Bacterial metal(loid) resistance genes (MRGs) and their variation and application in environment: A review

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.

The good, the bad, and the ugly of metals as antimicrobials

We are now moving into the antimicrobial resistance (AMR) era where more antibiotic resistant bacteria are now the majority, a problem brought on by both misuse and over use of antibiotics. Unfortunately, the antibiotic development pipeline dwindled away over the past decades as they are not very profitable compounds for companies to develop. Regardless researchers over the past decade have made strides to explore alternative options and out of this we see revisiting historical infection control agents such as toxic metals. From this we now see a field of research exploring the efficacy of metal ions and metal complexes as antimicrobials. Such antimicrobials are delivered in a variety of forms from metal salts, alloys, metal complexes, organometallic compounds, and metal based nanomaterials and gives us the broad term metalloantimicrobials. We now see many effective formulations applied for various applications using metals as antimicrobials that are effective against drug resistant strains. The purpose of the document here is to step aside and begin a conversation on the issues of use of such toxic metal compounds against microbes. This critical opinion mini-review in no way aims to be comprehensive. The goal here is to understand the benefits of metalloantimicrobials, but also to consider strongly the disadvantages of using metals, and what are the potential consequences of misuse and overuse. We need to be conscious of the issues, to see the entire system and affect through a OneHealth vision.

Heavy metal tolerance and detoxification mechanism mediated by heavy metal resistance genes in compost habitat

Heavy metal pollution from compost is one of the most concerned environmental problems, which poses a threat to the ecosystem and human health. This study aims to reveal the heavy metal tolerance and detoxification mechanism mediated by heavy metal resistance genes (HMRGs) in compost habitat through metagenomics combined with chemical speciation analysis of heavy metals. The results showed that there were 37 HMRGs corresponding to 7 common heavy metal(loid)s in composting, and they had the ability to transform heavy metals into stable or low-toxic speciation by regulating enzyme transport, redox, methylation, etc. This study summarized the heavy metal metabolism pathway mediated by HMRGs, providing a new perspective for understanding the transformation of heavy metals in the composting process.

Modifying humus-phosphorus-arsenic interactions in sludge composting: The strengthening of phosphorus availability and arsenic efflux detoxification mechanisms

Arsenic (As) in sewage sludge poses a significant threat to environmental and human health, which has attracted widespread attention. This study investigated the value of adding sodium percarbonate (SP) on phosphorus (P) availability and As efflux detoxification through HS-P-As interactions. Due to the unique structure of humus (HS) and the similar chemical properties of P and As, the conditions for HS-P-As interaction are provided. This study discussed the content, morphology and microbial communities of HS, P and As by using metagenomic and correlation analysis. The results showed that the humification index in the experiment group (SPC) was 2.34 times higher than that in the control group (CK). The available phosphorus (AP) content of SPC increased from 71.09 mg/kg to 126.14 mg/kg, and SPC was 1.11 times that of CK. The relative abundance of ACR3/ArsB increased. Pst, Actinomyces and Bacillus commonly participated in P and As conversion. The correlation analysis revealed that the humification process was enhanced, the AP was strengthened, and the As was efflux detoxified after SP amendment. All in all, this study elucidated the key mechanism of HS-P-As interaction and put forward a new strategy for sewage sludge resource utilization and detoxification.

Role of phosphate in microalgal-bacterial symbiosis system treating wastewater containing heavy metals

Phosphorus is one of the important factors to successfully establish the microalgal-bacterial symbiosis (MABS) system. The migration and transformation of phosphorus can occur in various ways, and the effects of phosphate on the MABS system facing environmental impacts like heavy metal stress are often ignored. This study investigated the roles of phosphate on the response of the MABS system to zinc ion (Zn2+). The results showed that the pollutant removal effect in the MABS system was significantly reduced, and microbial growth and activity were inhibited with the presence of Zn2+. When phosphate and Zn2+ coexisted, the inhibition effects of pollutants removal and microbial growth rate were mitigated compared to that of only with the presence of Zn2+, with the increasing rates of 28.3% for total nitrogen removal, 48.9% for chemical oxygen demand removal, 78.3% for chlorophyll-a concentration, and 13.3% for volatile suspended solids concentration. When phosphate was subsequently supplemented in the MABS system after adding Zn2+, both pollutants removal efficiency and microbial growth and activity were not recovered. Thus, the inhibition effect of Zn2+ on the MABS system was irreversible. Further analysis showed that Zn2+ preferentially combined with phosphate could form chemical precipitate, which reduced the fixation of MABS system for Zn2+ through extracellular adsorption and intracellular uptake. Under Zn2+ stress, the succession of microbial communities occurred, and Parachlorella was more tolerant to Zn2+. This study revealed the comprehensive response mechanism of the co-effects of phosphate and Zn2+ on the MABS system, and provided some insights for the MABS system treating wastewater containing heavy metals, as well as migration and transformation of heavy metals in aquatic ecosystems.

A critical review on bioremediation technologies of metal(loid) tailings: Practice and policy

Globally, most high-grade ores have already been exploited. Contemporary mining tends to focus on the extraction of lower-grade ores thereby leaving large stored tailings open to the environment. As a result, current mines have emerged as hotspots for the migration of metal(loid)s and resistance genes, thereby potentially contributing to a looming public health crisis. Therefore, the management and remediation of tailings are the most challenging issues in environmental ecology. Bioremediation, a cost-effective solution for the treatment of multi-element mixed pollution (co-contamination), shows promise for the restoration of mine tailings. This review focuses on the bioremediation technologies developed to untangle the issues of non-ferrous metal mine tailings. These technologies address the environmental risks of multi-element exposure to the ecosystem and human health risks. It provides a review and comparison of current bioremediation technologies used to mineralize metal(loid)s. The role of plant-microorganisms and their mechanisms in the remediation of tailings are also discussed. The importance of "treating waste with wastes" is crucial for advancing bioremediation technologies. This approach underscores the potential for waste materials to contribute to environmental cleanup processes. The concept of a circular economy is pertinent in this context, emphasizing recycling and reuse. There's an immediate need for international collaboration. Collaboration is needed in policy-making, funding, and data accessibility. Sharing data is essential for the growth of bioremediation globally.

Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes

The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.

Heavy Metals as Catalysts in the Evolution of Antimicrobial Resistance and the Mechanisms Underpinning Co-selection

The menace caused by antibiotic resistance in bacteria is acknowledged on a global scale. Concerns over the same are increasing because of the selection pressure exerted by a huge number of different antimicrobial agents, including heavy metals. Heavy metals are non-metabolizable and recalcitrant to degradation, therefore the bacteria can expel the pollutants out of the system and make it less harmful via different mechanisms. The selection of antibiotic-resistant bacteria may be influenced by heavy metals present in environmental reservoirs. Through co-resistance and cross-resistance processes, the presence of heavy metals in the environment can act as co-selecting agents, hence increasing resistance to both heavy metals and antibiotics. The horizontal gene transfer or mutation assists in the selection of mutant bacteria resistant to the polluted environment. Hence, bioremediation and biodegradation are sustainable methods for the natural clean-up of pollutants. This review sheds light on the occurrence of metal and antibiotic resistance in the environment via the co-resistance and cross-resistance mechanisms underpinning co-selection emphasizing the dearth of studies that specifically examine the method of co-selection in clinical settings. Furthermore, it is advised that future research incorporate both culture- and molecular-based methodologies to further our comprehension of the mechanisms underlying bacterial co- and cross-resistance to antibiotics and heavy metals.

Microbial antagonistic mechanisms of Hg(II) and Se(IV) in efficient wastewater treatment using granular sludge

The antagonistic effects of mercury (Hg) and selenium (Se) have been extensively studied in higher animals and plants. In this study, the microbial antagonistic effects of Hg and Se were utilized for wastewater treatment. We developed and optimized a new granular sludge approach to efficiently remove Hg(II) and Se(IV) from wastewater. Under anaerobic-oxic-anaerobic (AOA) conditions, the removal rates of Hg(II) and Se(IV) reached up to 99.91±0.07 % and 97.7 ± 0.8 %, respectively. The wastewater Hg(II) was mostly (97.43±0.01 %) converted to an inert mineral called tiemannite (HgSe) in the sludge, and no methylmercury (MeHg) was detected. The HgSe in sludge is less toxic, with almost no risk of secondary release, and it can be recovered with high purity. An inhibition experiment of mercury reduction and the high expression of the mer operon indicated that most Hg(II) (∼71 %) was first reduced to Hg0, and then Hg0 reacted with Se0 to synthesize HgSe. Metagenomic results showed that the final sludge (day 182) was dominated by two unclassified bacteria in the orders Rhodospirillales (27.7 %) and Xanthomonadales (6.3 %). Their metagenome-assembled genomes (MAGs) were recovered, suggesting that both of them can reduce Hg(II) and Se(IV). Metatranscriptomic analyses indicate that they can independently and cooperatively synthesize HgSe. In summary, granular sludge under AOA conditions is an efficient method for removing and recovering Hg from wastewater. The microbial transformation of Hg2+to Hg0 to HgSe may occur widely in both engineering and natural ecosystems.

Efficient and synergistic treatment of selenium (IV)-contaminated wastewater and mercury (II)-contaminated soil by anaerobic granular sludge: Performance and mechanisms

Wastewater containing selenium (Se) and soil contaminated by mercury (Hg) are two environmental problems, but they are rarely considered for synergistic treatment. In this work, anaerobic granular sludge (AnGS) was used to address both of the aforementioned issues simultaneously. The performance and mechanisms of Se(IV) removal from wastewater and Hg(II) immobilization in soil were investigated using various technologies. The results of the reactor operation indicated that the AnGS efficiently removed Se from wastewater, with a removal rate of 99.94 ± 0.05%. The microbial communities in the AnGS could rapidly reduce Se(IV) to Se0 nanoparticles (SeNPs). However, the AnGS lost the ability to reduce Se(IV) once the Se0 content reached the saturation value of 5.68 g Se/L. The excess sludge of Se0-rich AnGS was applied to remediate soil contaminated with Hg(II). The Se0-rich AnGS largely decreased the percentage of soil Hg in the mobile, extractable phase, with up to 99.1 ± 0.3% immobilization. Soil Hg(II) and Hg0 can react with Se (-II) and Se0, respectively, to form HgSe. The formation of inert HgSe was an important pathway for immobilizing Hg. Subsequently, the pot experiments indicated that soil remediation using Se0-rich AnGS significantly decreased the Hg content in pea plants. Especially, the content of Hg decreased from 555 ± 100 to 24 ± 3 μg/kg in roots after remediation. In summary, AnGS is an efficient and cost-effective material for synergistically treating Se-contaminated wastewater and Hg-contaminated soil.

Production of extracellular superoxide radical in microorganisms and its environmental implications: A review

Extracellular superoxide radical (O2•-) is ubiquitous in microbial environments and has significant implications for pollutant transformation. Microbial extracellular O2•- can be produced through multiple pathways, including electron leakage from the respiratory electron transport chain (ETC), NADPH oxidation by the transmembrane NADPH oxidase (NOX), and extracellular reactions. Extracellular O2•- significantly influences the geochemical processes of various substances, including toxic metals and refractory organic pollutants. On one hand, extracellular O2•- can react with variable-valence metals and detoxify certain highly toxic metals, such as As(III), Cr(VI), and Hg(II). On the other hand, extracellular O2•- can directly or indirectly (via Bio-Fenton) degrade many organic pollutants, including a variety of emerging contaminants. In this work, we summarize the production mechanisms of microbial extracellular O2•-, review its roles in the transformation of environmental pollutants, and discuss the potential applications, limiting factors, and future research directions in this field.

Characterization on nicotine degradation and research on heavy metal resistance of a strain Pseudomonas sp. NBB

The remediation of polluted sites containing multiple contaminants like nicotine and heavy metals poses significant challenges, due to detrimental effects like cell death. In this study, we isolated a new strain Pseudomonas sp. NBB capable of efficiently degrading nicotine even in high level of heavy metals. It degraded nicotine through pyrrolidine pathway and displayed minimum inhibitory concentrations of 2 mM for barium, copper, and lead, and 5 mM for manganese. In the presence of 2 mM Ba2+ or Pb2+, 3 g L-1 nicotine could be completely degraded within 24 h. Moreover, under 0.5 mM Cu2+ or 5 mM Mn2+ stress, 24.13% and 72.56% of nicotine degradation were achieved in 60 h, respectively. Strain NBB tolerances metal stress by various strategies, including morphological changes, up-regulation of macromolecule transporters, cellular response to DNA damage, and down-regulation of ABC transporters. Notably, among the 153 up-regulated genes, cds_821 was identified as manganese exporter (MneA) after gene disruption and recovery experiments. This study presents a novel strain capable of efficiently degrading nicotine and displaying remarkable resistance to heavy metals. The findings of this research provide valuable insights into the potential application of nicotine bioremediation in heavy metal-contaminated areas.

Enhanced anaerobic oxidation of methane with the coexistence of iron oxides and sulfate fertilizer in paddy soil

Iron oxides and sulfate are usually abundant in paddy soil, but their role in reducing methane emissions is little known. In this work, paddy soil was anaerobically cultivated with ferrihydrite and sulfate for 380 days. An activity assay, inhibition experiment, and microbial analysis were conducted to evaluate the microbial activity, possible pathways, and community structure, respectively. The results showed that anaerobic oxidation of methane (AOM) was active in the paddy soil. The AOM activity was much higher with ferrihydrite than sulfate, and an extra 10% of AOM activity was stimulated when ferrihydrite and sulfate coexisted. The microbial community was highly similar to the duplicates but totally different with different electron acceptors. The microbial abundance and diversity decreased due to the oligotrophic condition, but mcrA-carrying archaea increased 2-3 times after 380 days. Both the microbial community and the inhibition experiment implied that there was an intersection between iron and sulfur cycles. A "cryptic sulfur cycle" might link the two cycles, in which sulfate was quickly regenerated by iron oxides, and it might contribute 33% of AOM in the tested paddy soil. Complex links between methane, iron, and sulfur geochemical cycles occur in paddy soil, which may be significant in reducing methane emissions from rice fields.