[Effects of Supplementation of Different Amendments on Soil Heavy Metals and Enzyme Activities in Coastal Saline Land]

The supplementation of soil amendments may not only improve the soil physical and chemical properties but also lead to the accumulation of heavy metals in soil. This experiment included six treatments:control (CK), organic manure (OM), polyacrylamide+organic manure (PAM+OM), straw mulching+organic manure (SM+OM), buried straw+organic manure (BS+OM), and bio-organic manure+organic manure (BM+OM) to explore the effects of different soil amendments on heavy metals and soil enzyme activities in coastal saline land and the relationship between them. The results revealed that compared with that in the CK treatment, the contents of soil Cr, Cu, Ni, and Pb exhibited an upward trend after the supplementation of soil amendments, among which the SM+OM and PAM+OM treatments had the most significant effects on the contents of soil Cr and Cu, respectively, whereas the BM+OM treatment had the most significant effects on the contents of soil Ni and Pb. Compared with those in the CK treatment, the activities of soil invertase and urease increased significantly following supplementation of soil amendments, and the BM+OM treatment had the best effect. The alkaline phosphatase activity exhibited a slightly upward trend after the supplementation of soil amendments, whereas the catalase activity did not change significantly. The redundancy analysis revealed that the first two axes cumulatively accounted for 70.3% of the variability in enzyme activities, and the importance of single soil heavy metals on soil enzyme activity was as follows:Ni>Cu>Cr>Pb.

Antibiotic resistome and associated bacterial communities in agricultural soil following the amendments of swine manure-derived fermentation bed waste

The practice of utilizing animal manures on land is widespread in agriculture, but it has raised concerns about the possible spread of antibiotic resistance genes (ARGs) and the potential risk it poses to public health through food production. Fermentation bed culture is an effective circular agricultural practice commonly utilized in pig farming that minimizes the environmental impact of livestock farming. However, this method generates a significant amount of fermentation bed waste (FBW), which can be turned into organic fertilizer for land application. The objective of this research was to examine the impacts of amending agricultural soil samples with swine manure-derived FBW on microbial communities, mobile genetic elements (MGEs), and ARG profiles over different periods. The study findings indicated that the amendment of swine manure-derived FBW significantly increased the diversity and abundance of ARGs and MGEs during the early stages of amendment, but this effect diminished over time, and after 12 months of FBW amendments, the levels returned to those comparable to control samples. The shift in the bacterial communities played a significant role in shaping the patterns of ARGs. Actinobacteriota, Proteobacteria, and Bacteroidetes were identified as the primary potential hosts of ARGs through metagenomic binning analysis. Furthermore, the pH of soil samples was identified as the most important property in driving the composition of the bacterial community and soil resistome. These findings provided valuable insights into the temporal patterns and dissemination risks of ARGs in FBW-amended agriculture soil, which could contribute to the development of effective strategies to manage the dissemination risks of FBW-derived ARGs.

Nano-Selenium inhibited antibiotic resistance genes and virulence factors by suppressing bacterial selenocompound metabolism and chemotaxis pathways in animal manure

Numerous antibiotic resistance genes (ARGs) and virulence factors (VFs) found in animal manure pose significant risks to human health. However, the effects of graphene sodium selenite (GSSe), a novel chemical nano-Selenium, and biological nano-Selenium (BNSSe), a new bioaugmentation nano-Se, on bacterial Se metabolism, chemotaxis, ARGs, and VFs in animal manure remain unknown. In this study, we investigated the effects of GSSe and BNSSe on ARGs and VFs expression in broiler manure using high-throughput sequencing. Results showed that BNSSe reduced Se pressure during anaerobic fermentation by inhibiting bacterial selenocompound metabolism pathways, thereby lowering manure Selenium pollution. Additionally, the expression levels of ARGs and VFs were lower in the BNSSe group compared to the Sodium Selenite and GSSe groups, as BNSSe inhibited bacterial chemotaxis pathways. Co-occurrence network analysis identified ARGs and VFs within the following phyla Bacteroidetes (genera Butyricimonas, Odoribacter, Paraprevotella, and Rikenella), Firmicutes (genera Lactobacillus, Candidatus_Borkfalkia, Merdimonas, Oscillibacter, Intestinimonas, and Megamonas), and Proteobacteria (genera Desulfovibrio). The expression and abundance of ARGs and VFs genes were found to be associated with ARGs-VFs coexistence. Moreover, BNSSe disruption of bacterial selenocompound metabolism and chemotaxis pathways resulted in less frequent transfer of ARGs and VFs. These findings indicate that BNSSe can reduce ARGs and VFs expression in animal manure by suppressing bacterial selenocompound metabolism and chemotaxis pathways.

Effects of soil solarization combined with manure-amended on soil ARGs and microbial communities during summer fallow

Soil solarization (SS) is a technique for managing pathogens and weeds, which involves covering with transparent plastic to increase soil temperature during summer fallow (SF). However, SS also alters the diversity of bacterial communities. Therefore, during SF, various organic modifiers are used in combination with SS to improve its efficacy. Organic amendments may contain antibiotic resistance genes (ARGs). Greenhouse vegetable production (GVP) soils are vital to ensure food security and ecological balance. However, comprehensive study on the effects of SS combined with different types of manure on ARGs in GVP soils during SF remains unclear. Therefore, this study employed high-throughput qPCR to explore the effects of different organic amendments combined with SS on the abundance changes of ARGs and mobile genetic elements (MGEs) in GVP soils during SF. The abundance and diversity of ARGs and MGEs in GVP soils with different manure fertilization and SS decreased during SF. Horizontal gene transfer via MGEs (especially integrases 45.80%) induced by changes in environmental factors (NO3--N 14.7% and NH4+-N) was the main factor responsible for the changes in ARGs. Proteobacteria (14.3%) and Firmicutes were the main potential hosts of ARGs. Network analysis suggested that Ornithinimicrobium, Idiomarina and Corynebacterium had positive correlations with aminoglycosides, MLSB, and tetracycline resistance genes. These results provide new insights to understand the fate of ARGs in the GVP soils by manure-amended combined with SS during SF, which may help to reduce the spread of ARGs.

Investigation of 29 Antimicrobial Compounds in Soil Using Newly Developed UHPLC-MS/MS Method

While the prudent and reasonable use of veterinary antimicrobial agents in food-producing animals is necessary, researchers over the decades have shown that these antimicrobial agents can spread into the environment through livestock manure and wastewater. The analysis of the occurrence of antimicrobial compounds in soil samples is of a great importance to determine potential impacts on human and animal health and the environment. In this study, an affordable, rugged and simple analytical method has been developed for the determination of twenty-nine antimicrobial compounds from five different classes (tetracyclines, fluoro(quinolones), macrolides, sulfonamides and diaminopirimidines). Liquid-liquid extraction (LLE) with extract filtration combined with ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) was the best strategy for the simultaneous determination of all analytes. The developed method was validated according to the Commission Implementing Regulation (EU) 2021/808. The limit of detections (LODs) ranged from 0.5 to 2.0 µg/kg, while the limit of quantitation (LOQ) was established at 1.0 to 20.0 µg/kg. The developed method was successfully applied for the determination of antimicrobial residues in one hundred and eighteen soil samples obtained from four European countries (Austria, Czech Republic, Estonia and Portugal). Doxycycline in the concentration levels of 9.07 µg/kg-20.6 µg/kg was detected in eight of the analysed samples. Samples were collected from areas where natural fertilizers (swine or cow manure) were applied. Our method can be efficiently used to monitor anti-microbial compounds in soil samples.

Mitigating runoff nitrate loss from soil organic nitrogen mineralization in citrus orchard catchments using green manure

Nitrate-nitrogen (NO3--N) loss is a significant contributor to water quality degradation in agricultural catchments. The amount of nitrogen (N) fertilizer input in citrus orchard is relatively large and results in significant NO3--N loss, compared to cropland. To promote sustainable N fertilizer management, it is crucial to identify the sources of runoff NO3--N loss in citrus orchards catchments. Particularly, we poorly know the sources of NO3--N and the mitigation mechanisms in these areas, which are highly polluted with NO3--N in water bodies. In this study conducted in central China, we conducted a field experiment with four treatments (CK: no N fertilizer; CF: conventional N fertilizer, 371.3kg N ha-1 yr-1 urea; OM: CF with organic manure; GM: CF with legume green manure) and a catchment-scale experiment in two citrus orchards (34.3%; 51.6%) catchments. To determine the source of runoff NO3--N loss, we used the dual isotope tracer method (δ15N and δ18O of NO3-) to identify the sources of NO3--N, and a 15-day incubation experiment to determine the potential and rate of soil N mineralization. Our findings revealed that soil organic nitrogen (SON) mineralization was the primary contributor to runoff NO3--N loss, and soil N mineralization potential (0.65⁎⁎⁎) and rate (0.54⁎⁎⁎) were the key factors impacting NO3--N loss. Interestingly, organic manure significantly increased 29.0% of NO3--N loss derived from SON in the runoff by enhancing soil N mineralization potential (+36.6%) and rate (+77.1%). But green manure mulching significantly reduced the soil N mineralization rate (-18.6%) compared to organic manure application, making it the most effective measure to reduce NO3--N loss (-12.4%). Our study highlights the critical role of regulating SON mineralization in controlling NO3--N pollution in surface waters in citrus orchard catchments.

Influence of key factors on ammonia and nitrous oxide emission factors for excreta deposited by livestock and land-applied manure

Ammonia (NH3) and nitrous oxide (N2O) emissions from livestock manure management have a significant impact on air quality and climate change. There is an increasing urgency to improve our understanding of drivers influencing these emissions. We analysed the DATAMAN ("DATAbase for MANaging greenhouse gas and ammonia emissions factors") database to identify key factors influencing (i) NH3 emission factors (EFs) for cattle and swine manure applied to land and (ii) N2O EFs for cattle and swine manure applied to land, and (iii) cattle urine, dung and sheep urine deposited during grazing. Slurry dry matter (DM) content, total ammoniacal nitrogen (TAN) concentration and method of application were significant drivers of NH3 EFs from cattle and swine slurry. Mixed effect models explained 14-59 % of the variance in NH3 EFs. Apart from the method of application, the significant influence of manure DM, manure TAN concentration or pH on NH3 EFs suggests mitigation strategies should focus on these. Identifying key factors influencing N2O EFs from manures and livestock grazing was more challenging, likely because of the complexities associated with microbial processes and soil physical properties impacting N2O production and emissions. Generally, significant factors were soil-related e.g. soil water content, pH, clay content, suggesting mitigations may need to consider the conditions of the receiving environment for manure spreading and grazing deposition. Total variability explained by terms in mixed effect model was on average 66 %, with the random effect 'experiment identification number' explaining, on average, 41 % of the total variability in the models. We suspect this term captured the effect of non-measured manure, soil and climate factors and any biases in application and measurement technique effects associated with individual experiments. This analysis has helped to improve our understanding of key factors of NH3 and N2O EFs for inclusion within models. With more studies over time, insights into the underlying processes influencing emissions will be further improved.

Phenotypic link between protein efficiency and pig welfare suggests no apparent trade-offs for mitigating nitrogen pollution

Pig manure contributes significantly to environmental pollution through nitrogen compounds. Reducing protein in feed can help, but it may lead to damaging behaviors if pigs' nutritional needs are not met. Breeding pigs for higher protein efficiency (PE) is a long-term solution to reduce nitrogen pollution, but concerns about pig welfare remain. We studied 95 pigs involved in a project on the genetic basis of PE on a 20% protein restricted diet to investigate the phenotypic connection between PE and welfare. These pigs represented natural PE variations in the population. At around 100 days, before their PE was known, we observed their behaviors. Only three pigs engaged in tail biting and manipulation of vulnerable regions, but this was not associated with PE. There was no clear link between PE and manipulating pen mates' less vulnerable regions. Such behaviors are normal but can cause stress and injury if carried out excessively due to boredom or stress. Overall, pigs with higher PE showed no major behavioral abnormalities in this study. Considering the lack of genetic knowledge, the risk of increased harmful behaviors when selecting for higher PE appears low when inferred from this purely phenotypic association.

Mitigation effects and microbial mechanism of two ecological earthworms on the uptake of chlortetracycline and antibiotic resistance genes in lettuce

The contamination of greenhouse vegetable soils with antibiotics and antibiotic resistance genes (ARGs), caused by the application of livestock and poultry manure, is a prominent environmental problem. In this study, the effects of two ecological earthworms (endogeic Metaphire guillelmi and epigeic Eisenia fetida) on the accumulation and transfer of chlortetracycline (CTC) and ARGs in a soil-lettuce system were studied via pot experiments. The results revealed that earthworm application accelerated the removal of the CTC from the soil and lettuce roots and leaves, with the CTC content reducing by 11.7-22.8 %, 15.7-36.1 %, and 8.93-19.6 % compared with that of the control, respectively. Both earthworms significantly reduced the CTC uptake by lettuce roots from the soil (P < 0.05) but did not change the CTC transfer efficiency from the roots to leaves. The high-throughput quantitative PCR results showed that the relative abundance of ARGs in the soil and lettuce roots and leaves decreased by 22.4-27.0 %, 25.1-44.1 %, and 24.4-25.4 %, respectively, with the application of earthworms. Earthworm addition decreased the interspecific bacterial interactions and the relative abundance of mobile genetic elements (MGEs), which helped reduce the dissemination of ARGs. Furthermore, some indigenous soil antibiotic degraders (Pseudomonas, Flavobacterium, Sphingobium, and Microbacterium) were stimulated by the earthworms. The results of redundancy analysis indicated that the bacterial community composition, CTC residues, and MGEs were the main parameters affecting the distribution of ARGs, accounting for 91.1 % of the total distribution. In addition, the bacterial function prediction results showed that the addition of earthworms reduced the abundance of some pathogenic bacteria in the system. Overall, our findings imply that earthworm application can substantially reduce the accumulation and transmission risk of antibiotics and ARGs in soil-lettuce systems, providing a cost-effective soil bioremediation practice for addressing antibiotic and ARGs contamination to guarantee the safety of vegetables and human health.

Phosphorus recovery from aqueous product of hydrothermal carbonization of cow manure

The work studies the recovery of nutrients (phosphorus and nitrogen) from the process water of acid-assisted hydrothermal carbonization (HTC) of cow manure. Three organic acids (formic acid, oxalic acid, and citric acid) and sulfuric acid were evaluated as additives in HTC. Using 0.3 M sulfuric acid, more than 99% of phosphorus and 15.6% of nitrogen from manure are extracted and dissolved during HTC at 170 °C with 10 min reaction time in a batch reactor. Nutrients (mainly phosphorus) were recovered through precipitation from process water by raising the ionic strength of the solution by addition of salts of magnesium and ammonia, and by raising the pH to 9.5. Subsequently, phosphorus-rich solids were recovered containing almost all (greater than 95%) of the dissolved phosphorus in the sulfuric and formic acid assisted runs. Morphology and qualitative chemical analysis of the precipitates were determined. It is shown by XRD that the precipitate formed from process water generated by HTC with oxalic acid is crystalline, although the diffraction pattern could not be matched with any expected substance.

State-level trends in the greenhouse gas emission intensity of US milk production

The greenhouse gas emission intensity of US milk production (i.e., greenhouse gas emissions per unit of production) has varied across time and states. However, research has not examined how farm-sector trends affect the state-level emission intensity of production. We estimated fixed effects regressions with state-level panel data from 1992 through 2017 to test how US dairy farm-sector changes influenced the greenhouse gas emission intensity of production. We found that increases in per cow milk productivity reduced the enteric greenhouse gas emission intensity of milk production, while it had no statistically significant effect on the manure greenhouse gas emission intensity of production. In contrast, increases in average farm size and the number of farms reduced the manure greenhouse gas emission intensity of milk production, while they did not affect the enteric greenhouse gas emission intensity of production.

Fecal antibiotic resistance genes were transferred through the distribution of soil-lettuce-snail food chain

Massive antibiotic resistance genes (ARG) were detected in the soil modified by manure, which may affect human life safety through the food chain. However, the transmission of ARGs through the soil-plant-animal food chain is still unclear. Therefore, this study used high-throughput quantitative PCR technology to explore the effects of pig manure application on ARGs and bacterial communities in soil, lettuce phyllosphere, and snail excrement. The results showed that a total of 384 ARGs and 48 MEGs were detected in all samples after 75 days of incubation. The diversity of ARGs and MGEs in soil components increased significantly by 87.04% and 40% with the addition of pig manure. The absolute abundance of ARGs in the phyllosphere of lettuce was significantly higher than that of the control group, with a growth rate of 212.5%. Six common ARGs were detected between the three components of the fertilization group, indicating that there was internal transmission of fecal ARGs between the trophic levels of the food chain. Firmicutes and Proteobacteria were identified as the dominant host bacteria in the food chain system, which were more likely to be used as carriers of ARGs to promote the spread of resistance in the food chain. The results were used to assess the potential ecological risks of livestock and poultry manure. It provides theoretical basis and scientific support for the formulation of ARG prevention and control policies.

Risk assessment and dissemination mechanism of antibiotic resistance genes in compost

In recent years, the excessive of antibiotics in livestock and poultry husbandry, stemming from extensive industry experience, has resulted in the accumulation of residual antibiotics and antibiotic resistance genes (ARGs) in livestock manure. Composting, as a crucial approach for the utilization of manure resources, has the potential to reduce the levels of antibiotics and ARGs in manure, although complete elimination is challenging. Previous studies have primarily focused on the diversity and abundance of ARGs in compost or have solely examined the correlation between ARGs and their carriers, potentially leading to a misjudgment of the actual risk associated with ARGs in compost. To address this gap, this study investigated the transfer potential of ARGs in compost and their co-occurrence with opportunistic pathogenic bacteria by extensively analyzing metagenomic sequencing data of compost worldwide. The results demonstrated that the potential risk of ARGs in compost was significantly lower than in manure, suggesting that composting effectively reduces the risk of ARGs. Further analysis showed that the microbes shifted their life history strategy in manure and compost due to antibiotic pressure and formed metabolic interactions dominated by antibiotic-resistant microbes, increasing ARG dissemination frequency. Therefore, husbandry practice without antibiotic addition was recommended to control ARG evolution, dissemination, and abatement both at the source and throughout processing.

Assessment of the biochemical methane potential of in-house and outdoor stored pig and dairy cow manure by evaluating chemical composition and storage conditions

Biogas production is a suitable option for producing energy from dairy and pig manure types. During manure storage, organic matter degradation results in methane emissions decreasing the potential biogas yield. The present research advances the understanding of the biochemical methane potential (BMP) and the chemical characteristics of manure collected year-round from sequential stages of the liquid manure management chain of commercial dairy cow and pig farms. To this end, manure samples from six livestock farms in Germany were analyzed. The results showed that changes in chemical composition during storage led to a 20.5% decrease in the BMP of dairy manure from the barn to outdoor storage. For fattening pig manure samples, there was a 39.5% decrease in the BMP from intermediate to outdoor storage. An analysis of BMP according to manure age showed that pig manure degrades faster than dairy manure; the importance of promptly feeding manure to the biogas plant in order to avoid significant CH4 emission losses and reduction in energy producing capacity was highlighted. The best BMP predictors for dairy manure were the contents of dry matter, volatile solids and lignin, whereas best BMP predictors for pig manure were dry matter and volatile fatty acid (VFA) content. Prediction models performed well for samples from outdoor storages; refinements for predicting BMP of less aged samples presenting lower chemical variability would be necessary.

Scientific characterization methods for better utilization of cattle dung and urine: a concise review

Cattle are usually raised for food, manure, leather, therapeutic, and draught purposes. Biowastes from cattle, such as dung and urine, harbor a diverse group of crucial compounds, metabolites/chemicals, and microorganisms that may benefit humans for agriculture, nutrition, therapeutics, industrial, and other utility products. Several bioactive compounds have been identified in cattle dung and urine, which possess unique properties and may vary based on agro-climatic zones and feeding practices. Therefore, cattle dung and urine have great significance, and a balanced nutritional diet may be a key to improved quality of these products/by-products. This review primarily focuses on the scientific aspects of biochemical and microbial characterization of cattle biowastes. Various methods including genomics for analyzing cattle dung and gas chromatography-mass spectroscopy for cattle urine have been reviewed. The presented information might open doors for the further characterization of cattle resources for heterogeneous applications in the production of utility items and addressing research gaps. Methods for cattle's dung and urine characterization.

Identified factors and predicted unidentified-factors affecting ammonia emissions from a swine building

Large variabilities in ammonia (NH₃) released from animal manure and emitted from different livestock buildings were frequently reported, but the factors influencing the emissions were not sufficiently investigated. In this paper, continuously monitored data of NH₃ emissions and other relevant environmental variables under controlled conditions in a 12-room experimental swine building for a 155-d complete wean-to-finish cycle were studied. Measurement data mining was conducted at both spatial and temporal dimensions using panel data analysis with heterogeneous time trends. The pig diet, total pig weight, and the pit air temperature were identified as the major influencing factors for the variabilities by using multivariate linear regression. Two unidentified factors that imposed substantial influences on the NH₃ emission variabilities were predicted. They were most possibly related to variations in microenvironment and microbial activity inside the manure in the pit. The results suggest necessary future research to identify physical properties of the new NH₃ emissions factors in microbiological and biochemical processes.

Combining multi-isotope technology, hydrochemical information, and MixSIAR model to identify and quantify nitrate sources of groundwater and surface water in a multi-land use region

Accurate identification of nitrate (NO3-) sources is the premise of non-point source pollution control in watersheds. The multiple isotope techniques (δ15N-NO3-, δ18O-NO3-, δ2H-H2O, δ18O-H2O), combined with hydrochemistry characteristics, land use information, and Bayesian stable isotope mixing model (MixSIAR), were used to identify the sources and contributions of NO3- in the agricultural watershed of the upper Zihe River, China. A total of 43 groundwater (GW) and 7 surface water (SFW) samples were collected. The results showed that NO3- concentrations of 30.23% GW samples exceeded the WHO maximum permissible limit level, whereas SFW samples did not exceed the standard. The NO3- content of GW varied significantly among different land uses. The averaged GW NO3- content in livestock farms (LF) was the highest, followed by vegetable plots (VP), kiwifruit orchards (KF), croplands (CL), and woodlands (WL). Nitrification was the main transformation process of nitrogen, while denitrification was not significant. Hydrochemical analysis results combined with NO isotopes biplot showed that manure and sewage (M&S), NH4+ fertilizers (NHF), and soil organic nitrogen (SON) were the mixed sources of NO3-. The MixSIAR model summarized that M&S was the main NO3- contributor for the entire watershed, SFW, and GW. For contribution rates of sources in GW of different land use patterns, the main contributor in KF was M&S (contributing 59.00% on average), while M&S (46.70%) and SON (33.50%) contributed significantly to NO3- in CL. Combined with the traceability results and the situation that land use patterns are changing from CL to KF in this area, improving fertilization patterns and increasing manure use efficiency are necessary to reduce NO3- input. These research results will serve as a theoretical foundation for controlling NO3- pollution in the watershed and adjusting agricultural planting structures.

Field-scale nutrient loss assessment following cover crop and manure rate change

Eutrophication due to elevated nitrogen (N) and phosphorus (P) loss from croplands remains one of the most pressing water quality issues throughout the world. Understanding the effect of implementing conservation management practices is critical for meeting nutrient reduction goals as well as informing conservation programs and policies. A before-after-control-impact (BACI) analysis was used to evaluate the individual and combined effect of cover crops and manure application rate on discharge and nutrient loss using six water years (WY2014-WY2019) of measured data across four distinct drainage zones (1X-NCC; 1X-CC; 2X-NCC; 2X-CC) within an Ohio, USA, crop production field. White mustard significantly reduced mean monthly nitrate (NO₃^--N) concentration regardless of manure application rate (i.e., 65 m³ ha^-1 and 130 m³ ha^-1). However, neither the use of white mustard, doubling manure rate, or the combination of the two had a significant impact on mean monthly drainage discharge, dissolved-reactive P (DRP), or total P (TP) loss. Seasonal analysis confirmed that NO₃^--N concentration in the cover crop zones was signficantly less in fall, winter, and spring. However, significant increases in spring discharge, NO₃^--N, DRP, and TP loads as well as TP concentration were noted with cover crop and greater manure rate treatments. These findings confirm that cover crops have a reducing effect on NO₃^--N concentration but may not have any effect on addressing P concerns. Further research is warranted; however, this study highlights that the resource concern (e.g., N or P) should be considered prior to implementing cover crops as a conservation management practice.

Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant

Poultry farming is a major livelihood in South and Southeast Asian economies where it is undergoing rapid intensification to meet the growing human demand for dietary protein. Intensification of poultry production systems is commonly supported by increased antimicrobial drug use, risking greater selection and dissemination of antimicrobial resistance genes (ARGs). Transmission of ARGs through food chains is an emerging threat. Here, we investigated transmission of ARGs from chicken (broiler and layer) litter to soil and Sorghum bicolor (L.) Moench plants based on field and pot experiments. The results demonstrate ARGs transmission from poultry litter to plant systems under field as well as experimental pot conditions. The most common ARGs could be tracked for transmission from litter to soil to plants were identified as detected were cmx, ErmX, ErmF, lnuB, TEM-98 and TEM-99, while common microorganisms included Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Vibrio cholerae. Using next generation sequencing and digital PCR assays we detected ARGs transmitted from poultry litter in both the roots and stems of S. bicolor (L.) Moench plants. Poultry litter is frequently used as a fertiliser because of its high nitrogen content; our studies show that ARGs can transmit from litter to plants and illustrates the risks posed to the environment by antimicrobial treatment of poultry. This knowledge is useful for formulating intervention strategies that can reduce or prevent ARGs transmission from one value chain to another, improving understanding of impacts on human and environmental health. The research outcome will help in further understanding the transmission and risks posed by ARGs from poultry to environmental and human/animal health.

Comparison of phosphorus species in livestock manure and digestate by different detection techniques

Phosphorus (P) species characterize the effectiveness of the P fertilizer. In this study, the P species and distribution in different manures (pig manure, dairy manure and chicken manure) and their digestate were systematically investigated through combined characterization methods of Hedley fractionation (H₂OP, NaHCO₃-P, NaOH-P, HCl-P, and Residual), X-ray diffraction (XRD) and nuclear magnetic resonance (NMR) techniques. The results from Hedley fractionation showed that >80 % of P in the digestate was inorganic and the HCl-P content in manure increased significantly during anaerobic digestion (AD). XRD manifested that insoluble hydroxyapatite and struvite belonging to HCl-P were presented during AD, which was in agreement with the result of Hedley fractionation. ³¹P NMR spectral analysis revealed that some orthophosphate monoesters were hydrolyzed during AD, meanwhile the orthophosphate diester organic phosphorus like DNA and phospholipids content has increased. After characterizing P species by combining these methods, it was found that chemical sequential extraction could be an effective way to fully understand the P in livestock manure and digestate, with other methods used as auxiliary tool depending on the purpose of studies. Meanwhile, this study provided a basic knowledge of utilizing digestate as P fertilizer and minimizing the risk of P loss from livestock manure. Overall, applying digestates can minimize the risk of P loss from directly applied livestock manure while satisfying plant demands, and is an environmentally friendly P fertilizer.

Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land

Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a municipal wastewater treatment plant along the west coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARG mechanisms were observed between swine manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40-55 %), tetracyclines (30-45 %), beta-lactam-resistance (20-35 %), macrolides (18-30 %), and >50 % of the VFGs that the 24 microbiomes harbored were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. Metabolic reconstruction of metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with carbapenem resistance, multidrug resistance (MDR), and efflux pump. Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that the dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands, negatively impacting both soil and human health.

Heat balance analysis for self-heating torrefaction of dairy manure using a mathematical model

A self-heating torrefaction system was developed to overcome the difficulties in converting high-moisture biomass to biochar. In self-heating torrefaction, the ventilation rate and ambient pressure must be set properly to initiate the process. However, the minimum temperature at which self-heating begins is unclear because the effects of these operating variables on the heat balance are not theoretically understood. The present report presents a mathematical model for the self-heating of dairy manure based on the heat balance equation. The first step was to estimate the heat source; experimental data showed that the activation energy for the chemical oxidation of dairy manure is 67.5 kJ/mol. Next, the heat balance of feedstock in the process was analyzed. Results revealed that the higher the ambient pressure and the lower the ventilation rate at any given pressure, the lower the temperature at which self-heating is induced. The lowest induction temperature was 71 °C at a ventilation rate of 0.05 L min^-1 kg-AFS^-1 (AFS: ash-free solid). The model also revealed that the ventilation rate significantly affects the heat balance of feedstock and drying rate, suggesting an optimal range for ventilation.

Prevalence of veterinary antibiotics in natural and organic fertilizers from animal food production and assessment of their potential ecological risk

BACKGROUND

Veterinary antibiotics are emerging contaminants and enter into soil principally by agricultural application of organic fertilizers. This article presents the results of the research obtained for the analyzed 70 samples of fertilizers (pig and poultry manure and slurry and digestate) for various classes of antibiotics.

RESULTS

Doxycycline, oxytetracycline, tetracycline, lincomycin, tiamulin and enrofloxacin were found in tested samples. Doxycycline was found as a dominant compound, and its highest concentration was 175 mg/kg in pig manure. This investigation indicated that fertilization with manure, especially animal feces, might be the primary source of antibiotics. Additionally, a risk assessment based on a risk quotient was carried out, which showed that the determined concentrations of antibiotics in fertilizers may pose a threat to soil microorganisms.

CONCLUSIONS

Results suggested that the ecological risk effects of antibiotic contamination on soil bases and their potential adverse risk on human health needs special attention. © 2023 Society of Chemical Industry.

Potential output and risk of commonly administered veterinary antibiotics from small-scale livestock farms to surrounding areas in Northwest China

The concern over antibiotic pollution from animal husbandry has significantly increased over recent years. However, few studies on output and environmental risk of veterinary antibiotics (VAs) throughout different exposure matrices from small-scale livestock farms (SSLFs) have been explored. This study explored the output and environmental risk of three classes of VAs (sulfonamides (SAs), tetracyclines (TCs), fluoroquinolones (FQs)) in three different types of environmental media (manure, soil, and plants/vegetables) derived from four livestock feedlots in the Hexi Corridor of Northwest China. Following, a risk assessment was conducted to identify the hazardous potential of these VAs on the ecological health of the surrounding environment. A total of 108 soil, 36 manure, 12 plants/vegetables, and 15 animal product samples were collected from the animal feedlots for analysis. The results showed that each of the three groups of VAs were detected in the soil, manure and plant samples derived from all four feedlots in varying levels. In the soil samples, the detection rate of SAs (68%) was higher than the TCs (57%) and the FQs (27%). The total concentration of VAs ranged from not detected (n.d.) to 275 ng/g, while chlortetracycline (CTC) was the most abundant (275 ng/g) of the VAs in soil samples. The SAs had the highest detection rate (100%), followed by TCs (89%), and FQs (78%) in manure samples. The total concentration of VAs residues ranged from n. d. to 105 ng/g, of which CTC was as high as 91 ng/g in manures. In the plant/vegetable samples, the TCs had the highest detection rate (58%), while sulfamethazine (SDM) was the most abundant (32 ng/g). The total concentration of the VAs ranged from n. d. to 65 ng/g in the plant/vegetable samples. The target VAs were not detected in animal products. Measurements of the composition of VAs in soil samples at different vertical depths as well as horizontal distances from the manure accumulation sites showed that VAs were partially retained in the soil of the feedlots and were distributed into the surrounding environment both horizontally and vertically. It is suspected that the detected VAs could be accumulated in agricultural soils since they could be found in most of the sampled manures and soils in SSLFs. These results highlighted the necessity of considering SSLF practices to mange the accumulation and disposal of manure mitigating and controlling VA pollution.

Methane release from enteric fermentation and manure management of domestic water buffalo in Nepal

Methane (CH₄) emission in livestock arises from enteric fermentation (EnF) and manure management (MM). This study develops the country-specific CH₄ emission factors (EFs) in both EnF and MM for domestic water buffalo (Bubalus bubalis) and estimates total CH₄ emission in Nepal using Intergovernmental Panel on Climate Change (IPCC) Tier 2 methodology. Seasonal field data were collected on morphological characteristics, feed characteristics, and manure management practices of the buffalo. The buffalo population was divided into five age groups, and at least 35 buffalo individuals were measured from each age group in the Hilly and Plain regions of Nepal in the winter and summer seasons. Buffalo adult male (BAM) had the highest body weight of 530 ± 53 kg in the plain region and 514 ± 65 kg in the Hill region. Similarly, the weight of buffalo calf (BC) was 91 ± 25 kg in the plain region and 77 ± 26 kg in the Hill region. For different age groups of buffalo, EnF EFs ranged from 34 ± 8 to 90 ± 10 kg CH₄ head^-1 year^-1 and MM EFs ranged from 2.5 ± 0.5 to 7.5 ± 0.5 kg CH₄ head^-1 year^-1. The estimated EnF and MM EFs of buffalo were not statistically different by region (p > 0 .05). The total CH₄ flux from buffalo was 347.8 Gg year^-1 in Nepal, contributing 322.2 Gg year^-1 from EnF and 25.6 Gg year^-1 from MM. The country-specific EFs are highly recommended for precise computing of the national emissions and carrying out mitigation action.

Composting reduces the risks of antibiotic resistance genes in maize seeds posed by gentamicin fermentation waste

Using high-throughput quantitative PCR and next generation sequencing, the impact of land application of raw and composted gentamicin fermentation waste (GFW) on antibiotic resistance genes (ARGs) in maize seeds was studied in a three-year field trial. The raw and composted GFW changed both the bacterial community composition and the ARGs diversity in the maize seeds compared to non-amended controls and chemical fertilizer. The abundance of ARGs after raw GFW amendment was significantly higher than other treatments because of a high abundance of aadA1, qacEdeltal and aph(2')-Id-02; probably induced by gentamicin selection pressure in maize tissues. Meanwhile, the potential host of these three ARGs, pathogenic bacteria Tenacibaculum, also increased significantly in maize seeds after the application of raw GFW. But our result proved that composting could weaken the risk posed by GFW. We further reveal that the key biotic driver for shaping the ARG profiles in maize seeds is bacterial community followed by heavy metal resistance genes, and ARGs are more likely located on bacterial chromosomes. Our findings provide new insight into ARGs dispersal mechanism in maize seeds after long-term GFW application, demonstrate the potential benefits of composting the GFW to reduce risks as well as the potential efficient management method to GFW.

Calcium cyanamide reduces methane and other trace gases during long-term storage of dairy cattle and fattening pig slurry

Calcium cyanamide (CaCN₂) has been used in agriculture for more than a century as a nitrogen fertilizer with nitrification inhibiting and pest-controlling characteristics. However, in this study, a completely new application area was investigated, as CaCN₂ was used as a slurry additive to evaluate its effect on the emission of ammonia and greenhouse gases (GHG) consisting of methane, carbon dioxide, and nitrous oxide. Efficiently reducing these emissions is a key challenge facing the agriculture sector, as stored slurry is a major contributor to global GHG and ammonia emissions. Therefore, dairy cattle and fattening pig slurry was treated with either 300 mg kg^-1 or 500 mg kg^-1 cyanamide formulated in a low-nitrate CaCN₂ product (Eminex®). The slurry was stripped with nitrogen gas to remove dissolved gases and then stored for 26 weeks, during which gas volume and concentration were measured. Suppression of methane production by CaCN₂ began within 45 min after application and persisted until the storage end in all variants, except in the fattening pig slurry treated with 300 mg kg^-1, in which the effect faded after 12 weeks, indicating that the effect is reversible. Furthermore, total GHG emissions decreased by 99% for dairy cattle treated with 300 and 500 mg kg^-1 and by 81% and 99% for fattening pig, respectively. The underlying mechanism is related to CaCN₂-induced inhibition of microbial degradation of volatile fatty acids (VFA) and its conversion to methane during methanogenesis. This increases the VFA concentration in the slurry, lowering its pH and thereby reducing ammonia emissions.

Transfer and distribution of antibiotic resistance genes in the soil-peanut system receiving manure for years

Antibiotic resistance gene (ARG)-contaminated food from manure application is gaining widespread interest, but little is known about the distribution and uptake of ARGs in peanuts that are subjected to manure routinely. In this study, the ARG profile and bacterial community in soil and peanut plants from a 7-year manure-fertilized field were investigated using high-throughput qPCR and 16S rRNA gene sequencing. Manure application increased the abundance of ARGs in soil and peanuts by 59-72 and 4-10 fold, respectively. The abundance of ARGs from high to low was as follows: manure, shell-sphere soil, rhizosphere soil, bulk soil, stems, shells, needles, kernels, and roots. Source-tracker analyses were used to investigate the potential source of ARGs in peanut kernels, which revealed that the ARGs in peanut kernels may be primarily absorbed by the roots from the soil. The horizontal gene transfer (HGT) of ARGs was the primary factor in the spread of ARGs, and Proteobacteria were the primary agents of HGT between different parts of peanut plants. Additionally, norank_Chloroplast from the phylum Cyanobacteria was the most important contributor to the abundance of ARGs in peanut kernels. Overall, our findings fill a gap in our understanding of the distribution patterns of ARGs in peanut plants and the migratory pathways of ARGs from soil to peanut kernels.

Compaction effects on greenhouse gas and ammonia emissions from solid dairy manure

Waste management practices of solid dairy manures were evaluated under controlled conditions to study gas transport and emission inside manure piles. Three applied stresses and three moisture contents were tested to represent manure conditions managed at various pile depths. A Fourier-transform infrared spectroscopy monitor measured concentrations of greenhouses gases [methane, carbon dioxide, and nitrous oxide] and ammonia as part of gas flux rate calculations. Results showed that carbon dioxide dominated the greenhouse gas emissions under all test conditions. Gas transfer, primarily diffusion, was facilitated by manure with high mechanical strength and high permeability. Gas emission rates reduced dramatically when moisture content increased in manure with high water holding capacity, while compaction treatments did not as strongly affect the gas emission rates. Results provide fundamental insights into management strategies for reducing gas emissions from solid dairy manure.

Insights into the panorama of antibiotic resistome in cropland soils amended with vermicompost in China

The accumulation and propagation of animal-derived antibiotic resistance genes (ARGs) pose great challenges to agricultural ecosystems. Vermicompost has drawn global attention as a new type of eco-friendly organic fertilizer. However, the effects of vermicompost application on ARGs in soil are still unclear. Here, we conducted a nationwide large-scale survey to explore the impact of vermicompost application on ARGs and the host in cropland fields as well as their regional differences. Vermicompost application was found to alter the pattern of ARGs, reduce the transfer of mobile genetic elements (MGEs), and mitigate the proliferation of high-risk bla-ARGs in soil. Regional differences in vermicompost-derived ARGs were observed in croplands, with less ARG-spreading risk in brown and yellow-brown soils. Total ARG abundance was present at the lowest level (1.24 × 10⁵-3.57 × 10⁷ copies/g) in vermicomposted soil compared with the croplands using animal manure (e.g., swine, chicken, and cow manure). Furthermore, vermicompost application increased the abundance of beneficial bacteria like Ilumatobacter and Gaiella, while reducing the abundance of Acidobacteria and Pseudarthrobacter. Network analysis showed that vermicompost altered ARG host bacteria and reduced the numbers of potential ARG hosts in soil. Microbes played a key role in ARG changes in vermicompost-treated soil. Our study provides valuable insight into the response of soil ARGs and the host to vermicompost in cropland ecosystem, and also provides a novel pathway for controlling the propagation of animal-derived ARGs.

Geochemistry, stable isotopes and statistic tools to estimate threshold and source of nitrate in groundwater (Sardinia, Italy)

In the European Union, nitrate vulnerable zone (NVZ) should be designed for the mitigation of nitrate (NO₃^-) contamination caused by agricultural practices. Before establishing new NVZ, the sources of NO₃^- must be recognized. A geochemical and multiple stable isotopes approach (hydrogen, oxygen, nitrogen, sulfur and boron) and statistical tools were applied to define the geochemical characteristics of groundwater (60 samples), calculate the local NO₃^- threshold and assess potential sources of NO₃^- contamination in two study areas (hereafter Northern and Southern), located in a Mediterranean environment (Sardinia, Italy). Results of the integrated approach applied to two case study, permits to highlight the strengths of integrating geochemical and statistical methods to provide nitrate source identification as a reference by decision makers to remediate and mitigate nitrate contamination in groundwater. Hydrogeochemical features in the two study areas were similar: near neutral to slightly alkaline pH, electrical conductivity in the range of 0.3 to 3.9 mS/cm, and chemical composition ranging from Ca-HCO₃^- at low salinity to Na-Cl^- at high salinity. Concentrations of NO₃^- in groundwater were in the range of 1 to 165 mg/L, whereas the nitrogen reduced species were negligible, except few samples having NH₄⁺ up to 2 mg/L. Threshold values in the studied groundwater samples were between 4.3 and 6.6 mg/L NO₃^-, which was in agreement with previous estimates in Sardinian groundwater. Values of δ³⁴S and δ¹⁸O_SO4 of SO₄^2- in groundwater samples indicated different sources of SO₄^2-. Sulfur isotopic features attributed to marine SO₄^2- were consistent with groundwater circulation in marine-derived sediments. Other source of SO₄^2- were recognize due to the oxidation of sulfide minerals, to fertilizers, manure, sewage fields, and SO₄^2- derived from a mix of different sources. Values of δ¹⁵N and δ¹⁸O_NO3 of NO₃^- in groundwater samples indicated different biogeochemical processes and NO₃^- sources. Nitrification and volatilization processes might have occurred at very few sites, and denitrification was likely to occur at specific sites. Mixing among various NO₃^- sources in different proportions might account for the observed NO₃^- concentrations and the nitrogen isotopic compositions. The SIAR modeling results showed a prevalent NO₃^- source from sewage/manure. The δ¹¹B signatures in groundwater indicated the manure to be the predominant NO₃^- source, whereas NO₃^- from sewage was recognized at few sites. Geographic areas showing either a predominant process or a defined NO₃^- source where not recognize in the studied groundwater. Results indicate widespread contamination of NO₃^- in the cultivated plain of both areas. Point sources of contamination, due to agricultural practices and/or inadequate management of livestock and urban wastes, were likely to occur at specific sites.

Differential impacts of salinity on antibiotic resistance genes during cattle manure stockpiling are linked to mobility potentials revealed by metagenomic sequencing

Livestock manure is an important source of antibiotic resistance genes (ARGs), and its salinity level can change during stockpiling. To understand how the salinity changes affect the fate of ARGs, cattle manure was adjusted of salinity and stockpiled in laboratory microcosms at low (0.3% salt), moderate (3.0%) and high salinity levels (10.0%) for 44 days. Amongst the five ARGs (tetO, bla_TEM, sul1, tetM, and ermB) and the first-class integrase (intI1) monitored by qPCR, the relative abundance of tetO and bla_TEM exhibited no clear trend in response to salinity levels, while that of sul1, tetM, ermB and intI1 showed clear downward trends over time at the lower salinity levels (0.3% and 3%) but not at the high salinity level (10%). Metagenomic contig construction of cattle manure samples revealed that sul1, tetM and ermB genes were more likely to associate with mobile genetic elements (MGEs) than tetO and bla_TEM, suggesting that their slower decay at higher salinity levels was either caused by horizontal gene transfer or co-selection of ARGs and osmotic stress resistant determinants. Further analysis of metagenomic contigs showed that osmotic stress resistance can also be located on MGEs or in conjunction with ARGs.

Comprehensive analysis of the fates and risks of veterinary antibiotics in a small ecosystem comprising a pig farm and its surroundings in Northeast China

This study investigated the behavior of veterinary antibiotics (VAs) in a small farm ecosystem. Manure and environmental samples were collected around a large pig farm in northeast China. Thirty-four VAs in six categories were analyzed. Then, a multimedia fugacity model was used to estimate the fates of VAs in the environment. The results showed that VAs were prevalent in manure, soil, water, and sediment, but not in crops. Compared with fresh manure, VA levels were significantly lower in surface manure piles left in the open air for 3-6 months. The main VAs, tetracyclines and quinolones, decreased by 427.12 and 158.45 µg/kg, respectively. VAs from manure piles were transported to the surroundings and migrated vertically into deep soil. The concentrations of ∑VAs detected in agricultural soils were 0.03-4.60 µg/kg; > 94% of the mass inventory of the VAs was retained in soil organic matter (SOM), suggesting that SOM is the main reservoir for antibiotics in soil. Risk assessment and model analysis indicated that the negative impact of mixed antibiotics at low concentrations in farmland on crops may be mediated by indirect effects, rather than direct effects. Our findings highlight the environmental fates and risks of antibiotics from livestock farms.

Changes in cropland soil carbon through improved management practices in China: A meta-analysis

Recommended management practices (RMPs, e.g., manuring, no-tillage, crop residue return) can increase soil organic carbon (SOC), reduce greenhouse gas emissions, and maintain soil health in croplands. However, there is no consensus on how RMPs affect the SOC storage potential of cropland soils for climate change mitigation. Here, based on 2301 comparisons from 158 peer-reviewed papers, a meta-analysis was conducted to explore management-induced SOC stock changes and their variations under different conditions. The results show that SOC stocks in the 0-20 cm layer were increased by 31.8% when chemical fertilization combined with manure application was compared with no fertilizer; 9.98% when no-tillage was compared with plow tillage; and 10.84% when straw return was compared with removal. The RMPs favorably increased SOC stock in arid areas, and in alkaline and fine-textured soils. Initial SOC, carbon-nitrogen ratio, and experimental duration could also affect SOC storage. Compared with the initial SOC stock, RMPs increased the SOC sequestration potential by 2.6-4.5% in the 0-20 cm soil depth, indicating that these practices can help China achieve targets to increase SOC by 4.0‰. Hence, it is essential to implement RMPs for climate change mitigation and soil fertility improvement.

Identification of nitrogen pollution sources and transport transformation processes in groundwater of different landforms using C, H, N, and O isotope techniques: an example from the lower Weihe River

Nitrogen pollution in groundwater is an environmental issue of global concern. Identifying nitrogen pollution sources and determining migration and transformation processes are the major ways to prevent and control nitrogen pollution in the groundwater on a regional scale. In this study, groundwater in the lower Wei River was investigated by combining multi-isotope tracing techniques with the SIAR hybrid model (source resolution) to trace the nitrate sources and their contribution rate to nitrogen pollution in groundwater of different geomorphological units, considering types of geomorphology as the units. The multi-isotope tracing technique allows dynamic analysis of nitrate sources, and the combination of this technology can improve the accuracy of nitrogen source traceability. The results indicated that the pH of the water bodies in the study area ranged from 6.83 to 8.01, which is neutral and weakly alkaline. The nitrogen pollution was mainly due to nitrates. The significant factors affecting nitrogen migration in groundwater are the geomorphological type, the chemical characteristics of the groundwater, and the age of the groundwater. Nitrogen migration and transformation processes in the study area were dominated by nitrification, and sources of nitrate pollution were mainly animal manure and domestic sewage (32.6%), followed by atmospheric deposition (26.8%), soil nitrogen (20.9%), and chemical fertilizer (19.7%). The main sources of nitrate in groundwater from river flats, alluvial plains, and loess tableland were animal manure and domestic sewage (43.7%), animal manure and domestic sewage (59.1%), and atmospheric deposition (55.5%), respectively. The result is mainly related to the different structural characteristics of various geomorphic units and the intensity of human activities. This study can provide a theoretical basis for the relevant agencies to develop plans to combat groundwater pollution.

Characteristics and source analysis of polycyclic aromatic hydrocarbons in organisms and manure near Ardley Island, Antarctica

In order to better understand the migration and accumulation behavior of polycyclic aromatic hydrocarbons (PAHs) in biological chains in the cold environment around the Ardley Island, a variety of biological and penguin manure samples during China's 36th Antarctic Scientific expedition have been collected and studied. A certain difference in PAHs concentration was observed in the environmental samples, and the order of size was as follows: fish > limpets > krill > manure > brown alga > mosses. The percentage of PAHs with different ring numbers in brown alga, moss, and krill was in the following order: three rings > two rings > four rings > five rings > six rings. The proportion of HMW-PAHs in limpets and fish samples was higher than that in brown alga, moss, manure, and krill samples. The main source of PAHs in environmental samples near Ardley Island is oil, which may be due to the development of tourism in Antarctica, the number of ships and human activities around the region. Therefore, it is imperative to strengthen the protection of the ecological environment in the area around Ardley Island.

Co-occurrence of genes for antibiotic resistance and arsenic biotransformation in paddy soils

Paddy soils are potential hotspots of combined contamination with arsenic (As) and antibiotics, which may induce co-selection of antibiotic resistance genes (ARGs) and As biotransformation genes (ABGs), resulting in dissemination of antimicrobial resistance and modification in As biogeochemical cycling. So far, little information is available for these co-selection processes and specific patterns between ABGs and ARGs in paddy soils. Here, the 16S rRNA amplicon sequencing and high-throughput quantitative PCR and network analysis were employed to investigate the dynamic response of ABGs and ARGs to As stress and manure application. The results showed that As stress increased the abundance of ARGs and mobile genetic elements (MGEs), resulting in dissemination risk of antimicrobial resistance. Manure amendment increased the abundance of ABGs, enhanced As mobilization and methylation in paddy soil, posing risk to food safety. The frequency of the co-occurrence between ABGs and ARGs, the host bacteria carrying both ARGs and ABGs were increased by As or manure treatment, and remarkably boosted in soils amended with both As and manure. Multidrug resistance genes were found to have the preference to be co-selected with ABGs, which was one of the dominant co-occurring ARGs in all treatments, and manure amendment increased the frequency of Macrolide-Lincosamide-Streptogramin B resistance (MLSB) to co-occur with ABGs. Bacillus and Clostridium of Firmicutes are the dominant host bacteria carrying both ABGs and ARGs in paddy soils. This study would extend our understanding on the co-selection between genes for antibiotics and metals, also unveil the hidden environmental effects of combined pollution.

Evaluating the impact of heavy metals on antimicrobial resistance in the primary food production environment: A scoping review

Heavy metals are naturally occurring environmental compounds, which can influence antimicrobial resistance (AMR) dissemination. However, there is limited information on how heavy metals may act as a selective pressure on AMR in the primary food production environment. This review aims to examine the literature on this topic in order to identify knowledge gaps. A total of 73 studies, which met pre-established criteria, were included. These investigations were undertaken between 2008 and 2021, with a significant increase in the last three years. The majority of studies included were undertaken in China. Soil, water and manure were the most common samples analysed, and the sampling locations varied from areas with a natural presence of heavy metals, areas intentionally amended with heavy metals or manure, to areas close to industrial activity or mines. Fifty-four per cent of the investigations focused on the analysis of four or more heavy metals, and copper and zinc were the metals most frequently analysed (n = 59, n = 49, respectively). The findings of this review highlight a link between heavy metals and AMR in the primary food production environment. Heavy metals impacted the abundance and dissemination of mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs), with MGEs also observed as playing a key role in the spread of ARGs and metal resistance genes (MRGs). Harmonization of methodologies used in future studies would increase the opportunity for comparison between studies. Further research is also required to broaden the availability of data at a global level.

Effect of amendments on bioavailability of cadmium in soil-rice system: a field experiment study

The field experiment study investigated the effect of lime (L), manure compost (M), combination of lime and manure (LM), and combinations of lime with four kinds of passivators (LP1, LP2, LP3, and LP4) on the bioavailability of cadmium (Cd) in soil and Cd accumulation in rice plants. These four passivating products were composed of organic and inorganic compounds such as silicon-sulfhydryl group, CaO, SiO₂, and so on. The results indicated that the application of these amendments improved soil pH, organic matter content, and cation exchange capacity (CEC) by 0.19-0.73 unit, 0.6-8.2%, and 5.7-38.9%, respectively; meanwhile, decreased soil acid-extractable Cd by 4.0-13.9% compared with before remediation. Alleviating Cd stress to rice also resulted in a significant increase in rice grains yield, whereas the LP4 showed an increment of 15.8-27.6%. Among these amendments, LP4 had a relatively high effectiveness, it promoted the decrease of extractable Cd by 13.9% and the increase of residual Cd by 8.1%; meanwhile, the bioconcentration factor of rice grain in LP4 decreased by 71.3%. The high pH, CEC, and rich functional groups in amendments might cause soil Cd transform from mobile fraction to residual fraction, and the cation ions in amendments also competed with Cd ions due to the antagonism. Taken all of these effects, the amendments alleviated Cd pollution in soil-rice system, decreasing Cd migration from soil to grain. In future, the long-term field experiment will need to be done for verify the long-term effect of soil amendments.

N-Source Determines Barley Productivity, Nutrient Accumulation, and Grain Quality in Cyprus Rainfed Agricultural Systems

The Eastern Mediterranean and Middle East (EMME) region is already experiencing the negative effects of increased temperatures and the increase in prolonged drought periods. The use of organic fertilization could be a valuable tool to meet the main challenges of climate change and maintain the productivity, quality, and sustainability of rainfed agricultural ecosystems. In the current study, we compare the effect of manure, compost, and chemical fertilization (NH₄NO₃) on barley grain and straw yield in a field study for three consecutive growing seasons. The hypothesis that the barley productivity, nutrient accumulation, and grain quality remain similar among the different nutrient management strategies was tested. The results showed that both growing season and type of nutrient source significantly affected barley grain and straw yield (F_6,96 = 13.57, p < 0.01). The lowest productivity was noticed in the non-fertilized plots while chemical and organic fertilization exhibited similar grain yield, ranging from 2 to 3.4 t/ha throughout the growing seasons. For straw, the use of compost had no effect on the yield in any of the growing seasons examined. The use of manure and compost had a significant effect on grain macro- and micronutrient content but this was highly related to growing season. Principal component analysis (PCA) clearly demonstrated the discrimination of the different type of fertilization on barley performance during the course of the study, while the application of compost was highly associated with an increase in micronutrients in grain samples. Furthermore, structural equational modeling (SEM) showed that both chemical and organic fertilization had a direct positive effect on macro- (r = 0.44, p < 0.01) and micronutrient (r = 0.88, p < 0.01) content of barley grain and a positive indirect effect on barley productivity through N accumulation in grain (β = 0.15, p = 0.007). The current study showed that barley grain and straw yield was similar between manure and NH₄NO₃ treatments, while compost exhibited a residual positive effect causing an increase in grain yield during the growing season. The results highlight that N fertilization under rainfed conditions is beneficial to barley productivity through its indirect effects on N accumulation in grain and straw, while it improves grain quality through the increased accumulation of micronutrients.

Manure and biochar have limited effect on lettuce leaf endophyte resistome

Soil amendment with manure compost and biochar is widely adopted to improve soil fertility and promote plant growth, and their effects on soil microbial communities and resistome have been well documented. However, there is sparse information regarding their effects on vegetable endophytes, which represent a major source of human exposure to pathogens and antibiotic resistance genes (ARGs) when eaten raw. Here, we investigated the impacts of manure compost or biochar addition on the bacterial community compositions and ARGs in the soil-lettuce continuum including soil, seed, leaf, and root samples. A total of 137 ARGs and 31 mobile genetic elements (MGEs) were detected in all the samples after 60 days of cultivation. The relative abundance of ARGs and the diversity of bacteria communities presented a consistent decreasing trend from soil to root endophytes, then leaf endophytes. Manure compost addition increased the diversity and abundance of ARGs in soil, while significant changes in the ARG profiles and bacterial communities were not observed in leaf endophytes after manure compost or biochar addition, or both. Bipartite networks analysis suggested that seed microbiome was one of the major sources of plant endophytes and ARGs. Twenty potential human pathogens were isolated from lettuce, indicating potential exposure risk to pathogens via the consumption of raw lettuce. These results suggest limited impacts of manure compost and biochar addition on lettuce endophytes and highlight the contribution of seed microbiome to endophyte ARG profiles.

Cow dung putrefaction via vermicomposting using Eisenia fetida and its influence on seed sprouting and vegetative growth of Viola wittrockiana (pansy)

The current research was conducted at Vermi-tech Unit, Muzaffarabad in 2018 to evaluate the efficacy of cow dung and vermicompost on seed sprouting, seedlings, and vegetative developmental parameters of Viola x wittrokiana (pansy). In the current study, vermicompost was produced using Eisenia fetida. Physicochemical parameters of vermicompost and organic manure were recorded before each experimentation. The potting experiment was designed and comprised of eight germination mediums containing different combinations of soil, sand, cow dung, and various concentrations of vermicompost such as 10% VC, 15% VC, 20% VC, 25% VC, 30% VC, and 35% VC. Seed sprouting and seedling developmental parameters were observed for 28 days while vegetative plant growth parameters were recorded after 10 weeks of transplantation in various vermicompost amended germination media. Pre and post-physicochemical analysis of germination media were also recorded to check their quality and permanency. The current findings showed that 30% VC germination media was an effective dose for early seed germination initiation and all seed germination parameters. However, the significant vegetative plant growth and flowering parameters of pansy occurred at 35% VC. Findings revealed that vermicompost not only enhanced the seed germination and growth of pansy but also improved soil health. These results indicate that vermicompost can be exploited as a potent bio-fertilizer for ornamental plant production.

Application of earthworm and silicon can alleviate antibiotic resistance in soil-Chinese cabbage system with ARGs contamination

Organic fertilization is a major contributor to the spread of antibiotic resistance genes (ARGs) in the agroecosystem, which substantially increases the risk of ARGs acquisition and their transmission into human food chains. Earthworms are among the most vital soil faunas involved in the link between belowground and aboveground, and silicon is beneficial for soil health and plant stress resistance. This study aims to explore the effect of different amendment strategies (earthworm and/or silicon) and the related influencing factors on the alleviation of ARGs using high-throughput qPCR. The results showed that the application of earthworms and silicon fertilizers reduced the absolute abundance of ARGs in the rhizosphere soils, either singly or in combination. According to the structural equation model and random forest analysis, mobile genetic elements are the major factors enhancing ARGs transfers and the treatment affects ARGs in direct or indirect ways. Our results highlight the role of "rhizosphere effect" in alleviating antibiotic resistance and suggest that silicon fertilizers, together with the earthworms, can be considered as a sustainable and natural solution to mitigate high-risk ARGs spread in the soil-plant systems. Our findings provide guidance in formulating strategies for halting the spread of ARGs in the agroecosystem.

Ammonia emissions, impacts, and mitigation strategies for poultry production: A critical review

Confined animal feeding operations (CAFOs) are the main sources of air pollutants such as ammonia (NH₃) and greenhouse gases. Among air pollutants, NH₃ is one of the most concerned gasses in terms of air quality, environmental impacts, and manure nutrient losses. It is recommended that NH₃ concentrations in the poultry house should be controlled below 25 ppm. Otherwise, the poor air quality will impair the health and welfare of animals and their caretakers. After releasing from poultry houses, NH₃ contributes to the form of fine particulate matters in the air and acidify soil and water bodies after deposition. Therefore, understanding the emission influential factors and impacts is critical for developing mitigation strategies to protect animals' welfare and health, environment, and ecosystems. This review paper summarized the primary NH₃ emission influential factors, such as how poultry housing systems, seasonal changes, feed management, bedding materials, animal densities, and animals' activities can impact indoor air quality and emissions. A higher level of NH₃ (e.g., >25 ppm) results in lower production efficiency and poor welfare and health, e.g., respiratory disorder, less feed intake, lower growth rates or egg production, poor feed use efficiency, increased susceptibility to infectious diseases, and mortality. In addition, the egg quality (e.g., albumen height, pH, and condensation) was reduced after laying hens chronically exposed to high NH₃ levels. High NH₃ levels have detrimental effects on farm workers' health as it is a corrosive substance to eyes, skin, and respiratory tract, and thus may cause blindness, irritation (throat, nose, eyes), and lung illness. For controlling poultry house NH₃ levels and emissions, we analyzed various mitigation strategies such as litter additives, biofiltration, acid scrubber, dietary manipulation, and bedding materials. Litter additives were tested with 50% efficiency in broiler houses and 80-90% mitigation efficiency for cage-free hen litter at a higher application rate (0.9 kg m^-2). Filtration systems such as multi-stage acid scrubbers have up to 95% efficiency on NH₃ mitigation. However, cautions should be paid as mitigation strategies could be cost prohibitive for farmers, which needs assistances or subsidies from governments.

Exploring the abundance and influencing factors of antimicrobial resistance genes in manure plasmidome from swine farms

Plasmids play a critical role in the dissemination of antimicrobial resistance genes (ARGs), however, a systematical understanding of ARGs originated from plasmids in swine production is currently lacking. Herein, quantitative polymerase chain reaction was applied to determine the prevalence of ten ARGs and the class1 integron gene intI1 of plasmid source in swine manure from 44 farms in Sichuan, Hubei and Hebei provinces, China. All assayed ARGs were observed in plasmid DNA samples, and the average absolute abundance of aac(6')-Ib-cr, bla_NDM, bla_CTX-M, optrA, ermB, floR, mcr-1, qnrS, tetM, sul1 and intI1 were 7.09, 2.90, 4.67, 6.62, 7.55, 7.14, 4.08, 4.85, 7.16, 7.11 and 8.07 of 10 log copies/gram, respectively. IntI1 showed a high correlation (r > 0.8, P < 0.01) with the abundance of aac(6')-Ib-cr and sul1 in swine manure. Moreover, the farm scale (i.e., herd population) and geographical location were not found to be critical factors influencing the absolute abundance of ARGs of plasmid DNA in swine farms. However, the concentrations of florfenicol, Cu, Zn, Fe, total phosphorus (TP) and total potassium (TK) demonstrated a significant correlation with the abundance of several ARGs. Particularly, Cu and Zn had high correlations with optrA and bla_CTX-M, respectively. Our results demonstrated that antibiotics, heavy metals and environmental nutrients are likely jointly contributing to the long-term persistence of ARGs in swine production. This study provides insights into the abundance and influencing factors of ARGs from swine manure, which is of significance for assessing and reducing the public health risks in livestock production.

Nutrient concentrations affect the antimicrobial resistance profiles of cattle manures

Antimicrobial resistance (AMR) in cattle is widespread because of the increased use of antibiotics to combat microbial diseases and enhance milk production. The cattle excreta released into the environment can be a potent source of contamination in spreading antibiotic resistance, especially upon its application in agriculture. However, the correlation of AMR profile of manure with other physico-chemical parameters is limited. Therefore, the study aimed to generate AMR profiles for manure samples collected from 25 different sites of two agriculturally important states in India, Madhya Pradesh and Uttar Pradesh. Samples were tested for physico-chemical parameters, viz., electrical conductivity, pH, total nitrogen (N), total phosphorus (P), and total potassium (K). Bacterial community analysis was done by culture-dependent and culture-independent methods. The influence of feeding practices, nutrient concentration, and bacterial abundance on antibiotic resistance profiles was observed in collected manure samples. Manures of intensive feeding animals harbored highly resistant profiles of bacteria as compared to natural grazing cattle.

Effect of graphene and graphene oxide on antibiotic resistance genes during copper-contained swine manure anaerobic digestion

Copper is an important selectors for antibiotic resistance genes (ARGs) transfer because of metal-antibiotic cross-resistance and/or coresistance. Due to carbon-based materials' good adsorption capacity for heavy metals, graphene and graphene oxide have great potential to reduce ARGs abundance in the environment with copper pollution. To figure out the mechanics, this study investigated the effects of graphene and graphene oxide on the succession of ARGs, mobile genetic elements (MGEs), heavy metal resistance genes (HMRGs), and bacterial communities during copper-contained swine manure anaerobic digestion. Results showed that graphene and graphene oxide could reduce ARGs abundance in varying degrees with the anaerobic reactors that contained a higher concentration of copper. Nevertheless, graphene decreased the abundance of ARGs more effectively than graphene oxide. Phylum-level bacteria such as Firmicutes, Bacteroidetes, Spirochaetes, and Verrucomicrobiaat were significantly positively correlated with most ARGs. Network and redundancy analyses demonstrated that alterations in the bacterial community are one of the main factors leading to the changes in ARGs. Firmicutes, Bacteroidetes, and Spirochaetes were enriched lower in graphene reactor than graphene oxide in anaerobic digestion products, which may be the main reason that graphene is superior to graphene oxide in reduced ARGs abundance. Additionally, ARGs were close to HMRGs than MGEs in the treatments with graphene, the opposite in graphene oxide reactors. Therefore, we speculate that the reduction of HMRGs in graphene may contribute to the result that graphene is superior to graphene oxide in reduced ARGs abundance in anaerobic digestion.

Swine manure treatment technologies as drivers for circular economy in agribusiness: A techno-economic and life cycle assessment approach

Anaerobic digestion has been employed as a technology capable of adding value to waste coupled with environmental impact mitigation. However, many issues need to be elucidated to ensure the systems viability based on this technology. In this sense, the present study evaluated technically, environmentally, and economically, four configurations of swine waste treatment systems focused on the promotion of decarbonization and circularity of the swine chain. For this, a reference plant, based on a compact treatment process named SISTRATES® (Portuguese acronym for swine effluent treatment system) was adopted to serve as a model for comparison and validation. The results showed the importance of prioritization of the energy recuperation routes through anaerobic digestion, providing increased economic benefits and minimizing environmental damage. Thus, the SISTRATES® configuration was the one that presented the best designs in a circular context, maximizing the recovery of energy and nutrients, along with the reduction of greenhouse gas emissions, ensuring the sustainability of the pig production chain.

Insights into the Fate of the Novel Pesticide Vanisulfane from Animal Manure in Plant-Soil Systems: Assisted by Carbon-14 Labeling

Pesticide use can result in plant residues, which can be ingested by livestock consuming plant-derived feed and appear in manure. When this manure is applied as a fertilizer, pesticides can contaminate plant-soil systems. Few studies have focused on pesticide infiltration from applying pesticide-contaminated manure to land. In this study, the fate of pesticide vanisulfane from chicken manure was studied in radish-soil and cabbage-soil systems assisted by carbon-14 labeling. Vanisulfane and its metabolites mostly appeared as bound residues (BRs) after introduction, and BR release was found at 35 d. Notably, manure contaminated with vanisulfane and its metabolites exhibited higher plant accumulation and phytotoxicity than manure contaminated with only the parent. Four metabolites were identified, and germination toxicity assays illustrated that a metabolite with an aldehyde structure induced phytotoxicity. This study provides valuable information on pesticide contamination from manure and emphasizes the importance of considering pesticide metabolites when assessing environmental risks.

Organic amendment treatments for antimicrobial resistance and mobile element genes risk reduction in soil-crop systems

Agricultural fertilization with organic amendments of animal origin often leads to antibiotic resistance dissemination. In this study, we evaluated the effect of different treatments (anaerobic digestion, biochar application, ozonation, zerovalent iron nanoparticle application, and spent mushroom substrate addition) on the resistome in dairy cow manure-derived amendments (slurry, manure, and compost). Anaerobic digestion and biochar application resulted in the highest reduction in antibiotic resistance gene (ARG) and mobile genetic element (MGE) gene abundance. These two treatments were applied to cow manure compost, which was then used to fertilize the soil for lettuce growth. After crop harvest, ARG and MGE gene absolute and relative abundances in the soil and lettuce samples were determined by droplet digital PCR and high-throughput qPCR, respectively. Prokaryotic diversity in cow manure-amended soils was determined using 16S rRNA metabarcoding. Compared to untreated compost, anaerobic digestion led to a 38% and 83% reduction in sul2 and intl1 absolute abundances in the soil, respectively, while biochar led to a 60% reduction in intl1 absolute abundance. No differences in lettuce gene abundances were observed among treatments. We conclude that amendment treatments can minimize the risk of antibiotic resistance in agroecosystems.