Antibiotic resistance gene abundances associated with antibiotics and heavy metals in animal manures and agricultural soils adjacent to feedlots in Shanghai; China

Swine Manure Composting With Compound Microbial Inoculants: Removal of Antibiotic Resistance Genes and Their Associations With Microbial Community

In this study, compound microbial inoculants, including three Bacillus strains and one Yeast strain, were inoculated into swine manure composting to explore the effects on antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), microbial community structure, and pathogenic bacteria. The results indicated that the abundances of the detected ARGs ranged from 3.6 × 10³ to 1.13 × 10⁸ copies/g. The ARGs with the highest abundance was sul2, and the lowest was blaCTX. Composting removes most of the ARGs and MGEs by 22.8-99.7%. These ARGs were significantly reduced during the thermophilic phase of compost. The removal rate of ARGs at the different layers of compost pile was different as follows: middle layer > upper layer > lower layer. But some ARGs proliferated significantly in the maturation phase of compost, especially the sulfonamide resistance genes. Compound microbial inoculants increased the temperature of compost, accelerated water loss, nitrogen fixation, and increased the removal rate of β-lactamase resistance genes, the transposon gene tn916 and part of tetracycline resistance genes by 3.7-23.8% in compost. Compound microbial inoculants changed the community structure and increased the Bacillus abundance in the thermophilic phase of compost. And it was helpful for removing pathogens during composting. The addition of compound microbial inoculants causes the decrease of Firmicutes and the increase of Bacteroidetes, which may be related to the removal and proliferation of ARGs.

Struvite crystallization induced the discrepant transports of antibiotics and antibiotic resistance genes in phosphorus recovery from swine wastewater

Struvite (MgNH₄PO₃·6H₂O) crystallization is one of important methods of phosphorus recovery from wastewater. As to livestock wastewater, the high-strength occurrence of antibiotics and antibiotic resistance genes might induce struvite recovery to spread antibiotic resistance to the environment. However, limited information has been reported on the simultaneous transport of antibiotics and ARGs in struvite recovery. In the present study, tetracyclines (TCs) and tetracyclines antibiotic resistance genes (ARGs) were selected as the targeted pollutants, and their discrepant residues in struvite recovery from swine wastewater were investigated. TCs and ARGs were obviously detected, with their contents of 4.88-79.5 mg/kg and 6.99 × 10⁷-2.14 × 10¹¹ copies/g, notably higher than those of TCs 0.550-1.94 mg/kg and ARGs 3.98 × 10⁴-5.66 × 10⁷ copies/g obtained from synthetic wastewater. The correlational relationship revealed that predominant factors affecting TCs and ARGs transports were different. Results from network analyses indicated that among the total edges, the negative correlations between TCs and ARGs predominately occupied 18.0%. The redundancy analysis revealed that mineral components in the recovered products, including struvite, K-struvite and amorphous calcium phosphate, coupling with organic contents, displayed insignificant roles on TCs residues, where heavy metals exerted positive and remarkable functions to boost TCs migration. Unexpectedly, mineral components and heavy metals did not displayed significant promotion on ARGs transport as a whole.

Assessment of Bioavailability of Biochar-Sorbed Tetracycline to Escherichia coli for Activation of Antibiotic Resistance Genes

Human overuse and misuse of antibiotics have caused the wide dissemination of antibiotics in the environment, which has promoted the development and proliferation of antibiotic resistance genes (ARGs) in soils. Biochar (BC) with strong sorption affinity to many antibiotics is considered to sequester antibiotics and hence mitigate their impacts to bacterial communities in soils. However, little is known about whether BC-sorbed antibiotics are bioavailable and exert selective pressure on soil bacteria. In this study, we probed the bioavailability of tetracycline sorbed by BCs prepared from rice-, wheat-, maize-, and bean-straw feedstock using Escherichia coli MC4100/pTGM bioreporter strain. The results revealed that BC-sorbed tetracycline was still bioavailable to the E. coli attached to BC surfaces. Tetracycline sorbed by BCs prepared at 400 °C (BC400) demonstrated a higher bioavailability to bacteria compared to that sorbed by BCs prepared at 500 °C (BC500). Tetracycline could be sorbed primarily in the small pores of BC500 where bacteria could not access due to the size exclusion to bacteria. In contrast, tetracycline could be sorbed mainly on BC400 surfaces where bacteria could conveniently access tetracycline. Increasing the ambient humidity apparently enhanced the bioavailability of BC400-sorbed tetracycline. BC500-sorbed tetracycline exposed to varying levels of ambient humidity showed no significant changes in bioavailability, indicating that water could not effectively mobilize tetracycline from BC500 pores to surfaces where bacteria could access tetracycline. The results from this study suggest that BCs prepared at a higher pyrolysis temperature could be more effective to sequester tetracycline and mitigate the selective pressure on soil bacteria.

Antibiotic resistance genes (ARGs) in agricultural soils from the Yangtze River Delta, China

As an important reservoir of intrinsic antimicrobial resistance, soil is subjected to increasing anthropogenic activities that creates sustained selection pressure for the prevalence of antibiotic resistance genes (ARGs), thus constituting an important environmental dissemination pathway to human exposure. This study investigated the levels and spatial distributions of three classes of ARGs in relation to a range of co-occurring chemical mixtures and soil properties at a regional scale of the Yangtze River Delta (YRD), China. The selected eight ARGs were all detected in 241 agricultural soil samples with relative abundances ranging from 1.01 × 10^-7 to 2.31 × 10^-1 normalized to the 16S rRNA gene. The sulII and tetG were the dominant ARGs with a mean relative abundance of 6.67 × 10^-3 and 5.25 × 10^-3, respectively. The ARGs were mainly present in agricultural soils alongside Taihu Lake and Shanghai municipality, the most agriculturally and economically vibrant area of the YRD region. Antibiotics, rather than other co-occurring pollutants and soil properties, remain to be the dominant correlate to the ARGs, suggesting their co-introduction into the soils via irrigation and manure application or the sustained selection pressure of antibiotics from these sources for the proliferation of ARGs in the soils. While the current dataset provided useful information to assess the ARGs pollution for mitigation, future studies are warranted to reveal the complete picture on the potential transfer of antimicrobial resistance from soil to agricultural produces to human consumption and associated health implications.

Speciation, toxicity mechanism and remediation ways of heavy metals during composting: A novel theoretical microbial remediation method is proposed

Heavy metals (HM) pollution is a major limitation to the application of composting products. Therefore, mitigating the toxicity of HM has attracted wide attention during composting. The toxicity of HM is mainly acted on microorganisms during composting, and the toxicity of different HM speciation is obviously various. There are many pathways to change the speciation to reduce the toxicity during composting. Therefore, in this review, the speciation distribution, toxicity mechanism and remediation ways of HM during composting were discussed in order to better solve HM pollution. The microbial remediation technology holds enormous potential to remediate for HM without damaging composting, however, it is hard to extract HM. The innovation of this review was to outline microbial remediation strategies for HM during composting based on two mechanisms of microbial remediation: extracellular adsorption and intracellular sequestration, to solve the problem how to extract microbial agents from the compost. Ultimately, a novel theoretical method of microbial remediation was proposed to remove HM from the compost.

Antibiotic resistance genes, bacterial communities, and functions in constructed wetland-microbial fuel cells: Responses to the co-stresses of antibiotics and zinc

The effects of the continuous accumulation of Zinc (Zn) on the fate of antibiotic resistance genes (ARGs) in constructed wetland-microbial fuel cells (CW-MFCs) remain unclear. In this study, the impacts of Zn addition and a circuit mode on antibiotic removal, occurrence of ARGs, the bacterial community, and bacterial functions were investigated in three groups of CW-MFCs. The results showed that continuous Zn exposure enriched the target ARGs during the initial stage, while excessive Zn accumulation decreased antibiotic removal and the abundance of ARGs. A principal component analysis demonstrated that ARGs and the bacterial community distribution characteristics were significantly impacted by the mass accumulation of antibiotics and Zn, as well as the circuit mode. A redundancy analysis, partial least squares path modeling, and Procrustes analysis revealed that the accumulation of antibiotics and Zn, the composition of the bacterial community, the circuit mode, and the abundance of intI associated with horizontal gene transfer jointly contributed to the distributions of ARGs in the electrodes and effluent. Moreover, continuous exposure to Zn decreased the bacterial diversity and changed the composition and function of the bacterial community predicted using PICRUSt tool. The co-occurrence of ARGs, their potential hosts and bacterial functions were further revealed using a network analysis. A variation partition analysis also showed that the accumulation of target pollutants and the circuit mode had a significant impact on the bacterial community composition and functions. Therefore, the interaction among ARGs, the bacterial community, bacterial functions, and pollutant accumulations in the CW-MFC was complex. This study provides useful implications for the application of CW-MFCs for the treatment of wastewater contaminated with antibiotics and heavy metals.

Deciphering the toxic effects of metals in gold mining area: Microbial community tolerance mechanism and change of antibiotic resistance genes

Mine tailing dumps represent significant threats to ecological environments due to the presence of toxic substances. The present work investigated the relationship among microbial activity, the community, antibiotic resistance genes (ARGs) and trace metals in soil surrounding gold mine tailings. Using microbial metabolic activity and high-throughput sequencing analysis, we found the trace metals Cd and Hg could be main factors influencing the microbial community. According to bacterial co-occurrence pattern analysis, the effects of total cadmium and total mercury on bacterial diversity are potentially mediated by influencing bacteria community in the keystone module II. Additionally, most of metal-resistant bacteria belong to Actinobacteria and Proteobacteria, and the metal tolerance suggested to be linked with various functions including replication, recombination and repair, as well as inorganic ion transport and metabolism based on PICRUSt2 analysis. We also found that metals generated by mining activity may trigger the co-selection of antibiotic resistance in the phyla Actinobacteria and Proteobacteria due to co-resistance or cross resistance. Additionally, PLS-PM analysis revealed that metals could indirectly affect ARGs by influencing bacterial diversity in gold mining areas.

Long-lasting effect of mercury contamination on the soil microbiota and its co-selection of antibiotic resistance

Antibiotic resistance genes (ARGs) in the environment are an exposure risk to humans and animals and is emerging as a global public health concern. In this study, mercury (Hg) driven co-selection of ARGs was investigated under controlled conditions in two Australian non-agricultural soils with differing pH. Soils were spiked with increasing concentrations of inorganic Hg and left to age for 5 years. Both soils contained ARGs conferring resistance to tetracycline (tetA, tetB), sulphonamides (sul1), trimethoprim (dfrA1) and the ARG indicator class 1 integron-integrase gene, intI1, as measured by qPCR. The last resort antibiotic vancomycin resistance gene, vanB and quinolone resistance gene, qnrS were not detected. Hg driven co-selection of several ARGs namely intI1, tetA and tetB were observed in the alkaline soil within the tested Hg concentrations. No co-selection of the experimental ARGs was observed in the neutral pH soil. 16S rRNA sequencing revealed proliferation of Proteobacteria and Bacteriodetes in Hg contaminated neutral and alkaline soils respectively. Multivariate analyses revealed a strong effect of Hg, soil pH and organic carbon content on the co-selection of ARGs in the experimental soils. Additionally, although aging caused a significant reduction in Hg content, agriculturally important bacterial phyla such as Nitrospirae did not regrow in the contaminated soils. The results suggest that mercury can drive co-selection of ARGs in contaminated non-agricultural soils over five years of aging which is linked to soil microbiota shift and metal chemistry in the soil.

Fluoroquinolones and trace elements in poultry litter: estimation of environmental load based on nitrogen requirement for crops

Poultry litter soil application contributes to sustainability of agricultural systems and is in accordance with the United Nations Sustainable Development Goals (UN-SDG). Poultry litter recommended rates are based on crop nitrogen (N) needs, however, their application can be a potential source of antibiotics and trace elements overload. The aim of the study was to estimate the role of poultry litter application on soil contamination by fluoroquinolones [enrofloxacin (ENR) and ciprofloxacin (CIP)] and trace elements, based on N requirements for crops. Analytical and sampling techniques were used to estimate the loads from poultry litter application. Only CIP was found in poultry litter samples (283 ± 124 µg kg^-1) and its load was estimated to be of 9.89 ± 4.33 g ha^-1, for the poultry litter application (35 t ha^-1). The estimated loads (g ha^-1) of trace elements were: Cr 9.19 ± 3.26, Ni 12.3 ± 4.93, Pb 22.0 ± 8.26, Cu 229 ± 85.6, Mn 691 ± 259 and Zn 1,011 ± 378. These estimates were 900% higher than those recommended by the technical guidance, while N exceeded 600% the recommended application. In order to achieve UN-SDGs, local policies to disseminate knowledge and technologies are required for consolidating sustainable agricultural practices.

Impacts of Cu and Zn on the performance, microbial community dynamics and resistance genes variations during mesophilic and thermophilic anaerobic digestion of swine manure

In this work, fate of antibiotic resistance genes (ARGs), heavy metal resistance genes (MRGs) and intI1 were investigated during mesophilic (mAD) and thermophilic anaerobic digestion (tAD) of swine manure with presence of Cu and Zn. Results showed that metal reduced the lag phase time. Cu showed stronger inhibition than Zn on archaea community and metals inhibited the growth of acetoclastic methanogens during mAD. Although total concentration of metals increased after AD, they were transformed into stable state. The abundance of qnrS, sul1, sul2 and drfA7 increased 1.2-5.7 times after mAD, while reduced after tAD, showed that tAD was effective in ARGs removal. Structural equation model analysis suggested that intI1 had the most standardized direct effects on ARGs variation in mAD (R = 0.85, p < 0.01), while the co-occurrence of MRGs with ARGs showed significantly positive influences on ARGs variation in tAD (R = 0.82, p < 0.01).

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

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

A critical review on the occurrence of resistomes in the environment and their removal from wastewater using apposite treatment technologies: Limitations, successes and future improvement

Recent reports are pointing towards the potential increasing risks of resistomes in human host. With no permissible limit in sight, resistomes are continually multiplying at an alarming rate in the ecosystem, with a disturbing level in drinking water source. The morphology and chemical constituent of resistomes afford them to resist degradation, elude membrane and counter ionic charge, thereby, rendering both conventional and advanced water and wastewater treatment inefficient. Water and wastewater matrix may govern the propagation of individual resistomes sub-type, co-selection and specific interaction towards precise condition may have enhanced the current challenge. This review covers recent reports (2011-2019) on the occurrence of ARB/ARGs and ease of spread of resistance genes in the aquatic ecosystem. The contributions of water matrix to the spread and mitigation, treatment options, via bulk removal or capture, and intracellular and extracellular DNA lysis were discussed. A complete summary of recent occurrences of ARB/ARGs, fate after disinfection and optimum conditions of individual treatment technology or in tandem, including process limitations, with a brief assessment of removal or degradation mechanism were highlighted.

Stress responses and biological residues of sulfanilamide antibiotics in Arabidopsis thaliana

Sulfonamides (SAs) are antibiotics widely used in clinical practice, livestock and poultry production, and the aquaculture industry. The compounds enter the soil environment largely through livestock and poultry manure application to farmland. SAs not only affect plant growth, but also pose a potential threat to human health through SA residues in plant tissues. In particular, sulfamethoxazole (SMZ) has been classified as a Category 3 carcinogen by the World Health Organization, and thus its soil ecological toxicity and possible health risks are of concern. Using A. thaliana as a model plant, stress responses and biological residues of sulfadiazine (SD), sulfametoxydiazine (SMD), and SMZ were investigated in the present study. Root length and aboveground plant biomass were significantly inhibited by the three types of SA, whereas lateral roots exposed to SMD grew vigorously. The contents of chlorophyll a and chlorophyll b and photosystem II maximum photochemical quantum yield declined with increase in drug concentration, which indicated that exposure to SAs affected photosynthesis and inhibited chlorophyll synthesis in A. thaliana. With increase in drug concentration, reactive oxygen species (ROS) accumulation in the leaves increased significantly. Activities of the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT) were activated at low SA concentrations, but increased lipid peroxidation occurred with increase in SA concentration. Of the three compounds, SMZ was the most toxic to A. thaliana, followed by SD, and SMD was the least toxic. The results indicated that the risk of SMD entering an organism through the food chain is greater than that for SMZ and SD.

The incidence of antibiotic resistance within and beyond the agricultural ecosystem: A concern for public health

The agricultural ecosystem creates a platform for the development and dissemination of antimicrobial resistance, which is promoted by the indiscriminate use of antibiotics in the veterinary, agricultural, and medical sectors. This results in the selective pressure for the intrinsic and extrinsic development of the antimicrobial resistance phenomenon, especially within the aquaculture‐animal‐manure‐soil‐water‐plant nexus. The existence of antimicrobial resistance in the environment has been well documented in the literature. However, the possible transmission routes of antimicrobial agents, their resistance genes, and naturally selected antibiotic‐resistant bacteria within and between the various niches of the agricultural environment and humans remain poorly understood. This study, therefore, outlines an overview of the discovery and development of commonly used antibiotics; the timeline of resistance development; transmission routes of antimicrobial resistance in the agro‐ecosystem; detection methods of environmental antimicrobial resistance determinants; factors involved in the evolution and transmission of antibiotic resistance in the environment and the agro‐ecosystem; and possible ways to curtail the menace of antimicrobial resistance.

Insight into the fate of antibiotic resistance genes and bacterial community in co-composting green tea residues with swine manure

Green tea residues (GTRs) are byproducts of tea production and processing, and this type of agricultural waste retains nutritious components. This study investigated the co-composting of GTRs with swine manure, as well as the effects of GTRs on antibiotic resistance genes (ARGs) and the bacterial community during co-composting. The temperature and C/N ratio indicate compost was mature after processing. The addition of GTRs effectively promoted the reduction in the abundances of most targeted ARGs (tet and sul genes), mobile genetic element (MGE; intI1), and metal resistance genes (MRGs; pcoA and tcrB). Redundancy analysis (RDA) showed that GTRs can reduce the abundance of MRGs and ARGs by reducing the bioavailability of heavy metals. Network analysis shows that Firmicutes and Actinobacteria were the main hosts of ARGs and ARGs, MGEs, and MRGs shared the same potential host bacteria. Adding GTRs during composting may reduce ARGs transmission through horizontal gene transfer (HGT). GTRs affected the bacterial community, thereby influencing the variations in the ARG profiles and reducing the potential risk associated with the compost product.

Distribution of antibiotic resistance genes in an agriculturally disturbed lake in China: Their links with microbial communities, antibiotics, and water quality

In this study, six antibiotic resistance genes (ARGs), one mobile genetic element (int1), and their relation with microbial communities, antibiotics, and water quality were investigated in and around of an agriculturally disturbed lake, namely, Lake Honghu. The ARGs and int1 in the research area had a 100 % detection frequency in each sample during two sampling times. The ARGs were higher in the rivers and inlets than in Lake Honghu. Sul1 was the main ARG in this area. Antibiotics, nutrients, and dissolved oxygen were significantly, positively, and negatively correlated with nearly all of the ARGs, respectively. This finding suggests that reducing antibiotics and the eutrophication level could reduce the risk of ARGs. Microbial community shift had the most direct contribution to ARG variation. However, when the indirect effect was considered, environmental factors contributed 34 % to the ARGs' variance, the microbial community contributed 28 %, and their joint effect contributed 27 % to the ARG profiles. The abundance of Firmicutes, Gemmatimonadetes, Proteobacteria, etc. and their positive correlation with ARGs were significant, suggesting that these phyla probably carry ARGs. The study provides a systematic profile of ARG distribution and dissemination in a typical Chinese lake and new ideas to control this emerging contaminant in lakes.

Family livestock waste: An ignored pollutant resource of antibiotic resistance genes

The random discharge of livestock waste from family farms without utilization and treatment has caused great pressure on the rural ecological environment and gravely increased the environmental pollution. In this study, we targeted 26 family livestock farms to assess the occurrence characteristics of antibiotic resistance genes (ARGs) in livestock waste and its receiving farmland environment in Erhai Lake basin of China by real-time fluorescence quantitative PCR. The results showed that various common ARGs and some high-risk ARGs (i.e., bla_ampC, bla_OXA-1 and bla_TEM-1) were prevalent in family livestock waste, and the pollution of tetracycline resistance genes was the most serious in these family livestock farms. Meanwhile, we also found that the ARG levels were higher in family chicken farms than that in pig and cattle farms, and ARGs pollution in layer waste and sow waste was more severe than that in broiler waste and piglet/fattening pig waste, respectively. Troublesomely, significant ARGs levels could be discharged via manure application, further causing the increase of ARGs abundance in soil environment (approximately 11-36 times). This study demonstrated the high prevalence and severity of ARGs contamination in family livestock farms, also emphasizing that family livestock waste was a non-ignored important pollutant resource of ARGs in the environment.

Struvite-supported biochar composite effectively lowers Cu bio-availability and the abundance of antibiotic-resistance genes in soil

The accumulation of heavy metals and the accelerated dissemination of antibiotic-resistance genes (ARGs) in soil receiving long-term manure application are causing worldwide concern. In this study, struvite-supported biochar composite (MAP/BC) obtained by N and P recovery from pig slurry with Mg(OH)₂-modified biochar (Mg(OH)₂/BC) was used as a novel amendment for the remediation of Cu- and ARG-contaminated agricultural soil. The effects of MAP/BC on Cu immobilization, ARG distribution, and the bacterial community in the soil were investigated simultaneously. The results showed that the mechanisms involved in the immobilization of Cu by MAP/BC included the formation of copper-phosphate precipitation and a surface complex. With a 10% MAP/BC modification, the acid-soluble Cu content in soil decreased by 0.47-fold at day 56 while the residual Cu content increased 1.41-fold. Meanwhile, the abundances of most of the target ARGs (tetX, tetT, tetW, tetG, ermB, sulI, sulII, and intlI) were reduced by 11.35-99.95%, and the abundance of total ARGs was reduced by 30.69%. The redundancy analysis indicated that the bio-available Cu content played a crucial role in the variations of both ARGs and bacterial communities. The network analysis further suggested that potential hosts of soil ARGs were mainly Firmicutes and Actinobacteria. The above results suggested that the application of MAP/BC can mitigate Cu and ARG pollution in manured soil.

Dose and time-dependent response of single and combined artificial contamination of sulfamethazine and copper on soil enzymatic activities

The widespread contamination of antibiotics and heavy metals results in imbalance in the ecosystem. However, the effect of the interaction between sulfamethazine (SM2) and copper (Cu) on soil enzymatic activities is unclear. Therefore, this study investigated the effect of single and combined artificial contamination of SM2 and Cu (0, 1.6 mmol kg^-1 Cu and 0, 0.05, 0.2, 0.8 mmol kg^-1 SM2) on soil enzymatic activities (urease, sucrose, phosphatase, and RubisCO). A single application of Cu at a concentration of 1.6 mmol kg^-1 inhibited the urease, phosphatase and sucrase activities, while a stimulating effect on RubisCO activity was observed on day 7, 21, and 28 of incubation. The individual application of SM2 at higher concentration exhibited significant inhibition of sucrase, phosphatase, and urease activities while a stimulatory effect on RubisCO activity was observed on day 14 and 21 of incubation. The combined contamination of SM2 and Cu significantly inhibited the activities of urease, sucrase, and phosphatase. The effect of combined contamination of SM2 and Cu on the activity of RubisCO was different. The analysis results of interaction types show that there are synergistic or antagonistic effects between Cu and SM2, and these effects can amplify or reduce the effect of Cu or SM2 on soil enzyme activities. Integrated biological responses version 2 (IBRv2) analysis showed that the combined contamination of Cu and SM2 had a greater inhibitory or stimulatory effect on soil enzyme activities than the single contamination of Cu and SM2, depending upon dose and time.

Soil types influence the characteristic of antibiotic resistance genes in greenhouse soil with long-term manure application

Composted livestock and poultry manure, which may contain antibiotic resistance genes (ARGs), is widely used as natural fertilizer in China. But the influence of soil types on ARGs is not well characterized, particularly at greenhouse sites with long-term manure application. We investigated the distribution of ARGs in the cinnamon, fluvo-aquic and saline-alkali soils in greenhouse of Yellow River Delta region, China. A total of 193 ARGs subtypes were detected, with multidrug and aminoglycoside resistance genes as the most universal ARGs subtypes. Soil types influenced the ARGs distribution, where higher levels of diversity and relative abundance of ARGs in the fluvo-aquic and saline-alkali soils compared with those in the cinnamon soils. Among abiotic factors, sand, pH and Zn contributed more to the pattern of ARGs in the cinnamon soils, whereas sand and Cd, clay and Pb contributed the most in the fluvo-aquic and saline-alkali soils respectively. Furthermore, positive correlations between the relative abundances of ARGs and mobile genetic elements (MGEs) in the fluvo-aquic soils, suggesting higher dissemination potential of ARGs in this type of soil. Overall, MGEs played a positive primary role in the ARGs distribution in greenhouse soil than heavy metal co-selection and soil physicochemical properties.

Occurrence of ESBL-producing Escherichia coli in soils subjected to livestock grazing in Azores archipelago: an environment-health pollution issue?

Antibiotics are successful drugs used in human and animal therapy; however, they must be considered as environmental pollutants. This study aims to isolate and characterize the extended-spectrum β-lactamase (ESBL) producing Escherichia coli soil from Azores Archipelago subjected to livestock agricultural practices. Twenty-four soil samples were collected from three different pasture systems with different number of cattle heads, and from a control site. Antibiotic susceptibility method was performed by Kirby-Bauer disk diffusion method against 16 antibiotics, and the presence of genes encoding lactamases, antimicrobial resistance genes, virulence factors, and phylogenetic groups was determined by polymerase chain reaction (PCR). Nine ESBLs were recovered from the three grazing sites, and all isolates presented the beta-lactamase genes bla_CTX-M-3 and bla_SHV. E. coli isolates were resistance to tetracycline and streptomycin and harbored the tetB, strA, and strB genes. One isolate also showed resistance to sulfonamides, and the genes sul1 and sul2 were detected. The isolates were grouped into the following phylogenic groups: B1 (n = 6), D (n = 2), and A (n = 1). The presence of antibiotics and resistance genes in soils may be the source to the development of antimicrobial resistance, which may have negative consequences in human and animal health.

Manure fertilization increase antibiotic resistance in soils from typical greenhouse vegetable production bases, China

A large quantity of manure is applied in greenhouse vegetable production (GVP) soils, while manure fertilization often leads to the proliferation of antibiotic resistance genes (ARGs) in soils. However, comprehensive study on the effects of different types of manure on ARGs in GVP soils remains unknown, and the baseline level of ARGs in GVP soil is poorly quantified. This study conducted a comprehensive survey of ARGs in GVP soils using high-throughput quantitative PCR. We found elevated ARG diversity and absolute abundance in fertilized soil, whereas no significant difference in soil ARGs amended with different types of manure. Redundancy analysis indicated that the change of bacterial community compositions and environmental factors contributed partially to the shift in ARG profiles. Bipartite network analysis indicated that one ARG was detected in non-manured soils, while 50 ARGs and 4 mobile gene elements were exclusively detected in fertilized soils, suggesting introduction of ARGs from manure into soils largely explained the increased ARG diversity in fertilized soil. By comparison of ARG absolute abundance between manured and non-manured soil, we estimated the typical level of ARG absolute abundance in non-manured soil, which provided the first rough baseline level of ARGs to assess ARG contamination in GVP soils.

Characteristics of and variation in airborne ARGs among urban hospitals and adjacent urban and suburban communities: A metagenomic approach

Environmental antibiotic resistance genes (ARGs) have received much attention, while the characteristics of ARGs carried by particulate matter (PM) as a function of urban functional region are almost unknown. In this study, ARGs carried by PM_2.5 and PM₁₀ in an urban hospital, a nearby urban community and the nearest suburban community were detected using metagenomics. In total, 643 ARG subtypes belonging to 22 different ARG types were identified. The chloramphenicol exporter gene, sul1, bacA, and lnuA were the most abundant ARG subtypes in all air samples. The hospital exhibited higher ARG abundance and richness than the nearby communities. ARG profiles depended on functional region: hospital and suburban samples clustered separately, and samples from the nearby urban community interspersed among them. The representation of multidrug and quinolone resistance genes decayed with distance from the hospital to the urban community to the suburban community, indicating that hospital PM may be a hotspot for ARGs encoding proteins conferring multidrug and quinolone resistance. Airborne ARGs carried by PM in the hospital environment were more closely associated with clinically important pathogens than were those in nearby communities. In particular, carbapenemase genes, including bla_NDM,bla_KPC,bla_IMP,bla_VIM,and bla_OXA-48, were discovered in hospital PM. In the suburban community, crAssphage, a human host-specific bacteriophage, was applied to predict ARG abundance and found to be enriched due to anthropogenic pollution but showed no clear evidence for ARG selection. In the hospital and the nearby urban community, the drivers of ARGs were complex. Our results highlighted that PM ARGs were closely related to human activities and revealed a potential hotspot, which could provide new evidence for further research and consequently mitigate the formation of airborne ARGs and transfer risks.

The influence of variables on the bioavailability of heavy metals during the anaerobic digestion of swine manure

The speciation of heavy metals, besides the total concentrations, urgently need to be considered when assessing the eco-toxicity and the bioavailability of heavy metals in environment. This paper aims to investigate the distribution and chemical speciation (e.g. the acid extractable fraction (F1), the reducible fraction (F2), the oxidizable fraction (F3), and the residual fraction (F4)) of heavy metals during the anaerobic digestion process of swine manure. The majority of six heavy metals from the manure was located in biogas residue in the order of decreasing concentration Zn > Cu > Ni > As > Pb > Cd. The transformation of heavy metals among four fractions was observed during the digestion process, and the change of bioavailable fraction of Zn, Cu, Ni, Cd, As and Pb were 9.71%, -6.04%, -19.24%, 13.62%, -16.48% and -7.22%, respectively. The heat map of correlation coefficients and the stepwise linear regressions model were established to describe the correlation between the bioavailability of the metals and the given digestion variables to predict the influence of the selected variables on the bioavailability of heavy metals. The variations of heavy metal bioavailable fractions are attributed to three key digestion variables, NH₄⁺-N concentration, CH₄% in biogas daily yield and pH. These results provide a new perspective for analysis and control of heavy metals during the anaerobic digestion process.

Factors associated with elevated levels of antibiotic resistance genes in sewer sediments and wastewater

The sewer environment is a potential hotspot for the proliferation of antibiotic resistance genes (ARGs) and other hazardous microbial agents. Understanding the potential for ARG proliferation and retardation and/or accumulation in sewer sediments is of interest for protecting the health of sewage workers and the broader community in the event of sewer overflows as well as for interpreting sewage epidemiology data. To better understand this understudied environment for antibiotic resistance, a field survey was conducted to identify the factors that may control ARGs in sewer sediments and sewage. qPCR was performed for select ARGs and amplicon sequencing was performed for paired samples from combined and separate sanitary sewer systems. Metagenomic sequencing was performed on combined sewer sediments. The relative abundances of sul1, tet(O), tet(W), ermF, and vanA were higher in wastewater compared to sewer sediments, while NDM-1 was greater in sewer sediment and ermF was similar between the two matrices. NDM-1 was observed in sewer sediment but rarely above detection in wastewater in this study. This may indicate that larger/more frequent wastewater samples are needed for detection and/or that retardation and/or accumulation in sewage sediment may need to be considered when interpreting wastewater-based epidemiology data for ARGs. Random forest analyses indicated that season and conductivity were important variables and to a lesser extent so were pH, TSS, heavy metals, and sewer type for explaining the variance of the ARGs. These variables explained the 19-61% of the variance of sul1, tet(O), tet(G), and tet(W) quantified in wastewater. These variables performed less well for explaining the variance in sewer sediments (0.2-24%). Sewer sediment and wastewater had distinct microbial community structures and biomarkers for each are described. Metagenomics indicated that a high diversity of ARGs, including several of medical importance, were observed in the combined sewer sediment. This work provides insight into the complex sewer microbiome and the potential hazard posed by different sewer matrices.

The Effects of Tetracycline Residues on the Microbial Community Structure of Tobacco Soil in Pot Experiment

To evaluate the micro-ecological effects of tetracycline residues on tobacco soil, high-throughput sequencing technology was used to study the effects of the addition of different concentrations (0, 5, 50, and 500 mg·kg-1) of tetracycline on the abundance, diversity, and structure of bacterial and fungal communities in the rhizosphere and non-rhizosphere soil of flue-cured tobacco in China. Results showed that the presence of tetracycline had an important but varying effect on soil bacterial and fungal community richness, diversity, and structure. Changes in the diversity indices (Chao index and Shannon index) of soil bacterial and fungal communities showed a similar pattern after the addition of tetracycline; however, a few differences were found in the effects of tetracycline in the rhizosphere and non-rhizosphere soil, suggesting an evident rhizosphere-specific effect. The bacterial community at the phylum level in the rhizosphere closely clustered into one group, which might be the result of tobacco root secretions and rhizodeposition. Tetracycline showed a concentration-dependent effect on the soil bacterial community structure. The soil bacterial community structures observed after treatments with higher concentrations of tetracycline (50 and 500 mg·kg-1) were found to be closely related. Moreover, the effects of the treatments with higher concentrations of tetracycline, on the soil bacterial community at the phylum level, were different from those with lower concentrations of tetracycline (5 mg·kg-1), and CK treatments. This might have resulted from the induction of increasing selective pressure with increasing antibiotic concentration. Tetracycline continued to affect the soil bacterial community throughout the experiment. Tetracycline was found to have a varying impact on the community structure of soil fungi compared to that of soil bacteria, and the addition of an intermediate concentration of tetracycline (50 mg·kg-1) significantly increased the soil fungal diversity in the non-rhizosphere soil. The biological effects of tetracycline on the soil fungal community and the fungal-bacterial interactions, therefore, require further elucidation, warranting further research.

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

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

Potential of industrial composting and anaerobic digestion for the removal of antibiotics, antibiotic resistance genes and heavy metals from chicken manure

Composting and anaerobic digestion techniques are widely used for manure recycling, but these methods have shown conflicting results in the removal of antibiotics, antibiotic resistance genes (ARGs), and heavy metals. In the present study, anaerobically digested chicken manure and various types of composted chicken manure were investigated on an industrial scale. Antibiotics, ARGs, and heavy metals had shown inconsistent results for anaerobic digestion and composting. The different composting processes either declined or completely removed the blaCTX-M, intl1 and oqxB genes. In addition, composting processes decreased the absolute abundance of aac6'-Ib and aadA genes, while increased the absolute abundance of qnrD, sul1, and tet(A) genes. On the other hand, anaerobic digestion of chicken manure increased the absolute abundance of ere(A) and tet(A). High throughput sequencing showed that Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria dominated the total bacterial composition of composted and anaerobically digested samples. Network analysis revealed the co-occurrence of ARGs and intl1. The redundancy analysis showed a significant correlation between some heavy metals and ARGs. Similarly, the bacterial composition showed a positive correlation with the prevalence of ARGs in treated manure. These findings suggest that bacterial community, heavy metals, and mobile genetic elements can play a significant role in the abundance and variation of ARGs during composting and anaerobic digestion. In conclusion, anaerobic digestion and composting methods at industrial scale need to be improved for the effective removal of antibiotics, ARGs and heavy metals from chicken manure.

Time-dependent evolution of Zn(II) fractions in soils remediated by wheat straw biochar

Biochar is a cost-effective and multifunctional carbon material, which can be used to immobilize heavy metal (HM) in soil. To date, the immobilization of different HM by various biochars are well-studied, however, little is known about the release condition of the immobilized HM. As the released HM may bring a threat to the soil environment, it is critical to understand the release pattern of biochar-sorbed HM in soil. Herein, six wheat straw-derived biochars (WBs) pyrolyzed under different temperature and duration time were loaded with zinc(Zn (II)), and the evolution of Zn(II) fractions in soils remediated by WBs over time was investigated by Community Bureau of Reference (BCR) three-step sequential extraction method. The main Zn(II) species sorbed on WBs were the Zn(II) sorbed on the acidic functional groups of WB and that sorbed on WB surface via electrostatic interaction. Generally, Zn(II) sorbed on high-temperature WB was more mobile than that sorbed on low-temperature WB. In the red soil, the soluble and exchangeable Zn(II) (i.e., Zn(II) in Fraction 1) in WB was inclined to transform to organic matter associated-Zn(II) (i.e., Zn(II) in Fraction 3) and residual Zn(II) (i.e., Zn(II) in Fraction 4). In the yellow-brown soil, the soluble and exchangeable Zn(II) in WB was prone to convert into amorphous Fe/Mn oxide associated-Zn(II) (i.e., Zn(II) in Fraction 2) and residual Zn(II). These results imply that Zn(II) sorbed by WB has the risk to be released into the soil environment, and WB produced at low temperature are more suitable to remediate soils with low/neutral pH.

Heavy metal copper accelerates the conjugative transfer of antibiotic resistance genes in freshwater microcosms

Recent studies have consistently demonstrated increasing abundances of antibiotic resistance genes (ARGs) in the absence of antibiotic use. There is a large amount of quantitative data that has correlated the elevated ARGs levels with the concentrations of heavy metals in environments with anthropogenic impact. However, the mechanisms by which heavy metals facilitate the proliferation and horizontal gene transfer of ARGs among environmental bacteria were still unknown. This study validated effects of four typical heavy metals (Cu, Cd, Pb, Zn) on the plasmid RP4 mediated conjugative transfer of ARGs in freshwater microcosms. The results suggested that the typical heavy metals including Cu, Pb and Zn would promote conjugative transfer of the plasmid RP4, and Cu (5.0 μg/L) had the greatest ability to increase conjugative transfer by 16-fold higher than the control groups. In conjugative transfer microcosms, the species of each cultivable transconjugant were isolated, and their minimum inhibitory concentrations (MICs) were assessed via antibiotic susceptibility testing. The mechanism of the increased conjugative transfer of Cu was that Cu induced cell damage and the reduced conjugative transfer of Cd was that Cd increased the content of extracellular polymers substances (EPS). This study confirms that heavy metal Cu facilitates the conjugative transfer of environmental-mediated plasmid RP4 by cell damage effect, therefore accelerating the transmission and proliferation of ARGs.

Occurrence, distribution, and source track of antibiotics and antibiotic resistance genes in the main rivers of Chongqing city, Southwest China

In this study, the occurrence of 14 antibiotics, four corresponding antibiotic resistance genes (ARGs) and two microbial source tracker (MST) indicators were analyzed in two rivers of Chongqing city, southwest China. The results showed that 13 antibiotics were detected in all 12 sites and their detection frequencies were much higher in September, but concentrations were lower than that in March. Of them, erythromycin (ETM) and ofloxacin (OFL) were the predominant antibiotics in both seasons. The remarkably higher concentration of antibiotics in sediments of these rivers than those in other rivers were found. Environmental risk assessment found that four antibiotics posed high risk toward some sensitive algae. For ARGs, their relative abundances were higher in waters than those in sediments, higher in March than in September. Correlation analysis showed that antibiotics were not the exclusive selective pressure of ARGs; many environmental factors like dry matter contents on a mass basis, organic matter, total organic carbon, dissolved organic carbon, temperature, oxidation reduction potential and nitrite could affect the occurrence of ARGs. MST indicators analysis demonstrated that this river basin was largely polluted by human and pig feces, and human feces might be one main source of the four ARGs and five antibiotics.

Preservatives accelerate the horizontal transfer of plasmid-mediated antimicrobial resistance genes via differential mechanisms

Increasing concentrations of preservatives have been detected in environments due to the overuse and misuse of preservatives in food and personal care products. Recent studies have relied heavily on the toxicity, biodegradability, and fate of preservatives in the environment. However, the biological effects of preservatives on antimicrobial resistance, which poses great threats to public health worldwide, are largely unknown. This study investigated three preservatives for their ability and mechanisms of promoting horizontal transfer of antimicrobial resistance genes (ARGs). The results demonstrated that these preservatives (sodium nitrite, sodium benzoate, and triclocarbon), under daily-use concentrations, led to concentration-dependent increases in conjugative transfer by 1.24-2.63, 6.79-7.05, and 2.17-4.31 folds compared with the control group. Even these three preservatives had different patterns on generating intracellular reactive oxidative species (ROS) and reactive nitrogen species (RNS), all of them could stimulate radical-induced RpoS regulon and SOS response, increase cell membrane permeability, and regulate conjugative transfer-related genes, subsequently promoting horizontal transfer of ARGs. The present results expanded the understanding of biological effects induced by preservatives, and provided mechanistic insight into the preservatives-induced resistance. This study also opens an intriguing question on the roles of emerging contaminants including preservatives in the emerging and spread of ARGs in various environments.

Using Selection by Nonantibiotic Stressors to Sensitize Bacteria to Antibiotics

Evolutionary adaptation of bacteria to nonantibiotic selective forces, such as osmotic stress, has been previously associated with increased antibiotic resistance, but much less is known about potentially sensitizing effects of nonantibiotic stressors. In this study, we use laboratory evolution to investigate adaptation of Enterococcus faecalis, an opportunistic bacterial pathogen, to a broad collection of environmental agents, ranging from antibiotics and biocides to extreme pH and osmotic stress. We find that nonantibiotic selection frequently leads to increased sensitivity to other conditions, including multiple antibiotics. Using population sequencing and whole-genome sequencing of single isolates from the evolved populations, we identify multiple mutations in genes previously linked with resistance to the selecting conditions, including genes corresponding to known drug targets or multidrug efflux systems previously tied to collateral sensitivity. Finally, we hypothesized based on the measured sensitivity profiles that sequential rounds of antibiotic and nonantibiotic selection may lead to hypersensitive populations by harnessing the orthogonal collateral effects of particular pairs of selective forces. To test this hypothesis, we show experimentally that populations evolved to a sequence of linezolid (an oxazolidinone antibiotic) and sodium benzoate (a common preservative) exhibit increased sensitivity to more stressors than adaptation to either condition alone. The results demonstrate how sequential adaptation to drug and nondrug environments can be used to sensitize bacteria to antibiotics and highlight new potential strategies for exploiting shared constraints governing adaptation to diverse environmental challenges.

Evaluation of the fate of nutrients, antibiotics, and antibiotic resistance genes in sludge treatment wetlands

The aim of this research was to analyze the elimination of nutrients, antibiotics as well as antibiotic resistance genes (ARGs) in different sludge treatment wetlands (STWs) with or without reeds and aeration tubes. Five antibiotics, including oxytetracycline, tetracycline, azithromycin, sulfamethoxazole, and sulfadiazine; five ARGs, including two tetracycline ARGs (tetC and tetA), one macrolide ARGs (ermB), and two sulfonamide ARGs (sul1 and sul2); and one integrase gene (intI1) were determined in the surface and bottom layers of three STWs, respectively. The removal efficiencies of antibiotics in the bottom layer were lower than that in the surface layer, while the elimination efficiencies of ARGs showed opposite trend. Strong correlations were observed among the contents of antibiotics as well as related ARGs, and the abundance of ARGs had a strong correlation with intI1. The results demonstrated that the contents of these pollutants decreased during the resting period in all the STWs, while the wetland had reeds and aeration tubes performed the best.

The legacy of industrial pollution in estuarine sediments: spatial and temporal variability implications for ecosystem stress

The direct impacts of anthropogenic pollution are widely known public and environmental health concerns, and details on the indirect impact of these are starting to emerge, for example affecting the environmental microbiome. Anthropogenic activities throughout history with associated pollution burdens are notable contributors. Focusing on the historically heavily industrialised River Clyde, Scotland, we investigate spatial and temporal contributions to stressful/hostile environments using a geochemical framework, e.g. pH, EC, total organic carbon and potentially toxic elements: As, Co, Cr, Cu, Ni, Pb and Zn and enrichment indicators. With regular breaches of the sediment quality standards in the estuarine system we focused on PTE correlations instead. Multivariate statistical analysis (principle component analysis) identifies two dominant components, PC1: As, Cr, Cu, Pb and Zn, as well as PC2: Ni, Co and total organic carbon. Our assessment confirms hot spots in the Clyde Estuary indicative of localised inputs. In addition, there are sites with high variability indicative of excessive mixing. We demonstrate that industrialised areas are dynamic environmental sites dependant on historical anthropogenic activity with short-scale variation. This work supports the development of 'contamination' mapping to enable an assessment of the impact of historical anthropogenic pollution, identifying specific 'stressors' that can impact the microbiome, neglecting in estuarine recovery dynamics and potentially supporting the emergence of antimicrobial resistance in the environment.

The bacterial microbiota in florfenicol contaminated soils: The antibiotic resistome and the nitrogen cycle

Soil antibiotic resistome and the nitrogen cycle are affected by florfenicol addition to manured soils but their interactions have not been fully described. In the present study, antibiotic resistance genes (ARGs) and nitrogen cycle genes possessed by soil bacteria were characterized using real-time fluorescence quantification PCR (qPCR) and metagenomic sequencing in a short-term (30 d) soil model experiment. Florfenicol significantly changed in the abundance of genes conferring resistance to aminoglycosides, β-lactams, tetracyclines and macrolides. And the abundance of Sphingomonadaceae, the protein metabolic and nitrogen metabolic functions, as well as NO reductase, nitrate reductase, nitrite reductase and N₂O reductase can also be affected by florfenicol. In this way, ARG types of genes conferring resistance to aminoglycosides, β-lactamases, tetracyclines, colistin, fosfomycin, phenicols and trimethoprim were closely associated with multiple nitrogen cycle genes. Actinobacteria, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia played an important role in spreading of ARGs. Moreover, soil physicochemical properties were important factors affecting the distribution of soil flora. This study provides a theoretical basis for further exploration of the transmission regularity and interference mechanism of ARGs in soil bacteria responsible for nitrogen cycle.

Selectively enrichment of antibiotics and ARGs by microplastics in river, estuary and marine waters

The partition of antibiotics and antibiotic resistant genes (ARGs) between the microplastics (MPs) and the surrounding water with various salinity are still unclear. In this study, we hypothesized that adsorption of antibiotics on MPs might cause a significant change of the structure of microbial communities, diversity and abundance of ARGs on MPs and this might be further affected by change of salinity. In this study, we investigated adsorption of four common antibiotics (sulfamerazine, tetracycline, chloramphenicol and tylosin) to polyethylene (PE) MPs in river, estuary and marine waters, and the differences of antibiotic resistant genes (ARGs) and bacterial communities on MPs and in the three waters. The results showed that MPs can enrich antibiotics, ARGs and microbes from the surrounding water. Elevated salinity could reduce adsorption of antibiotics to MPs and the abundance of ARGs. For example, MPs can concentrate more antibiotics and ARGs in the fresh river water than in the estuary and the marine waters. In addition, ARGs and bacterial communities on MPs at various salinity were significantly different under the pressure of four antibiotics. On MPs, sul1, sulA/folP-01, tetA, tetC, tetX and ermE increased significantly but a few new ARGs such as sulA/folP-01 and tetA appeared. The structure of the bacterial communities on MPs was different from the surrounding water since some bacteria species found on MPs were barely detected in the surrounding water while some genera on MPs vanished after exposure to antibiotics. As the antibiotics adsorbed and the ARGs on MPs decreased with the water salinity, the structure of the communities on MPs thus varied with salinity change. These findings are important to understand the effects of MPs on the transport, fate and ecological risk of antibiotics and ARGs in different aquatic environments.

Antibiotic Resistance Genes in Antibiotic-Free Chicken Farms

Rising concern about the use of antibiotics in food production has resulted in many studies on the occurrence of antibiotic resistance genes (ARGs) in animal-associated bacterial communities. There are few baseline data on the abundance of ARGs on farms where chickens are intensively raised with little or no use of antibiotics. This study used a high-throughput quantitative PCR array to survey two antibiotic-free chicken farms for the occurrence of ARGs and mobile genetic elements known to enhance the spread of ARGs. No antibiotics had been used on the study farms for five years prior to this study. The results provide a baseline for the occurrence of resistance genes in the chicken production system without direct selective pressure.

Biochar-induced migration of tetracycline and the alteration of microbial community in agricultural soils

Recently, biochar is widely used as a soil amendment to improve soil properties, which might affect the fate and behavior of contaminants in soil. In this study, we investigated the effect of biochar on the migration of tetracycline (TC) in soil and their combined impacts on microbiome. Due to the strong interaction between soil and TC, adsorption, rather than photolysis or biodegradation, was the dominating dissipation way of TC in soil. Moreover, biochar could promote the vertical migration of TC through the decreased soil bulk density and its lower adsorption capacity. After 90-day incubation, only slight impact of TC on soil bacterial community was observed due to the rapid dissipation of TC in soil, whereas more available C supply induced by biochar significantly altered bacterial community via the enhancement of copiotrophic bacteria. Besides, biochar could decrease the soil pH and thus change the composition of fungal community. The effect of TC on fungal community was partially counteracted by biochar, which could adsorb part of TC and thus decrease the contact of TC with microorganisms. This work will improve our understanding of the fate of organic pollutants and evolution of microbiome in soil where biochar servers as soil amendment.

Occurrence and human health risk assessment of pharmaceuticals and personal care products in real agricultural systems with long-term reclaimed wastewater irrigation in Beijing, China

Reclaimed wastewater (RW) is increasingly used to irrigate agricultural land and to alleviate agricultural water shortages worldwide. This usage has resulted in concerns about soil contamination by pharmaceuticals and personal care products (PPCPs) and the human health risks associated with dietary crop intake. In this study, we systematically analysed the occurrence and accumulation of 11 PPCPs and one active metabolite in soils and various crops (cucumber, eggplant, long bean and wheat) from realistic RW irrigation fields with different irrigation histories (20, 30 and 40 years) in Beijing and evaluated the human health risks associated with the consumption of these crops. The 11 PPCPs and one active metabolite were detected at concentrations ranging from 0.67 to 22.92 ng L^-1 in RW, 0.029-28.13 μg kg^-1 in irrigated soil, and <0.01-28.01 μg kg^-1 in crops. The concentrations of N4-acetyl-sulfamethoxazole and triclosan were higher than those of other PPCPs, with respective concentrations of 14.39-31.44 ng L^-1 and 15.93-26.23 ng L^-1 in RW, 10.92-23.29 μg kg^-1 and 20.22-28.13 μg kg^-1 in irrigated soil and 17.92-28.01 μg kg^-1 and 8.92-14.91 μg kg^-1 in crops. However, the estimated threshold of toxicological concern (TTC) and hazard quotient (HQ) values revealed that the concentrations of N4-acetyl-sulfamethoxazole and triclosan in crops irrigated with RW should be considered a de minimis risk to human health. The concentrations of 11 PPCPs and one active metabolite in soils and crops and the calculated fruit bioconcentration factors (BCFs) did not display obvious increases associated with the duration of RW irrigation in real agricultural systems (P > 0.05). The concentrations of the studied PPCPs in the RW used for irrigation followed different patterns from the concentrations detected in the irrigated soils and crops. Although the concentrations of sulfamethoxazole, sulfisoxazole, sulfamethazine and trimethoprim in RW were higher than those of many other studied PPCPs, their respective values in the irrigated soils and crops did not display a similar tendency. The uptake and accumulation of PPCPs varied among the crop species (P < 0.05). Although PPCPs were detected in eggplant, long bean and wheat (BCFs: not applicable-1.67, 0.03-1.35 and 0.01-5.01, respectively), PPCPs accumulated at increased levels in cucumber (BCFs 0.03-18.98). The estimated TTC and HQ values showed that the consumption of crops irrigated long-term with RW presents a de minimis risk to human health. However, further studies with more PPCPs and additional crop species need to be conducted, the synergistic effects of chemical mixtures of multiple PPCPs and the toxic effects of PPCP metabolites should be elucidated to obtain more reliable information on the safety of wastewater reuse for irrigation.

Contribution of antibiotics to the fate of antibiotic resistance genes in anaerobic treatment processes of swine wastewater: A review

Antibiotic resistance genes (ARGs) in water environment have become a global health concern. Swine wastewater is widely considered to be one of the major contributors for promoting the proliferation of ARGs in water environments. This paper comprehensively reviews and discusses the occurrence and removal of ARGs in anaerobic treatment of swine wastewater, and contributions of antibiotics to the fate of ARGs. The results reveal that ARGs' removal is unstable during anaerobic processes, which negatively associated with the presence of antibiotics. The abundance of bacteria carrying ARGs increases with the addition of antibiotics and results in the spread of ARGs. The positive relationship was found between antibiotics and the abundance and transfer of ARGs in this review. However, it is necessary to understand the correlation among antibiotics, ARGs and microbial communities, and obtain more knowledge about controlling the dissemination of ARGs in the environment.

Responses of microbial communities to a gradient of pig manure amendment in red paddy soils

Microbial communities play a key role in maintaining agroecosystem functioning and sustainability, but their response to excessive animal manure application and relevant mechanisms have not been thoroughly elucidated to date. This study investigated the responses of soil bacterial and fungal communities to pig manure (PM) amendment in red paddy soils. High-throughput sequencing revealed that PM amendment significantly reduced the relative abundance of Acidobacteria yet increased that of Bacteroidetes, Ignavibacteriae, Firmicutes, and Rozellomycota. The Cu and available phosphorus were the primary impact factors influencing bacterial and fungal diversity, respectively. Bacterial alpha-diversity tended to sharply decrease when the content of soil Cu was >30.70 mg kg^-1, while fungal alpha-diversity did not continuously increase when the content of soil available phosphorus was >82.84 mg kg^-1. Bacterial communities with a wider niche breadth showed significantly lower structural variation, whereas fungal communities with a narrower niche breadth showed greater variation in community structure. Soil heavy metals, primarily Cu and Zn, were the primary factors that affected bacterial communities, whereas soil fungal communities were mainly influenced by soil phosphorus. Bacterial and fungal communities showed distinct co-occurrence patterns, with bacterial communities showing a higher degree, a clustering coefficient, and betweenness centrality, but a lower closeness centrality. The findings highlighted that bacteria and fungi responded differently to PM amendment because of their discrepant niche breadth, interspecific relationships, and different tolerance to heavy metal and soil nutrient.

New insight into fates of sulfonamide and tetracycline resistance genes and resistant bacteria during anaerobic digestion of manure at thermophilic and mesophilic temperatures

This study investigated the variations in antibiotic (sulfonamide and tetracycline) resistance genes (ARGs) and resistant bacteria (ARB) during manure anaerobic digestion (AD) at 35 ℃ and 55 ℃, and discussed the mechanisms of variations in ARGs. The AD lasted for 60 days, five ARGs and intI1 each decreased in abundance after AD at the thermophilic temperature, while only half decreased at the mesophilic temperature. On days 10, 30, and 60, sulfonamide and tetracycline ARB were screened on selective media. During thermophilic AD, ARB numbers reduced by 4-log CFUs per gram dry manure, but only by approximately 1-log CFU at the mesophilic temperature. However, ARB composition analysis showed that at either temperature, no significant reduction in identified ARB species was observed. Furthermore, 72 ARB clones were randomly selected to detect the ARGs they harbored, and the results showed that each ARG was harbored by various hosts, and no definitive link existed between ARGs and bacterial species. In addition, by comparison with the identified host by culture method, the host prediction results based on the correlation analysis between ARGs and the bacterial community was proven to be unreliable. Overall, these findings indicated that relationships between ARB and ARGs were intricate.

Both silver ions and silver nanoparticles facilitate the horizontal transfer of plasmid-mediated antibiotic resistance genes

Antibiotic resistance in bacteria is a growing threat to global human health. Horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) is recognized as the primary contributor to antibiotic resistance dissemination. Silver nanoparticles (AgNPs) are widely used in personal care products as antimicrobial agents. While heavy metals are known to induce antibiotic resistance in bacteria, it is not known whether AgNPs in the environment can stimulate the HGT of ARGs. Here, we report that both AgNPs and ionic silver Ag⁺, at environmentally relevant and sub-lethal concentrations, facilitate the conjugative transfer of plasmid-borne ARGs across bacterial genera (from the donor Escherichia coli K-12 LE392 to the recipient Pseudomonas putida KT2440). The underlying mechanisms of the Ag⁺- or AgNPs-promoted HGT were unveiled by detecting oxidative stress and cell membrane permeability, combined with genome-wide RNA sequencing and proteomic analyses. It was found that both Ag⁺ and AgNPs exposure induced various bacterial responses that included reactive oxygen species (ROS) generation, membrane damage and the SOS response. This study exposes the potential ecological risks of environmental levels of AgNPs and Ag⁺ for promoting the spread of ARGs and highlights concerns regarding the management of nanoparticles and heavy metals.

Profiles of ARGs and their relationships with antibiotics, metals and environmental parameters in vertical sediment layers of three lakes in China

Antibiotic resistance is a global health problem, and the role of antibiotics and metal pollution in antibiotic resistance in sediment biocenosis is limited. The occurrence and relationship between antibiotic resistance genes (ARGs), antibiotics, metals and environmental parameters were investigated in vertical layers of sediments in rural and urban lakes. Generally, the total concentrations of seven antibiotics were significantly higher in the rural lake (Lake Taihu = 96%) than in the urban lakes (Xuanwu = 0.3%, Wulongtan = 3%), while similar concentrations were observed for metals (Taihu (34%), Xuanwu (33%) and Wulongtan (33%)). The concentration of metals and antibiotics were mostly higher in the surface sediment layers than the deeper ones (for antibiotics; surface layers = 89%, deeper layer = 11%, for metals; surface = 65%, deep = 35%). The ARGs showed no significant difference between surface and deeper sediments (surface = 48%, deep = 52%, p < 0.05). The potential ecological risk index of Ni, Cu, Zn, Cr, Mn, As, Cd, and Pb contamination showed that Lake Taihu and Wulongtan had moderate ecological risks while Lake Xuanwu had a low ecological risk. Pearson coefficient and network analysis showed that direct and indirect relationship existed among antibiotics, metals, environmental parameters, and ARGs, and the relationship was linked by key environmental components. tetA, bla_TEM, SDZ, TOC, OFL, Cd, OTC, NOR, Ni, sulA, AUR, TC, DOX and TN were the major factors that influence the distribution of resistance genes, forming a complex network mechanism of antibiotic resistance. Our study revealed that antibiotics and heavy metals are widely distributed in the surficial sediments and the proliferation of ARGs are influenced by some key environmental components.

Environmental antibiotics drives the genetic functions of resistome dynamics

The increasing prevalence of antibiotic-resistant microorganisms imposes a global threat to public health. The over reliant use of antibiotics in the food industry has contributed considerably to the dissemination of antibiotics into various environments, yet the mechanisms by which antibiotic dissemination influences the assembly of the microbial community continues to remain obscure. Here, we examine bacterial and fungal community assemblies in swine manure, compost, compost amended, and unamended agricultural soil in five suburban areas of Beijing, China. Total antibiotic concentration decreased by factors of 10-1000 from manure and compost to soils. The bacterial α-diversity was found to be low in manure and compost samples, while the fungal α-diversity was similar across all samples. We detected significantly (p < 0.05) higher relative abundances of well recognized pathogenic microbial taxa, virulence associated genes, and antibiotic resistance genes (ARGs) in manure and compost than those in agricultural soils, revealing the higher microbial capacity of pathogenicity, virulence and antibiotic resistance. Unexpectedly, the relative abundances of both bacterial and fungal taxa did not predict the antibiotic concentration. A possible explanation was that bacterial and fungal communities were mainly shaped by random assemblies. Rather, antibiotic concentration could be well predicted by relative abundances of antibiotic resistance, stress and virulence associated genes. Despite the weak interconnection between ARGs and the microbiome, we demonstrate that microbial genes should be the focal point in tracking the ecological effects of antibiotic dissemination by revealing microbial community patterns along the dissemination chain of antibiotics.

Co-selection and stability of bacterial antibiotic resistance by arsenic pollution accidents in source water

Frequent heavy-metal pollution accidents severely deteriorated the source water quality of drinking water treatment plants (DWTP). Limited data have explicitly addressed the impact of these incidents on bacterial antibiotic resistance (BAR). In present study, we investigated the shift of antibiotic resistome caused by heavy metal pollution incidents via simulating an arsenic shock loading [As (III)], along with the associated risks imposed on drinking water systems. The results indicated that a quick co-selection of antibiotic resistant bacteria (ARB) was achieved after exposure to 0.2-1 mg/L As (III) for only 6 h, meanwhile, there was an increase of relative abundance of antibiotic resistance genes (ARGs) and mobile genetic elements. Most of the co-selected BAR could be maintained for at least 4 days in the absence of As (III) and antibiotics, implying that the pollution in source water possibly contributed to the preservation and proliferation of antibiotic resistance determinants in the subsequent DWTP. Bacterial community structure analysis showed a strong correlation between bacterial community shift and BAR promotion, and enrichment of opportunistic bacteria (e.g. Escherichia-Shigella, Empedobacter sp. and Elizabethkingia sp.). The results indicated a potential epidemiological threat to the public due to accident-level arsenic contamination in the source water. This study gave insight into understanding the source water pollution accidents from the perspective of bio-hazard and biological risks, and highlighted a neglected important source of BAR in drinking water systems.

Insight into the effects of sulfamethoxazole and norfloxacin on nitrogen transformation functional genes during swine manure composting

The effects of sulfamethoxazole and norfloxacin on nitrogen functional genes were investigated in four composting treatments of swine manure: CK (no antibiotics), SMZ (spiked with 5 mg kg^-1 dry weight (DW) sulfamethoxazole), NOR (spiked with 5 mg kg^-1DW norfloxacin), and SN (spiked with 5 mg kg^-1DW sulfamethoxazole and 5 mg kg^-1DW norfloxacin). Antibiotics decreased relative abundance of bacterial amoA and nxrA, while increased nosZ/nirK. The decline in amoA/16S rRNA increased the total NH₃ emission in SMZ and NOR from 1027.05 to 1144.39 and 1278.22 mg kg^-1DW. The decrease of nxrA/16S rRNA enhanced the NO₂^--N content and N₂O emission in SMZ in the initial composting. Additionally, the increase in nosZ/nirK probably was the main reason for the lower N₂O emission in SN than other treatments in the cooling phase. The inhibition on nitrification process and increase in NH₃ emission resulted from antibiotics is worthy of attention in the future.