Differential distribution characteristics of heavy metal resistance genes and driving mechanisms of heavy metal speciation in river-lake system sediments.

Composting is an effective method for stabilizing and valorizing pig manure, which is rich in nutrients but also contains heavy metals such as chromium (Cr). These heavy metals can promote the development of heavy metal resistance genes (MRGs) during composting, posing environmental and health risks. In this study, pig manure composting supplemented with pyridine carboxylate chromium was applied to investigate its effects on heavy metal speciation and MRG abundance and explore the influence factors of the dynamics of MRGs during composting. The results showed that the addition of Cr significantly influenced the composting process, including temperature fluctuations and nutrient dynamics. Specifically, the addition of Cr weakened the impact of water addition on temperature, as evidenced by the failure of the Cr-amended treatment to re-enter the thermophilic phase after water addition. The speciation of Cr changed during composting, with a significant reduction in high-bioavailable Cr forms (e.g., a 54.56% reduction in high-bioavailable Cr in the Cr-amended treatment) and an increase in low-bioavailable forms. The abundance of MRGs, particularly copper resistance genes, increased over time, with more pronounced fluctuations in the Cr-amended treatment. The primary factors influencing the dynamics of these MRGs during composting were identified as heavy metal speciation, microbial community structure, and specific physicochemical properties such as pH, electrical conductivity, and dissolved organic carbon. The present study offers valuable insights into the complex interactions between heavy metals and microbial communities during composting and provides inspiration for managing heavy metals to minimize the spread of MRGs.

Characterizations of heavy metal contamination, microbial community, and resistance genes in a tailing of the largest copper mine in China.

Zero-valent iron drives the passivation of Zn and Cu during composting: Fate of heavy metal resistant bacteria and genes

Heavy metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) in bacteria can respond to the inducement of heavy metals. However, the co-occurrence of MRGs and ARGs in the long-term heavy metal contaminated area is still poorly understood. Here, we investigated the relationship between the abundance of soil bacteria MRGs, ARGs and heavy metal pollution in a copper tailing dam area of northern China. We found that arsC and ereA genes coding for resistance mechanisms to arsenic and to macrolides, respectively, are the most abundant MRG and ARG in the study area. The abundance of MRGs is positively correlated with cadmium (Cd) concentration, and this indicates the importance of Cd in the selection of MRGs. The network analysis results show that sulII and MRGs co-occur and copB occur with ARGs, which suggests that MRGs and ARGs can be co-selected in the soil contaminated by heavy metal. The network analysis also reveals the co-occurrence of Cd and MRGs, and thus heavy metal with a high ‘toxic-response’ factor can be used as the indicator of MRGs. This study improves the understanding of the relationship between bacterial resistance and multi-metal contamination, and underlies the exploration of the adaptive mechanism of microbes in the multi-metal contaminated environment.

Response of heavy metal and antibiotic resistance genes and related microorganisms to different heavy metals in activated sludge

The emergence and persistence of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs) has aroused growing public concern for its risk to human health and ecological safety. Moreover, heavy metals concentrated in sewage and sludge could potentially favour co-selection of ARGs and heavy metal resistance genes (HMRGs). In this study, the profile and abundance of antibiotic and metal resistance genes in influent, sludge and effluent were characterized based on the Structured ARG Datebase (SARG) and Antibacterial Biocide and Metal Resistance Gene Datebase (BacMet) by metagenomic analysis. Sequences were aligning against the INTEGRALL, ISFinder, ICEberg and NCBI RefSeq databases to obtain the diversity and abundance of mobile genetic elements (MGEs, e.g.plasmid and transposon). Among them, 20 types of ARGs and 16 types of HMRG were detected in all samples, the influent metagenomes contained many more resistance genes (both ARGs and HMRGs) than the sludge and the influent sample, large reductions in the relatively abundance and diversity of ARG were achieved by biological treatment. ARGs and HMRGs cannot be completely eliminated during the oxidation ditch. A total of 32 species of the potential pathogens were detected, relative abundances of pathogens had no obvious changes. It is suggested that more specific treatments are required to limit their proliferation in the environment. This study can be helpful for further understanding the removal of antibiotic resistance genes in the sewage treatment process via metagenomic sequencing.

Sustainability assessment of topsoil ecology in Chongqing, China based on the application of livestock and poultry manure

Persistent use of pesticides and animal manure in agricultural soils inadvertently introduced heavy metals and antibiotic/antibiotic resistance genes (ARGs) into the soil with deleterious consequences. The microbiome and heavy metal and antibiotic resistome of a pesticide and animal manure inundated agricultural soil (SL6) obtained from a vegetable farm at Otte, Eiyenkorin, Kwara State, Nigeria, was deciphered via shotgun metagenomics and functional annotation of putative ORFs (open reading frames). Structural metagenomics of SL6 microbiome revealed 29 phyla, 49 classes, 94 orders, 183 families, 366 genera, 424 species, and 260 strains with the preponderance of the phyla Proteobacteria (40%) and Actinobacteria (36%), classes Actinobacteria (36%), Alphaproteobacteria (18%), and Gammaproteobacteria (17%), and genera Kocuria (16%), Sphingobacterium (11%), and Brevundimonas (10%), respectively. Heavy metal resistance genes annotation conducted using Biocide and Metal Resistance Gene Database (BacMet) revealed the detection of genes responsible for the uptake, transport, detoxification, efflux, and regulation of copper, cadmium, zinc, nickel, chromium, cobalt, selenium, tungsten, mercury, and several others. ARG annotation using the Antibiotic Resistance Gene-annotation (ARG-ANNOT) revealed ARGs for 11 antibiotic classes with the preponderance of β-lactamases, mobilized colistin resistance determinant (mcr-1), macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside resistance genes, among others. The persistent use of pesticide and animal manure is strongly believed to play a major role in the proliferation of heavy metal and antibiotic resistance genes in the soil. This study revealed that agricultural soils inundated with pesticide and animal manure use are potential hotspots for ARG spread and may accentuate the spread of multidrug resistant clinical pathogens.

The large-scale manganese mining causes severe heavy metal contamination, posing a significant potential risk to human health. Songtao County is one of the most important manganese mining areas in China, where the disorderly mining and extensive production has inevitably caused serious pollution. However, it's still unclear how Mn production activities affect agricultural soils located relatively far from the mining sites. Therefore, we investigated the horizontal and vertical distribution of heavy metal contamination, microbial communities, and resistance genes in the agricultural soils located at Songtao County. Metagenomic sequencing revealed that Proteobacteria, Acidobacteria, Rokubacteria, Chloroflexi, and Actinobacteria were the most abundant phyla. The diversity and composition of the bacterial communities varied significantly between different sampling sites and depths. Redundancy and Spearman correlation analysis indicated that total nitrogen, total organic carbon, total K, and Mn were the primary environmental factors determining the distribution of bacterial communities. The bacterial communities in Wuluo were influenced by Hg, Zn, Cu, Ni, and As, whereas in Mushu, it was primarily affected by Mn levels. A large account of heavy metal resistance genes, manganese resistance genes, and antibiotics resistance genes were identified. The relative abundances and correlation analysis of these resistance genes exhibited observed correlations based on the potential co-selection mechanisms, suggesting that Mn and heavy metals, as well as antibiotics, might shape the microbiome and resistome in this agricultural soil. These findings provide an insight for the surveillance, maintenance, and remediation of the agricultural soil and offer theoretical evidence for improving the agricultural soil environment.

Seasonal variation and co-occurrence of metal resistance and virulence genes in landfill leachate pathogens: Implications for environmental risk management.

Copper resistance in phytopathogens is a major challenge to crop production globally and is known to be driven by excessive use of copper-based pesticides. However, recent studies have shown co-selection of multiple heavy metal and antibiotic resistance genes in bacteria exposed to heavy metal and xenobiotics, which may impact the epidemiology of plant, animal, and human diseases. In this study, multi-resistance to heavy metals and antibiotics were evaluated in local Xanthomonas campestris pv. campestris (Xcc) and co-isolated Xanthomonas melonis (Xmel) strains from infected crucifer plants in Trinidad. Resistance to cobalt, cadmium, zinc, copper, and arsenic (V) was observed in both Xanthomonas species up to 25 mM. Heavy metal resistance (HMR) genes were found on a small plasmid-derived locus with ~ 90% similarity to a Stenotrophomonas spp. chromosomal locus and a X. perforans pLH3.1 plasmid. The co-occurrence of mobile elements in these regions implies their organization on a composite transposon-like structure. HMR genes in Xcc strains showed the lowest similarity to references, and the cus and ars operons appear to be unique among Xanthomonads. Overall, the similarity of HMR genes to Stenotrophomonas sp. chromosomal genomes suggest their origin in this genus or a related organism and subsequent spread through lateral gene transfer events. Further resistome characterization revealed the presence of small multidrug resistance (SMR), multidrug resistance (MDR) efflux pumps, and bla (Xcc) genes for broad biocide resistance in both species. Concurrently, resistance to antibiotics (streptomycin, kanamycin, tetracycline, chloramphenicol, and ampicillin) up to 1000 µg/mL was confirmed.

Heavy metal pollution and antimicrobial resistance genes (ARGs) are global challenges in aquatic ecosystems. They are commonly produced from agricultural waste, industrial effluents, and untreated sewage. Heavy metals, including cadmium, copper, and zinc, can exert pressure on microbial communities, leading to the co-selection of antimicrobial resistance genes (ARGs) and metal resistance genes (MRGs). This occurs through cross-resistance mechanisms, shared mobile genetic elements, and co-regulation under selective pressure. Metagenomics is known for its effectiveness and culture- independent nature, providing an advanced way to detect and profile ARGs and MRGs in environmental samples to facilitate the identification of functional genes and uncultured microorganisms. Findings from case studies from the Yamuna River (India) and Pear River (China) demonstrate strong relationships between concentrations of heavy metals and abundance of ARG/MRG, which supports the assumption that heavy metal contamination plays an integral role in sustaining antimicrobial resistance genes in aquatic systems. This paper also highlights metagenomics as a key tool for defining dynamics of co-selection, integrating biological indicators into monitoring water quality, and informing risk assessment. It establishes that standardized protocols, cross-sectoral frameworks, and long-term monitoring are vital for mitigating spread of antimicrobial resistance genes. Embedding genomics data with environmental parameters suggests that metagenomics support early interventions while strengthening environmental governance and minimizing public health risks for its environmental dissemination.

Effects of H3PO4 modified biochar on heavy metal mobility and resistance genes removal during swine manure composting

Distribution of antibiotic and metal resistance genes in two glaciers of North Sikkim, India

Heavy metal and disinfectant resistance genes among livestock-associated methicillin-resistant Staphylococcus aureus isolates