Bacterial survival strategies and responses under heavy metal stress: a comprehensive overview

Arsenic behavior in soil-plant system under the manure application with the combination of antibiotic and roxarsone

Limited attention has been given to the interaction between antibiotics and arsenic in the soil-plant system. In this investigation, Medicago sativa seedlings were grown in soil treated with cow manure containing oxytetracycline (OTC) or sulfadiazine (SD), as well as arsenic (introduced through roxarsone, referred to as ROX treatment). The study revealed a notable increase in As(III) and dimethylarsinic acid (DMA(V)) levels in rhizosphere soils and plant root tissues as arsenic contamination intensified in the presence of antibiotics, while concentrations of As(V) and monomethylarsonic acid (MMA(V)) decreased. Conversely, elevated antibiotic presence resulted in higher levels of As(V) but reduced DMA concentrations in both rhizosphere soils and plant root tissues in the presence of arsenic. The arsenic biotransformation gene aioA was inhibited by arsenic contamination when antibiotics were present, and suppressed by antibiotic contamination in the presence of arsenic, especially in SD treatments, resulting in reduced expression levels at higher SD concentrations. Conversely, the arsM gene exhibited consistent upregulation under all conditions. However, its expression was found to increase with higher concentrations of ROX in the presence of antibiotics, decrease with increasing SD concentrations, and initially rise before declining with higher levels of OTC in the presence of arsenic. Bacterial genera within the Proteobacteria phylum, such as Geobacter, Lusitaniella, Mesorhizobium, and Methylovirgula, showed significant co-occurrence with both aioA and arsM genes. Correlation analysis demonstrated associations between the four arsenic species and the two arsenic biotransformation genes, emphasizing pH as a critical factor influencing the transformation and uptake of different arsenic species in the soil-plant system. The combined stress of antibiotics and arsenic has the potential to modify arsenic behavior and associated risks in soil-plant systems, highlighting the necessity of considering this interaction in future research endeavors.

Biological assessment and radiological impact in Keana, North Central Nigeria: environmental implication and metabolites production

The objective of the research was to examine microbial characteristics, metabolites produced, and the potential radiological risks present in mining soils located in Keana, North Central Nigeria. Soil samples were collected from various locations within Keana, Nasarawa State. Bacterial isolation was carried out, and molecular techniques were employed to characterize the bacteria found in the collected soil samples. Additionally, the susceptibility of these isolates to antibiotics was determined, and the bacteria screened for their ability to produce metabolites. The isolated bacteria were classified into three groups: Actinobacteria, Firmicutes, and Proteobacteria. The analysis of the spectra revealed that 1595 compounds were produced, including carboxylic acids, nitro compounds, aldehydes, anhydrides, esters, ketones, amides, phenols, alcohols, alkanes, alkenes, alkynes, and arenes. Some of the metabolites produced were oleic acid, 1,3-dioxolane, linoelaidic acid and oleic acid, 1-nonadecene, butylated hydroxytoluene, diisooctyl phthalate, bis(2-ethylhexyl) phthalate among others, and 1,2-benzenedicarboxylic acid (85.32%) as the most produced metabolite. Among the antibiotics tested, levofloxacin and ciprofloxacin exhibited the strongest antibacterial properties against the isolates. Airborne gamma-ray spectrometry analysis identified elevated levels of potassium, thorium, and uranium in the soils, indicating potential environmental hazards. However, no significant correlation was found between the presence of bacteria and radioactive elements. These findings emphasize the importance of comprehensive environmental monitoring in Keana to address potential health risks associated with microbial contamination and radioactive materials. Additionally, the study highlighted the role of microbial diversity in Keana soils in promoting the production of secondary metabolites with potential applications in pharmaceutical and industrial sectors..

Bacterial community composition and function vary with farmland type and soil depth around a mining area

Heavy metal pollution can have adverse impacts on microorganisms, plants and even human health. To date, the impact of heavy metals on bacteria in farmland has yielded poor attention, and there is a paucity of knowledge on the impact of land type on bacteria in mining area with heavy metal pollution. Around a metal-contaminated mining area, two soil depths in three types of farmlands were selected to explore the composition and function of bacteria and their correlations with the types and contents of heavy metals. The compositions and functions of bacterial communities at the three different agricultural sites were disparate to a certain extent. Some metabolic functions of bacterial community in the paddy field were up-regulated compared with those at other site. These results observed around mining area were different from those previously reported in conventional farmlands. In addition, bacterial community composition in the top soils was relatively complex, while in the deep soils it became more unitary and extracellular functional genes got enriched. Meanwhile, heavy metal pollution may stimulate the enrichment of certain bacteria to protect plants from damage. This finding may aid in understanding the indirect effect of metal contamination on plants and thus putting forward feasible strategies for the remediation of metal-contaminated sites. MAIN FINDINGS OF THE WORK: This was the first study to comprehensively explore the influence of heavy metal pollution on the soil bacterial communities and metabolic potentials in different agricultural land types and soil depths around a mining area.

The abundance and pathogenicity of microbes in automobile air conditioning filters across the typical cities of China and Europe

Bioaerosols are widely distributed in urban air and can be transmitted across the atmosphere, biosphere, and anthroposphere, resulting in infectious diseases. Automobile air conditioning (AAC) filters can trap airborne microbes. In this study, AAC filters were used to investigate the abundance and pathogenicity of airborne microorganisms in typical Chinese and European cities. Culturable bacteria and fungi concentrations were determined using microbial culturing. High-throughput sequencing was employed to analyze microbial community structures. The levels of culturable bioaerosols in Chinese and European cities exhibited disparities (Analysis of Variance, P < 0.01). The most dominant pathogenic bacteria and fungi were similar in Chinese (Mycobacterium: 18.2-18.9 %; Cladosporium: 23.0-30.2 %) and European cities (Mycobacterium: 15.4-37.7 %; Cladosporium: 18.1-29.3 %). Bartonella, Bordetella, Alternaria, and Aspergillus were also widely identified. BugBase analysis showed that microbiomes in China exhibited higher abundances of mobile genetic elements (MGEs) and biofilm formation capacity than those in Europe, indicating higher health risks. Through co-occurrence network analysis, heavy metals such as zinc were found to correlate with microorganism abundance; most bacteria were inversely associated, while fungi exhibited greater tolerance, indicating that heavy metals affect the growth and reproduction of bioaerosol microorganisms. This study elucidates the influence of social and environmental factors on shaping microbial community structures, offering practical insights for preventing and controlling regional bioaerosol pollution.

Microbial community structure in an uranium-rich acid mine drainage site: implication for the biogeochemical release of uranium

The generation of acid mine drainage (AMD) characterized by high acidity and elevated levels of toxic metals primarily results from the oxidation and dissolution of sulfide minerals facilitated by microbial catalysis. Although there has been significant research on microbial diversity and community composition in AMD, as well as the relationship between microbes and heavy metals, there remains a gap in understanding the microbial community structure in uranium-enriched AMD sites. In this paper, water samples with varying levels of uranium pollution were collected from an abandoned stone coal mine in Jiangxi Province, China during summer and winter, respectively. Geochemical and high-throughput sequencing analyses were conducted to characterize spatiotemporal variations in bacterial diversity and community composition along pollution groups. The results indicated that uranium was predominantly concentrated in the AMD of new pits with strong acid production capacity, reaching a peak concentration of 9,370 μg/L. This was accompanied by elevated acidity and concentrations of iron and total phosphorus, which were identified as significant drivers shaping the composition of bacterial communities, rather than fluctuations in seasonal conditions. In an extremely polluted environment (pH < 3), bacterial diversity was lowest, with a predominant presence of acidophilic iron-oxidizing bacteria (such as Ferrovum), and a portion of acidophilic heterotrophic bacteria synergistically coexisting. As pollution levels decreased, the microbial community gradually evolved to cohabitation of various pH-neutral heterotrophic species, ultimately reverting back to background level. The pH was the dominant factor determining biogeochemical release of uranium in AMD. Acidophilic and uranium-tolerant bacteria, including Ferrovum, Leptospirillum, Acidiphilium, and Metallibacterium, were identified as playing key roles in this process through mechanisms such as enhancing acid production rate and facilitating organic matter biodegradation.

The Cd resistant mechanism of Proteus mirabilis Ch8 through immobilizing and detoxifying

Cadmium (Cd) pollution is a serious global environmental problem, which requires a global concern and practical solutions. Microbial remediation has received widespread attention owing to advantages, such as environmental friendliness and soil amelioration. However, Cd toxicity also severely deteriorates the remediation performance of functional microorganisms. Analyzing the mechanism of bacterial resistance to Cd stress will be beneficial for the application of Cd remediation. In this study, the bacteria strain, up to 1400 mg/L Cd resistance, was employed and identified as Proteus mirabilis Ch8 (Ch8) through whole genome sequence analyses. The results indicated that the multiple pathways of immobilizing and detoxifying Cd maintained the growth of Ch8 under Cd stress, which also possessed high Cd extracellular adsorption. Firstly, the changes in surface morphology and functional groups of Ch8 cells were observed under different Cd conditions through SEM-EDS and FTIR analyses. Under 100 mg/L Cd, Ch8 cells exhibited aggregation and less flagella; the Cd biosorption of Ch8 was predominately by secreting exopolysaccharides (EPS) and no significant change of functional groups. Under 500 mg/L Cd, Ch8 were present irregular polymers on the cell surface, some cells with wrapping around; the Cd biosorption capacity exhibited outstanding effects (38.80 mg/g), which was mainly immobilizing Cd by secreting and interacting with EPS. Then, Ch8 also significantly enhanced the antioxidant enzyme activity and the antioxidant substance content under different Cd conditions. The activities of SOD and CAT, GSH content of Ch8 under 500 mg/L Cd were significantly increased by 245.47%, 179.52%, and 241.81%, compared to normal condition. Additionally, Ch8 significantly induced the expression of Acr A and Tol C (the resistance-nodulation-division (RND) efflux pump), and some antioxidant genes (SodB, SodC, and Tpx) to reduce Cd damage. In particular, the markedly higher expression levels of SodB under Cd stress. The mechanism of Ch8 lays a foundation for its application in solving soil remediation.

An assessment of metal absorption competence of indigenous metal tolerant bacterial species- an in-vitro study

Heavy metals pose a serious global threat to the environment. Hence, removing hazardous metals from soil samples has become complicated over the past few years. The current work looked into the remediation of heavy metals from aqueous solutions using a bacterial community and a unique bacterium obtained from metal-contaminated soil. In this investigation, the isolates of Bacillus anthracis A1-7, Bacillus. thuringiensis A1-3, Bacillus. cereus A1-5, and Pseudomonas aeruginosa A-33 actively demonstrated metal tolerances to various tested metals. Furthermore, an in-vitro biosorption study was performed under ideal concentration. The bacterial consortia achieved the highest biosorption effectiveness for Cu & Zn, 92.7% and 90.3%, respectively. When compared with a single bacterium, the group exhibited inferior Pb biosorption (86%). Since then, P. aeruginosa A33 has had the highest Pb biosorption. Finally, a bacterial consortium has devised an intriguing strategy for eliminating Cu and Pb from the polluted medium. P. aeruginosa A33 was found to be a mighty microbe that extracts Zn from polluted water. This metal-tolerant bacterium also exhibited specific proportions of selective commercially available antibiotics, which were analyzed using the Multiple Antibiotic Resistance (MAR) Index. In conclusion, these findings indicated that bacterial consortia composed of four bacterial isolates can remove metals from a metal-polluted medium.

Comparative transcriptomics revealed the mechanism of Stenotrophomonas rhizophila JC1 response and biosorption to Pb2

Nowadays, there is limited research focusing on the biosorption of Pb2+ through microbial process, particularly at the level of gene expression. To overcome this knowledge gap, we studied the adsorption capacity of Stenotrophomonas rhizophila JC1 to Pb2+, and investigated the physiological mechanism by means of SEM, EDS, FTIR, membrane permeability detection, and investigated the molecular mechanism through comparative transcriptomics. The results showed that after 16 h of cultivation, the biosorption capacity of JC1 for 100 mg/L of Pb2+ reached at 79.8%. The main mechanism of JC1 adsorb Pb2+ is via intracellular accumulation, accounting for more than 90% of the total adsorption. At the physiological level, Pb2+ can precipitate with anion functional groups (e.g., -OH, -NH) on the bacterial cell wall or undergo replacement reaction with cell component elements (e.g., Si, Ca) to adsorb Pb2+ outside of the cell wall, thus accomplishing extracellular adsorption of Pb2+ by strains. Furthermore, the cell membrane acts as a "switch" that inhibits the entry of metal ions into the cell from the plasma membrane. At the molecular level, the gene pbt specificity is responsible for the adsorption of Pb2+ by JC1. In addition, phosphate permease is a major member of the ABC transporter family involved in Pb2+, and czcA/cusA or Co2+/Mg2+ efflux protein plays an important role in the efflux of Pb2+ in JC1. Further, cellular macromolecule biosynthesis, inorganic cation transmembrane transport, citrate cycle (TCA) and carbon metabolism pathways all play crucial roles in the response of strain JC1 to Pb2+ stress.

LCMS-Metabolomic Profiling and Genome Mining of Delftia lacustris DSM 21246 Revealed Lipophilic Delftibactin Metallophores

Bacteria have evolved various strategies to combat heavy metal stress, including the secretion of small molecules, known as metallophores. These molecules hold a potential role in the mitigation of toxic metal contamination from the environment (bioremediation). Herein, we employed combined comparative metabolomic and genomic analyses to study the metallophores excreted by Delftia lacustris DSM 21246. LCMS-metabolomic analysis of this bacterium cultured under iron limitation led to a suite of lipophilic metallophores exclusively secreted in response to iron starvation. Additionally, we conducted genome sequencing of the DSM 21246 strain using nanopore sequencing technology and employed antiSMASH to mine the genome, leading to the identification of a biosynthetic gene cluster (BGC) matching the known BGC responsible for delftibactin A production. The isolated suite of amphiphilic metallophores, termed delftibactins C-F (1-4), was characterized using various chromatographic, spectroscopic, and bioinformatic techniques. The planar structure of these compounds was elucidated through 1D and 2D NMR analyses, as well as LCMS/MS-based fragmentation studies. Notably, their structures differed from previously known delftibactins due to the presence of a lipid tail. Marfey's and bioinformatic analyses were employed to determine the absolute configuration of the peptide scaffold. Delftibactin A, a previously identified metallophore, has exhibited a gold biomineralizing property; compound 1 was tested for and also demonstrated this property.

Omics technology draws a comprehensive heavy metal resistance strategy in bacteria

The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.

Detoxification of copper and zinc from anaerobic digestate effluent by indigenous bacteria: Mechanisms, pathways and metagenomic analysis

The presence of organic-complexed copper and zinc in anaerobic digestate effluent (ADE) poses persistent ecological toxicity. This study investigated the detoxification performance and biotic responses of indigenous bacteria against ethylene diamine tetraacetic acid (EDTA)-complexed Cu(II) and Zn(II). Heavy metals (HMs) stress induced reactive oxygen species (ROS) generation and enhanced extracellular polymeric substances (EPS) secretion. At a Cu(II) influent concentration of 20.0 mg·L-1, indigenous bacteria removed 88.2% of Cu(II) within nine days. The majority of copper and zinc sequestered by bacteria were stored in the cell envelope, with over 50% of copper and 60% of zinc being immobilized. Transmission electron microscopy mapping (TEM-mapping) revealed significant mineralization of copper and zinc on the cell wall. Proteins abundant in EPS, alongside humic acid-like substances, effectively adsorbed HMs. Indigenous bacteria exhibited the capacity to reduce cupric to the cuprous state and cupric is preferentially reduced to cuprous before reaching reducing capacity saturation. Sulfur precipitation emerges as a crucial pathway for Zn(II) removal. Metagenomic analysis indicated that indigenous bacteria upregulated genes related to HMs homeostasis, efflux, and DNA repair, enhancing its resistance to high concentrations HMs. This study provided theoretical guidance for employing bacterial consortia to eliminate HMs in complex aquatic environments.

Atomic Pyridinic Nitrogen as Highly Active Metal-Free Coordination Sites at the Biotic-Abiotic Interface for Bio-Electrochemical CO2 Reduction

Bio-electrochemical conversion of anthropogenic CO2 into value-added products using cost-effective metal-free catalysts represents a promising strategy for sustainable fuel production. Herein, N-doped carbon nanosheets synthesized via pyrolysis of the zeolitic-imidazolate framework (ZIF) are developed for constructing efficient biohybrids to facilitate CO2-to-CH4 conversion. The microbial enrichment and bio-interfacial charge transfer are significantly affected by the proportion of the co-existed graphitic-N, pyridinic-N, and pyrrolic-N in the defective carbon nanosheets. It is unfolded that pyridinic-N and pyrrolic-N with the doped N atoms near the edge can significantly enhance the adsorption of their adjacent C atoms toward O, leading to improved microbe enrichment. Especially, pyridinic-N which can provide one p electron to the aromatic π system, greatly enhances the electron-donating capability of the carbon nanosheets to the microorganisms. Correspondingly, due to its largest amount of pyridinic-N doping, the N-doped carbon nanosheets derived from ZIF pyrolysis at 900 °C (denoted 900-NC) achieve the highest methane production of ≈215.7 mmol m-2 day-1 with a high selectivity (Faradaic efficiency = ≈94.2%) at -0.9 V versus Ag/AgCl. This work demonstrates the effectiveness of N-doped carbon catalysts for bio-electrochemical CO2 fixation and contributes to the understanding of N functionalities toward microbiome response and biotic-abiotic charge transfer in various bio-electrochemical systems.

Unveiling the inhibitory mechanisms of chromium exposure on microbial reductive dechlorination: Kinetics and microbial responses

Chromium and organochlorine solvents, particularly trichloroethene (TCE), are pervasive co-existing contaminants in subsurface aquifers due to their extensive industrial use and improper disposal practices. In this study, we investigated the microbial dechlorination kinetics under different TCE-Cr(Ⅲ/VI) composite pollution conditions and elucidated microbial response mechanisms based on community shift patterns and metagenomic analysis. Our results revealed that the reductive dechlorinating consortium had high resistance to Cr(III) but extreme sensitivity to Cr(VI) disturbance, resulting in a persistent inhibitory effect on subsequent dechlorination. Interestingly, the vinyl chloride-respiring organohalide-respiring bacteria (OHRB) was notably more susceptible to Cr(III/VI) exposure than the trichloroethene-respiring one, possibly due to inferior competition for growth substrates, such as electron donors. In terms of synergistic non-OHRB populations, Cr(III/VI) exposure had limited impacts on lactate fermentation but significantly interfered with H2-producing acetogenesis, leading to inhibited microbial dechlorination due to electron donor deficiencies. However, this inhibition can be effectively mitigated by the amendment of exogenous H2 supply. Furthermore, being the predominant OHRB, Dehalococcoides have inherent Cr(VI) resistance defects and collaborate with synergistic non-OHRB populations to achieve concurrent bio-detoxication of Cr(VI) and TCE. Our findings expand the understanding of the response patterns of different functional populations towards Cr(III/VI) stress, and provide valuable insights for the development of in situ bioremediation strategies for sites co-contaminated with chloroethene and chromium.

Effects of heavy metals and metalloids on the biodegradation of organic contaminants

Heavy metals and metalloids (HMMs) inhibit the biodegradation of organic pollutants. The degree of inhibition depends not only on the concentration and bioavailability of HMMs but also on additional factors, such as environmental variables (e.g., inorganic components, organic matter, pH, and redox potential), the nature of the metals, and microbial species. Based on the degradation pattern and metal concentrations causing half biodegradation rate reductions (RC50s), the inhibition of biodegradation was: Hg2+, As2O3 > Cu2+, Cd2+, Pb2+, Cr3+ > Ni2+, Co2+ > Mn2+, Zn2+ > Fe3+. Four patterns were observed: inhibition increases with increasing metal concentration; low concentrations stimulate, while high concentrations inhibit; high concentrations inhibit less; and mild inhibition remains constant. In addition, metal ion mixtures have more complex inhibitory effects on the degradation of organic pollutants, which may be greater than, similar to, or less than that of individual HMMs. Finally, the inhibitory mechanism of HMMs on biodegradation is reviewed. HMMs generally have little impact on the biodegradation pathway of organic pollutants for bacterial strains. However, when pollutants are biodegraded by the community, HMMs may activate microbial populations harbouring different transformation pathways. HMMs can affect the biodegradation efficiency of organic pollutants by changing the surface properties of microbes, interfering with degradative enzymes, and interacting with general metabolism.

Adsorption of Hg2+/Cr6+ by metal-binding proteins heterologously expressed in Escherichia coli

BACKGROUND

Removal of heavy metals from water and soil is a pressing challenge in environmental engineering, and biosorption by microorganisms is considered as one of the most cost-effective methods. In this study, the metal-binding proteins MerR and ChrB derived from Cupriavidus metallidurans were separately expressed in Escherichia coli BL21 to construct adsorption strains. To improve the adsorption performance, surface display and codon optimization were carried out.

RESULTS

In this study, we constructed 24 adsorption engineering strains for Hg2+ and Cr6+, utilizing different strategies. Among these engineering strains, the M'-002 and B-008 had the strongest heavy metal ion absorption ability. The M'-002 used the flexible linker and INPN to display the merRopt at the surface of the E. coli BL21, whose maximal adsorption capacity reached 658.40 μmol/g cell dry weight under concentrations of 300 μM Hg2+. And the B-008 overexpressed the chrB in the intracellular, its maximal capacity was 46.84 μmol/g cell dry weight under concentrations 500 μM Cr6+. While in the case of mixed ions solution (including Pb2+, Cd2+, Cr6+ and Hg2+), the total amount of ions adsorbed by M'-002 and B-008 showed an increase of up to 1.14- and 4.09-folds, compared to the capacities in the single ion solution.

CONCLUSION

The construction and optimization of heavy metal adsorption strains were carried out in this work. A comparison of the adsorption behavior between single bacteria and mixed bacteria systems was investigated in both a single ion and a mixed ion environment. The Hg2+ absorption capacity is reached the highest reported to date with the engineered strain M'-002, which displayed the merRopt at the surface of chassis cell, indicating the strain's potential for its application in practical environments.

Elimination of copper obstacle factor in anaerobic digestion effluent for value-added utilization: Performance and resistance mechanisms of indigenous bacterial consortium

The presence of excessive residual Cu(II), a high-risk heavy metal with potential toxicity and biomagnification property, substantially impede the value-added utilization of anaerobic digestion effluent (ADE). This study adapted indigenous bacterial consortium (IBCs) to eliminate Cu(II) from ADE, and their performances and resistance mechanisms against Cu(II) were analyzed. Results demonstrated that when the Cu(II) exposure concentration exceeded 7.5 mg/L, the biomass of IBCs decreased significantly, cells produced a substantial amount of ROS and EPS, at which time the intracellular Cu(II) content gradually decreased, while Cu(II) accumulation within the EPS substantially increased. The combined features of a high PN/PS ratio, a reversed Zeta potential gradient, and abundant functional groups within EPS collectively render EPS a primary diffusion barrier against Cu(II) toxicity. Mutual physiological and metagenomics analyses reveal that EPS synthesis and secretion, efflux, DNA repair along with coordination between each other were the primary resistance mechanisms of IBCs against Cu(II) toxicity. Furthermore, IBCs exhibited enhanced resistance by enriching bacteria carrying relevant resistance genes. Continuous pretreatment of actual ADE with IBCs at a 10-day hydraulic retention time (HRT) efficiently eliminated Cu(II) concentration from 5.01 mg/L to ∼0.68 mg/L by day 2. This elimination remained stable for the following 8 days of operation, further validated their good Cu(II) elimination stability. Notably, supplementing IBCs with 200 mg/L polymerized ferrous sulfate significantly enhanced their settling performance. By elucidating the intricate interplay of Cu(II) toxicity and IBC resistance mechanisms, this study provides a theoretical foundation for eliminating heavy metal barriers in ADE treatment.

Spectra metrology for interaction of heavy metals with extracellular polymeric substances (EPS) of Pseudomonas aeruginosa OMCS-1 reveals static quenching and complexation dynamics of EPS with heavy metals

The adsorption behavior and interaction mechanisms of extracellular polymeric substances (EPS) of Pseudomonas aeruginosa OMCS-1 towards chromium (Cr), lead (Pb), and cadmium (Cd) were investigated. EPS-covered (EPS-C) cells exhibited significantly higher (p < 0.0001; two-way ANOVA) removal of Cr (85.58 ± 0.39%), Pb (81.98 ± 1.02%), and Cd (73.88 ± 1%) than EPS-removed (EPS-R) cells. Interactions between EPS-heavy metals were spontaneous (ΔG<0). EPS-Cr(VI) and EPS-Pb(II) binding were exothermic (ΔH<0), while EPS-Cd(II) binding was endothermic (ΔH>0) process. EPS bonded to Pb(II) via inner-sphere complexation by displacement of surrounding water molecules, while EPS-Cr(VI) and EPS-Cd(II) binding occurred through outer-sphere complexation via electrostatic interactions. Increased zeta potential of Cr (29.75%), Pb (41.46%), and Cd (46.83%) treated EPS and unchanged crystallinity (CIXRD=0.13), inferred EPS-metal binding via both electrostatic interactions and complexation mechanism. EPS-metal interaction was predominantly promoted through hydroxyl, amide, carboxyl, and phosphate groups. Metal adsorption deviated EPS protein secondary structures. Strong static quenching mechanism between tryptophan protein-like substances in EPS and heavy metals was evidenced. EPS sequestered heavy metals via complexation with C-O, C-OH, CO/O-C-O, and NH/NH2 groups and ion exchange with -COOH group. This study unveils the fate of Cr, Pb, and Cd on EPS surface and provides insight into the interactions among EPS and metal ions for metal sequestration.

The Cd immobilization mechanisms in paddy soil through ureolysis-based microbial induced carbonate precipitation: Emphasis on the coexisting cations and metatranscriptome analysis

Microbial induced carbonate precipitation (MICP) can immobilize metals and reduce their bioavailability. However, little is known about the immobilization mechanism of Cd in the presence of soil cations and the triggered gene expression and metabolic pathways in paddy soil. Thus, microcosmic experiments were conducted to study the fractionation transformation of Cd and metatranscriptome analysis. Results showed that bioavailable Cd decreased from 0.62 to 0.29 mg/kg after 330 d due to the MICP immobilization. This was ascribed to the increase in carbonate bound, Fe-Mn oxides bound, and residual Cd. The underlying immobilization mechanisms could be attributed to the formation of insoluble Cd-containing precipitates, the complexation and lattice substitution with carbonate and Fe, Mn and Al (hydr)oxides, and the adsorption on functional group on extracellular polymers of cell. During the MICP immobilization process, up-regulated differential expression urease genes were significantly enriched in the paddy soil, corresponding to the arginine biosynthesis, purine metabolism and atrazine degradation. The metabolic pathway of bacterial chemotaxis, flagellum assembly, and peptidoglycan biosynthesis and the expression of cadA gene related to Cd excretion enhanced Cd resistance of soil microbiome. Therefore, this study provided new insights into the immobilization mechanisms of Cd in paddy soils through ureolysis-based MICP process.

Responses of a polycyclic aromatic hydrocarbon-degrading bacterium, Paraburkholderia fungorum JT-M8, to Cd (II) under P-limited oligotrophic conditions

For the bioremediation of mixed-contamination sites, studies on polycyclic aromatic hydrocarbon (PAH) degradation or Cd (II) tolerance in bacteria are commonly implemented in nutrient-rich media. In contrast, in the field, inocula usually encounter harsh oligotrophic habitats. In this study, the environmental strain Paraburkholderia fungorum JT-M8 was used to explore the overlooked Cd (II) defense mechanism during PAH dissipation under P-limited oligotrophic condition. The results showed that the growth and PAH degradation ability of JT-M8 under Cd (II) stress were correlated with phosphate contents and exhibited self-regulating properties. Phosphates mainly affected the Cd (II) content in solution, while the cellular distribution of Cd (II) depended on Cd (II) levels; Cd (II) was mainly located in the cytoplasm when exposed to less Cd (II), and vice versa. The unique Cd (II) detoxification pathways could be classified into three aspects: (i) Cd (II) ionic equilibrium and dose-response effects regulated by environmental matrices (phosphate contents); (ii) bacterial physiological self-regulation, e.g., cell surface-binding, protein secretion and active transport systems; and (iii) specific adaptive responses (flagellum aggregation). This study emphasizes the importance of considering culture conditions when assessing the metal tolerance and provides new insight into the bacterial detoxification process of complex PAH-Cd (II) pollutants.

Removing Heavy Metals: Cutting-Edge Strategies and Advancements in Biosorption Technology

This article explores recent advancements and innovative strategies in biosorption technology, with a particular focus on the removal of heavy metals, such as Cu(II), Pb(II), Cr(III), Cr(VI), Zn(II), and Ni(II), and a metalloid, As(V), from various sources. Detailed information on biosorbents, including their composition, structure, and performance metrics in heavy metal sorption, is presented. Specific attention is given to the numerical values of the adsorption capacities for each metal, showcasing the efficacy of biosorbents in removing Cu (up to 96.4%), Pb (up to 95%), Cr (up to 99.9%), Zn (up to 99%), Ni (up to 93.8%), and As (up to 92.9%) from wastewater and industrial effluents. In addition, the issue of biosorbent deactivation and failure over time is highlighted as it is crucial for the successful implementation of adsorption in practical applications. Such phenomena as blockage by other cations or chemical decomposition are reported, and chemical, thermal, and microwave treatments are indicated as effective regeneration techniques. Ongoing research should focus on the development of more resilient biosorbent materials, optimizing regeneration techniques, and exploring innovative approaches to improve the long-term performance and sustainability of biosorption technologies. The analysis showed that biosorption emerges as a promising strategy for alleviating pollutants in wastewater and industrial effluents, offering a sustainable and environmentally friendly approach to addressing water pollution challenges.

Utilization of biochar for remediation of heavy metals in aqueous environments: A review and bibliometric analysis

Biochar usage for removing heavy metals from aqueous environments has emerged as a promising research area with significant environmental and economic benefits. Using the PICO approach, the research question aimed to explore using biochar to remove heavy metals from aqueous media. We merged the data from Scopus and the Web of Science Core Collection databases to acquire a comprehensive perspective of the subject. The PRISMA guidelines were applied to establish the search parameters, identify the appropriate articles, and collect the bibliographic information from the publications between 2010 and 2022. The bibliometric analysis showed that biochar-based heavy metal remediation is a research field with increasing scholarly attention. The removal of Cr(VI), Pb(II), Cd(II), and Cu(II) was the most studied among the heavy metals. We identified five main clusters centered on adsorption, water treatment, adsorption models, analytical techniques, and hydrothermal carbonization by performing keyword co-occurrence analysis. Trending topics include biochar reusability, modification, acid mine drainage (AMD), wastewater treatment, and hydrochar. The reutilization of heavy metal-loaded spent biochar includes transforming it into electrodes for supercapacitors or stable catalyst materials. This study provides a comprehensive overview of biochar-based heavy metal remediation in aquatic environments and highlights knowledge gaps and future research directions.

Adsorption of copper by naturally and artificially aged polystyrene microplastics and subsequent release in simulated gastrointestinal fluid

Microplastics, especially aged microplastics can become vectors of metals from environment to organisms with potential negative effects on food chain. However, a few studies focused on the bioavailability of adsorbed metals and most studies related to aged microplastics used artificial method that cannot entirely reflect actual aging processes. In this study, virgin polystyrene was aged by ozone (PS-O3), solar simulator (PS-SS) and lake (PS-lake) to investigate adsorption of Cu by virgin, artificially and naturally aged microplastics and subsequent release in simulated gastrointestinal fluids (SGF). Characterization results show carbonyl was formed in PS-O3 and PS-SS, and the oxidation degree was PS-O3 > PS-SS > PS-lake. However, Cu adsorption capacity followed this order PS-lake (158 μg g-1) > PS-SS (117 μg g-1) > PS-O3 (65 μg g-1) > PS-virgin (0). PS-O3 showed highest Cu adsorption capacity at 0.5 h (71 μg g-1), but it dropped dramatically later (10 μg g-1, 120 h), because PS-O3 could break up and the adsorbed Cu released in solutions subsequently. For PS-lake, precipitation of metallic oxides contributes to the accumulation of Cu. The addition of dissolved organic matter (DOM) could occupy adsorption sites on PS and compete with Cu, but also can attach PS and adsorb Cu due to its rich functional groups. The simultaneous ingestion of microplastics with food suggested that adsorbed Cu is solubilized mostly from aged PS to SGF.

Biological roles of soil microbial consortium on promoting safe crop production in heavy metal(loid) contaminated soil: A systematic review

Heavy metal(loid) (HM) pollution of agricultural soils is a growing global environmental concern that affects planetary health. Numerous studies have shown that soil microbial consortia can inhibit the accumulation of HMs in crops. However, our current understanding of the effects and mechanisms of inhibition is fragmented. In this review, we summarise extant studies and knowledge to provide a comprehensive view of HM toxicity on crop growth and development at the biological, cellular and the molecular levels. In a meta-analysis, we find that microbial consortia can improve crop resistance and reduce HM uptake, which in turn promotes healthy crop growth, demonstrating that microbial consortia are more effective than single microorganisms. We then review three main mechanisms by which microbial consortia reduce the toxicity of HMs to crops and inhibit HMs accumulation in crops: 1) reducing the bioavailability of HMs in soil (e.g. biosorption, bioaccumulation and biotransformation); 2) improving crop resistance to HMs (e.g. facilitating the absorption of nutrients); and 3) synergistic effects between microorganisms. Finally, we discuss the prospects of microbial consortium applications in simultaneous crop safety production and soil remediation, indicating that they play a key role in sustainable agricultural development, and conclude by identifying research challenges and future directions for the microbial consortium to promote safe crop production.

Potential applications of extremophilic bacteria in the bioremediation of extreme environments contaminated with heavy metals

Protecting the environment from harmful pollutants has become increasingly difficult in recent decades. The presence of heavy metal (HM) pollution poses a serious environmental hazard that requires intricate attention on a worldwide scale. Even at low concentrations, HMs have the potential to induce deleterious health effects in both humans and other living organisms. Therefore, various strategies have been proposed to address this issue, with extremophiles being a promising solution. Bacteria that exhibit resistance to metals are preferred for applications involving metal removal due to their capacity for rapid multiplication and growth. Extremophiles are a special group of microorganisms that are capable of surviving under extreme conditions such as extreme temperatures, pH levels, and high salt concentrations where other organisms cannot. Due to their unique enzymes and adaptive capabilities, extremophiles are well suited as catalysts for environmental biotechnology applications, including the bioremediation of HMs through various strategies. The mechanisms of resistance to HMs by extremophilic bacteria encompass: (i) metal exclusion by permeability barrier; (ii) extracellular metal sequestration by protein/chelator binding; (iii) intracellular sequestration of the metal by protein/chelator binding; (iv) enzymatic detoxification of a metal to a less toxic form; (v) active transport of HMs; (vi) passive tolerance; (vii) reduced metal sensitivity of cellular targets to metal ions; and (viii) morphological change of cells. This review provides comprehensive information on extremophilic bacteria and their potential roles for bioremediation, particularly in environments contaminated with HMs, which pose a threat due to their stability and persistence. Genetic engineering of extremophilic bacteria in stressed environments could help in the bioremediation of contaminated sites. Due to their unique characteristics, these organisms and their enzymes are expected to bridge the gap between biological and chemical industrial processes. However, the structure and biochemical properties of extremophilic bacteria, along with any possible long-term effects of their applications, need to be investigated further.

Extracellular proteins enhance Cupriavidus pauculus nickel tolerance and cell aggregate formation

Heavy metal-resistant bacteria secrete extracellular proteins (e-PNs). However, the role of e-PNs in heavy metal resistance remains elusive. Here Fourier Transform Infrared Spectroscopy implied that N-H, C = O and NH2-R played a crucial role in the adsorption and resistance of Ni2+ in the model organism Cuprividus pauculus 1490 (C. pauculus). Proteinase K treatment reduced Ni2+ resistance of C. pauculus underlining the essential role of e-PNs. Further three-dimension excitation-emission matrix fluorescence spectroscopy analysis demonstrated that tryptophan proteins as part of the e-PNs increased significantly with Ni2+ treatment. Proteomic and quantitative real-time polymerase chain reaction data indicated that major changes were induced in the metabolism of C. pauculus in response to Ni2+. Among those lipopolysaccharide biosynthesis, general secretion pathways, Ni2+-affiliated transporters and multidrug efflux play an essential role in Ni2+ resistance. Altogether the results provide a conceptual model for comprehending how e-PNs contribute to bacterial resistance and adsorption of Ni2+.

Metal accumulation and genetic adaptation of Oryza sativa to Cadmiun and Chromium heavy metal stress: A hydroponic and RAPD analyses

This research was performed to assess the influence of Cd and Cr metals on growth, pigments, antioxidant, and genomic stability of Oryza sativa indica and Oryza sativa japonica were investigated under hydroponic conditions. The results revealed that significant metal influence on test crop growth, pigment content, metal stress balancing antioxidant activity in a dose dependent manner. Since, while at elevated (500 ppm) concentration of Cd as well as Cr metals the pigment (total chlorophyll, chlorophyll a, b and carotenoids) level was reduced than control; however antioxidant activity (total antioxidant, H2O2, and NO) was considerably improved as protective mechanisms to combat the metal toxicity and support the plant growth. Furthermore, the test crops under typical hydroponic medium (loaded with Cd and Cr as 200, 300, 400, and 500 ppm) growth conditions, effectively absorb the metals from medium and accumulated in the root and least quantity was translocated to the shoot of this test crops. Furthermore, typical RAPD analysis with 10 universal primers demonstrated that the genomic DNA of the test crops was adaptable to develop metal resistance and ensure crop growth under increased concentrations (500 ppm) of tested heavy metals. These findings suggest that these edible crops have the ability to accumulate Cd along with Cr metals, and additionally that their genetic systems have the ability to adapt to metal-stressed environments.

Copper stress shapes the dynamic behavior of amoebae and their associated bacteria

Amoeba-bacteria interactions are prevalent in both natural ecosystems and engineered environments. Amoebae, as essential consumers, hold significant ecological importance within ecosystems. Besides, they can establish stable symbiotic associations with bacteria. Copper plays a critical role in amoeba predation by either killing or restricting the growth of ingested bacteria in phagosomes. However, certain symbiotic bacteria have evolved mechanisms to persist within the phagosomal vacuole, evading antimicrobial defenses. Despite these insights, the impact of copper on the symbiotic relationships between amoebae and bacteria remains poorly understood. In this study, we investigated the effects of copper stress on amoebae and their symbiotic relationships with bacteria. Our findings revealed that elevated copper concentration adversely affected amoeba growth and altered cellular fate. Symbiont type significantly influenced the responses of the symbiotic relationships to copper stress. Beneficial symbionts maintained stability under copper stress, but parasitic symbionts exhibited enhanced colonization of amoebae. Furthermore, copper stress favored the transition of symbiotic relationships between amoebae and beneficial symbionts toward the host's benefit. Conversely, the pathogenic effects of parasitic symbionts on hosts were exacerbated under copper stress. This study sheds light on the intricate response mechanisms of soil amoebae and amoeba-bacteria symbiotic systems to copper stress, providing new insights into symbiotic dynamics under abiotic factors. Additionally, the results underscore the potential risks of copper accumulation in the environment for pathogen transmission and biosafety.

Bacterial heavy metal resistance related to environmental conditions

Contaminated water bodies such as rivers provide reservoirs for bacterial resistance. This field study tested the water quality and the bacterial resistance to heavy metals of Qishan River water pollution. Wastewater discharged to environmental surface waters is a major pathway of heavy metals and heavy metal-resistant bacteria. Contaminated water bodies such as rivers provide reservoirs for bacterial resistance. This field study tested the water quality and bacterial resistance to heavy metals of Qishan River water pollution. Guided by our research hypothesis that an overall increase in downstream heavy metal resistance levels was following an increase in human settlements were eight sites sampled along the Qishan River. These were situated upstream and downstream to the confluence of the Qishan River with the Kaoping River. In the laboratory bacterial heavy metal resistance was bio-assayed by disk diffusion and micro-dilution with six widely used heavy metals. The comparison of bacterial resistance was among Qishan River upstream sites (sites 1-6) and downstream sites (sites 7-9). Multi-drug-resistant bacteria and co-resistance against heavy metals and antibacterials appeared at site 8. This research discusses the correlation between environmental factors, and antibacterial and heavy metal resistance. The results provide stakeholders and authorities responsible for environmental pollution with a reference for risk assessment and management of bacterial resistance.

Deciphering the impacts of chromium contamination on soil bacterial communities: A comparative analysis across various soil types

Addressing the widespread concern of chromium (Cr) pollution, this study investigated its impacts on bacterial communities across eight soil types, alongside the potential Cr transformation-related genes. Utilizing real-time PCR, 16S rRNA gene sequencing and gene prediction, we revealed shifts in bacterial community structure and function at three Cr exposure levels. Our results showed that the bacterial abundance in all eight soil types was influenced by Cr to varying extents, with yellow‒brown soil being the most sensitive. The bacterial community composition of different soil types exhibited diverse responses to Cr, with only the relative abundance of Proteobacteria decreasing with increasing Cr concentration across all soil types. Beta diversity analysis revealed that while Cr concentration impacted the assembly process of bacterial communities to a certain extent, the influence on the compositional structure of bacterial communities was primarily driven by soil type rather than Cr concentration. The study also identified biomarkers for each soil type under three Cr levels, offering a basis for monitoring changes in Cr pollution. By predicting crucial functional genes related to Cr transformation, it was observed that the relative abundance of chrA (chromate transporter) in yellow‒brown soil significantly exceeded that in all other soil types, suggesting its potential for Cr adaptation. The study also revealed correlations among soil physicochemical properties, Cr concentration, and these functional genes, providing a foundation for future research aimed at more precise functional analysis and the development of effective soil remediation strategies.

Genome-wide transcriptional response to silver stress in extremely halophilic archaeon Haloferax alexandrinus DSM 27206 T

BACKGROUND

The extremely halophilic archaeon Haloferax (Hfx.) alexandrinus DSM 27206 T was previously documented for the ability to biosynthesize silver nanoparticles while mechanisms underlying its silver tolerance were overlooked. In the current study, we aimed to assess the transcriptional response of this haloarchaeon to varying concentrations of silver, seeking a comprehensive understanding of the molecular determinants underpinning its heavy metal tolerance.

RESULTS

The growth curves confirmed the capacity of Hfx. alexandrinus to surmount silver stress, while the SEM-EDS analysis illustrated the presence of silver nanoparticles in cultures exposed to 0.5 mM silver nitrate. The RNA-Seq based transcriptomic analysis of Hfx. alexandrinus cells exposed to 0.1, 0.25, and 0.5 mM silver nitrate revealed the differential expression of multiple sets of genes potentially employed in heavy-metal stress response, genes mostly related to metal transporters, basic metabolism, oxidative stress response and cellular motility. The RT-qPCR analysis of selected transcripts was conducted to verify and validate the generated RNA-Seq data.

CONCLUSIONS

Our results indicated that copA, encoding the copper ATPase, is essential for the survival of Hfx. alexandrinus cells in silver-containing saline media. The silver-exposed cultures underwent several metabolic adjustments that enabled the activation of enzymes involved in the oxidative stress response and impairment of the cellular movement capacity. To our knowledge, this study represents the first comprehensive analysis of gene expression in halophillic archaea facing increased levels of heavy metals.

The copper resistance mechanism in a newly isolated Pseudoxanthomonas spadix ZSY-33

Resolving the heavy metal resistance mechanisms of microbes is crucial for understanding the bioremediation of the ecological environment. In this study, a multiple heavy metal resistance bacterium, Pseudoxanthomonas spadix ZSY-33 was isolated and characterized. The copper resistance mechanism was revealed by analysis of the physiological traits, copper distribution, and genomic and transcriptomic data of strain ZSY-33 cultured with different concentrations of copper. The growth inhibition assay in basic medium showed that the growth of strain ZSY-33 was inhibited in the presence of 0.5 mM copper. The production of extracellular polymeric substances increased at a lower concentration of copper and decreased at a higher concentration of copper. Integrative analysis of genomic and transcriptomic, the copper resistance mechanism in strain ZSY-33 was elucidated. At a lower concentration of copper, the Cus and Cop systems were responsible for the homeostasis of intracellular copper. As the concentration of copper increased, multiple metabolism pathways, including the metabolism of sulfur, amino acids, and pro-energy were cooperated with the Cus and Cop systems to deal with copper stress. These results indicated a flexible copper resistance mechanism in strain ZSY-33, which may acquire from the long-term interaction with the living environment.

Heavy-metal tolerant bacterial strains isolated from industrial sites and scrap yards in Kashmir, India

Heavy metal pollution has posed a severe danger to environmental stability due to its high toxicity and lack of biodegradability. The present study deals with the appraisement of tolerance shown by various bacteria in varied copper and iron concentrations. Among the 20 isolates, four isolates, GN2, SC5, SC8, and SC10, exhibiting more significant iron and copper tolerance, were selected and identified by 16 S ribosomal ribonucleic acid (rRNA) gene sequence analysis as Pantoea agglomerans strain GN2, Pantoea sp. strain SC5, Bacillus sp. strain SC8 and Priestia aryabhattaistrain SC10. The minimum inhibitory concentration of molecularly identified strains revealed that P. agglomerans strain GN2 showed tolerance to iron sulfate and copper sulfate upto 600 and 400 µg/mL, whereas Bacillus sp. SC8 (OQ202165) showed tolerance of 700 and 250 µg/mL were tolerant to iron sulfate and copper sulfate up to 700 and 150 µg/mL, respectively. Pantoea sp. strain SC5 showed significant tolerance to both heavy metals. The isolates were further studied for their ability to grow at varying temperatures and pH ranges. Most of the isolates showed optimal growth at 37°C and pH 7. However, Pantoea sp. SC5 was competent to have prominent growth at 45°C and pH 8.0. Microbial remediation, which is eco-friendly, has proven the most effective method for bioremediation of heavy metal-contaminated environments. Using heavy metal-resistant bacteria for microbial remediation of iron and copper-contaminated environments could be a viable and valuable strategy. These isolates could also be used to decontaminate heavy metal-polluted agricultural soils.

Mitigation of heavy metal stress in the soil through optimized interaction between plants and microbes

Agricultural as well as industrial processes, such as mining and textile activities, are just a few examples of anthropogenic activities that have a long-term negative impact on the environment. Each of the aforementioned factors increases the concentration of heavy metals in soil. Heavy metal contamination in soil causes a wide range of environmental issues and is harmful to microbes, plants, and animals. Because of their non-biodegradability and toxic effects, preventing additional metal contamination and remediating the vast majority of contaminated sites around the world is critical. Hence, this review focuses on the effects of metal contamination on soil microbes, as well as plant-microbe interactions. Plant-associated probiotics reduce metal accumulation; the introduction of beneficial microbes is regarded as one of the most promising approaches to improving metal stress tolerance; thus, the study focuses on plant-microbe interactions as well as their actual implications via phytoremediation. Plant-microbe interaction can play an important role in acclimating vegetation (plants) to metalliferous conditions and should thus be studied to improve microbe-aided metal tolerance in plants. Plant-interacted microbes reduce metal accumulation in plant cells and metal bioaccumulation in the soil through a variety of processes. A novel phytobacterial approach, such as genetically modified microbes, is now being used to improve heavy metal cleanup as well as stress tolerance among plants. This review examines our current understanding of such negative consequences of heavy metal stresses, signaling responses, and the role of plant-associated microbiota in heavy metal stress tolerance and interaction.

Quantitative proteomic analysis of the mechanism of Cd toxicity in Enterobacter sp. FM-1: Comparison of different growth stages

Enterobacter sp. are widely used in bioremediation, but the mechanism of Cadmium (Cd) toxicity in Enterobacter sp. has been poorly studied. In the present study, we determined the tolerance of Enterobacter sp. FM-1 to Cd by analyzing the physiological and biochemical responses of FM-1 induced under Cd stress. Differentially expressed proteins (DEPs) under exposure to different Cd environments were analyzed by 4D-label-free proteomics to provide a comprehensive understanding of Cd toxicity in FM-1. The greatest total number of DEPs, 1148, was found in the High concentration vs. Control comparison group at 10 h. When protein expression was compared after different incubation times, FM-1 showed the highest Cd tolerance at 48 h. Additionally, with an increasing incubation time, different comparison groups gradually began to show similar growth patterns, which was reflected in the GO enrichment analysis. Notably, only 815 proteins were identified in the High concentration vs. Control group, and KEGG enrichment analysis revealed that these proteins were significantly enriched in the pyruvate metabolism, oxidative phosphorylation, peroxisome, glyoxylate and dicarboxylate metabolism, and citrate cycle pathways. These results suggested that an increased incubation time allows FM-1 adapt and survive in an environment with Cd toxicity, and protein expression significantly increased in response to oxidative stress in a Cd-contaminated environment during the pre-growth period. This study provides new perspectives on bacterial participation in bioremediation and expands our understanding of the mechanism of bacterial resistance under Cd exposure.

The effects of arsenic on dechlorination of trichloroethene by consortium DH: Microbial response and resistance

Inorganic arsenic and organochlorines are frequently co-occurring contaminants in anoxic groundwater environments, and the bioremediation of their composite pollution has long been a rigorous predicament. Currently, the dechlorination behaviors and stress responses of microbial dechlorination consortia to arsenic are not yet fully understood. This study assessed the reductive dechlorination performance of a Dehalococcoides-bearing microcosm DH under gradient concentrations of arsenate [As(V)] or arsenite [As(III)] and investigated the response patterns of different functional microorganisms. Our results demonstrated that although the dechlorination rates declined with increasing arsenic concentrations in both As(III/V) scenarios, the inhibitory impact was more pronounced in As(III)-amended groups compared to As(V)-amended groups. Moreover, the vinyl chloride (VC)-to-ethene step was more susceptible to arsenic exposure compared to the trichloroethene (TCE)-to-dichloroethane (DCE) step, while high levels of arsenic exposure [e.g. As(III) > 75 μM] can induce significant accumulation of VC. Functional gene variations and microbial community analyses revealed that As(III/V) affected reductive dechlorination by directly inhibiting organohalide-respiring bacteria (OHRB) and indirectly inhibiting synergistic populations such as acetogens. Metagenomic results indicated that arsenic metabolic and efflux mechanisms were identical among different Dhc strains, and variations in arsenic uptake pathways were possibly responsible for their differential responses to arsenic exposures. By comparison, fermentative bacteria showed high potential for arsenic resistance due to their inherent advantages in arsenic detoxification and efflux mechanisms. Collectively, our findings expanded the understanding of the response patterns of different functional populations to arsenic stress in the dechlorinating consortium and provided insights into modifying bioremediation strategies at co-contaminated sites for furtherance.

Plant growth-promoting and heavy metal-resistant Priestia and Bacillus strains associated with pioneer plants from mine tailings

Open mine tailings dams are extreme artificial environments containing sizeable potentially toxic elements (PTEs), including heavy metals (HMs), transition metals, and metalloids. Furthermore, these tailings have nutritional deficiencies, including assimilable phosphorus sources, organic carbon, and combined nitrogen, preventing plant colonization. Bacteria, that colonize these environments, have mechanisms to tolerate the selective pressures of PTEs. In this work, several Priestia megaterium (formerly Bacillus megaterium), Bacillus mojavensis, and Bacillus subtilis strains were isolated from bulk tailings, anthills, rhizosphere, and endosphere of pioneer plants from abandoned mine tailings in Zacatecas, Mexico. Bacillus spp. tolerated moderate HMs concentrations, produced siderophores and indole-3-acetic acid (IAA), solubilized phosphates, and reduced acetylene in the presence of HMs. The strains harbored different PIB-type ATPase genes encoding for efflux pumps and Cation Diffusion Facilitator (CDF) genes. Moreover, nifH and nifD nitrogenase genes were detected in P. megaterium and B. mojavensis genomic DNA. They showed similarity with sequences of the beta-Proteobacteria species, which may represent likely horizontal transfer events. These Bacillus species precede the colonization of mine tailings by plants. Their phenotypic and genotypic features could be essential in the natural recovery of the sites by reducing the oxidative stress of HMs, fixing nitrogen, solubilizing phosphate, and accumulating organic carbon. These traits of the strains reflect the adaptations of Bacillus species to the mine tailings environment and could contribute to the success of phytoremediation efforts.

Genome-resolved metagenomics provides insights into the ecological roles of the keystone taxa in heavy-metal-contaminated soils

Microorganisms that exhibit resistance to environmental stressors, particularly heavy metals, have the potential to be used in bioremediation strategies. This study aimed to explore and identify microorganisms that are resistant to heavy metals in soil environments as potential candidates for bioremediation. Metagenomic analysis was conducted using microbiome metagenomes obtained from the rhizosphere of soil contaminated with heavy metals and mineral-affected soil. The analysis resulted in the recovery of a total of 175 metagenome-assembled genomes (MAGs), 73 of which were potentially representing novel taxonomic levels beyond the genus level. The constructed ecological network revealed the presence of keystone taxa, including Rhizobiaceae, Xanthobacteraceae, Burkholderiaceae, and Actinomycetia. Among the recovered MAGs, 50 were associated with these keystone taxa. Notably, these MAGs displayed an abundance of genes conferring resistance to heavy metals and other abiotic stresses, particularly those affiliated with the keystone taxa. These genes were found to combat excessive accumulation of zinc/manganese, arsenate/arsenite, chromate, nickel/cobalt, copper, and tellurite. Furthermore, the keystone taxa were found to utilize both organic and inorganic energy sources, such as sulfur, arsenic, and carbon dioxide. Additionally, these keystone taxa exhibited the ability to promote vegetation development in re-vegetated mining areas through phosphorus solubilization and metabolite secretion. In summary, our study highlights the metabolic adaptability and ecological significance of microbial keystone taxa in mineral-affected soils. The MAGs associated with keystone taxa exhibited a markedly higher number of genes related to abiotic stress resistance and plant growth promotion compared to non-keystone taxa MAGs.

Endophytic Plant Growth-Promoting Bacterium Bacillus subtilis Reduces the Toxic Effect of Cadmium on Wheat Plants

Heavy metal ions, in particular cadmium (Cd), have a negative impact on the growth and productivity of major crops, including wheat. The use of environmentally friendly approaches, in particular, bacteria that have a growth-stimulating and protective effect, can increase the resistance of plants. The effects of the pre-sowing seed treatment with the plant growth-promoting endophyte Bacillus subtilis 10-4 (BS) on cadmium acetate (Cd)-stressed Triticum aestivum L. (wheat) growth, photosynthetic pigments, oxidative stress parameters, roots' lignin content, and Cd ions accumulation in plants were analyzed. The results showed that the tested Cd-tolerant BS improved the ability of wheat seeds to germinate in the presence of different Cd concentrations (0, 0.1, 0.5, and 1 mM). In addition, the bacterial treatment significantly decreased the damaging effects of Cd stress (1 mM) on seedlings' linear dimensions (lengths of roots and shoots), biomass, as well as on the integrity and permeability of the cell walls (i.e., lipid peroxidation and electrolyte leakage) and resulted in reduced H₂O₂ generation. The pretreatment with BS prevented the Cd-induced degradation of the leaf photosynthetic pigments chlorophyll (Chl) a, Chl b, and carotenoids. Moreover, the bacterial treatment intensified the lignin deposition in the roots under normal and, especially, Cd stress conditions, thereby enhancing the barrier properties of the cell wall. This manifested in a reduced Cd ions accumulation in the roots and in the restriction of its translocation to the aboveground parts (shoots) of the bacterized plants under Cd stress in comparison with non-bacterized controls. Thus, the pre-sowing seed treatment with the endophyte BS may serve as an eco-friendly approach to improve wheat production in Cd-contaminated areas.

Unexpected enrichment of antibiotic resistance genes and organic remediation genes in high-altitude lakes at Eastern Tibetan Plateau

Elevation has a strong effect on aquatic microbiome. However, we know little about the effects of elevation on functional genes, especially antibiotic resistance genes (ARGs) and organic remediation genes (ORGs) in freshwater ecosystems. In this study, we analyzed five classes of functional genes including ARGs, metal resistance genes (MRGs), ORGs, bacteriophages, and virulence genes between two high-altitude lakes (HALs) and two low-altitude lakes (LALs) in Mountain Siguniang at Eastern Tibetan Plateau by means of GeoChip 5.0. No differences (Student's t-test, p > 0.05) of gene richness including ARGs, MRGs, ORGs, bacteriophages, and virulence genes in HALs and LALs were found. The abundance of most ARGs and ORGs was higher in HALs than in LALs. For MRGs, the abundance of macro metal resistance genes of potassium, calcium, and aluminum was higher in HALs than in LALs (Student's t-test, p < 0.05; all Cohen's d > 0.8). The abundance of some heavy metal resistance genes of lead and mercury was lower in HALs than in LALs (Student's t-test, p < 0.05; all Cohen's d < -0.8). The composition of these functional genes in HALs differed significantly from in LALs. The functional gene network in HALs was also more complex than that in LALs. We speculate that enrichment of ARGs and ORGs in HALs is related to different microbial communities, exogenous ARGs, and enriched persistent organic pollutants through long-range atmospheric transport driven by the Indian monsoon. This study highlights the unexpected enrichment of ARGs, MRGs, and ORGs in remote lakes at high elevations.

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

Toxic metal(loid)s are widespread and permanent in the biosphere, and bacteria have evolved a wide variety of metal(loid) resistance genes (MRGs) to resist the stress of excess metal(loid)s. Via active efflux, permeability barriers, extracellular/intracellular sequestration, enzymatic detoxification and reduction in metal(loid)s sensitivity of cellular targets, the key components of bacterial cells are protected from toxic metal(loid)s to maintain their normal physiological functions. Exploiting bacterial metal(loid) resistance mechanisms, MRGs have been applied in many environmental fields. Based on the specific binding ability of MRGs-encoded regulators to metal(loid)s, MRGs-dependent biosensors for monitoring environmental metal(loid)s are developed. MRGs-related biotechnologies have been applied to environmental remediation of metal(loid)s by using the metal(loid) tolerance, biotransformation, and biopassivation abilities of MRGs-carrying microorganisms. In this work, we review the historical evolution, resistance mechanisms, environmental variation, and environmental applications of bacterial MRGs. The potential hazards, unresolved problems, and future research directions are also discussed.

Virulence regulation of Zn2+ uptake system znuABC on mesophilic Aeromonas salmonicida SRW-OG1

Psychrophilic Aeromonas salmonicida could not grow above 25°C and therefore thought unable to infect mammals and humans. In our previous study, a mesophilic A. salmonicida SRW-OG1 was isolated from Epinephelus coioides with furunculosis. Through the analysis of preliminary RNA-seq, it was found that the Zn2+ uptake related genes znuA, znuB and znuC might be involved in the virulence regulation of A. salmonicida SRW-OG1. Therefore, the purpose of this study was to explore the effect of znuABC silencing on the virulence regulation of A. salmonicida SRW-OG1. The results showed that the growth of the znuA-RNAi, znuB-RNAi, and znuC-RNAi strains was severely restricted under the Fe2+ starvation, but surprisingly there was no significant difference under the Zn2+ restriction. In the absence of Zn2+ and Fe2+, the expression level of znuABC was significantly increased. The motility, biofilm formation, adhesion and hemolysis of the znuA-RNAi, znuB-RNAi, and znuC-RNAi strains were significantly reduced. We also detected the expression of znuABC under different growth periods, temperatures, pH, as well as Cu2+ and Pb2+ stresses. The results showed that znuABC was significantly up-regulated in the logarithmic phase and the decline phase of A. salmonicida. Interestingly, the trend of expression levels of the znuABC at 18, 28, and 37°C was reversed to another Zn2+ uptake related gene zupT. Taken together, these indicated that the znuABC was necessary for A. salmonicida SRW-OG1 pathogenicity and environmental adaptability, and was cross regulated by iron starvation, but it was not irreplaceable for A. salmonicida SRW-OG1 Zn2+ uptake in the host.

Use of nanoparticle-coated bacteria for the bioremediation of organic pollution: A mini review

Nanoparticle (NP)-coated (immobilized) bacteria are an effective method for treating environmental pollution due to their multifarious benefits. This review collates a vast amount of existing literature on organic pollution treatment using NP-coated bacteria. We discuss the features of bacteria, NPs, and decoration techniques of NP-bacteria assemblies, with special attention given to the surface modification of NPs and connection mechanisms between NPs and cells. Furthermore, the performance of NP-coated bacteria was examined. We summarize the factors that affect bioremediation efficiency using coated bacteria, including pH, temperature, and agitation, and the possible mechanisms involving them are proposed. From future perspectives, suitable surface modification of NPs and wide application in real practice will make the NP-coated bacterial technology a viable treatment strategy.

Biodegradation of Crystalline and Nonaqueous Phase Liquid-Dissolved ATRAZINE by Arthrobacter sp. ST11 with Cd2+ Resistance

A newly isolated cadmium (Cd)-resistant bacterial strain from herbicides-polluted soil in China could use atrazine as the sole carbon, nitrogen, and energy source for growth in a mineral salt medium (MSM). Based on 16S rRNA gene sequence analysis and physiochemical tests, the bacterium was identified as Arthrobacter sp. and named ST11. The biodegradation of atrazine by ST11 was investigated in experiments, with the compound present either as crystals or dissolved in di(2-ethylhexyl) phthalate (DEHP) as a non-aqueous phase liquid (NAPL). After 48 h, ST11 consumed 68% of the crystalline atrazine in MSM. After being dissolved in DEHP, the degradation ratio of atrazine was reduced to 55% under the same conditions. Obviously, the NAPL-dissolved atrazine has lower bioavailability than the crystalline atrazine. Cd2+ at concentrations of 0.05–1.5 mmol/L either had no effect (<0.3 mmol/L), slight effects (0.5–1.0 mmol/L), or significantly (1.5 mmol/L) inhibited the growth of ST11 in Luria-Bertani medium. Correspondingly, in the whole concentration range (0.05–1.5 mmol/L), Cd2+ promoted ST11 to degrade atrazine, whether crystalline or dissolved in DEHP. Refusal to adsorb Cd2+ may be the main mechanism of high Cd resistance in ST11 cells. These results may provide valuable insights for the microbial treatment of arable soil co-polluted by atrazine and Cd.

Genomic Characterization of Aureimonas altamirensis C2P003-A Specific Member of the Microbiome of Fraxinus excelsior Trees Tolerant to Ash Dieback

Some European ash trees show tolerance towards dieback caused by the invasive pathogen Hymenoscyphus fraxineus. The microbiome of these trees harbours a range of specific bacterial groups. One of these groups belonging to the species Aureimonas altamirensis was studied in detail by genome analysis and a plant inoculation trial. The strain group was shown to be phylogenetically distinct from clinical isolates by 16S rRNA analysis and phylogenomics. Genome analysis of a representative strain C2P003 resulted in a large number of unique gene sequences in comparison to other well-studied strains of the species. A functional analysis of the genome revealed features associated with the synthesis of exopolysaccharides, protein secretion and biofilm production as well as genes for stress adaptation, suggesting the ability of C2P003 to effectively colonize ash leaves. The inoculation of ash seedlings with C2P003 showed a significant positive effect on the plant health of the seedlings that were exposed to H. fraxineus infection. This effect was maintained over a period of three years and was accompanied by a significant shift in the bacterial microbiome composition one year after inoculation. Overall, the results indicate that C2P003 may suppress H. fraxineus in or on ash leaves via colonization resistance or indirectly by affecting the microbiome.

Impact of key parameters involved with plant-microbe interaction in context to global climate change

Anthropogenic activities have a critical influence on climate change that directly or indirectly impacts plant and microbial diversity on our planet. Due to climate change, there is an increase in the intensity and frequency of extreme environmental events such as temperature rise, drought, and precipitation. The increase in greenhouse gas emissions such as CO2, CH4, NOx, water vapor, increase in global temperature, and change in rainfall patterns have impacted soil–plant-microbe interactions, which poses a serious threat to food security. Microbes in the soil play an essential role in plants’ resilience to abiotic and biotic stressors. The soil microbial communities are sensitive and responsive to these stressors. Therefore, a systemic approach to climate adaptation will be needed which acknowledges the multidimensional nature of plant-microbe-environment interactions. In the last two scores of years, there has been an enhancement in the understanding of plant’s response to microbes at physiological, biochemical, and molecular levels due to the availability of techniques and tools. This review highlights some of the critical factors influencing plant-microbe interactions under stress. The association and response of microbe and plants as a result of several stresses such as temperature, salinity, metal toxicity, and greenhouse gases are also depicted. New tools to study the molecular complexity of these interactions, such as genomic and sequencing approaches, which provide researchers greater accuracy, reproducibility, and flexibility for exploring plant-microbe–environment interactions under a changing climate, are also discussed in the review, which will be helpful in the development of resistant crops/plants in present and future.

A Review of the Role of Extracellular Polymeric Substances (EPS) in Wastewater Treatment Systems

A review of the characterization and functions of extracellular polymeric substances (EPS) of microbial aggregates in biological wastewater treatment systems is presented in this paper. EPS represent the complex high-molecular-weight mixture of polymers excreted by microorganisms generated from cell lysis as well as adsorbed inorganic and organic matter from wastewater. EPS exhibit a three-dimensional, gel-like, highly hydrated matrix that facilitates microbial attachment, embedding, and immobilization. EPS play multiple roles in containments removal, and the main components of EPS crucially influence the properties of microbial aggregates, such as adsorption ability, stability, and formation capacity. Moreover, EPS are important to sludge bioflocculation, settleability, and dewatering properties and could be used as carbon and energy sources in wastewater treatment. However, due to the complex structure of EPS, related knowledge is incomplete, and further research is necessary to understand fully the precise roles in biological treatment processes.

Distribution Pattern and Influencing Factors of Heavy Metal Resistance Genes in the Yellow River Sediments of Henan Section

The transformation of heavy metal resistance genes (MRGs) in the environment has attracted increasing attention in recent years. However, few studies have reported the MRG content in the Yellow River, one of the main irrigation water sources in the North China Plain. In this study, we quantified MRG abundance by a metagenomic approach, and assessed the influence on MRGs of both bioavailable and total heavy metal (HM) content. The results indicate that Cu-resistant genes are the most common genes, and the prevalence of arsM needs more attention. Comamonadaceae is the dominant family in the Yellow River, and the presence of organic pollutants may contribute to the prevalence of Vicinamibacteraceae, Nocardioidaceae, and Flavobacteriacea. The results of the Mantel test and Spearman analysis indicate that both the bioavailable fractions and total content of HMs could have little influence on MRGs. Network analysis results indicate that some dominant bacteria could be the potential hosts of some prevalent MRGs, which may exert an adverse impact on human health.

Synergistic Antibacterial Activity of Green Synthesized Silver Nanomaterials with Colistin Antibiotic against Multidrug-Resistant Bacterial Pathogens

The high frequency of nosocomial bacterial infections caused by multidrug-resistant pathogens contributes to significant morbidity and mortality worldwide. As a result, finding effective antibacterial agents is of critical importance. Hence, the aim of the present study was to greenly synthesize silver nanoparticles (AgNPs) utilizing Salvia officinalis aqueous leaf extract. The biogenic AgNPs were characterized utilizing different physicochemical techniques such as energy-dispersive X-ray spectroscopy (EDX), ultraviolet-visible spectrophotometry (UV-Vis), X-ray diffraction analysis (XRD), transmission electron microscopy (TEM), and Fourier transform infrared spectroscopy (FT-IR) analysis. Additionally, the synergistic antimicrobial effectiveness of the biosynthesized AgNPs with colistin antibiotic against multidrug-resistant bacterial strains was evaluated utilizing the standard disk diffusion assay. The bioformulated AgNPs revealed significant physicochemical features, such as a small particle size of 17.615 ± 1.24 nm and net zeta potential value of −16.2 mV. The elemental mapping of AgNPs revealed that silver was the main element, recording a relative mass percent of 83.16%, followed by carbon (9.51%), oxygen (5.80%), silicon (0.87%), and chloride (0.67%). The disc diffusion assay revealed that AgNPs showed antibacterial potency against different tested bacterial pathogens, recording the highest efficiency against the Escherichia coli strain with an inhibitory zone diameter of 37.86 ± 0.21 mm at an AgNPs concentration of 100 µg/disk. In addition, the antibacterial activity of AgNPs was significantly higher than that of colistin (p ≤ 0.05) against the multidrug resistant bacterial strain namely, Acinetobacter baumannii. The biosynthesized AgNPs revealed synergistic antibacterial activity with colistin antibiotic, demonstrating the highest synergistic percent against the A. baumannii strain (85.57%) followed by Enterobacter cloacae (53.63%), E. coli (35.76%), Klebsiella pneumoniae (35.19%), Salmonella typhimurium (33.06%), and Pseudomonas aeruginosa (13.75%). In conclusion, the biogenic AgNPs revealed unique physicochemical characteristics and significant antibacterial activities against different multidrug-resistant bacterial pathogens. Consequently, the potent synergistic effect of the AgNPs–colistin combination highlights the potential of utilizing this combination for fabrication of highly effective antibacterial coatings in intensive care units for successful control of the spread of nosocomial bacterial infections.

A critical review of mineral-microbe interaction and coevolution: mechanisms and applications

The mineral-microbe interactions play important roles in environmental change, biogeochemical cycling of elements, and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation, and precipitation of minerals through their activity, resulting in either genetically-controlled or metabolism-induced biomineralization. Through these interactions minerals and microbes coevolve through Earth history. The mineral-microbe interactions typically occur at microscopic scale but the effect is often manifested at global scale. Despite advances achieved through decades of research, major questions remain. Four areas are identified for future research: integrating mineral and microbial ecology, establishing mineral biosignatures, linking laboratory mechanistic investigation to field observation, and manipulating mineral-microbe interactions for the benefit of humankind.

Biochemical and Metabolomic Responses of Antarctic Bacterium Planococcus sp. O5 Induced by Copper Ion

Heavy metal pollution in the Antarctic has gone beyond our imagination. Copper toxicity is a selective pressure on Planococcus sp. O5. We observed relatively broad tolerance in the polar bacterium. The heavy metal resistance pattern is Pb2+ > Cu2+ > Cd2+ > Hg2+ > Zn2+. In the study, we combined biochemical and metabolomics approaches to investigate the Cu2+ adaptation mechanisms of the Antarctic bacterium. Biochemical analysis revealed that copper treatment elevated the activity of antioxidants and enzymes, maintaining the bacterial redox state balance and normal cell division and growth. Metabolomics analysis demonstrated that fatty acids, amino acids, and carbohydrates played dominant roles in copper stress adaptation. The findings suggested that the adaptive mechanisms of strain O5 to copper stress included protein synthesis and repair, accumulation of organic permeable substances, up-regulation of energy metabolism, and the formation of fatty acids.