Bacterial Heavy-Metal and Antibiotic Resistance Genes in a Copper Tailing Dam Area in Northern China

Comprehensive analysis of metal(loid)s and associated metal(loid) resistance genes in atmospheric particulate matter

Despite global concerns about metal(loid)s in atmospheric particulate matter (PM), the presence of metal(loid) resistance genes (MRGs) in PM remains unknown. Therefore, we conducted a comprehensive investigation of the metal(loid)s and associated MRGs in PMs in two seasons (summer and winter) in Xiamen, China. According to the geoaccumulation index (Igeo), most metal(loid)s, except for V and Mn, exhibited enrichment in PM, suggesting potential anthropogenic sources. By employing Positive Matrix Factorization (PMF) model, utilizing a dataset encompassing both total and bioaccessible metal(loid)s, along with backward trajectory simulations, traffic emissions were determined to be the primary potential contributor of metal(loid)s in summer, whereas coal combustion was observed to have a dominant contribution in winter. The major contributor to the carcinogenic risk of metal(loid)s in both summer and winter was predominantly attributed to coal combustion, which serves as the main source of bioaccessible Cr. Bacterial communities within PMs showed lower diversity and network complexity in summer than in winter, with Pseudomonadales being the dominant order. Abundant MRGs, including the As(III) S-adenosylmethionine methyltransferase gene (arsM), Cu(I)-translocating P-type ATPase gene (copA), Zn(II)/Cd(II)/Pb(II)-translocating P-type ATPase gene (zntA), and Zn(II)-translocating P-type ATPase gene (ziaA), were detected within the PMs. Seasonal variations were observed for the metal(loid) concentration, bacterial community structure, and MRG abundance. The bacterial community composition and MRG abundance within PMs were primarily influenced by temperature, rather than metal(loid)s. This research offers novel perspectives on the occurrence of metal(loid)s and MRGs in PMs, thereby contributing to the control of air pollution.

Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria

The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.

Distribution, source apportionment, and ecological risk assessment of soil antibiotic resistance genes in urban green spaces

Urban green spaces play a crucial role in cities by providing near-natural environments that greatly impacts the health of residents. However, these green spaces have recently been scrutinized as potential reservoirs of antibiotic resistance genes (ARGs), posing significant ecological risks. Despite this concern, our understanding of the distribution, sources, and ecological risks associated with ARGs remains limited. In this study, we investigated the spatial distribution of soil ARGs using spatial interpolation and auto-correlation analysis. To apportion the source of soil ARGs in urban green spaces of Tianjin, Geo-detector method (GDM) was employed. Furthermore, we evaluated the ecological risk posed by ARGs employing risk quotients (RQ). The results of our study showed a significantly higher abundance of Quinolone resistance genes in the soil of urban green spaces in Tianjin. These genes were mainly found in the northwest, central, and eastern regions of the city. Our investigation identified three main factors contributing to the presence of soil ARGs: antibiotic production, precipitation, livestock breeding, and hospital. The results of ecological risk in RQ value showed a high risk associated with Quinolone resistance genes, followed by Aminoglycoside, Tetracycline, Multidrug, MLSB, Beta Lactam, Sulfonamide, and Chloramphenicol. Mantel-test and correlation analysis revealed that the ecological risk of ARGs was greatly influenced by soil properties and heavy metals. This study provides a new perspective on source apportionment and the ecological risk assessment of soil ARGs in urban green spaces.

The effect of dietary zinc and zinc physiological status on the composition of the gut microbiome in vivo

Zinc serves critical catalytic, regulatory, and structural roles. Hosts and their resident gut microbiota both require zinc, leading to competition, where a balance must be maintained. This systematic review examined evidence on dietary zinc and physiological status (zinc deficiency or high zinc/zinc overload) effects on gut microbiota. This review was conducted according to PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses) guidelines and registered in PROSPERO (CRD42021250566). PubMed, Web of Science, and Scopus databases were searched for in vivo (animal) studies, resulting in eight selected studies. Study quality limitations were evaluated using the SYRCLE risk of bias tool and according to ARRIVE guidelines. The results demonstrated that zinc deficiency led to inconsistent changes in α-diversity and short-chain fatty acid production but led to alterations in bacterial taxa with functions in carbohydrate metabolism, glycan metabolism, and intestinal mucin degradation. High dietary zinc/zinc overload generally resulted in either unchanged or decreased α-diversity, decreased short-chain fatty acid production, and increased bacterial metal resistance and antibiotic resistance genes. Additional studies in human and animal models are needed to further understand zinc physiological status effects on the intestinal microbiome and clarify the applicability of utilizing the gut microbiome as a potential zinc status biomarker.

Perspectives of pteridophytes microbiome for bioremediation in agricultural applications

The microbiome is the synchronised congregation of millions of microbial cells in a particular ecosystem. The rhizospheric, phyllospheric, and endospheric microbial diversity of lower groups of plants like pteridophytes, which includes the Ferns and Fern Allies, have also given numerous alternative opportunities to achieve greener and sustainable agriculture. The broad-spectrum bioactivities of these microorganisms, including bioremediation of heavy metals (HMs) in contaminated soil, have been drawing the attention of agricultural researchers for the preparation of bioformulations for applications in climate-resilient and versatile agricultural production systems. Pteridophytes have an enormous capacity to absorb HMs from the soil. However, their direct application in the agricultural field for HM absorption seems infeasible. At the same time, utilisation of Pteridophyte-associated microbes having the capacity for bioremediation have been evaluated and can revolutionise agriculture in mining and mineral-rich areas. In spite of the great potential, this group of microbiomes has been less studied. Under these facts, this prospective review was carried out to summarise the basic and applied research on the potential of Pteridophyte microbiomes for soil bioremediation and other agricultural applications globally. Gaps have also been indicated to present scopes for future research programmes.

Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms

In this study, we present a mathematical model for plasmid spread in a growing biofilm, formulated as a nonlocal system of partial differential equations in a 1-D free boundary domain. Plasmids are mobile genetic elements able to transfer to different phylotypes, posing a global health problem when they carry antibiotic resistance factors. We model gene transfer regulation influenced by nearby potential receptors to account for recipient-sensing. We also introduce a promotion function to account for trace metal effects on conjugation, based on literature data. The model qualitatively matches experimental results, showing that contaminants like toxic metals and antibiotics promote plasmid persistence by favoring plasmid carriers and stimulating conjugation. Even at higher contaminant concentrations inhibiting conjugation, plasmid spread persists by strongly inhibiting plasmid-free cells. The model also replicates higher plasmid density in biofilm's most active regions.

Crucifer Lesion-Associated Xanthomonas Strains Show Multi-Resistance to Heavy Metals and Antibiotics

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.

Analysis of Antimicrobial Resistance in Bacterial Pathogens Recovered from Food and Human Sources: Insights from 639,087 Bacterial Whole-Genome Sequences in the NCBI Pathogen Detection Database

Understanding the role of foods in the emergence and spread of antimicrobial resistance necessitates the initial documentation of antibiotic resistance genes within bacterial species found in foods. Here, the NCBI Pathogen Detection database was used to query antimicrobial resistance gene prevalence in foodborne and human clinical bacterial isolates. Of the 1,843,630 sequence entries, 639,087 (34.7%) were assigned to foodborne or human clinical sources with 147,788 (23.14%) from food and 427,614 (76.88%) from humans. The majority of foodborne isolates were either Salmonella (47.88%), Campylobacter (23.03%), Escherichia (11.79%), or Listeria (11.3%), and the remaining 6% belonged to 20 other genera. Most foodborne isolates were from meat/poultry (95,251 or 64.45%), followed by multi-product mixed food sources (29,892 or 20.23%) and fish/seafood (6503 or 4.4%); however, the most prominent isolation source varied depending on the genus/species. Resistance gene carriage also varied depending on isolation source and genus/species. Of note, Klebsiella pneumoniae and Enterobacter spp. carried larger proportions of the quinolone resistance gene qnrS and some clinically relevant beta-lactam resistance genes in comparison to Salmonella and Escherichia coli. The prevalence of mec in S. aureus did not significantly differ between meat/poultry and multi-product sources relative to clinical sources, whereas this resistance was rare in isolates from dairy sources. The proportion of biocide resistance in Bacillus and Escherichia was significantly higher in clinical isolates compared to many foodborne sources but significantly lower in clinical Listeria compared to foodborne Listeria. This work exposes the gaps in current publicly available sequence data repositories, which are largely composed of clinical isolates and are biased towards specific highly abundant pathogenic species. We also highlight the importance of requiring and curating metadata on sequence submission to not only ensure correct information and data interpretation but also foster efficient analysis, sharing, and collaboration. To effectively monitor resistance carriage in food production, additional work on sequencing and characterizing AMR carriage in common commensal foodborne bacteria is critical.

Characterization of heavy metal, antibiotic pollution, and their resistance genes in paddy with secondary municipal-treated wastewater irrigation

Secondary municipal-treated wastewater irrigation may introduce residual antibiotics into the agricultural systems contaminated with certain heavy metals, ultimately leading to the coexistence of antibiotics and heavy metals. The coexistence may induce synergistic resistance to both in the microbial community. Here, we investigated the effects of long-term municipal-treated irrigation for rice on the microbiome and resistome. The results showed that the target antibiotics were undetectable in edible grains, and the heavy metal concentrations did not exceed the standard in edible rice grains. Heavy metal resistance genes (MRGs) ruvB and acn antibiotic resistance genes (ARGs) sul1 and sul2 were the dominating resistant genes. The coexistence of antibiotics and heavy metals affected the microbial community and promoted metal and antibiotic resistance. Network analysis revealed that Proteobacteria were the most influential hosts for MRGs, ARGs, and integrons, and co-selection may serve as a potential mechanism for resistance maintenance. MRG czcA and ARG sul1 can be recommended as model genes to study the co-selection of ARGs and MRGs in environments. The obtained results highlight the importance of considering the co-occurrence of heavy metals and antibiotics while developing effective methods to prevent the transmission of ARGs. These findings are critical for assessing the possible human health concerns associated with secondary municipal-treated wastewater irrigation for agriculture and improving the understanding of the coexistence of heavy metals and antibiotics.

Meta-analysis addressing the characterization of antibiotic resistome in global hospital wastewater

Hospital wastewater (HWW) is a significant environmental reservoir of antibiotic resistance genes (ARGs). However, currently, no comprehensive understanding exists of the antibiotic resistome in global HWW. In this study, we attempted to address this knowledge gap through an in silico reanalysis of publicly accessible global HWW metagenomic data. We reanalyzed ARGs in 338 HWW samples from 13 countries in Africa, Asia, and Europe. In total, 2420 ARG subtypes belonging to 30 ARG types were detected, dominated by multidrug, beta-lactam, and aminoglycoside resistance genes. ARG composition in Europe differed from that in Asia and Africa. Notably, the ARGs presented co-occurrence with mobile genetic elements (MGEs), metal resistance genes (MRGs), and human bacterial pathogens (HBP), indicating a potential dissemination risk of ARGs in the HWW. Multidrug resistance genes presented co-occurrence with MGEs, MRGs, and HBP, is particularly pronounced. The abundance of contigs that contained ARG, contigs that contained ARG and HBP, contigs that contained ARG and MGE, contigs that contained ARG and MRG were used for health and transmission risk assessment of antibiotic resistome and screened out 40 high risk ARGs in the global HWW. This study first provides a comprehensive characterization and risk of the antibiotic resistome in global HWW.

Insights into antibiotic and heavy metal resistance interactions in Escherichia coli isolated from livestock manure and fertilized soil

Heavy metal and antibiotic-resistant bacteria from livestock feces are ecological and public health problems. However, the distribution and relationships of antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs), and virulence factors (VFs) and their transmission mechanisms remain unclear. Therefore, we investigated the resistance of Escherichia coli, the prevalence of its ARGs, HMRGs, and VFs, and their transmission mechanisms in livestock fresh feces (FF), composted feces (CF), and fertilized soil (FS). In total, 99.54% (n = 221) and 91.44% (n = 203) of E. coli were resistant to at least one antibiotic and one heavy metal, respectively. Additionally, 72.52% (n = 161) were multi-drug resistant (MDR), of which Cu-resistant E. coli accounted for 72.67% (117/161). More than 99.34% (88/89) of E. coli carried multidrug ARGs, VFs, and the Cu resistance genes cueO and cusABCRFS. The Cu resistance genes cueO and cusABCRFS were mainly located on chromosomes, and cueO and cusF were positively associated with HMRGs, ARGs, and VFs. The Cu resistance genes pcoABCDRS were located on the plasmid pLKYL-P02 flanked by ARGs in PF18C from FF group and on chromosomes flanked by HMRGs in SAXZ1-1 from FS group. These results improved our understanding of bacterial multidrug and heavy metal resistance in the environment.

Draft genome analysis for Enterobacter kobei, a promising lead bioremediation bacterium

Lead pollution of the environment poses a major global threat to the ecosystem. Bacterial bioremediation offers a promising alternative to traditional methods for removing these pollutants, that are often hindered by various limitations. Our research focused on isolating lead-resistant bacteria from industrial wastewater generated by heavily lead-containing industries. Eight lead-resistant strains were successfully isolated, and subsequently identified through molecular analysis. Among these, Enterobacter kobei FACU6 emerged as a particularly promising candidate, demonstrating an efficient lead removal rate of 83.4% and a remarkable lead absorption capacity of 571.9 mg/g dry weight. Furthermore, E. kobei FACU6 displayed a remarkable a maximum tolerance concentration (MTC) for lead reaching 3,000 mg/L. To further investigate the morphological changes in E. kobei FACU6 in response to lead exposure, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were employed. These analyses revealed significant lead adsorption and intracellular accumulation in treated bacteria in contrast to the control bacterium. Whole-genome sequencing was performed to gain deeper insights into E. kobei's lead resistance mechanisms. Structural annotation revealed a genome size of 4,856,454 bp, with a G + C content of 55.06%. The genome encodes 4,655 coding sequences (CDS), 75 tRNA genes, and 4 rRNA genes. Notably, genes associated with heavy metal resistance and their corresponding regulatory elements were identified within the genome. Furthermore, the expression levels of four specific heavy metal resistance genes were evaluated. Our findings revealed a statistically significant upregulation in gene expression under specific environmental conditions, including pH 7, temperature of 30°C, and high concentrations of heavy metals. The outstanding potential of E. kobei FACU6 as a source of diverse genes related to heavy metal resistance and plant growth promotion makes it a valuable candidate for developing safe and effective strategies for heavy metal disposal.

High prevalence of antibiotic-resistant and metal-tolerant cultivable bacteria in remote glacier environment

Studies of antibiotic-resistant bacteria (ARB) have mainly originated from anthropic-influenced environments, with limited information from pristine environments. Remote cold environments are major reservoirs of ARB and have been determined in polar regions; however, their abundance in non-polar cold habitats is underexplored. This study evaluated antibiotics and metals resistance profiles, prevalence of antibiotic resistance genes (ARGs) and metals tolerance genes (MTGs) in 38 ARB isolated from the glacier debris and meltwater from Baishui Glacier No 1, China. Molecular identification displayed Proteobacteria (39.3%) predominant in debris, while meltwater was dominated by Actinobacteria (30%) and Proteobacteria (30%). Bacterial isolates exhibited multiple antibiotic resistance index values > 0.2. Gram-negative bacteria displayed higher resistance to antibiotics and metals than Gram-positive. PCR amplification exhibited distinct ARGs in bacteria dominated by β-lactam genes blaCTX-M (21.1-71.1%), blaACC (21.1-60.5%), tetracycline-resistant gene tetA (21.1-60.5%), and sulfonamide-resistant gene sulI (18.4-52.6%). Moreover, different MTGs were reported in bacterial isolates, including mercury-resistant merA (21.1-63.2%), copper-resistant copB (18.4-57.9%), chromium-resistant chrA (15.8-44.7%) and arsenic-resistant arsB (10.5-44.7%). This highlights the co-selection and co-occurrence of MTGs and ARGs in remote glacier environments. Different bacteria shared same ARGs, signifying horizontal gene transfer between species. Strong positive correlation among ARGs and MTGs was reported. Metals tolerance range exhibited that Gram-negative and Gram-positive bacteria clustered distinctly. Gram-negative bacteria were significantly tolerant to metals. Amino acid sequences of blaACC,blaCTX-M,blaSHV,blaampC,qnrA, sulI, tetA and blaTEM revealed variations. This study presents promising ARB, harboring ARGs with variations in amino acid sequences, highlighting the need to assess the transcriptome study of glacier bacteria conferring ARGs and MTGs.

Validation and calibration of a novel GEM biosensor for specific detection of Cd2+, Zn2+, and Pb2

BACKGROUND

In this study, we designed a novel genetic circuit sensitive to Cd2+, Zn2+ and Pb2+ by mimicking the CadA/CadR operon system mediated heavy metal homeostasis mechanism of Pseudomonas aeruginosa. The regular DNA motifs on natural operon were reconfigured and coupled with the enhanced Green Fluorescent Protein (eGFP) reporter to develop a novel basic NOT type logic gate CadA/CadR-eGFP to respond metal ions mentioned above. A Genetically Engineered Microbial (GEM)-based biosensor (E.coli-BL21:pJET1.2-CadA/CadR-eGFP) was developed by cloning the chemically synthesised CadA/CadR-eGFP gene circuit into pJET1.2-plasmid and transforming into Escherichia coli (E. coli)-BL21 bacterial cells.

RESULTS

The GEM-based biosensor cells indicated the reporter gene expression in the presence of Cd2+, Zn2+ and Pb2+ either singly or in combination. Further, the same biosensor cells calibrated for fluorescent intensity against heavy metal concentration generated linear graphs for Cd2+, Zn2+ and Pb2+ with the R2 values of 0.9809, 0.9761 and 0.9758, respectively as compared to non-specific metals, Fe3+ (0.0373), AsO43- (0.3825) and Ni2+ (0.8498) making our biosensor suitable for the detection of low concentration of the former metal ions in the range of 1-6 ppb. Furthermore, the GEM based biosensor cells were growing naturally within the concentration range of heavy metals, at 37 °C and optimum pH = 7.0 in the medium, resembling the characteristics of wildtype E.coli.

CONCLUSION

Finally, the novel GEM based biosensor cells developed in this study can be applied for detection of targeted heavy metals in low concentration ranges (1-6 ppb) at normal bacterial physiological conditions.

Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region

The occurrence and spread of antibiotic resistance genes (ARGs) in environmental microorganisms, particularly in poly-extremophilic bacteria, remain underexplored and have received limited attention. This study aims to investigate the prevalence of ARGs and metal resistance genes (MRGs) in shotgun metagenome sequences obtained from water and salt crust samples collected from Lake Afdera and the Assale salt plain in the Danakil Depression, northern Ethiopia. Potential ARGs were characterized by the comprehensive antibiotic research database (CARD), while MRGs were identified by using BacMetScan V.1.0. A total of 81 ARGs and 39 MRGs were identified at the sampling sites. We found a copA resistance gene for copper and the β-lactam encoding resistance genes were the most abundant the MRG and ARG in the study area. The abundance of MRGs is positively correlated with mercury (Hg) concentration, highlighting the importance of Hg in the selection of MRGs. Significant correlations also exist between heavy metals, Zn and Cd, and ARGs, which suggests that MRGs and ARGs can be co-selected in the environment contaminated by heavy metals. A network analysis revealed that MRGs formed a complex network with ARGs, primarily associated with β-lactams, aminoglycosides, and tetracyclines. This suggests potential co-selection mechanisms, posing concerns for both public health and ecological balance.

CTX-M-producing Escherichia coli ST602 carrying a wide resistome in South American wild birds: Another pandemic clone of One Health concern

Wild birds have emerged as novel reservoirs and potential spreaders of antibiotic-resistant priority pathogens, being proposed as sentinels of anthropogenic activities related to the use of antimicrobial compounds. The aim of this study was to investigate the occurrence and genomic features of extended-spectrum β-lactamase (ESBL)-producing bacteria in wild birds in South America. In this regard, we have identified two ESBL (CTX-M-55 and CTX-M-65)-positive Escherichia coli (UNB7 and GP188 strains) colonizing Creamy-bellied Thrush (Turdus amaurochalinus) and Variable Hawk (Geranoaetus polyosoma) inhabiting synanthropic and wildlife environments from Brazil and Chile, respectively. Whole-genome sequence (WGS) analysis revealed that E. coli UNB7 and GP188 belonged to the globally disseminated clone ST602, carrying a wide resistome against antibiotics (β-lactams), heavy metals (arsenic, copper, mercury), disinfectants (quaternary ammonium compounds), and pesticides (glyphosate). Additionally, E. coli UNB7 and GP188 strains harbored virulence genes encoding hemolysin E, type II and III secretion systems, increased serum survival, adhesins and siderophores. SNP-based phylogenomic analysis, using an international genome database, revealed genomic relatedness (19-363 SNP differences) of GP188 with livestock and poultry strains, and genomic relatedness (61-318 differences) of UNB7 with environmental, human and livestock strains (Table S1), whereas phylogeographical analysis confirmed successful expansion of ST602 as a global clone of One Health concern. In summary, our results support that ESBL-producing E. coli ST602 harboring a wide resistome and virulome have begun colonizing wild birds in South America, highlighting a potential new reservoir of critical priority pathogens.

A critical review on the migration and transformation processes of heavy metal contamination in lead-zinc tailings of China

The health risks of lead-zinc (Pb-Zn) tailings from heavy metal (HMs) contamination have been gaining increasing public concern. The dispersal of HMs from tailings poses a substantial threat to ecosystems. Therefore, studying the mechanisms of migration and transformation of HMs in Pb-Zn tailings has significant ecological and environmental significance. Initially, this study encapsulated the distribution and contamination status of Pb-Zn tailings in China. Subsequently, we comprehensively scrutinized the mechanisms governing the migration and transformation of HMs in the Pb-Zn tailings from a geochemical perspective. This examination reveals the intricate interplay between various biotic and abiotic constituents, including environmental factors (EFs), characteristic minerals, organic flotation reagents (OFRs), and microorganisms within Pb-Zn tailings interact through a series of physical, chemical, and biological processes, leading to the formation of complexes, chelates, and aggregates involving HMs and OFRs. These interactions ultimately influence the migration and transformation of HMs. Finally, we provide an overview of contaminant migration prediction and ecological remediation in Pb-Zn tailings. In this systematic review, we identify several forthcoming research imperatives and methodologies. Specifically, understanding the dynamic mechanisms underlying the migration and transformation of HMs is challenging. These challenges encompass an exploration of the weathering processes of characteristic minerals and their interactions with HMs, the complex interplay between HMs and OFRs in Pb-Zn tailings, the effects of microbial community succession during the storage and remediation of Pb-Zn tailings, and the importance of utilizing process-based models in predicting the fate of HMs, and the potential for microbial remediation of tailings.

Assessing the nonlinear association of environmental factors with antibiotic resistance genes (ARGs) in the Yangtze River Mouth, China

The emergence of antibacterial resistance (ABR) is an urgent and complex public health challenge worldwide. Antibiotic resistant genes (ARGs) are considered as a new pollutant by the WHO because of their wide distribution and emerging prevalence. The role of environmental factors in developing ARGs in bacterial populations is still poorly understood. Therefore, the relationship between environmental factors and bacteria should be explored to combat ABR and propose more tailored solutions in a specific region. Here, we collected and analyzed surface water samples from Yangtze Delta, China during 2021, and assessed the nonlinear association of environmental factors with ARGs through a sigmoid model. A high abundance of ARGs was detected. Amoxicillin, phosphorus (P), chromium (Cr), manganese (Mn), calcium (Ca), and strontium (Sr) were found to be strongly associated with ARGs and identified as potential key contributors to ARG detection. Our findings suggest that the suppression of ARGs may be achieved by decreasing the concentration of phosphorus in surface water. Additionally, Group 2A light metals (e.g., magnesium and calcium) may be candidates for the development of eco-friendly reagents for controlling antibiotic resistance in the future.

Response of heavy-metal and antibiotic resistance genes and their related microbe in rice paddy irrigated with treated municipal wastewaters

Paddy irrigation with secondary effluents from municipal wastewater treatment plants (MWTPs) is a well-established practice to alleviate water scarcity. However, the reuse might lead to more complicated contamination caused by interactions between residual antibiotics in effluents and heavy metals in paddy soil. To date, no information is available for the potential effects of dual stress of heavy metals and antibiotics on heavy-metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). Here, this study investigated the response of heavy metal and antibiotic resistance genes, and related microorganisms to the dual threat of antibiotics and heavy metals under the long-term MWTP effluent irrigation for rice paddy using metagenome. The results showed that there was not a negative effect on rice consumption if MWTP effluent was used to irrigate rice for a long time. The concentration of antibiotics could reshape the ARGs and MRG profiles in rice paddy soil. The findings revealed the co-occurrence of ARGs and MRGs in rice paddy soils, thus highlighting the need for simultaneous elimination of antibiotics and heavy metals to effectively reduce ARGs and MRGs. Acn and sul1 genes encoding Iron and sulfonamides resistance mechanisms are the most abundant MRG and ARG, respectively. Network analysis revealed the possibility that IntI1 plays a role in the co-transmission of MRG and ARG to host microbes, and that Proteobacteria are the most dominant hosts for MRG, ARG, and integrons. The presence of antibiotics in irrigated MWTP effluents has been found to stimulate the proliferation of heavy metal and antibiotic resistances by altering soil microbial communities. This study will enhance our comprehension of the co-selection between ARGs and MRGs, as well as reveal the concealed environmental impacts of combined pollution. The obtained results have important implications for food safety and human health in rice.

Geochemical fractionation, bioaccessibility and ecological risk of metallic elements in the weathering profiles of typical skarn-type copper tailings from Tongling, China

Nonferrous metal tailings have long posed a significant threat to the surrounding environment and population. Previous studies have primarily focused on heavy metal pollution in the vicinity of sulfide tailings, while little attention was given to metal mobility and bioavailability within skarn-type tailings profile during weathering. Therefore, this study aimed to investigate the fractionation, bioaccessibility, and ecological risk associated with metallic elements (MEs, including Pb, Cd, Cr, Zn, and Cu) in two representative weathering copper-tailings profiles of Tongling mine (China). This was achieved through the use of mineralogical analyses, BCR extractions (F1: exchangeable, F2: reducible, F3: oxidizable, F4: residual fraction), in-vitro gastrointestinal simulation test (PBET) and risk assessment models. The mineral compositions of two weathering profiles were similar, with quartz and calcite being the dominant minerals, along with minor amounts of siderite, hematite and spangolite. The mean concentration in the tailings profile was approximately 0.31 (Cr), 1.8 (Pb), 12 (Zn), 33 (Cd) or 34 (Cu) times of the local background values (LBVs). The mean content of the bottom weakly-weathering layer in profile was about 0.36 (Cr), 0.91 (Pb), 1.91 (Cd), 2.73 (Zn) or 2.68 (Cu) times of the surface oxide layer, indicating a strong weathering-leaching effect. The average proportion of BCR-F1 fraction for Cd (30.94 %) was the highest among the five MEs, possibly due to its association with calcite. The PBET-extracted fractions for Cd, Zn and Cu were significantly positively correlated with the F1, F2 and F3 fractions of BCR, suggesting that these elements have higher bioavailability/bioaccessibility. The assessment results indicated that Cd posed a higher health risk, while the risk of Cu, Zn, and Pb is relatively low and Cr is safe. In conclusion, this study provides valuable insights into the environmental geochemical behavior and potential risks of MEs in skarn-type non-ferrous metal tailings ponds.

Genotypic detection of β-lactamase-producing Escherichia coli isolates obtained from Seven Crater Lakes of San Pablo, Laguna, Philippines

The extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is becoming a global public health concern. More comprehensive surveillance of β-lactam resistance in E. coli would improve monitoring strategies and control resistance transmission in contaminated environments. This study investigated the prevalence of β-lactamase genes in E. coli isolated from the Seven Crater Lakes in San Pablo, Laguna, Philippines. Water samples from lakes were collected for the isolation of E. coli (n = 846) and molecular characterization by detecting the presence of the uidA gene. The isolates were then tested for the presence of β-lactamase genes using PCR. Among the screened genes, blaAmpC was the most dominant (91%). Other β-lactamase genes such as blaTEM, blaSHV, and blaCTXM were also detected with percentage occurrence of 34, 5, and 1%, respectively. Multiple genes within individual isolates were also observed, wherein blaTEM/AmpC was the most prevalent gene combination. Moreover, a significant negative correlation between blaAmpC with blaSHV and blaCTXM was depicted in this study. Overall, these findings demonstrate the presence of β-lactamase genes in E. coli in the Seven Crater Lakes of San Pablo and can be used in developing effective strategies to control antibiotic resistance in environmental waters.

Mining-related multi-resistance genes in sulfate-reducing bacteria treatment of typical karst nonferrous metal(loid) mine tailings in China

Management of tailings at metal mine smelter sites can reduce the potential hazards associated with exposure to toxic metal(loid)s and residual organic flotation reagents. In addition, microbes in the tailings harboring multi-resistance genes (e.g., tolerance to multiple antimicrobial agents) can cause high rates of morbidity and global economic problems. The potential co-selection mechanisms of antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) during tailings sulfate-reducing bacteria (SRB) treatment have been poorly investigated. Samples were collected from a nonferrous metal mine tailing site treated with an established SRB protocol and were analyzed for selected geochemical properties and high throughput sequencing of 16S rRNA gene barcoding. Based on the shotgun metagenomic analysis, the bacterial domain was dominant in nonferrous metal(loid)-rich tailings treated with SRB for 12 months. KEGGs related to ARGs and MRGs were detected. Thiobacillus and Sphingomonas were the main genera carrying the bacA and mexEF resistance operons, along with Sulfuricella which were also found as the main genera carrying MRGs. The SRB treatment may mediate the distribution of numerous resistance genes. KOs based on the metagenomic database indicated that ARGs (mexNW, merD, sul, and bla) and MRGs (czcABCR and copRS genes) were found on the same contig. The SRB strains (Desulfosporosinus and Desulfotomaculum), and the acidophilic strain Acidiphilium significantly contributed to the distribution of sul genes. The functional metabolic pathways related to siderophores metabolism were largely from anaerobic genera of Streptomyces and Microbacterium. The presence of arsenate reductase, metal efflux pump, and Fe transport genes indicated that SRB treatment plays a key role in the metal(loid)s transformation. Overall, our findings show that bio-treatment is an effective tool for managing ARGs/MRGs and metals in tailings that contain numerous metal(loid) contaminants.

Impact of soil supplemented with pig manure on the abundance of antibiotic resistant bacteria and their associated genes

This study was conducted to evaluate the abundance of antibiotic resistant bacteria and their resistance genes from agriculture soil supplemented with pig manure. Uncultivable soil sample was supplemented with pig manure samples under microcosm experimental conditions and plated on Luria-Bertani (LB) agar incorporated with commercial antibiotics. The supplementation of soil with 15% pig manure resulted in the highest increase in the population of antibiotic resistant bacteria (ARB)/multiple antibiotic resistant bacteria (MARB). Seven genera that included Pseudomonas, Escherichia, Providencia, Salmonella, Bacillus, Alcaligenes and Paenalcaligenes were the cultivable ARB identified. A total of ten antibiotic resistant bacteria genes (ARGs) frequently used in clinical or veterinary settings and two mobile genetic elements (MGEs) (Class 1 and Class 2 integrons) were detected. Eight heavy metal, copper, cadmium, chromium, manganese, lead, zinc, iron, and cobalt were found in all of the manure samples at different concentrations. Tetracycline resistance genes were widely distributed with prevalence of 50%, while aminoglycoside and quinolone-resistance gene had 16% and 13%, respectively. Eighteen ARB isolates carried more than two ARGs in their genome. Class 1 integron was detected among all the 18 ARB with prevalence of 90-100%, while Class 2 integron was detected among 11 ARB. The two classes of integron were found among 10 ARB. Undoubtedly, pig manure collected from farms in Akure metropolis are rich in ARB and their abundance might play a vital role in the dissemination of resistance genes among clinically-relevant pathogens.

A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments

The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, little effort has been made to monitor AMR outside of clinical and veterinary settings. Partially, this is caused by a lack of comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish a baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey, identifying 150 scientific papers containing relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data included 1594 samples distributed across 30 different countries and 12 sample types, in a time span from 2001 to 2020. We found that for most ARGs, the typically reported abundances in human impacted environments fell in an interval from 10-5 to 10-3 copies per 16S rRNA, roughly corresponding to one ARG copy in a thousand bacteria. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.

Metagenomics combined with metabolomics reveals the effect of Enterobacter sp. inoculation on the rhizosphere microenvironment of Bidens pilosa L. in heavy metal contaminated soil

Metagenomics analysis was performed to determine the effects of Enterobacter sp. FM-1 (FM-1) on key genera as well as functional genes in the rhizosphere of Bidens pilosa L. (B. pilosa L.). Moreover, metabolomics was used to reveal the differences among rhizosphere metabolites after FM-1 inoculation. FM-1 inoculation significantly increased the activity of enzymes associated with the carbon cycle in soil; among them, invertase activity increased by 5.52 units compared to a control. Specifically, the relative abundance of beneficial genera increased significantly, such as Lysobacter (0.45-2.58 unit increase) in low-contamination soils (LC) and Pseudomonas (31.17-45.99 unit increase) in high-contamination soils (HC). Comparison of different transformation processes of the C cycle revealed that inoculation of FM-1 increased the abundance of functional genes related to the carbon cycle in LC soil. In contrast, the nitrogen cycling pathway was significantly elevated in both the LC and HC soils. FM-1 inoculation reduced HM resistance gene abundance in the rhizosphere soil of B. pilosa L. in the LC soil. Moreover, FM-1 and B. pilosa L. interactions promoted the secretion of rhizosphere metabolites, in which lipids and amino acids played important roles in the phytoremediation process. Overall, we explored the rhizosphere effects induced by plantmicrobe interactions, providing new insights into the functional microbes and rhizosphere metabolites involved in phytoremediation.

Antibiotic, Heavy Metal, and Biocide Concentrations in a Wastewater Treatment Plant and Its Receiving Water Body Exceed PNEC Limits: Potential for Antimicrobial Resistance Selective Pressure

Although the rise in antimicrobial resistance has been attributed mainly to the extensive and indiscriminate use of antimicrobials such as antibiotics and biocides in humans, animals and on plants, studies investigating the impact of this use on water environments in Africa are minimal. This study quantified selected antibiotics, heavy metals, and biocides in an urban wastewater treatment plant (WWTP) and its receiving water body in Kwazulu-Natal, South Africa, in the context of the predicted no-effect concentrations (PNEC) for the selection of antimicrobial resistance (AMR). Water samples were collected from the WWTP effluent discharge point and upstream and downstream from this point. Heavy metals were identified and quantified using the United States Environmental Protection Agency (US EPA) method 200.7. Biocides and antibiotic residues were determined using validated ultra-high-performance liquid chromatography with tandem mass spectrometry-based methods. The overall highest mean antibiotic, metal and biocide concentrations were observed for sulfamethoxazole (286.180 µg/L), neodymium (Nd; 27.734 mg/L), and benzalkonium chloride (BAC 12) (7.805 µg/L), respectively. In decreasing order per sampling site, the pollutant concentrations were effluent > downstream > upstream. This implies that the WWTP significantly contributed to the observed pollution in the receiving water. Furthermore, most of the pollutants measured recorded values exceeding the recommended predicted no-effect concentration (PNEC) values, suggesting that the microbes in such water environments were at risk of developing resistance due to the selection pressure exerted by these antimicrobials. Further studies are required to establish such a relationship.

Profiles and spatial distributions of heavy metals, microbial communities, and metal resistance genes in sediments from an urban river

The occurrence and propagation of resistance genes due to exposure to heavy metals (HMs) in rivers is an emerging environmental issue. Little is known about resistance genes in microbial communities in river sediments with low HM concentrations. The profiles and spatial distributions of HMs, the microbial community, and metal resistance genes (MRGs) were analyzed in sediment samples from the Zhilong River basin in Yangjiang city, near the Pearl River Delta. Concentrations of copper (Cu), cadmium (Cd), lead (Pb), chromium (Cr), and nickel (Ni) were relatively low compared with those in other urban river sediments in China. HM chemical composition and fractions and the structure of the microbial community varied along the main channel, but the composition and abundance of MRGs were relatively homogeneous. Variations in HMs and microbial communities in mid- to upstream areas were related to the presence of tributaries, whose inputs were one of the major factors affecting HM chemical fractions and genera structure in mainstream sediments. There were no significant correlations (p < 0.05) between HM concentrations, bacterial communities, and the MRG profiles; thus, HM concentrations were not the main factor affecting MRGs in sediments. These results contribute to understanding the propagation of MRGs in urban rivers in developing cities.

Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils

Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.

Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India

Aquatic ecosystems are regarded as a hub of antibiotic and metal resistance genes. River Ganges is a unique riverine system in India with socio-cultural and economic significance. However, it remains underexplored for its microbiome and associated resistomes along its anthropogenically impacted course. The present study utilized a nanopore sequencing approach to depict the microbial community structure in the sediments of the river Ganges harboring antibiotic and metal resistance genes (A/MRGs) in lower stretches known for anthropogenic impact. Comprehensive microbiome analyses revealed resistance genes against 23 different types of metals and 28 classes of antibiotics. The most dominant ARG category was multidrug resistance, while the most prevalent MRGs conferred resistance against copper and zinc. Seasonal differences dismally affected the microbiota of the Ganges. However, resistance genes for fosmidomycin and tetracycline varied with season ANOVA, p < 0.05. Interestingly, 333 and 334 ARG subtypes were observed at all the locations in pre-monsoon and post-monsoon, respectively. The taxa associated with the dominant ARGs and MRGs were Pseudomonas and Burkholderia, which are important nosocomial pathogens. A substantial phage diversity for pathogenic and putrefying bacteria at all locations attracts attention for its use to tackle the dissemination of antibiotic and metal-resistant bacteria. This study suggests the accumulation of antibiotics and metals as the driving force for the emergence of resistance genes and the affiliated bacteria trafficking them. The present metagenomic assessment highlights the need for comprehensive, long-term biological and physicochemical monitoring and mitigation strategies toward the contaminants associated with ARGs and MRGs in this nationally important river.

Does biochar in combination with compost effectively promote phytostabilization of heavy metals in soil under different temperature regimes?

The article presents the effect of a combined amendment, i.e., biochar+compost (BC), on the process of Cd, Cu, Ni, Pb and Zn immobilization in soil cultivated with L. perenne under freezing and thawing conditions (FTC). In particular, the speciation analysis of the examined elements in phytostabilized soils based on their response using the sequential extraction, and the variability of the soil microbiome using 16S rRNA gene amplicon sequencing were systematically assessed. Metal stability in soils was evaluated by the reduced distribution index (Ir). Plants were grown in pots for 52 days under greenhouse conditions. After termination, phytostabilization was continued in a temperature chamber for 64 days to provide FTC. As a result, it was noted that biomass yield of L. perenne was promoted by BC (39 % higher than in the control pots) and reduced by FTC (45 % lower than in the BC-enriched soil not exposed to FTC). An efficacious level of phytostabilization, i.e., higher content of heavy metals in plant roots, was found in the BC-enriched soil, regardless of the changes in soil temperature conditions. BC improved soil pH before applying FTC more than after applying FTC. BC had the greatest impact on increasing Cu stability by redistributing it from the F1 and F2 fractions to the F3 and F4 fractions. For most metals, phytostabilization under FTC resulted in an increase in the proportion of the F1 fraction and a decrease in its stability. Only for Pb and Zn, FTC had greater impact on their stability than BC addition. In all soil samples, the core genera with about 2-3 % abundances were Sphingomonas sp. and Mycobacterium sp. FTC favored the growth of Bacteroidetes and Proteobacteria in soil. Microbial taxa that coped well with FTC but only in the absence of BC were Rhodococcus, Alkanindiges sp., Flavobacterium sp., Williamsia sp. Thermomonas sp.

River sediment microbial community composition and function impacted by thallium spill

Thallium (Tl) is widely used in various industries, which increases the risk of leakage into the environment. Since Tl is highly toxic, it can do a great harm to human health and ecosystem. In order to explore the response of freshwater sediment microorganisms to sudden Tl spill, metagenomic technique was used to elucidate the changes of microbial community composition and functional genes in river sediments. Tl pollution could have profound impacts on microbial community composition and function. Proteobacteria remained the dominance in contaminated szediments, indicating that it had a strong resistance to Tl contamination, and Cyanobacteria also showed a certain resistance. Tl pollution also had a certain screening effect on resistance genes and affected the abundance of resistance genes. Metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) were enriched at the site near the spill site, where Tl concentration was relatively low among polluted sites. When Tl concentration was higher, the screening effect was not obvious and the resistance genes even became lower. Moreover, there was a significant correlation between MRGs and ARGs. In addition, co-occurrence network analysis showed that Sphingopyxis had the most links with resistance genes, indicating that it was the biggest potential host of resistance genes. This study provided new insight towards the shifts in the composition and function of microbial communities after sudden serious Tl contamination.

Efflux Pump Inhibitors in Controlling Antibiotic Resistance: Outlook under a Heavy Metal Contamination Context

Multi-drug resistance to antibiotics represents a growing challenge in treating infectious diseases. Outside the hospital, bacteria with the multi-drug resistance (MDR) phenotype have an increased prevalence in anthropized environments, thus implying that chemical stresses, such as metals, hydrocarbons, organic compounds, etc., are the source of such resistance. There is a developing hypothesis regarding the role of metal contamination in terrestrial and aquatic environments as a selective agent in the proliferation of antibiotic resistance caused by the co-selection of antibiotic and metal resistance genes carried by transmissible plasmids and/or associated with transposons. Efflux pumps are also known to be involved in either antibiotic or metal resistance. In order to deal with these situations, microorganisms use an effective strategy that includes a range of expressions based on biochemical and genetic mechanisms. The data from numerous studies suggest that heavy metal contamination could affect the dissemination of antibiotic-resistant genes. Environmental pollution caused by anthropogenic activities could lead to mutagenesis based on the synergy between antibiotic efficacy and the acquired resistance mechanism under stressors. Moreover, the acquired resistance includes plasmid-encoded specific efflux pumps. Soil microbiomes have been reported as reservoirs of resistance genes that are available for exchange with pathogenic bacteria. Importantly, metal-contaminated soil is a selective agent that proliferates antibiotic resistance through efflux pumps. Thus, the use of multi-drug efflux pump inhibitors (EPIs) originating from natural plants or synthetic compounds is a promising approach for restoring the efficacy of existing antibiotics, even though they face a lot of challenges.

Heavy Metal Pollution Impacts Soil Bacterial Community Structure and Antimicrobial Resistance at the Birmingham 35th Avenue Superfund Site

Heavy metals (HMs) are known to modify bacterial communities both in the laboratory and in situ. Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease. IMPORTANCE Heavy metals cross-select for antimicrobial resistance in laboratory experiments, but few studies have documented this effect in polluted soils. Moreover, despite decades of awareness of heavy metal contamination at the EPA Superfund site in North Birmingham, Alabama, this is the first analysis of the impact of this pollution on the soil microbiome. Specifically, this work advances the understanding of the relationship between heavy metals, microbial diversity, and patterns of antibiotic resistance in North Birmingham soils. Our results suggest that polluted soils carry a risk of increased exposure to antibiotic-resistant infections in addition to the direct health consequences of heavy metals. Our work provides important information relevant to both political and scientific efforts to advance environmental justice for the communities that call Superfund neighborhoods home.

Chimeric MerR-Family Regulators and Logic Elements for the Design of Metal Sensitive Genetic Circuits in Bacillus subtilis

Whole-cell biosensors are emerging as promising tools for monitoring environmental pollutants such as heavy metals. These sensors constitute a genetic circuit comprising a sensing module and an output module, such that a detectable signal is produced in the presence of the desired analyte. The MerR family of metal-responsive regulators offers great potential for the construction of metal sensing circuits, due to their high sensitivity, tight transcription control, and large diversity in metal-specificity. However, the sensing diversity is broadest in Gram-negative systems, while chassis organisms are often selected from Gram-positive species, particularly sporulating bacilli. This can be problematic, because Gram-negative biological parts, such as promoters, are frequently observed to be nonfunctional in Gram-positive hosts. Herein, we combined construction of synthetic genetic circuits and chimeric MerR regulators, supported by structure-guided design, to generate metal-sensitive biosensor modules that are functional in the biotechnological work-horse species Bacillus subtilis. These chimeras consist of a constant Gram-positive derived DNA-binding domain fused to variable metal binding domains of Gram-negative origins. To improve the specificity of the whole-cell biosensor, we developed a modular "AND gate" logic system based on the B. subtilis two-subunit σ-factor, SigO-RsoA, designed to maximize future use for synthetic biology applications in B. subtilis. This work provides insights into the use of modular regulators, such as the MerR family, in the design of synthetic circuits for the detection of heavy metals, with potentially wider applicability of the approach to other systems and genetic backgrounds.

Sulfur: a neglected driver of the increased abundance of antibiotic resistance genes in agricultural reclaimed subsidence land located in coal mines with high phreatic water levels

Due to the shallow burial of groundwater in coal mines with a high phreatic water level, a large area of subsidence lakes is formed after the mine collapses. Agricultural and fishery reclamation activities have been carried out, which introduced antibiotics and exacerbated the contamination of antibiotic resistance genes (ARGs), but this has received limited attention. This study analyzed ARG occurrence in reclaimed mining areas, the key impact factors, and the underlying mechanism. The results show that sulfur is the most critical factor impacting the abundance of ARGs in reclaimed soil, which is due to changes in the microbial community. The species and abundance of ARGs in the reclaimed soil were higher than those in the controlled soil. The relative abundances of most ARGs increased with the depth of reclaimed soil (from 0 to 80 cm). In addition, the microbial structures of the reclaimed and controlled soils were significantly different. Proteobacteria, was the most dominant microbial phylum in the reclaimed soil. This difference is likely related to the high abundance of sulfur metabolism functional genes in the reclaimed soil. Correlation analysis showed that the differences in ARGs and microorganisms in the two soil types were highly correlated with the sulfur content. High levels of sulfur promoted the proliferation of sulfur-metabolizing microbial populations such as Proteobacteria and Gemmatimonadetes in the reclaimed soils. Remarkably, these microbial phyla were the main antibiotic-resistant bacteria in this study, and their proliferation created conditions for the enrichment of ARGs. Overall, this study underscores the risk of the abundance and spread of ARGs driven by high-level sulfur in reclaimed soils and reveals the mechanisms.

Metals to combat antimicrobial resistance

Bacteria, similar to most organisms, have a love-hate relationship with metals: a specific metal may be essential for survival yet toxic in certain forms and concentrations. Metal ions have a long history of antimicrobial activity and have received increasing attention in recent years owing to the rise of antimicrobial resistance. The search for antibacterial agents now encompasses metal ions, nanoparticles and metal complexes with antimicrobial activity ('metalloantibiotics'). Although yet to be advanced to the clinic, metalloantibiotics are a vast and underexplored group of compounds that could lead to a much-needed new class of antibiotics. This Review summarizes recent developments in this growing field, focusing on advances in the development of metalloantibiotics, in particular, those for which the mechanism of action has been investigated. We also provide an overview of alternative uses of metal complexes to combat bacterial infections, including antimicrobial photodynamic therapy and radionuclide diagnosis of bacterial infections.

Co-occurrence of antibiotic and metal resistance in long-term sewage sludge-amended soils: influence of application rates and pedo-climatic conditions

Urban sewage sludge (USS) is increasingly being used as an alternative organic amendment in agriculture. Because USS originates mostly from human excreta, partially metabolized pharmaceuticals have also been considered in risk assessment studies after reuse. In this regard, we investigated the cumulative effect of five annual USS applications on the spread of antibiotic-resistant bacteria (ARB) and their subsequent resistance to toxic metals in two unvegetated soils. Eventually, USS contained bacterial strains resistant to all addressed antibiotics with indices of resistance varying between 0.25 for gentamicin to 38% for ampicillin and azithromycin. Sludge-amended soils showed also the emergence of resistome for all tested antibiotics compared to non-treated controls. In this regard, the increase of sludge dose generally correlated with ARB counts, while soil texture had no influence. On the other hand, the multi-antibiotic resistance (MAR) of 52 isolates selected from USS and different soil treatments was investigated for 10 most prescribed antibiotics. Nine isolates showed significant MAR index (≥ 0.3) and co-resistance to Cd, As and Be as well. However, events including an extreme flash flood and the termination of USS applications significantly disrupted ARB communities in all soil treatments. In any case, this study highlighted the risks of ARB spread in sludge-amended soils and a greater concern with the recent exacerbation of antibiotic overuse following COVID-19 outbreak.

Heavy metal co-resistance with antibiotics amongst bacteria isolates from an open dumpsite soil

Heavy metal co-resistance with antibiotics appears to be synergistic in bacterial isolates via similar mechanisms. This synergy has the potential to amplify antibiotics resistance genes in the environment which can be transferred into clinical settings. The aim of this study was to assess the co-resistance of heavy metals with antibiotics in bacteria from dumpsite in addition to physicochemical analysis. Sample collection, physicochemical analysis, and enumeration of total heterotrophic bacteria counts (THBC) were all carried out using standard existing protocols. Identified bacteria isolates were subjected to antibiotics sensitivity test using the Kirby Bauer disc diffusion technique and the resulting multidrug resistant (MDR) isolates were subjected to heavy metal tolerance test using agar dilution technique with increasing concentrations (50, 100, 150, 200 and to 250 μg/ml) of our study heavy metals. THBC ranged from 6.68 to 7.92 × 105 cfu/g. Out of the 20 isolates subjected to antibiotics sensitivity, 50% (n = 10) showed multiple drug resistance and these were B. subtilis, B. cereus, C. freundii, P. aeruginosa, Enterobacter sp, and E. coli (n = 5). At the lowest concentration (50 μg/ml), all the MDR isolates tolerated all the heavy metals, but at 250 μg/ml, apart from cadmium and lead, all test isolates were 100% sensitive to chromium, vanadium and cobalt. The control isolate was only resistant to cobalt and chromium at 50 μg/ml, but sensitive to other heavy metals at all concentrations The level of co-resistance shown by these isolates is a call for concern.

Draft genome of Raoultella planticola, a high lead resistance bacterium from industrial wastewater

Isolation of heavy metals-resistant bacteria from their original habitat is a crucial step in bioremediation. Six lead (Pb) resistant bacterial strains were isolated and identified utilizing 16S rRNA to be Enterobacter ludwigii FACU 4, Shigella flexneri FACU, Microbacterium paraoxydans FACU, Klebsiella pneumoniae subsp. pneumonia FACU, Raoultella planticola FACU 3 and Staphylococcus xylosus FACU. It was determined that all these strains had their Minimum inhibitory concentration (MIC) to be 2500 ppm except R. planticola FACU 3 has a higher maximum tolerance concentration (MTC) up to 2700 ppm. We evaluated the survival of all six strains on lead stress, the efficiency of biosorption and lead uptake. It was found that R. planticola FACU 3 is the highest MTC and S. xylosus FACU was the lowest MTC in this evaluation. Therefore, transmission electron microscopy (TEM) confirmed the difference between the morphological responses of these two strains to lead stress. These findings led to explore more about the genome of R. planticola FACU 3 using illumine Miseq technology. Draft genome sequence analysis revealed the genome size of 5,648,460 bp and G + C content 55.8% and identified 5526 CDS, 75 tRNA and 4 rRNA. Sequencing technology facilitated the identification of about 47 genes related to resistance to many heavy metals including lead, arsenic, zinc, mercury, nickel, silver and chromium of R. planticola FACU 3 strain. Moreover, genome sequencing identified plant growth-promoting genes (PGPGs) including indole acetic acid (IAA) production, phosphate solubilization, phenazine production, trehalose metabolism and 4-hydroxybenzoate production genes and a lot of antibiotic-resistant genes.

Development of a GIS-based knowledge hub for contaminants of emerging concern in South African water resources using open-source software: Lessons learnt

With population growth and dwindling freshwater sources, protecting such sources has come to the forefront of water resource management. Historically, society's response to a problem is based on funding availability, current threat, and public outcry. Achieving this is largely dependent on the knowledge of the factors that are resulting in compromised water sources. These factors are constantly changing as novel contaminants are introduced into surface water sources. As we are in the information age, the interest in contaminants of emerging concern (CEC) is gaining ground. Whilst research is being conducted to identify contaminants in South African water sources, the research outputs and available information is not collated and presented to the science community and stakeholders in readily available formats and platforms. Current research outcomes need to be made known to regulators in order to develop environmental laws. By using fourth industrial revolution technology, we were able to collate available data in literature and display these in a user-friendly online format to regulatory bodies as well as researchers. A standardized excel spreadsheet was developed and uploaded to a PostgreSQL, running a PostGIS extension and was then processed in the GeoServer to allow for visualization on an interactive map which can be continuously updated. The near real-time access to information will reduce the possibility of duplication of research efforts, enhance collaboration in the discipline, and act as a CEC early warning system.

Metal-containing landfills as a source of antibiotic tolerance

To unveil the potential effect of metal presence to antibiotic tolerance proliferation, four sites of surface landfills containing tailings from metal processing in Slovakia (Hnúšťa, Hodruša, Košice) and Poland (Tarnowskie Góry) were investigated. Tolerance and multitolerance to selected metals (Cu, Ni, Pb, Fe, Zn, Cd) and antibiotics (ampicillin, tetracycline, chloramphenicol, and kanamycin) and interrelationships between them were evaluated. A low bacterial diversity (Shannon-Wiener index from 0.83 to 2.263) was detected in all sampling sites. Gram-positive bacteria, mostly belonging to the phylum Actinobacteria, dominated in three of the four sampling sites. The recorded percentages of tolerant bacterial isolates varied considerably for antibiotics and metals from 0 to 57% and 0.8 to 47%, respectively, among the sampling sites. Tolerances to chloramphenicol (45-57%) and kanamycin (32-45%) were found in three sites. Multitolerance to several metals and antibiotics in the range of 24 to 48% was recorded for three sites. A significant positive correlation (p < 0.05) for the co-occurrence of tolerance to each studied metal and at least one of the antibiotics was observed. Exposure time to the metal (landfill duration) was an important factor for the development of metal- as well as antibiotic-tolerant isolates. The results show that metal-contaminated sites represent a significant threat for human health not only for their toxic effects but also for their pressure to antibiotic tolerance spread in the environment.

Evaluation of cadmium tolerance and remediated efficacy of wild and mutated Enterobacter species isolated from potassium nitrate (KNO₃) processing unit contaminated soil

The purpose of this study was to find the most cadmium (Cd²⁺) tolerant and remediated bacteria isolate from KNO₃ processing unit contaminated soil. One isolate out of 19 isolates possessed excellent Cd²⁺ tolerance than others, which was recognized as Enterobacter hormaechei SFC3 through molecular characterization (16S rRNA sequencing). The identified E. hormaechei SFC3 contained 55% and 45% of GC and AT content, respectively. The wild and acridine orange mutated E. hormaechei SFC3 exhibited excellent resistance to Cd²⁺ up to the concentration of 1500 μg mL^-1. Furthermore, the wild E. hormaechei SFC3 and mutated E. hormaechei SFC3 showed 82.47% and 90.21% of Cd²⁺ remediation on 6th days of treatment respectively. Similarly, the Cd²⁺ tolerant wild and mutated E. hormaechei SFC3 showed considerable resistance to all the tested antibiotics. The findings indicate that E. hormaechei SFC3 isolated from KNO₃ processing unit contaminated soil is a promising candidate for microbial remediation of Cd²⁺ contamination.

Metagenomic insight into the distribution of metal resistance genes within cascade reservoir waters: Synergic impacts of geographic variation and anthropogenic pollution

Metal resistance genes (MRGs) are potential bio-indicators to diagnose contamination stress on riverine ecosystems. Within reservoir systems, river damming weakens hydrodynamic condition and enriches metal contaminants. But, little is known about the synergic impacts of geographic variation and anthropogenic pollution on MRGs. In this study, the abundance, composition and microbes of MRGs in four cascade reservoirs along the Jinsha River, southwestern China were investigated via high-throughput metagenomics. The results showed significant enrichment of chromium, cadmium and lead in Ludila and Xiluodu reservoirs with moderate ecological risks based on the criteria of drinking water quality and aquatic life protection. Nevertheless, at watershed scale, these metals played little role in up-regulating MRGs abundance owing to the limited toxic stress on microbes. Accordingly, geographic variation showed stronger impacts on MRGs composition than metals as revealed by the distance-decay relationship (Pearson correlation, r_geo = 0.24-0.57, r_metal = 0.10-0.41) and co-occurrence network (Node degree to MRGs subtype, n_geo = 180, n_metal = 6). River damming, as an artificial isolation of geographic space, significantly affected MRGs composition. The longer operation history, smaller storage capacity and higher regulation frequency caused the higher dissimilarity of MRGs composition between the reservoir's upstream and downstream areas. In conclusion, the metal pollution level is a prerequisite regulating MRGs; while under the lowly-polluted conditions, geographic variation had stronger impacts on MRGs than metal pollution via altered assembly of microbial communities. This study provides an important guidance for the future environmental management and ecological protection of river-reservoir ecosystems.

Bioremediation of hexavalent chromium by transformation of Escherichia coli DH5α with chromate reductase (ChrR) genes of Pseudomonas putida isolated from tannery effluent

AIMS

Hexavalent chromium Cr(VI), a toxic heavy metal, is a serious pollutant of tannery effluent, and its accumulation in soil and water causes severe environmental concerns of increasing public health issues. The present study focus on the isolation and identification of chromium-reducing bacteria collected from the tannery industry in Dindigul, Tamil Nadu. Chromium-reducing bacteria Pseudomonas putida were identified by 16S rRNA sequencing followed by BLAST search. The plasmid with Cr(VI) reductase gene was isolated from Pseudomonas putida and transferred to E. coli DH5α for further studies.

METHODS AND RESULTS

The bacterial cultures were kept under controlled conditions for 72 h to observe the growth rates and bacterial resistance to chromium. When strains wild type and transformant E. coli DH5α were grown in chromium supplemented media revealed significant growth, but strains cured type Pseudomonas putida and E. coli DH5α were minimum growth. The Cr(VI) reduction employed by transformant E. coli DH5α and wild Pseudomonas putida was 42.52 ± 1.48% and 44.46 ± 0.55%, respectively. The culture supernatant of the wild Pseudomonas putida and transformant E. coli DH5α showed an increased reduction of Cr(VI) compared to cell extract supernatant and cell debris due to the extracellular activity of chromium reductase has been responsible for Cr(VI) reduction. Besides, the chromium reductase gene was confirmed in the isolated Pseudomonas putida and transformant E. coli DH5α.

CONCLUSIONS

Transformant bacteria could employ an alternative method for heavy metal detoxification in contaminated environments like tannery effluent and mining processes.

Cytobacillus pseudoceanisediminis sp. nov., A Novel Facultative Methylotrophic Bacterium with High Heavy Metal Resistance Isolated from the Deep Underground Saline Spring

In this study, we present the characterization of the BNO1^T bacterial strain isolated from the deep subsurface saline spring at the Baksan Neutrino Observatory INR RAS (Kabardino-Balkaria, Russia). The complete genome sequence of the strain BNO1^T is 5,347,902 bp, with a GC content 41 and 49%. The cell wall peptidoglycan contains meso-diaminopimelic acid. The major isoprenoid quinone is MK-7 and the polar lipids are diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The major fatty acids are anteiso-C_15:0 (23.34%), iso-C_15:0 (20.10%), C_16:0 (11.96%), iso-C_16:0 (10.88%), and anteiso-C_17:0 (10.79%). The 16S rRNA gene sequence clearly demarcated the strain as belonging to Cytobacillus genera. Based on the phylogenetic analysis, ANI (average nucleotide identity) and dDDH (digital DNA-DNA hybridization) assessments we propose to assign the strain BNO1^T and other related strains to new species and to name it Cytobacillus pseudoceanisediminis sp. nov. (The values of ANI and dDDH between BNO1^T and Cytobacillus oceanisediminis CGMCC 1.10115 ^T are 80.65% and 24.7%, respectively; values of ANI and dDDH between BNO1^T and Cytobacillus firmus NCTC 10335 ^T are 89% and 38%, respectively). Genomic analysis of strain BNO1^T revealed pathways for C1 compounds oxidation and two pathways for C1 compounds assimilation: serine and ribulose monophosphate pathways. In addition, strain BNO1^T contains a plasmid (342,541 bp) coding multiple genes involved in heavy metal ion balance. Moreover, heavy metal toxicity testing confirmed the high potential of the strain BNO1^T as a source of metal resistance genes and enzymes. The type strain is BNO1^T (= BIM B-1921 ^T = VKM B-3664 ^T).

Developing erythromycin resistance gene by heavy metals, Pb, Zn, and Co, in aquatic ecosystems

Industrial development is the main cause of environmental pollution with various substances such as antibiotics and heavy metals. Many heavy metals with antimicrobial properties could contribute to antibiotic resistance and the emergence of antibiotic resistance genes due to the co-selection phenomenon. The aim of this study was to investigate the concurrent presence and correlation between several heavy metals and the erythromycin resistance genes in six aquatic ecosystems of Iran. Distribution and assessment of 11 erythromycin resistance genes were investigated using specific primers and online enrichment and triple-quadrupole LC-MS/MS. The concentration of heavy metals was measured using inductively coupled plasma atomic emission spectroscopy by Thermo electron corporation. Principal component analysis was performed to globally compare and to determine the similarities and differences among different aquatic ecosystems in different parts of the world in terms of the concentration of zinc and lead in their water. The results of the simple logistic regression analysis for the correlation between erythromycin resistance genes and heavy metals concentrations revealed the most significant correlation between erythromycin resistance genes and Pb concentration, followed by Co and Zn concentrations.

Coupling of metataxonomics and culturing improves bacterial diversity characterization and identifies a novel Rhizorhapis sp. with metal resistance potential in a multi-contaminated waste sediment

Long-term contaminated environments have been recognized as potential hotspots for bacterial discovery in taxonomic and functional terms for bioremediation purposes. Here, bacterial diversity in waste sediment collected from a former industrial dumpsite and contaminated with petroleum hydrocarbon and heavy metals was investigated through the parallel application of culture-independent (16S rRNA gene amplicon sequencing) and -dependent (plate culturing followed by colony picking and identification of isolates by 16S rRNA gene Sanger sequencing) approaches. The bacterial diversities retrieved by both approaches greatly differed. Bacteroidetes and Proteobacteria were dominant in the culture-independent community, while Firmicutes and Actinobacteria were the main culturable groups. Only 2.7% of OTUs (operational taxonomic units) in the culture-independent dataset were cultured. Most of the culturable OTUs were absent or in very low abundances in the culture-independent dataset, revealing that culturing is a useful tool to study the rare bacterial biosphere. One culturable OTUs (comprising only the isolate SPR117) was identified as a potential new species in the genus Rhizorhapis (class Alphaproteobacteria) and was selected for further characterization. Phytopathogenicity tests showed that Rhizorhapis sp. strain SPR117 (ATCC TSD-228) is not pathogenic to lettuce, despite the only described species in this genus, Rhizorhapis suberifaciens, is causal agent of the lettuce corky root disease. The genome of the strain SPR117 was sequenced, assembled in 256 contigs, with a length of 4,419,522 bp and a GC content of 59.9%, and its further annotation revealed the presence of genes related to the resistance to arsenic, copper, iron, and mercury, among other metals. Therefore, the coupling of metataxonomics and culturing is a useful tool to obtain not only an improved description of bacterial communities in contaminated environments, but also to isolate microorganisms with bioremediation potential.

Comparative genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium from Irish hospitals

Introduction. Enterococcus faecium has emerged as an important nosocomial pathogen, which is increasingly difficult to treat due to the genetic acquisition of vancomycin resistance. Ireland has a recalcitrant vancomycin-resistant bloodstream infection rate compared to other developed countries.

Hypothesis/Gap statement. Vancomycin resistance rates persist amongst E. faecium isolates from Irish hospitals. The evolutionary genomics governing these trends have not been fully elucidated.

Methodology. A set of 28 vancomycin-resistant isolates was sequenced to construct a dataset alongside 61 other publicly available Irish genomes. This dataset was extensively analysed using in silico methodologies (comparative genomics, pangenomics, phylogenetics, genotypics and comparative functional analyses) to uncover distinct evolutionary, coevolutionary and clinically relevant population trends.

Results. These results suggest that a stable (in terms of genome size, GC% and number of genes), yet genetically diverse population (in terms of gene content) of E. faecium persists in Ireland with acquired resistance arising via plasmid acquisition (vanA) or, to a lesser extent, chromosomal recombination (vanB). Population analysis revealed five clusters with one cluster partitioned into four clades which transcend isolation dates. Pangenomic and recombination analyses revealed an open (whole genome and chromosomal specific) pangenome illustrating a rampant evolutionary pattern. Comparative resistomics and virulomics uncovered distinct chromosomal and mobilomal propensity for multidrug resistance, widespread chromosomal point-mutation-mediated resistance and chromosomally harboured arsenals of virulence factors. Interestingly, a potential difference in biofilm formation strategies was highlighted by coevolutionary analysis, suggesting differential biofilm genotypes between vanA and vanB isolates.

Conclusions. These results highlight the evolutionary history of Irish E. faecium isolates and may provide insight into underlying infection dynamics in a clinical setting. Due to the apparent ease of vancomycin resistance acquisition over time, susceptible E. faecium should be concurrently reduced in Irish hospitals to mitigate potential resistant infections.

Ecological Responses of Maize Rhizosphere to Antibiotics Entering the Agricultural System in an Area with High Arsenicals Geological Background

Metal(loid)s can promote the spread and enrichment of antibiotic resistance in the environmental ecosystem through a co-selection effect. Little is known about the ecological effects of entering antibiotics into the environment with long-term metal(loid)s' resistance profiles. Here, cow manure containing oxytetracycline (OTC) or sulfadiazine (SA) at four concentrations (0 (as control), 1, 10, and 100 mg/kg) was loaded to a maize cropping system in an area with high a arsenicals geological background. Results showed that exogenous antibiotics entering significantly changed the nutrient conditions, such as the concentration of nitrate nitrogen, ammonium nitrogen, and available phosphorus in the maize rhizosphere soil, while total arsenic and metals did not display any differences in antibiotic treatments compared with control. Antibiotics exposure significantly influenced nitrate and nitrite reductase activities to reflect the inhibition of denitrification rates but did not affect the soil urease and acid phosphatase activities. OTC treatment also did not change soil dehydrogenase activities, while SA treatment posed promotion effects, showing a tendency to increase with exposure concentration. Both the tested antibiotics (OTC and SA) decreased the concentration of arsenite and arsenate in rhizosphere soil, but the inhibition effects of the former were higher than that of the latter. Moreover, antibiotic treatment impacted arsenite and arsenate levels in maize root tissue, with positive effects on arsenite and negative effects on arsenate. As a result, both OTC and SA treatments significantly increased bioconcentration factors and showed a tendency to first increase and then decrease with increasing concentration. In addition, the treatments decreased translocation capacity of arsenic from roots to shoots and showed a tendency to increase translocation factors with increasing concentration. Microbial communities with arsenic-resistance profiles may also be resistant to antibiotics entering.

Arsenic resistance and horizontal gene transfer are associated with carbon and nitrogen enrichment in bacteria

Coastal waters are confluences receiving large amounts of point and non-point sources of pollution. An attempt was made to explore microbial community interactions in response to carbon, nitrogen and metal pollution. Additionally, experiments were designed to analyze the influence of these factors on horizontal gene transfer (HGT). Shift in bacterial diversity dynamics by arsenic stress and nutrient addition in coastal waters was explored by metagenomics of microcosm setups. Phylogenetic analysis revealed equal distribution of Gammaproteobacteria (29%) and Betaproteobacteria (28%) in control microcosm. This proportional diversity from control switched to unique distribution of Gammaproteobacteria (44.5%)> Flavobacteria (17.7%)> Bacteriodia (11.92%)> Betaproteobacteria (11.52%) in microcosm supplemented with carbon, nitrogen and metal (C + N + M). Among metal-stressed systems, alpha diversity analysis indicated highest diversity of genera in C + N + M followed by N + M > C+M> metal alone. Arsenic and ampicillin sensitive E. coli XL1 blue and environmental strains (Vibrio tubiashii W85 and E. coli W101) were tested for efficiency of uptake of plasmid (P) pUCminusMCS (arsB^Ramp^R) under varying stress conditions. Transformation experiments revealed that combined effect of carbon, nitrogen and metal on horizontal gene transfer (HGT) was significantly higher (p < 0.01) than individual factors. The effect of carbon on HGT was proved to be superior to nitrogen under metal stressed conditions. Presence of arsenic in experimental setups (P + M, P + N + M and P + C + M) enhanced the HGT compared to non-metal counterparts supplemented with carbon or nitrogen. Arsenic resistant bacterial isolates (n = 200) were tested for the ability to utilize various carbon and nitrogen substrates and distinct positive correlation (p < 0.001) was found between arsenic resistance and utilization of urea and nitrate. However, evident positive correlation was not found between carbon sources and arsenic resistance. Our findings suggest that carbon and nitrogen pollution in aquatic habitats under arsenic stress determine the microbial community dynamics and critically influence uptake of genetic material from the surrounding environment.