Prevalence of quinolone resistance genes, copper resistance genes, and the bacterial communities in a soil-ryegrass system co-polluted with copper and ciprofloxacin

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

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

Effects of norfloxacin, copper, and their interactions on microbial communities in estuarine sediment

The discharge of antibiotics and metals in estuaries is of great concern since they threaten microbial communities that are critical for maintaining ecosystem function. To understand single and combined effects of norfloxacin (0-20 μg g^-1) and copper (40 μg g^-1) on microbial ecology in estuaries, we evaluated changes in bacteria population, inhibition rates, and microbial composition in estuarine sediments over a 28-day period. Bacteria population significantly decreased following single and combined exposure to norfloxacin and copper throughout the incubation period, except on Day 28 in treatments exposed to copper, 20 μg g^-1 norfloxacin, or both. These three treatment groups had lower Shannon diversity and Simpson's indices on Day 28 than other treatments and the controls suggesting recovery in bacteria population did not correspond with recovery in richness and evenness. Furthermore, functional predictions revealed that the effect of time and contaminants were significantly different on some microbial community functions on Day 28, especially the combination of Cu and high concentration NFX, including aerobic chemoheterotrophy, methanol oxidation and methylotrophy. Thus, norfloxacin and copper had significant adverse effects on microbial communities in estuarine sediments; however, the combined effects were variable and depended on exposure duration and antibiotic concentration.

Joint effects of bacterium and biochar in remediation of antibiotic-heavy metal contaminated soil and responses of resistance gene and microbial community

Soils containing both veterinary antibiotics (VAs) and heavy metals necessitate effective remediation approaches, and microbial and molecular levels of the results should be further examined. Here, a novel material combining waste fungus chaff-based biochar (WFCB) and Herbaspirillum huttiense (HHS1) was established to immobilize copper (Cu) and zinc (Zn) and degrade oxytetracycline (OTC) and enrofloxacin (ENR). Results showed that the combined material exhibited high immobilization of Cu (85.5%) and Zn (64.4%) and great removals of OTC (41.9%) and ENR (40.7%). Resistance genes including tet(PB), tetH, tetR, tetS, tetT, tetM, aacA/aphD, aacC, aadA9, and czcA were reduced. Abundances of potential hosts of antibiotic resistance genes (ARGs) including phylum Proteobacteria and genera Brevundimonas and Rhodanobacter were altered. Total phosphorus and pH were the factors driving the VA degrading microorganisms and potential hosts of ARGs. The combination of WFCB and HHS1 can serve as an important bioresource for immobilizing heavy metals and removing VAs in the contaminated soil.

Tracking antibiotic resistance genes (ARGs) during earthworm conversion of cow dung in northern China

Using cow dung to breed earthworms poses a risk of environmental transmission of antibiotic resistance genes (ARGs). The purpose of this study was to address the occurrence, persistence and environmental fate of ARGs during earthworm conversion of cow dung. The results showed that ARGs persisted through the whole process. Notably, earthworm conversion effectively reduced some ARGs in cow dung, but a definite concentration of ARGs still remained in earthworms and vermicompost (up to 10^-1 and 10^-2 copies/16S copies, respectively). We found that tet-ARGs were the most abundant in 15 earthworm farms (10^-6~10^-1 copies/16S copies) and some high-risk ARGs (i.e., bla_ampC, bla_OXA-1 and bla_TEM-1) were even prevalent in these farms. Interestingly, although ARGs differ widely in cow dung (10^-10~10^-1 copies/16S copies), the ARGs levels were comparable in vermicompost samples from different farms (10^-8~10^-2 copies/16S copies). Notably, earthworm conversion effectively reduced some ARGs in cow dung, but significant level of ARGs still remained in earthworms and vermicompost (up to 10^-1 and 10^-2 copies/16S copies, respectively). Nevertheless, the concentrations of some heavy metals (Cu, Zn and Ni), the abundance of mobile genetic elements (MGEs) and total nitrogen content were confirmed to be correlated to the enrichment of some ARGs. Overall, this study demonstrated the high prevalence of ARGs contamination in earthworm farms, and also highlighted the dissemination risk of ARGs during the earthworm conversion of cow dung.

Profiles of antibiotic resistance genes in an inland salt-lake Ebinur Lake, Xinjiang, China: The relationship with antibiotics, environmental factors, and microbial communities

Lakes in arid northwestern China, as the main pollutant-holding water bodies in the typical ecologically fragile areas, are facing the unknown risk of exposure to antibiotics and antibiotic resistance genes (ARGs). In this study, five ARGs and one mobile genetic element (intI1) and their relation with antibiotics, microbial communities and water quality were investigated in Ebinur Lake Basin, a typical salt-lake of China. Quantitative PCR analysis indicated that ARGs decreasing order in both surface water and sediment was sul1 >sul2 >tetW>ermB>qnrS, which means sulfonamide resistance genes were the main pollution ARGs. Macrolide antibiotics were the predominant antibiotics in the surface water and sediment in winter, while sulfonamides and quinolones accounted for a high proportion in summer. There was a non-corresponding relationship between ARGs and antibiotics. Moreover, the relationship between ARGs and microbial communities were defined. Sulfonamide resistance genes were carried by a greater diversity of potential host bacteria (76 genera) than other ARGs (9 genera). And their positive correlation with intI1 (p < 0.05) which promotes their migration and provides possibility of their co-occurrence in bacterial populations (e.g., Nitrospira). Bacterial genera were the main driver of ARGs distribution pattern in highly saline lake sediment. Environmental factors like salinity, total nitrogen and organic matter could have a certain influence on the occurrence of ARGs by affecting microorganisms. The results systematically show the distribution and propagation characteristics of ARGs in typical inland salt-lakes in China, and preliminarily explored the relationship between ARGs and antibiotics, resistance genes and microorganisms in lakes in ecologically fragile areas.

Effects of chlorotetracycline on antibiotic resistance genes and the bacterial community during cattle manure composting

Chlorotetracycline (CTC) is one of the most antibiotics present in cattle manure. In present study, three levels of CTC (0, 20 and 40 mg kg^-1) were added to cattle manure composting systems to investigate its effects on the distribution of antibiotic-resistant genes (ARGs) and succession of bacterial community. Adding CTC hindered the removal of ARGs during composting; the high level of CTC significantly increased the relative abundance (RA) of 9/11 ARGs and four MGEs. The bacterial community could be clustered according to the composting time under various treatments, with the high level of CTC having a more persistent effect on the bacterial community. Based on redundancy analysis, bacterial community explained the most variation in ARGs (50.1%), whereas based on network analysis, Firmicutes and Proteobacteria were the main hosts for ARGs. In conclusion, the presence of CTC increased the risks of spreading ARGs in compost products.

Environmentally Friendly Quinolones Design for a Two-Way Choice between Biotoxicity and Genotoxicity through Double-Activity 3D-QSAR Model Coupled with the Variation Weighting Method

Quinolone (QN) antibiotics are widely used, which lead to their accumulation in soil and toxic effects on ryegrass in pasture. In this study, we employed ryegrass as the research object and selected the total scores of 29 QN molecules docked with two resistant enzyme structures, superoxide dismutase (SOD, PDB ID: 1B06) and proline (Pro, PPEP-2, PDB ID: 6FPC), as dependent variables. The structural parameters of QNs were used as independent variables to construct a QN double-activity 3D-QSAR model for determining the biotoxicity on ryegrass by employing the variation weighting method. This model was constructed to determine modification sites and groups for designing QNs molecules. According to the 3D contour map of the model, by considering enrofloxacin (ENR) and sparfloxacin (SPA) as examples, 23 QN derivatives with low biotoxicity were designed, respectively. The functional properties and environmental friendliness of the QN derivatives were predicted through a two-way selection between biotoxicity and genotoxicity before and after modification; four environmentally friendly derivatives with low biotoxicity and high genotoxicity were screened out. Mixed toxicity index and molecular dynamics methods were used to verify the combined toxicity mechanism of QNs on ryegrass before and after modification. By simulating the combined pollution of ENR and its derivatives in different soils (farmland, garden, and woodland), the types of combined toxicity were determined as partial additive and synergistic. Binding energies were calculated using molecular dynamics. The designed QN derivatives with low biotoxicity, high genotoxicity, and environmental friendliness can highly reduce the combined toxicity on ryegrass and can be used as theoretic reserves to replace QN antibiotics.

Response of Cyperus involucratus to sulfamethoxazole and ofloxacin-contaminated environments: Growth physiology, transportation, and microbial community

Plant-microbe is a complementary coupling system for antibiotics removing in constructed wetlands (CWs), but how plant and rhizosphere microbiomes respond to antibiotics exposure and the occurrence of ARGs in this microenvironment have seldom been researched. Thus, the response of the plant-microbe coupling system to different levels of antibiotics (sulfamethoxazole (SMZ) and ofloxacin (OFL)) was investigated. The results showed that two antibiotic stressors have hormetic effects on plant growth, physiology, and microbial community evolution, and the antibiotic toxic effects presented as SMZ + OFL > SMZ > OFL. Antibiotic accumulation in the plants was in the order of roots > stems > leaves. Notably, the root attachments affected antibiotic transportation. The accumulation of antibiotics in the under-ground parts affected the rhizosphere microbial community structure, and the microorganisms were more sensitive to SMZ + OFL than the plants, with inflection points of 0.5 mg L^-1 and 1 mg L^-1, respectively. Pseudomonas was highly resistant to antibiotics, while Acidovorax and Devosia may play a role in antibiotic degradation. Correlation analysis and network analysis showed that antibiotic enrichment and the bacterial community contributed significantly to the abundance of antibiotic-resistant genes (ARGs), further revealing the co-occurrence of int1, ARGs, and the potential bacterial hosts.

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.

Arsenic and cadmium as predominant factors shaping the distribution patterns of antibiotic resistance genes in polluted paddy soils

Heavy metals have been recognized as potential factors driving the evolution and development of antibiotic resistance. However, the relative effects of cadmium (Cd) and arsenic (As) on the prevalence and distribution of antibiotic resistance genes (ARGs) remain unclear. We investigated the co-selection effects of Cd and As on ARGs in 45 paddy soils polluted by heavy metals, using high-throughput quantitative PCR. A total of 119 ARGs and 9 mobile genetic elements (MGEs) were detected in all samples. Regression analysis showed that the single pollution index (PI_As and PI_Cd) and Nemerow integrated pollution index (NIPI) both had significant and positive correlations with ARGs (P <  0.05), indicating the co-selective effects of Cd and As on ARGs distribution. The significant correlations between bacterial taxa and different ARGs in network analysis revealed potential hosts of ARGs. Structural equation models indicated that the effects of As on ARGs were stronger than that of Cd. The profile of ARGs could be impacted by Cd and As indirectly by strongly affecting the bacterial abundance. Overall, this study extended our knowledge about the co-selection of Cd and As on ARGs in paddy soil, and had important implications for assessing the potential risks of ARGs in paddy soils.

Effect of the coexposure of sulfadiazine, ciprofloxacin and zinc on the fate of antibiotic resistance genes, bacterial communities and functions in three-dimensional biofilm-electrode reactors

Three-dimensional biofilm electrode reactors (3D-BERs) with high treatment efficiency were constructed to treat wastewater containing sulfadiazine (SDZ) and ciprofloxacin (CIP) coexposure with Zinc (Zn). The results showed that coexposure to target antibiotics and Zn increased the absolute and relative abundances of target antibiotic resistance genes (ARGs). Additionally, the target ARG abundances were higher on cathode of 3D-BER compared with ordinary anaerobic reactor while the abundances of total ARGs were decreased in the effluent. Meanwhile, redundancy analysis results revealed that the composition of bacteria carrying ARGs was greatly influenced in the cathode by the accumulation of Zn and antibiotic, which dominated the changes of ARG abundances. Additionally, ARGs with their host bacteria revealed by network analysis were partially deposited on electrode substrates when being removed from wastewater. Thus, 3D-BER exhibits capability of simultaneously eliminating antibiotic and Zn, and greatly reduces the risks of ARGs spread.

Research and Technological Advances Regarding the Study of the Spread of Antimicrobial Resistance Genes and Antimicrobial-Resistant Bacteria Related to Animal Husbandry

The extensive use of antimicrobials in animal farms poses serious safety hazards to both the environment and public health, and this trend is likely to continue. Antimicrobial resistance genes (ARGs) are a class of emerging pollutants that are difficult to remove once introduced. Understanding the environmental transfer of antimicrobial-resistant bacteria (ARB) and ARGs is pivotal for creating control measures. In this review, we summarize the research progress on the spread and detection of ARB and ARG pollution related to animal husbandry. Molecular methods such as high-throughput sequencing have greatly enriched the information about ARB communities. However, it remains challenging to delineate mechanisms regarding ARG induction, transmission, and tempo-spatial changes in the whole process, from animal husbandry to multiple ecosystems. As a result, future research should be more focused on the mechanisms of ARG induction, transmission, and control. We also expect that future research will rely more heavily on metagenomic -analysis, metatranscriptomic sequencing, and multi-omics technologies

Short term changes in the abundance of nitrifying microorganisms in a soil-plant system simultaneously exposed to copper nanoparticles and atrazine

Copper nanoparticles (NCu) may co-exist with other pollutants in agricultural soils, such as pesticides. However, this has been little evaluated yet. Thus, possible effects of the simultaneous applications of pesticides and NCu on biogeochemical cycles are expected, for example on the nitrogen cycle. Therefore, the aim of this work was to evaluate the effect of simultaneous application of the herbicide atrazine (ATZ) and NCu on the abundance of total bacteria and nitrifying communities: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Moreover, the ATZ dissipation was evaluated. A soil-plant system containing ATZ at field dose (3 mg a.i. kg^-1) was mixed with two doses of NCu (0.05% or 0.15% w/w). Changes in the abundance of 16S rRNA and ammonia monooxygenase (amoA) genes of AOA and AOB were evaluated by real-time quantitative PCR (qPCR) at three sampling times (1, 15 and 30 days). The residual ATZ and nitrate production were also measured. The results showed significant differences in microbial composition and abundance over the 30 days of the experiment. Particularly, an initial decrease was observed in total bacterial abundance due to the presence of ATZ and NCu respect to ATZ alone (~60%). The abundance of AOA was also remarkably reduced (~85%), but these communities gradually recovered towards the end of the experiment. Conversely, AOB abundance initially increased (>100%) and remained mainly unaltered in soil exposed to ATZ and NCu 0.15% w/w, where nitrate formation was also constant. Moreover, NCu decreased the ATZ dissipation, which was translated in a 2-fold increase on the ATZ half-life values (T_1/2). This study demonstrates that the simultaneous presence of NCu and ATZ may represent a risk for the total bacteria present in soil and sensitive microorganisms such as nitrifying communities, and changes in the dissipation of the pesticide could influence this process.

Continuous degradation of ciprofloxacin in a manganese redox cycling system driven by Pseudomonas putida MnB-1

Ciprofloxacin (CIP), as an extensively used antibiotic, has been widely detected at a high level in the environment and has raised environmental pollution concerns. Thus, efficient and cost-effective methods for CIP degradation are highly desired. Biologically produced manganese oxides (BioMnO_x) offer a promising perspective for CIP degradation because of their catalytic reactivity and cost-effectiveness. However, the release of Mn(II) from BioMnO_x prevents the further oxidation of pollutants. As a consequence, continuous CIP degradation by BioMnO_x is not feasible. In this work, a manganese redox cycling system driven by Pseudomonas putida MnB-1 was constructed for continuous degradation of CIP. In such a system CIP was oxidized continuously and rapidly by re-oxidizing the formed Mn(II) to regenerate reactive BioMnO_x, which also protected the strain from CIP toxicity. CIP was degraded through N-dealkylation passway. No significant loss of BioMnO_x reactivity was observed in three-cycle CIP degradation process, suggesting the stability of this system. An overlooked intracellular BioMnO_x, which was involved in CIP degradation, was discovered in P. putida MnB-1. Moreover, the important role of Mn(III) in facilitating CIP removal in this system was also identified. This work provides useful information to better understand the degradation of antibiotic compounds mediated by microbes in environments.