Experimental Evidence for Manure-Borne Bacteria Invasion in Soil During a Coalescent Event: Influence of the Antibiotic Sulfamethazine.

The fertilization of agricultural soil by organic amendment that may contain antibiotics, like manure, can transfer bacterial pathogens and antibiotic-resistant bacteria to soil communities. However, the invasion by manure-borne bacteria in amended soil remains poorly understood. We hypothesized that this kind of process is both influenced by the soil properties (and those of its microbial communities) and by the presence of contaminants such as antibiotics used in veterinary care. To test that, we performed a microcosm experiment in which four different soils were amended or not with manure at an agronomical dose and exposed or not to the antibiotic sulfamethazine (SMZ). After 1 month of incubation, the diversity, structure, and composition of bacterial communities of the soils were assessed by 16S rDNA sequencing. The invasion of manure-borne bacteria was still perceptible 1 month after the soil amendment. The results obtained with the soil already amended in situ with manure 6 months prior to the experiment suggest that some of the bacterial invaders were established in the community over the long term. Even if differences were observed between soils, the invasion was mainly attributable to some of the most abundant OTUs of manure (mainly Firmicutes). SMZ exposure had a limited influence on soil microorganisms but our results suggest that this kind of contaminant can enhance the invasion ability of some manure-borne invaders.

Sorption and transport of five sulfonamide antibiotics in agricultural soil and soil-manure systems.

Animal manure application is a main spreading route of veterinary antibiotics in soil and groundwater. The sorption and leaching behavior of five commonly used sulfonamides in five typical soil and soil/manure mixtures from China were investigated in this study. Results showed that the empirical Freundlich equation fits well the sorption behavior of selected sulfonamides (r(2) was between 0.803 and 0.999, 1/n was between 0.68 and 1.44), and pH and soil organic carbon (OC) were the key impact factors to sorption and leaching. Addition of manure was found to increase the Kd values of sulfonamides in five different soils, following the rules that the more polar substances, the more increased extent of sorption after manure amendment (5.87 times for sulfadiazine with Log Kow = -0.09, and 2.49 times for sulfamethoxazole with Log Kow = 0.89). When the simulated rainfall amount reached 300 mL (180 mm), sulfonamides have high migration potential to the groundwater, especially in the soil with low OC and high pH. However, manure amendment increased the sorption capacity of sulfonamides in the top layer, thus it might play a role in decreasing the mobility of sulfonamides in soils. The systematic study would be more significant to assess the ecological risks and suggest considering the influence of manure amendment for the environmental fate of antibiotics.

Recalcitrant components accumulation in dissolved organic matter decreases microbial metabolic quotient of red soil under long-term manuring.

Microbial metabolism is closely related to soil carbon dioxide emissions, which in turn is related to environmental issues such as global warming. Dissolved organic matter (DOM) affects many fundamental biogeochemical processes such as microbial metabolism involved in soil carbon cycle, not only directly by its availability, but also indirectly by its chemodiversity. However, the association between the DOM chemodiversity and bioavailability remains unclear. To address this knowledge gap, soils from two agro-ecological experimental sites subjected to various long-term fertilizations in subtropical area was collected. The chemodiversity of DOM was detected by multi-spectroscopic techniques including ultraviolet-visible spectrophotometry, Fourier transform infrared spectroscopy and excitation emission matrices fluorescence spectroscopy. Results showed that long-term manure amendments significantly decreased microbial metabolic quotient (qCO2) by up to 57%. We also observed that long-term manure amendments significantly increased recalcitrant components of DOM (indicated by the aromaticity, humification index, the ratio of aromatic carbon to aliphatic carbon, and the relative abundances of humic-like components) and decreased labile components of DOM. Negatively correlation between the qCO2 and the proportion of recalcitrant components of DOM supported that accumulation in recalcitrant components of DOM increased microbial carbon utilization efficiency. Random forest models also showed the highest contribution of the relative abundances of humic-like components and the aromaticity of DOM in affecting qCO2. Both of the redundancy analysis and structural equation modeling further indicated the decisive role of soil pH in influencing the DOM chemodiversity. Soil pH explained 56.7% of the variation in the chemodiversity of DOM. The accumulation of recalcitrant components in DOM with increasing soil pH might be attributed to the accelerated microbial consumption of bioavailability components and/or to the negative impact on the solubility of bioavailability components. Overall, this research highlights the significance of long-term manure amendments in regulating qCO2 by altering the chemodiversity of soil DOM.

Evaluating antibiotic occurrence, degradation, and environmental risks in poultry litter within Argentina's agricultural hub.

This study explores the relationship between poultry farming's antibiotic administration practices and residual antibiotic levels in the litter before its application onto agricultural soils. Twenty-three antibiotics were performed across 19 Argentinean farms representing diverse antibiotic management practices. Analysis revealed up to 20 antibiotics from eight chemical classes in poultry litter samples, with tylosin, enrofloxacin, and salinomycin being the most relevant drugs. Farms with restricted antibiotic use in feed exhibited lower residual concentrations. A self-heating treatment was tested to reduce litter antibiotic levels. Although a 60 % reduction of antibiotics was found after treatment, prevalent compounds persisted at residual levels. Regulatory measures and comprehensive litter treatments pre-application are crucial to mitigate environmental risks. This is the first study that provides insight on the occurrence of >20 drugs in real poultry production scenarios from Latin America and demonstrates how relatively simple treatments can be readily applied to decrease the associated environmental risks.

Enhancing Soybean and Maize Yields through Improved Nitrogen and Soil Water Use Efficiencies: A 40-Year Study on the Impact of Farmyard Manure Amendment in Northeast China.

The combined application of manure and chemical fertilizers has been recognized as a critical factor driving significant changes in crop yield and nutrient use efficiency, holding the potential to optimize agricultural management to achieve high yields. In this 40-year study, we investigated the effect of manure amendment on soybean and maize yields, water and nitrogen use efficiencies (WUE and NUE), and water and mineral N storage at 0-100 cm soil depths from 2017 to 2018 to explore the optimization of fertilization management strategies for soybean and maize production in Northeast China. To elucidate the impact of chemical fertilizers and manure, twelve treatments-control (CK); single N fertilizer at a low rate (N1) and that at a high rate (N2); N1, phosphorus (P), and potassium (K) fertilizer (N1PK); manure alone at 13.5 and 27 t ha-1 (M1 and M2); and those combined with N, P, or K fertilizer (M1N1, M1N2, and M1N1PK and M2N1, M2N2, and M2N1PK)-were selected and studied. The results showed that long-term amendment with manure significantly increased crop biomass and yield in the soybean-maize-maize rotation system. Combining with manure increased the WUE, the partial factor productivity of N fertilizer (PFPN), and N physiological efficiency (PEN) in both the soybean and maize seasons; conserved soil water (mainly at 40-60 cm); and increased soil N retention (in the upper 60 cm layer), which reduced the risk of N leaching, with a better effect being observed after the application of 13.5 t ha-1 manure. These results provide insight into the potential of using fertilization management strategies that include amendment with 13.5 t ha-1 manure in combination with N, P, and K fertilizer in the maize season and only chemical fertilizer in the soybean season, as these results indicate that such strategies can achieve high yields and be used to implement agricultural sustainable development in brown soil regions in Northeast China.

Roadside ditches as conduits of fecal indicator organisms and sediment: implications for water quality management.

Roadside ditches are ubiquitous, yet their role in water pollution conveyance has largely been ignored, especially for bacteria and sediment. The goal of this study was to determine if roadside ditches are conduits for fecal indicator organisms and sediment, and if land use, specifically manure amendment, affects the concentrations and loadings. Seven roadside ditches in central New York, adjacent to either manure amended fields or predominately forested land, were monitored for one year for Escherichia coli (E. coli), total suspended solids (TSS) and flow. E. coli concentrations in water samples following storms averaged 4616 MPN of E. coli/100 mL. Concentrations reached as high as >241,960 MPN of E. coli/100 mL and frequently exceeded New York State and US EPA recommendations. Concentrations peaked in both summers following manure spreading, with declining levels thereafter. However, viable organisms were detected throughout the year. The concentrations were also high in the forested sites, with possible sources including wildlife, pets, septic wastes and livestock. E. coli concentrations and loadings were related to TSS concentrations and loadings, whether manure had been spread in the last 30 days and for concentrations only, antecedent rainfall. Viable E. coli were also present in ditch sediment between storm events and were available for resuspension and transport. Total suspended solids concentrations averaged 0.51 g/L and reached as high as 52.2 g/L. Loads were similarly high, at an average of 631.6 kg/day. Both concentrations and loads tended to be associated with discharge and rainfall parameters. The cumulative pollutant contribution from the ditch network was estimated to be large enough to produce detectable and sometimes high concentrations in a receiving stream in a small, rural watershed. Roadside drainage networks need to be actively managed for water quality improvements, because they capture and rapidly shunt stormwater and associated contaminants to streams.

Fluoride accumulation characteristics in a northern China apple orchard that has had long-term phosphate fertilization.

Phosphate fertilizer can cause fluoride accumulation in the soil and excessive fluoride poses potential risks to soil and food crop safety. However, the effects of fertilization on soil and fruit fluoride accumulations through long-term positioning trials, especially in high-fertilizer application situations such as apple orchards, have received little attention. To close this knowledge gap, we conducted a field experiment to demonstrate the effects among five long-term (13-year) fertilizer treatments on fluoride accumulations at different soil depths and in the fruits of an apple orchard in Baishui, Shaanxi, China. The five treatments included no fertilization (CK); manure application (M); nitrogen and phosphate fertilization (NP); nitrogen, phosphorus, and potassium fertilization (NPK); and groundcover with nitrogen and phosphate fertilization (GNP). The results confirmed that all phosphate fertilizer treatments (NP, NPK, and GNP) had significant increases in total fluoride (TF) and water-soluble fluoride (WF) accumulations in the topsoil (0-20 cm). Among the phosphate fertilizer treatments, NP topsoil accumulated the most TF and WF, 79.4 and 7.7 mg kg-1 more than CK, respectively, and an average annual TF increase of 6 mg kg-1. However, the M treatment both experienced reduced fluoride content in the topsoil and had TF and WF contents 8.1 and 0.67 mg kg-1 lower than CK, respectively. There was no significant difference between all fertilizer treatments and CK in apple fluoride content. Furthermore, TF and WF accumulated mainly in the topsoil and the differences in soil fluoride content among the treatments decreased with soil depth. These findings showed that long-term phosphate fertilization increases the risk of fluoride accumulation in orchard topsoil. Altogether, these results improve the understanding of the characterization of soil and fruit fluoride accumulations in apple orchards under long-term fertilizer conditions and provide new insights into the use of manure as a possible alternative fertilization strategy that reduces fluoride accumulation.

Conversion of swine manure into biochar for soil amendment: Efficacy and underlying mechanism of dissipating antibiotic resistance genes.

Livestock manure amendment, a common fertilization method for agricultural practice, can exacerbate antibiotic resistance gene (ARG) pollution, thus threatening food safety and human health. On the other hand, manure can also be produced as biochar to improve soil quality, which may reduce ARGs inside manure. However, it is unclear how and why shifting manure to biochar for soil amendment reduces ARG pollution. Thus, this study investigated the variations of ARGs and microbial communities in soil amended with swine manure (2 % and 5 %) and its biochar (2 % and 5 %) and then explored how shifting swine manure to biochar reduced ARG contamination. After 28 d incubation, ARG number in soil without amendment, manure-amended soils, and biochar-amended soils were 47, 112-136, and 43-52, respectively. ARG abundance in soil without amendment, manure-amended soils, and biochar-amended soils were 7.66 × 107, 4.32 × 109 - 1.42 × 1011, and 8.44 × 107-9.67 × 107 copies g-1 dry soil, respectively. Compared to manure-amended soils, its biochar amendments reduced ARG abundance by 2-4 orders of magnitude and ARG number by 70-93 in soil. Besides, manure amendment altered while biochar did not alter bacterial diversity and composition. The changed soil properties and mobile genetic elements (MGEs) could explain the changes in ARGs. Relative to manure amendments, its biochar amendments reduced mobile genetic elements (MGEs), Proteobacteria and Bacteroidetes in soil, which explained the reduced abundance and diversity of ARGs; however, the multidrug-resistance genes harbored in Proteobacteria and Bacteroidetes were still abundant in biochar-amended soil. This study suggests that converting manure to biochar as a soil amendment can help control the spread of manure ARGs.

Thriving beneath olive trees: The influence of organic farming on microbial communities.

Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 106 ± 1.62 × 105 (CM) to 4.54 × 106 ± 8.07 × 105 (OM) copies of the 18 S rRNA gene g-1 soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.

Effect of long-term manure slurry application on the occurrence of antibiotic resistance genes in arable purple soil (entisol).

The application of animal manure is a highly recommended traditional agricultural practice for soils of relatively low fertility. However, for the farmland purple soils that are widely distributed in the upper Yangtze River region, little knowledge has been established in previous studies about the changes in the antibiotic resistome upon manure amendment. In the present study, the impact of long-term pig manure slurry application on the occurrence of antibiotic resistance genes (ARGs) and bacterial community was assessed in arable calcareous purple soil using high-throughput quantitative polymerase chain reaction and Illumina sequencing. Four treatments, including a non-fertilization control (CK) and pig manure (OM), OM plus mineral N fertilizer (OMN) and OM plus mineral NPK fertilizer (OMNPK) treatments were investigated. Across all the soil samples receiving different treatments, a total of 139 unique ARGs and 6 mobile genetic element genes were detected, with multidrug and beta-lactam the two most dominant types of ARGs. The results of the principal coordinate analysis (PCoA) suggest that the profiles of soil ARGs in the two treatments of OM combined with mineral fertilizer(s) (i.e., OMN and OMNPK) were similar to those in the control treatment, while the soil receiving only pig manure application had a different pattern of ARGs from the soils in the other three treatments. A clear reduction of soil ARGs was observed in the OM treatment. Significant and positive relationships were found not only among ARGs but also between mobile genetic elements (MGEs) and ARGs. However, no significant relationships were detected between ARG patterns and bacterial community composition. These results imply that the long-term application of pig manure slurry to purple soil does not lead to the prevalence of ARGs; however, the potential for the horizontal transfer of ARGs in calcareous purple soil should not be ignored.