure is widely used in agricultural practices as soil fertilizer worldwide. However, several antibiotic residues, antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria are frequently detected in manure and manure-amended soils. This review explores the role of manure in the persistence and dissemination of ARGs in the environment, analyzes the procedures used to decrease antimicrobial resistance in manure and the potential impact of manure application in public health. We highlight that manure shows unique features as a hotspot for antimicrobial gene dissemination by horizontal transfer events: richness in nutrients, a high abundance and diversity of bacteria populations and antibiotic residues that may exert a selective pressure on bacteria and trigger gene mobilization; reduction methodologies are able to reduce the concentrations of some, but not all, antimicrobials and microorganisms. Conjugation events are often seen in the manure environment, even after composting. Antibiotic resistance is considered a growing threat to human, animal and environmental health. Therefore, it is crucial to reduce the amount of antimicrobials and the load of antimicrobial resistant bacteria that end up in soil.

Long-term monitoring of sulfonamides and tetracyclines in manure amended soils and leachate samples - A follow-up study

Antibiotics can be detected in manure and digestate samples worldwide. As manure is a frequently used fertilizer, antibiotics are found in soil and leachate samples. Only little is known about the long-term fate of antibiotics in the soil environment. One shortcut is the lack of appropriate monitoring studies. Here we present the results of an unequalled soil monitoring study over 18 years from an agricultural field site in Lower Saxony (Germany). Sulfonamides and tetracycline are mainly fixed in the upper soil layer. Contents showed a sharp decrease below sampling depth of 30 cm (plough depth). Sulfaguanidine and sulfamethazine (SMZ) were detected down to 90 cm. Water samples taken below the field site revealed the transfer of sulfonamides into leachate. High variances were observed between sampling points emphasizing the need for sampling strategies for environmental studies. In addition, field lysimeters with defined input of sulfonamides enabled a long-term monitoring and mass balance of antibiotic transfer into leachate over 10 years. SMZ showed the highest mobility with concentrations up to 65 ng L−1. Less than 0.5% of the applied SMZ was transferred into the leachate. Data of lysimeter and field water samples support the theory of a steady state process with a continuous input of sulfonamides such as SMZ into leachate. Soils contaminated with antibiotics can be a long-term source for the input of antibiotic active compounds into deeper soil layers and groundwater.

Environmental Drivers for Persistence of Escherichia coli and Salmonella in Manure-Amended Soils: A Meta-Analysis

Application of organic amendments to agricultural land improves soil quality and provides nutrients essential for plant growth; however, they are also a reservoir for zoonotic pathogens whose presence poses a significant risk to public health. The persistence of bacteria in manure-amended soil, and differences in manure handling practices, are important issues from a food safety perspective. The primary objective of this study was to quantitatively summarize the variations in the rate of decline of Escherichia coli and Salmonella spp. in manure-amended soil under laboratory and field conditions, and to assess the impact of environmental factors. Available literature data on persistence of E. coli and Salmonella spp. in manure-amended soil from 42 primary research studies were extracted and statistically analyzed using a mixed-effect regression model. The results indicated that temperature (soil and air combined) was the most prominent factor affecting persistence of both E. coli and Salmonella spp. under laboratory conditions (P < 0.001), and of E. coli under field conditions (P < 0.05). The time required for a log reduction of E. coli under field conditions was significantly higher at low temperature (0 to 10°C) than at high temperature (greater than 20°C) (P < 0.05). In addition, application method was identified as a significant factor, with manure incorporation to soil inducing longer survival compared with surface application by approximately 1.2 times. The significant variation observed among primary research studies of bacterial persistence has highlighted that mitigation strategies associated with the use of manures in fresh produce production need to be improved by addressing factors such as climate, soil management, application method, and initial microbial levels. These findings may be used to support guidelines establishing exclusion periods between manure fertilization and the grazing or harvesting of crops, and may be useful for the generation of quantitative microbial risk models for fresh produce.

Effect of soil type and temperature on survival of Salmonella enterica in poultry manure-amended soils.

The effects of soil type and temperature on the survival of a cocktail of five Salmonella enterica serotypes (Enteritidis, Infantis, Montevideo, Typhimurium and Zanzibar) in manure-amended soils under controlled laboratory conditions was assessed. Containers of clay loam or sandy soil, unaltered or amended with 2% (w/w) poultry manure, were inoculated with S. enterica (~5 log10 CFU per gram) and held at 5, 21 or 37°C for 6weeks. Statistical analysis of the persistence of S. enterica identified a significant three-way interaction between soil type, manure amendment and temperature. Clay loam soils and lower temperatures tended to support S. enterica persistence over 6weeks with only 1- and 2-log reductions respectively. In contrast, sand and higher temperatures resulted in a 4-log and either 3- to 4-log reductions respectively. Manure amendment had an overarching effect of reducing die-off of S. enterica in comparison with unamended soils. This study highlights that a large component of variation of the rate of S. enterica reduction in soils may be attributed to combinations of environmental factors, in particular, soil type and temperature. It further underscores the importance of risk management strategies and industry guidelines based on local data and that reflect the diversity of prevailing horticultural production environments. SIGNIFICANCE AND IMPACT OF THE STUDY: The persistence of Salmonella enterica in soil environments was shown to be significantly influenced by a range of individual and interacting environmental effects, including temperature, soil type and amendment addition. This indicates that current horticultural food safety management systems which employ a uniform prescribed exclusion period between application of manure and time of harvest may be unfit for purpose under certain conditions by either underestimating or overestimating pathogen die-off. These findings support exclusion periods that account for a range of environmental factors including temperature, soil type and growing region that may be more appropriate to manage microbiological risks associated with soil which has been amended with manure.

Application of poultry manure in agriculture fields leads to food plant contamination with potentially toxic elements and causes health risk

Abstract Potentially toxic elements (PTEs) are used in the poultry feed as additives and growth promoters which can transfer to food plants grown on manure-amended agricultural soils. The consumption of food plants grown on manure-amended soil can cause health risk due to presence of high level of PTEs. In this study, PTE concentrations in poultry-manure, soil and food plants of agriculture fields, collected from eleven districts of Khyber Pakhtunkhwa, Pakistan, were analyzed using Inductive Coupled Plasma Mass Spectrophotometer. The selected PTEs including cadmium (Cd), chromium (Cr), nickel (Ni), cobalt (Co), copper (Cu), barium (Ba) and lead (Pb) were observed below the permissible limits set by United States Environmental Protection Agency (US-EPA) in the samples of manure and soils. The concentrations of Cu (0.81-247 mg kg−1) and Cr (0.18-9.81 mg kg−1) in most of the food plants were significantly (p 1) bioaccumulation values in the selected plants like radish, garlic, barley and wheat. Among selected PTEs, Co, Ni and Ba shown lower bioaccumulation values and assumed to have no serious health risk. The HRI values were found >1 in barley (for Cu and Cd), wheat and radish (for Cu, Cd and Pb only), pea and onion (for Cd only) that may cause potential health risk to the local community. This study revealed that application of poultry-manure contaminates agricultural soil and food plants that might cause health risk therefore, necessary steps should be taken to ensure safe management of poultry manure in farm lands and also enable decision makers in farming sector to establish satisfactory standards for the use of manure in conventional and organic farming.

Organic Manure Amended with Phosphate Solubilizing Bacteria on Soil Phosphorous Availability

Purpose : Combine use of phosphate solubilizing microorganisms and organic manure has greater agronomic utility as it could improve phosphorous (P) utilization efficiency through conversion of insoluble P to accessible forms. Therefore, the present study was conducted to assess the effect of different organic manures (poultry manure, goat manure and cow dung) with phosphate solubilizing microorganism on phosphorous availability.Research Method : The phosphate solubilizing bacterial (PSB) strain employed in this study was isolated from soil samples collected from agricultural lands in Matara District of Sothern Sri Lanka. The strain was identified as Enterobacter cancerogenous. Eight treatment combinations each replicated three times were used in the study. Findings : P availability of organic manure amended soils was progressively increased irrespectively the inoculation of PSB strain. The bulk of the increment occurred during the first 2 to 3 weeks of the incubation followed by slight reductions at the later stages. P availability of the soil amended with organic manures was significantly (P ≤ 0.05) higher than that of the control. Furthermore, the specified were much higher when PSB was inoculated to the soil amended with organic manures. PSB inoculants were used with poultry manure showed the highest P availability.Originality / Value : The availability of soil phosphorous is enhanced by combine use of organic manures and PSB inoculants; the practice is suggested to be employed in integrated nutrient management strategies.

Manure-borne pathogens as an important source of water contamination: An update on the dynamics of pathogen survival/transport as well as practical risk mitigation strategies.

Enteropathogen contamination of water resources is a global concern. Several sources and routes of pathogen contamination of water resources have been identified including agriculture. Land spreading or disposal of manure/livestock wastes is a notable source of public health relevant microorganisms into water. Microorganisms can be transported from manure-amended soils into water, from where they can reach animals and humans and may cause infection. This review explores the public health relevance of manure-borne-pathogens, highlighting some of the diseases that manure associated pathogens cause. It also examines the dynamics of overland transport of pathogens into surface waters and percolation through soils into groundwater. Factors that influence the survival and transport of pathogens into respective water resources are discussed. The actual number of pathogens shed, pathogen release rate, requisite flow conditions, precipitation characteristics and pathogen inactivation potential are some general factors, examined in this review. Pathogen adaptation and survival in the soil environment is extensively discussed because soils significantly influence pathogen transfer into water. In addition to soil characteristics, environmental variables such as moisture, temperature and pH as well as soil biology are relevant aspects, considered herein. Manure and farm management practices such as manure source and type, storage and treatment, also influence the occurrence, survival and transport potential of pathogens. Optimized and recommended manure treatment techniques like composting, which has been demonstrated to satisfactorily inactivate enteric pathogens in manure are discussed. The need for proper composting by observing recommended manuring stipulations is emphasized and finally, practical strategies to protect water resources from pathogenic contamination are elucidated.

Tracking resistomes, virulence genes, and bacterial pathogens in long-term manure-amended greenhouse soils

Organic manure has been implicated as an important source of antibiotic resistance genes (ARGs) in agricultural soils. However, the profiles of biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence genes (VGs) and their bacterial hosts in manure-amended soils remain largely unknown. Herein, a systematic metagenome-based survey was conducted to comprehensively explore the changes in resistomes, VGs and their bacterial hosts, mobile genetic elements (MGEs), and pathogenic bacteria in manure-amended greenhouse soils. Many manure-borne ARGs, BRGs, MRGs, VGs, and bacterial pathogens could be transferred into soils by applying manures, and their abundance and diversity were markedly positively correlated with greenhouse planting years (manure amendment years). The main ARGs transferred from manures to soils conferred resistance to tetracycline, aminoglycoside, and macrolide-lincosamide-streptogramin. Both statistical analysis and gene arrangements showed a good positive co-occurrence pattern of ARGs/BRGs/MRGs/VGs and MGEs. Furthermore, bacterial hosts of resistomes and VGs were significantly changed in the greenhouse soils in comparison with the field soils. Our findings confirmed the migration and dissemination of resistomes, VGs, and bacterial pathogens, and their accumulation and persistence were correlated with the continuous application of manures.

Effect of Sulfadimethoxine, Oxytetracycline, and Streptomycin Antibiotics in Three Types of Crop Plants—Root, Leafy, and Fruit

(1) Background: Plants act as the natural sink for a variety of toxins in the environment, including veterinary antibiotics (VAs). The objective of this study was to evaluate the uptake and fate of sulfadimethoxine (SDZ), oxytetracycline (OTC), and streptomycin (STR) in lettuce (Lactuca sativa L.), carrot (Daucus carota), and pepper (Capsicum annum) grown in VAs amended soil. (2) Methods: 0, 50, and 100 mg kg−1 VA laced manure was applied in a sandy clay loam soil. (3) Results: 30-d (lettuce) and 60-d (carrot and pepper) greenhouse experiment showed that SDZ and OTC were taken up by all three plants, with concentrations in plant tissue ranging from 0.1 to 1.2 mg kg−1 dry weight. The concentration of VAs in plant tissues increased with a corresponding increase of antibiotics in manure. The highest plant tissue concentrations were found in carrot and lettuce, followed by pepper. An increase in NADPH P450 reductase and glutathione-s-transferase enzyme activity with increasing SDZ and OTC concentration was evident, signifying the induction of the detoxification process. The activity of plant detoxification enzymes under STR treatment was found not to be significantly different from control. (4) Conclusions: These results raise potential human health concerns of consuming low levels of antibiotics from produce grown on manure-amended soils. The result indicates that SDZ, OTC, and STR antibiotics posed high, medium, and low acute ecological risks in lettuce, carrot, and pepper plants when grown in sandy clay loam soil.

Alleviated Antibiotic-Resistant Genes in the Rhizosphere of Agricultural Soils with Low Antibiotic Concentration.

The influence of the rhizosphere on the abundance and diversity of antibiotic resistance genes (ARGs) has been recognized but there is a lack of consensus because of broad ranges of plant species and antibiotic concentrations across different habitats and the elusive underlying mechanisms. Here, we profiled antibiotic concentrations and resistomes in the rhizosphere and bulk soils by cultivating 10 types of crops in manure-amended agricultural soils. Rhizosphere effects altered the antibiotic resistome structure, significantly increased the absolute abundance of the antibiotic resistome, and decreased their relative abundance, contrasting previous studies. Such plantation-driven variation in ARGs resulted from the boost of bacterial lineages with negative relationships with ARGs and the constraint of the potential ARG-hosts in the rhizosphere of plants cultivated in soils with low antibiotic concentrations as the selective pressure. This mechanism is not reported previously and deepens our understanding about the rhizosphere effects on ARGs.

Molecular Scale Studies of Phosphorus Speciation and Transformation in Manure Amended and Microdose Fertilized Indigenous Vegetable Production Systems of Nigeria and Republic of Benin

This study investigated the speciation, transformation, and availability of P during indigenous vegetable production by employing a combination of chemical and spectroscopic techniques. The study focused on sites in two ecozones of SSA, the dry savanna (lna, Republic of Benin) and rainforest (Ilesha, Nigeria). Both sites were cultivated with two indigenous vegetable species: local amaranth (Amaranthus cruentus (AC)) and African eggplant (Solanum macrocarpon (SM)). The soils were treated with 5 t/ha poultry manure and urea fertilizer at the rates of 0, 20, 40, 60, and 80 kg N/ha. Soil samples were collected before planting and after harvest. Phosphorus K-edge X-ray absorption near-edge structure (XANES) spectroscopy was used to determine P speciation in these soils. Quantitative analysis showed that adsorbed and organic P were the two dominant P species in the manure amended dry savanna (DS) soils before planting and after harvest in soils cultivated with both AC and SM, with the addition of urea (40 kg N/ha) causing an increase in the organic P form in dry savanna soils cultivated with AC. Soils of the rainforest (RF) cultivated with AC initially had large amounts of apatite P in the manure amended soils prior to planting, which was transformed to adsorbed and organic P after harvest. Urea addition to the rainforest soils shifted the dominant P species from organic P to adsorbed and apatite P, which was likely to limit P availability. Soils cultivated with SM had similar proportions of both organic and adsorbed P forms, with 40 kg N/ha addition slightly increasing the proportion of adsorbed P.

Fate and transport of antibiotics and antibiotic resistance genes in runoff and soil as affected by the timing of swine manure slurry application

Land application of swine manure slurry is a common practice to supplement nutrients to soil for crop production. This practice can introduce antibiotic residues and antibiotic resistance genes (ARGs) into the environment. Field testing is critical in identifying manure management practices effective in minimizing the environmental impacts of manure-borne antibiotic and ARGs. The objective of this study was to determine how the timing of swine manure application relative to rainfall events impacts the fate and transport of antibiotics and ARGs in surface runoff and manure-amended soil. Swine manure slurry was either broadcast or injected on test plots in the field. A set of three 30-min simulated rainfall events, 24 h apart, were initiated on manured plots 1 day, 1 week, 2 weeks, or 3 weeks after the manure application. Results showed that an interval longer than 2 weeks between application and rainfall often significantly reduced the levels of antibiotics and ARGs tested in runoff with the exception of tet(X). For soil samples from broadcast plots, concentrations of two of the three antibiotics tested (lincomycin and tiamulin) decreased substantially in the first two weeks after manure application. In contrast, concentrations of most of the ARGs tested (tet(Q), tet(X), and erm(A)) in soil did not change significantly during the test period. Information obtained from the study can be beneficial in designing manure management practices and estimating the environmental loading of antibiotics and ARGs resulting from manure application.

The influence of oxytetracycline on the degradation and enantioselectivity of the chiral pesticide beta-cypermethrin in soil

Pesticide residues most likely coexist with antibiotics due to the application of animal-based fertilizers in agriculture. In this study, the degradation and enantioselectivity of beta-cypermethrin in soil and chicken manure-amended soil were investigated. The effects of oxytetracycline on the soil microbial community were also estimated. The results showed that the half-life of beta-cypermethrin in the soil was 16.9 days and that the (+)-enantiomer was degraded preferentially in both pairs of enantiomers. The metabolites cis/trans-DCCA(3-(2′,2′-dichlorovinyl)-2,2-dimethylcyclopropane carboxylic acid) and 3-PBA (3-Phenoxybenzoic acid) were detected. The trans-DCCA concentrations ranged from 0.094 to 0.120 mg/kg, which were higher than the concentrations of cis-DCCA (0.091–0.120 mg/kg) and 3-PBA (0.022–0.061 mg/kg). In the presence of oxytetracycline, beta-cypermethrin degradation was inhibited slightly, while the enantioselectivity was not affected. Oxytetracycline increased the enrichment and persistence of the metabolites. Addition of chicken manure decreased the cis-DCCA residue levels in the soil and alleviated the effect of oxytetracycline; however, chicken manure increased the accumulation and persistence of 3-PBA. In addition, oxytetracycline perturbed the structure of the soil microbial community. The abundance of Proteobacteria increased, while the abundances of Firmicutes and Actinobacteria decreased. These changes might affect the biodegradation of beta-cypermethrin and its metabolites. Combined pollution with antibiotics should be considered for its potential impact on pesticide residues.

Nitrogen Uptake Efficiency and Total Soil Nitrogen Accumulation in Long-Term Beef Manure and Inorganic Fertilizer Application

Livestock manure is a common soil amendment for crop-livestock production systems. However, the efficiency of crop nitrogen (N) uptake from the manure-amended soil may not equate with that from inorganic N sources. The objective of this paper was to determine the efficiency of N uptake, grain yield, and total soil nitrogen (TSN) accumulation in beef manure-amended soil compared to the inorganic N fertilizer-amended soil. Data (1990–2015) from a long-term continuous winter wheat (Triticum aestivum L.) fertility experiment at Stillwater in Oklahoma, USA, were used in this report. Three of the six “Magruder Plot” treatments used in this study were manure, NPK plus lime (NPKL), and a check (no nutrients applied). Pre-plant N, P, and K were applied annually at 67, 14.6, and 27.8 kg·ha−1, respectively, while beef manure was applied every 4 years at 269 kg N·ha−1. The results indicated that grain N uptake in the manure treatment (48.1 kg·ha−1) was significantly (p&lt;0.05) lower than that in the NPKL treatment (60.2 kg·ha−1). This represents 20.1% efficiency of inorganic N uptake than the manure N uptake. The average grain yield (1990–2015) from the manure and NPKL treatments was 2265.7 and 2510.5 kg·ha−1, respectively, and was not significantly different. There was a trend of TSN increase over the study period for both manure and NPKL treatments. The average TSN from manure and NPKL treatments was 0.92 and 0.91 g·kg−1 soil, respectively, and was not significantly different. While no significant difference between manure and NPKL grain yield was observed, there was a significantly lower uptake efficiency of manure N compared to inorganic N. Furthermore, the low uptake efficiency of the manure N could suggest a potential for environmental pollution. Appropriate timing and application rate of manure N sources could optimize crop use efficiency and limit potential threat to the environment.

Transfer of antibiotic resistance from manure-amended soils to vegetable microbiomes

The increasing antimicrobial resistance in manure-amended soil can potentially enter food chain, representing an important vehicle for antibiotic resistance genes (ARGs) transmission into human microbiome. However, the pathways for transmission of ARGs from soil to plant remain unclear. Here, we explored the impacts of poultry and cattle manure application on the patterns of resistome in soil and lettuce microbiome including rhizosphere, root endosphere, leaf endosphere and phyllosphere, to identify the potential transmission routes of ARGs in the soil-plant system. After 90 days of cultivation, a total of 144 ARGs were detected in all samples using high-throughput quantitative PCR. Rhizosphere soil samples harbored the most diverse ARGs compared with other components of lettuce. Cattle manure application increased the abundance of ARGs in root endophyte, while poultry manure application increased ARGs in rhizosphere, root endophyte and phyllosphere, suggesting that poultry manure may have a stronger impact on lettuce resistomes. The ARG profiles were significantly correlated with the bacterial community, and the enrichment of soil and plant resistomes was strongly affected by the bacterial taxa including Solibacteres, Chloroflexi, Acidobacteria, Gemm-1 and Gemmatimonadetes, as revealed by the network analyses. Moreover, the overlaps of ARGs between lettuce tissues and soil were identified, which indicated that plant and environmental resistomes are interconnected. Our findings provide insights into the transmission routes of ARGs from manured soil to vegetables, and highlight the potential risks of plant resistome migration to the human food chain.

Trophic Transfer of Antibiotic Resistance Genes in a Soil Detritus Food Chain.

The presence and spread of antibiotic resistance genes (ARGs) are causing substantial global public concern; however, the dispersal of ARGs in the food chain is poorly understood. Here, we experimented with a soil collembolan ( Folsomia candida)-predatory mite ( Hypoaspis aculeifer) model food chain to study trophic transfer of ARGs in a manure-contaminated soil ecosystem. Our results showed that manure amendment of soil could significantly increase ARGs in the soil collembolan microbiome. With the ARGs in the prey collembolan microbiome increasing, an increase in ARGs in the predatory mite microbiome was also observed, especially for three high abundant ARGs ( blaSHV, fosX and aph6ia). Three unique ARGs were transferred into the microbiome of the predatory mite from manure amended soil via the prey collembolan ( aac(6' )-lb(akaaacA4), yidY_mdtL and tolC). Manure amendment altered the composition and structure and reduced the diversity of the microbiomes of the prey collembolan and the predatory mite. We further reveal that bacterial communities and mobile genetic elements were two important drivers for the trophic transfer of ARGs, not just for ARGs distribution in the samples. These findings suggest that the importance of food chain transmission of ARGs for the dispersal of resistance genes in soil ecosystems may be underestimated.

Collembolans accelerate the dispersal of antibiotic resistance genes in the soil ecosystem

Soils have become an important sink for antibiotic resistance genes (ARGs). To better understand the impacts of ARGs on the soil ecosystem, the transport of ARGs is a basic question. So far, however, the role of soil animals in the dispersal of ARGs is not understood. Here, two treatments (without collembolans and with collembolans) were established, each treatment included unamended and manure-amended soil, and soil samples were collected at 14, 28 and 56 days after incubation. The effects of the collembolan Folsomia Candida on dispersal of ARGs in the soil ecosystem were explored using high-throughput qPCR combined with Illumina sequencing. As the culture time increased, more shared ARGs and OTUs were detected between the unamended and manured soil, especially in the treatment with collembolans. Vancomycin, aminoglycoside and MLSB genes may have been more readily transported by the collembolan. On the 28th day after incubation, a high abundance of mobile genetic elements (MGEs) was found in the treatment with collembolans. These results clearly reveal that collembolans can accelerate the dispersal of ARGs in the soil ecosystem. Procrustes analysis and the Mantel test both indicate that soil bacterial communities were significantly correlated with ARG profiles. Furthermore, partial redundancy analysis indicates that soil bacterial communities can explain 41.28% of the variation in ARGs. These results suggest that the change of soil microbial community have an important contribution to the dispersal of ARGs by the collembolan.

Prevalence and concentration of stx+ E. coli and E. coli O157 in bovine manure from Florida farms.

Fresh produce outbreaks due to Shiga toxin-producing Escherichia coli (STEC) continue to occur in the United States (US). Manure-amended soils can pose a public health risk when used for growing raw agricultural commodities. Knowing the prevalence and concentration of STEC in untreated biological soil amendments of animal origin (BSAAO) is important to help guide the most appropriate pre-harvest interval(s) following application to limit risks from these soil amendments. Bovine manure samples were collected from 12 farms in Florida, including samples from piles, lagoons, barns, and screened solids. Two methods were used to detect stx1/2 and rfbE genes in samples. A prevalence rate of 9% for stx1 and/or stx2 and 19% for rfbE was observed from the 518 bovine manure samples evaluated. A most probable number (MPN) assay was performed on stx+ samples when applicable. The geometric mean for stx+ samples (n = 20) was 3.37 MPN g-1 (0.53 log MPN g-1) with a maximum value of 6,800 MPN g-1 (3.83 log MPN g-1). This research was part of a larger nationwide geographical study on the prevalence and concentration of STEC in bovine manure to help guide regulations on feasible pre-harvest intervals for the application of untreated BSAAO.