A subcellular level study of copper speciation reveals the synergistic mechanism of microbial cells and EPS involved in copper binding in bacterial biofilms

Interaction of biochar with extracellular polymers of resistant bacteria restrains Pb(II) adsorption onto their composite: Macro and micro scale investigations

Pb(II) sequestration in extracellular polymers-biochar composites (EPS-BC) was explored using macroscopic models and microscopic technology. The results showed that the actual adsorption capacity of EPS-BC was 52.2% lower than the calculated capacity based on adsorption onto pure components due to the interaction of polysaccharide and amide group in extracellular polymers with biochar, which masked the reactive sites related to Pb(II) in EPS-BC. The bond of Pb-O (40.8%) and Pb-OOC (31.5%) mainly contributed to Pb(II) speciation on the EPS-BC surfaces. Furthermore, each Pb atom coordinated with 6O atoms in the first shell and with 0.5C atoms in the second shell, indicating that the carboxyl group in composite was complexed with Pb(II) as a monodentate inner-sphere structure. The findings provide an in-depth understanding of the adsorption mechanism of heavy metals by extracellular polymers coupled with biochar at molecular scale, guiding bioremediation with respect to heavy metal contamination.

Absence of synergistic effects between microplastics and copper ions on the spread of antibiotic resistance genes within aquatic bacteria at the community level

Microplastics and copper ions (Cu2+) are favorable in accelerating the propagation of antibiotic resistance genes (ARGs) in the plastisphere, however, their combined effects on the ARG spread within the bacterial community of the natural environment were less understood. The influence of microplastic types and Cu2+ concentrations on the horizontal gene transfer (HGT) of ARGs mediated by RP4 plasmid within natural bacterial communities in aquatic environments was investigated. Both biodegradable polybutylene succinate (PBS) and non-biodegradable polyvinyl chloride (PVC) microplastics significantly enhanced the transfer of ARGs, with PBS showing a significant higher effect compared to PVC. Cu2+ also increased transconjugation rates at environmentally relevant concentrations (5 μg L-1), but higher levels (50 μg L-1) lead to decreased rates due to severe bacterial cell membrane damage. The transconjugation rates in the presence of both microplastics and Cu2+ were lower than the sum of their individual effects, indicating no synergistic effects between them on transconjugation. Proteobacteria dominated the composition of transconjugates for all the treatment. Transmission electron microscope images and reactive oxygen species production in bacterial cells indicated that the increased contact frequency due to extracellular polymeric substances, combined with enhanced membrane permeability induced by microplastics and Cu2+, accounted for the increasing transconjugation rates. The study provides valuable insight into the potential effects of microplastics and heavy metals on the spread of ARGs from donors to bacterial communities in natural environments.

Deletion of pyoverdine-producing pvdA increases cadmium stabilization by Pseudomonas umsongensis CR14 in cadmium-polluted solutions

In this study, the effects of the Cd-resistant and pyoverdine-producing strain Pseudomonas umsongensis CR14 on Cd stabilization and the mechanisms were investigated. Compared with the control, CR14 markedly reduced the Cd concentration in a Cd-containing solution. The genes pvdA, 4498, 4499, and pchF, which are associated with pyoverdine production, were identified in CR14. Subsequently, CR14 and the CR14ΔpvdA, CR14Δ4498, CR14Δ4499, and CR14ΔpchF mutants were characterized for their effects on Cd stabilization in solution. After 72 h of incubation, the CR14ΔpchF and CR14ΔpvdA mutants significantly decreased Cd concentrations compared with CR14. Notably, the CR14ΔpvdA mutant showed a greater impact on Cd stabilization than the other mutants. Compared with CR14, this mutant brought a lower Cd concentration in the solution, with higher levels of cell surface-adsorbed and intracellular accumulated Cd, content of lipopolysaccharide (LPS), expression of the LPS-producing genes lptD and lpxL, and cell surface particles. Additionally, compared with CR14, the CR14ΔpvdA mutant demonstrated increased interactions between the hydroxyl, carboxyl, amino, or ether groups and Cd. These results suggest that the CR14ΔpvdA mutant immobilized Cd by increasing LPS production and cell surface particle numbers, upregulating the expression of LPS-producing genes, and increasing cell surface adsorption and intracellular accumulation in Cd-polluted solutions.

A comparative biomonitoring study of trace metals and organic compounds bioaccumulation in marine biofilms and caged mussels along the French Mediterranean coast

The bioaccumulation potential of contaminants in marine environments was investigated in biofilms and compared with caged mussels for a wide range of both organic and metallic contaminants across a large geographic area. Marine biofilms were sampled after three months of sub-surface immersion at 49 locations along the 1800 km of the French Mediterranean coast. Ten chemical elements (i.e. As, Cd, Co, Cr, Cu, Hg, Mn, Ni, Pb, and Zn) and 57 organic compounds (i.e., 18 polycyclic aromatic hydrocarbons (PAHs), 8 dioxin-like and 6 non-dioxin-like polychlorinated biphenyls (PCBs) and 25 organochlorine pesticides (OCPs)) were quantified in triplicates, revealing different multi-contaminated profiles depending on sites. Most of contaminants exhibited higher concentrations in biofilms than in mussels. Moreover, a remarkable significant and positive correlation between the concentrations in both biological matrices was observed for PAHs and PCBs, and more contaminant-dependent for OCPs and metals. These results highlighted the potential of biofilms as relevant bioindicators of the marine chemical contamination.

Synergistic bioremediation of petroleum-contaminated soil using immobilized consortium of Rhodococcus rhodochrous and Bacillus subtilis laccase

Petroleum-contaminated soil represents a significant environmental and public health challenge on a global scale. Microbial bioremediation has shown potential, yet the role of enzymes in enhancing petroleum degradation remains underexplored. In this study, the synergistic effects of Rhodococcus rhodochrous (R.rh) and Bacillus subtilis-derived laccase (BsLac) was investigated in the remediation of petroleum-contaminated soil. Immobilized R.rh (PSIMRH) and BsLac (ADIMLac) exhibited higher petroleum degradation rates than their free state, achieving 78.3% and 56.3% degradation in liquid systems, respectively. The combined treatment of PSIMRH and ADIMLac demonstrated a synergistic effect on petroleum degradation, achieving 43.6% with a maximum degradation constant of 0.0335 d-1, representing a 202.7% improvement over untreated soil. PSIMRH enhanced petroleum degradation through microbial metabolism, while ADIMLac accelerated the initial breakdown of complex hydrocarbons into simpler, more bioavailable ones via enzymatic oxidation, providing growth substrates for microbes and significantly improving petroleum degradation rates. The microbial analysis revealed an increase abundance of known petroleum-degrading bacterial genera, including Rhodococcus, Lysobacter, Micromonospora, and Streptomyces. However, the presence of BsLac appeared to reduce the competitive advantage of Rhodococcus, promoting the proliferation of indigenous strains like Lysobacter and Streptomyces. These results suggest that enzyme-microbe synergy can enhance the bioremediation process by altering microbial community dynamics and accelerating petroleum degradation. This study attempts to remediate petroleum-contaminated pollution with the combined use of strains and enzymes, providing a new approach for the remediation of other pollution problems.

Microbial extracellular polymeric substances in the environment, technology and medicine

Microbial biofilms exhibit a self-produced matrix of extracellular polymeric substances (EPS), including polysaccharides, proteins, extracellular DNA and lipids. EPS promote interactions of the biofilm with other cells and sorption of organics, metals and chemical pollutants, and they facilitate cell adhesion at interfaces and ensure matrix cohesion. EPS have roles in various natural environments, such as soils, sediments and marine habitats. In addition, EPS are relevant in technical environments, such as wastewater and drinking water treatment facilities, and water distribution systems, and they contribute to biofouling and microbially influenced corrosion. In medicine, EPS protect pathogens within the biofilm against the host immune system and antimicrobials, and emerging evidence suggests that EPS can represent potential virulence factors. By contrast, EPS yield a wide range of valuable products that include their role in self-repairing concrete. In this Review, we aim to explore EPS as a functional unit of biofilms in the environment, in technology and in medicine.

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.

Transport and transformations of cadmium in water-biofilm-sediment phases as affected by hydrodynamic conditions

Hydrodynamic conditions play a crucial role in governing the fate, transport, and risks of metal elements. However, the contribution of hydrodynamic conditions to the fate and transport of heavy metals among water, sediment, and biofilm phases is poorly understood. In our study, we conducted experiments in controlled hydrodynamic conditions using a total of 6 two-phase and 9 three-phase mesocosms consisting of water, biofilm, and sediment. We also measured Cd (cadmium) specification in different phases to assess how hydrodynamic forces control Cd bioavailability. We found that turbulent flow destroyed the surface morphology of the biofilm and significantly decreased the content of extracellular polymeric substances (p < 0.05). This led to a decrease in the biofilm's adsorption capacity for Cd, with the maximum adsorption capacity (0.124 mg/g) being one-tenth of that under static conditions (1.256 mg/g). The Cd chemical forms in the biofilm and sediment were significantly different, with the highest amount of Cd in the biofilm being acid-exchangeable, accounting for up to 95.1% of the total Cd content. Cd was more easily released in the biofilm due to its weak binding state, while Cd in the sediment existed in more stable chemical forms. Hydrodynamic conditions altered the migration behavior and distribution characteristics of Cd in the system by changing the adsorption capacity of the biofilm and sediment for Cd. Cd mobility increased in laminar flow but decreased in turbulent flow. These results enhance our understanding of the underlying mechanisms that control the mobility and bioavailability of metals in aquatic environments with varying hydrodynamic conditions.

Integrative chemical, physiological, and metabolomics analyses reveal nanospecific phytotoxicity of metal nanoparticles

The increasing application of metal nanoparticles (NPs) via agrochemicals and sewage sludge results in non-negligible phytotoxicological risks. Herein, the potential phytotoxicity of ZnO and CuO NPs on wheat was determined using integrative chemical, physiological, and metabolomics analyses, in comparison to Zn2+ and Cu2+. It was found that ZnO or CuO NPs had a stronger inhibitory effect on wheat growth than Zn2+ or Cu2+. After exposure to ZnO or CuO NPs, wheat seedlings accumulated significantly higher levels of Zn or Cu than the corresponding Zn2+ or Cu2+ treatments, indicating the active uptake of NPs via wheat root. TEM analysis further confirmed the intake of NPs. Moreover, ZnO or CuO NPs exposure altered micronutrients (Fe, Mn, Cu, and Zn) accumulation in the tissues and decreased the activities of antioxidant enzymes. The metabolomics analysis identified 312, 357, 145, and 188 significantly changed metabolites (SCMs) in wheat root exposed to ZnO NPs, CuO NPs, Zn2+, and Cu2+, respectively. Most SCMs were nano-specific to ZnO (80%) and CuO NPs (58%), suggesting greater metabolic reprogramming by NPs than metal ions. Overall, nanospecific toxicity dominated the phytotoxicity of ZnO and CuO NPs, and our results provide a molecular perspective on the phytotoxicity of metal oxide NPs.

Distribution of copper-binding ligands in Fram Strait and influences from the Greenland Shelf (GEOTRACES GN05)

The Fram Strait represents the major gateway of Arctic Ocean waters towards the Nordic Seas and North Atlantic Ocean and is a key region to study the impact of climate change on biogeochemical cycles. In the region, information about trace metal speciation, such as copper, is scarce. This manuscript presents the concentrations and conditional stability constants of copper-binding ligands (LCu and log KcondCu2+L) in the water column of Fram Strait and the Greenland shelf (GEOTRACES cruise GN05). Cu-binding ligands were analysed by Competitive Ligand Exchange-Adsorptive Cathodic Stripping Voltammetry (CLE-ACSV) using salicylaldoxime (SA) as competitive ligand. Based on water masses and the hydrodynamic influences, three provinces were considered (coast, shelf, and Fram Strait) and differences were observed between regions and water masses. The strongest variability was observed in surface waters, with increasing LCu concentrations (mean values: Fram Strait = 2.6 ± 1.0 nM; shelf = 5.2 ± 1.3 nM; coast = 6.4 ± 0.8 nM) and decreasing log KcondCu2+L values (mean values: Fram Strait = 15.7 ± 0.3; shelf = 15.2 ± 0.3; coast = 14.8 ± 0.3) towards the west. The surface LCu concentrations obtained above the Greenland shelf indicate a supply from the coastal environment to the Polar Surface Water (PSW) which is an addition to the ligand exported from the central Arctic to Fram Strait. The significant differences (in terms of LCu and log KcondCu2+L) between shelf and coastal samples were explained considering the processes which modify ligand concentrations and binding strengths, such as biological activity in sea-ice, phytoplankton bloom in surface waters, bacterial degradation, and meltwater discharge from 79NG glacier terminus. Overall, the ligand concentration exceeded those of dissolved Cu (dCu) and kept the free copper (Cu2+) concentrations at femtomolar levels (0.13-21.13 fM). This indicates that Cu2+ toxicity limits were not reached and dCu levels were stabilized in surface waters by organic complexes, which favoured its transport to the Nordic Seas and North Atlantic Ocean and the development of microorganism.

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.

The co-presence of polystyrene nanoplastics and ofloxacin demonstrates combined effects on the structure, assembly, and metabolic activities of marine microbial community

Nanoplastic is increasing in environments and can address toxic effects on various organisms. Particle size, concentration, and surface functionalization most influence nanoplastic toxicity. Besides, nanoplastic can adsorb other contaminants (e.g., antibiotics) to aggravate its adverse effects. The combined effects of nanoplastics and antibiotics on planktonic/benthic microbial communities, however, are still largely unknown. In this study, the combined effects of polystyrene nanoplastic and ofloxacin on the structure, assembly, and metabolic activities of marine microbial communities were investigated based on amplicon sequencing data. The results mainly demonstrate that: (1) nanoplastic and ofloxacin have greater impacts on prokaryotic communities than eukaryotic ones; (2) niche breadths of planktonic prokaryotes and benthic eukaryotes were shrank with both high nanoplastic and ofloxacin concentrations; (3) increased ofloxacin mainly reduces nodes/edges of co-occurrence networks, while nanoplastic centralizes network modularity; (4) increased nanoplastic under high ofloxacin concentration induces more differential prokaryotic pathways in planktonic communities, while benthic communities are less influenced. The present work indicates that co-presence of nanoplastics and ofloxacin has synergistic combined effects on community structure shifts, niche breadth shrinking, network simplifying, and differential prokaryotic pathways inducing in marine microbial communities, suggesting nanoplastics and its combined impacts with other pollutions should be paid with more concerns.

New Insights on Biological Activities, Chemical Compositions, and Classifications of Marine Actinomycetes Antifouling Agents

Biofouling is the assemblage of undesirable biological materials and macro-organisms (barnacles, mussels, etc.) on submerged surfaces, which has unfavorable impacts on the economy and maritime environments. Recently, research efforts have focused on isolating natural, eco-friendly antifouling agents to counteract the toxicities of synthetic antifouling agents. Marine actinomycetes produce a multitude of active metabolites, some of which acquire antifouling properties. These antifouling compounds have chemical structures that fall under the terpenoids, polyketides, furanones, and alkaloids chemical groups. These compounds demonstrate eminent antimicrobial vigor associated with antiquorum sensing and antibiofilm potentialities against both Gram-positive and -negative bacteria. They have also constrained larval settlements and the acetylcholinesterase enzyme, suggesting a strong anti-macrofouling activity. Despite their promising in vitro and in vivo biological activities, scaled-up production of natural antifouling agents retrieved from marine actinomycetes remains inapplicable and challenging. This might be attributed to their relatively low yield, the unreliability of in vitro tests, and the need for optimization before scaled-up manufacturing. This review will focus on some of the most recent marine actinomycete-derived antifouling agents, featuring their biological activities and chemical varieties after providing a quick overview of the disadvantages of fouling and commercially available synthetic antifouling agents. It will also offer different prospects of optimizations and analysis to scale up their industrial manufacturing for potential usage as antifouling coatings and antimicrobial and therapeutic agents.

A mini-review on indigenous microbial biofilm from various wastewater for heavy-metal removal - new trends

Biofilm, as a form of the microbial community in nature, represents an evolutionary adaptation to the influence of various environmental conditions. In nature, the largest number of microorganisms occur in the form of multispecies biofilms. The ability of microorganisms to form a biofilm is one of the reasons for antibiotic resistance. The creation of biofilms resistant to various contaminants, on the other hand, improves the biological treatment process in wastewater treatment plants. Heavy metals cannot be degraded, but they can be transformed into non-reactive and less toxic forms. In this process, microorganisms are irreplaceable as they interact with the metals in a variety of ways. The environment polluted by heavy metals, such as wastewater, is also a source of undiscovered microbial diversity and specific microbial strains. Numerous studies show that biofilm is an irreplaceable strategy for heavy metal removal. In this review, we systematize recent findings regarding the bioremediation potential of biofilm-forming microbial species isolated from diverse wastewaters for heavy metal removal. In addition, we include some mechanisms of action, application possibilities, practical issues, and future prospects.

Heavy metal removal by the photosynthetic microbial biomat found within shallow unit process open water constructed wetlands

Nature-based solutions offer a sustainable alternative to labor and chemical intensive engineered treatment of metal-impaired waste streams. Shallow, unit process open water (UPOW) constructed wetlands represent a novel design where benthic photosynthetic microbial mats (biomat) coexist with sedimentary organic matter and inorganic (mineral) phases, creating an environment for multiple-phase interactions with soluble metals. To query the interplay of dissolved metals with inorganic and organic fractions, biomat was harvested from two distinct systems: the demonstration-scale UPOW within the Prado constructed wetlands complex ("Prado biomat", 88 % inorganic) and a smaller pilot-scale system ("Mines Park (MP) biomat", 48 % inorganic). Both biomats accumulated detectable background concentrations of metals of toxicological concern (Zn, Cu, Pb, and Ni) by assimilation from waters that did not exceed regulatory thresholds for these metals. Augmentation in laboratory microcosms with a mixture of these metals at ecotoxicologically relevant concentrations revealed a further capacity for metal removal (83-100 %). Experimental concentrations encapsulated the upper range of surface waters in the metal-impaired Tambo watershed in Peru, where a passive treatment technology such as this could be applied. Sequential extractions demonstrated that metal removal by mineral fractions is more important in Prado than MP biomat, possibly due to a higher proportion and mass of iron and other minerals from Prado-derived materials. Geochemical modeling using PHREEQC suggests that in addition to sorption/surface complexation of metals to mineral phases (modeled as iron (oxyhydr)oxides), diatom and bacterial functional groups (carboxyl, phosphoryl, and silanol) also play an important role in soluble metal removal. By comparing sequestered metal phases across these biomats with differing inorganic content, we propose that sorption/surface complexation and incorporation/assimilation of both inorganic and organic constituents of the biomat play a dominant role in metal removal potential by UPOW wetlands. This knowledge could be applied to passively treat metal impaired waters in analogous and remote regions.

Microbial extracellular polymeric substances alleviate cadmium toxicity in rice (Oryza sativa L.) by regulating cadmium uptake, subcellular distribution and triggering the expression of stress-related genes

Cadmium (Cd) accumulation in crops causes potential risks to human health. Microbial extracellular polymeric substances (EPS) are a complex mixture of biopolymers that can bind various heavy metals. The present work examined the alleviating effects of EPS on Cd toxicity in rice and its detoxification mechanism. The 100 μM Cd stress hampered the overall plant growth and development, damaged the ultrastructures of both leaf and root cells, and caused severe lipid peroxidation in rice plants. However, applying EPS at a concentration of 100 mg/L during Cd stress resulted in increased biomass, reduced Cd accumulation and transport, and minimized the oxidative damage. EPS application also enhanced Cd retention in the shoot cell walls and root vacuoles, and actively altered the expression of genes involved in cell wall formation, antioxidant defense systems, transcription factors, and hormone metabolism. These findings provide new insights into EPS-mediated mitigation of Cd stress in plants and help us to develop strategies to improve crop yield in Cd-contaminated soils in the future.

The stringent response gene rsh plays multiple roles in Novosphingobium pentaromativorans US6-1's accommodation to different environmental pollutants: Phenanthrene, copper and nZVI

The rsh based stringent response system is widely employed by bacteria to cope with environmental stresses. However, how does the stringent response involve in bacterial accommodation to environmental pollutant is largely unexplored. In this study, to comprehensively understand the roles of rsh in Novosphingobium pentaromativorans US6-1's metabolism and accommodation to different pollutants, three distinct pollutants, phenanthrene, copper and nanoparticulated zero valent iron (nZVI) were selected as exposure substances. Results indicated that rsh played important roles in US6-1's multiplication and metabolism, including survival rate at stationary phase, amino acid and nucleotide metabolism, extracellular polymeric substance (EPS) production, redox homeostasis, etc. The deletion of rsh affected phenanthrene removal rates through regulating the multiplication of US6-1 and increasing the expression of degradation related genes. The rsh mutant showed higher resistance to copper than the wild type, largely due to higher EPS production and enhanced expression of copper resistance related genes. Finally, the rsh based stringent response helped maintain the redox homeostasis when US6-1 confronted nZVI particles that exerted oxidative stress, thereby improving the survival rate. Overall, this study provides firsthand data that rsh plays multiple roles in US6-1's accommodation to environmental pollutants. The stringent response system could be a powerful tool for environmental scientists and engineers to harness bacterial activities for bioremediation purposes.

Multi-omics eco-surveillance of bacterial community function in legacy contaminated estuary sediments

Complex legacy contamination is a major issue for many estuaries, with toxicity affecting change in bacterial communities, and their provision of associated goods and services. Sequencing surveys of bacterial community composition provide inferred function; however, additional insights may be generated by measurement of realised metabolic phenotypes. We apply multi-omics (genomics, lipidomics, and metabolomics), with traditional sediment quality analyses, to characterise sediment-associated bacterial communities in an estuary subject to legacy metal contamination (Zn, Hg, As, Cd, Cu and Pb). Analyses of bacterial composition and inferred function (genomics) are coupled with measurements of realised bacterial phenotype (metabolomics and lipidomics) at multiple industrialised and reference sites. At sites with the highest sediment metal concentrations (NTB), we also observed increased abundances of hydrocarbon and sulphuric acid metabolites, indicating additional sediment contamination. Bacterial phyla across sampled sites were dominated by Proteobacteria and Desulfobacteria. NTB sites were enriched with metabolically versatile, cooperative and biofilm forming phyla including, Zixibacteria, Spirochaetota, SAR324 clade, Proteobacteria, Latescibacterota, Desulfobacterota, Deferrisomtota and Acidobateriota; with inferred functions characterised by sulphur metabolism, pathways associated with the degradation of complex organic molecules, and fermentation. Reference sites were characterised by enhanced vitamin biosynthesis, cell wall, cofactor and carbohydrate biosynthesis, and CO₂ fixation. Measured metabolic phenotypes at NTB sites supported predicted functions, with most consistent change observed to naphthalene and aminobenzoate degradation pathways and carbohydrate metabolism (galactose, amino and nucleotide sugar). Change in NTB metabolite profiles was most highly correlated with sediment Hg concentrations, indicative of toxic exposure and potential for Hg methylation. Lipid profiles generated further insight into potential functional (hydroxy fatty acids) and community level change (ceramide phosphoethanolamines, unsaturated glycerides). Multi-omics outputs provided insights into bacterial community functions, modes of contaminant toxicity and expressed mechanisms of adaptation, necessary to better inform management decisions and predictive models in increasingly human-influenced environments.

Transcriptome analysis of the biofilm formation mechanism of Vibrio parahaemolyticus under the sub-inhibitory concentrations of copper and carbenicillin

Biofilm formation of Vibrio parahaemolyticus enhanced its tolerance to the environment, but caused many serious problems to food safety and human health. In this paper, the effects of copper and carbenicillin (CARB) stress on the formation of the biofilms of V. parahaemolyticus organisms were studied, and RNA sequencing technology was used to compare the differences in transcriptome profiles of the biofilm-related genes of V. parahaemolyticus organisms under different sub-inhibitory stresses. The results proved that V. parahaemolyticus had a large growth difference under the two stresses, copper and CARB at 1/2 minimal inhibitory concentration (MIC), and it could form a stable biofilm under both stress conditions. The amount of biofilm formed under CARB stress was significantly higher than that of copper stress (p < 0.05). Based on the analysis of transcriptome sequencing results 323, 1,550, and 1,296 significantly differential expressed genes were identified in the three treatment groups namely 1/2 MIC CARB, Cu²⁺, and Cu²⁺+CARB. Through COG annotation, KEGG metabolic pathway analysis and gene expression analysis related to biofilm formation, the functional pathways of transcriptome changes affecting V. parahaemolyticus were different in the three treatment groups, and the CARB treatment group was significantly different from the other two groups. These differences indicated that the ABC transport system, two-component system and quorum sensing were all involved in the biofilm formation of the V. parahaemolytic by regulating flagellar motility, extracellular polysaccharides and extracellular polymer synthesis. Exploring the effects of different stress conditions on the transcriptome of V. parahaemolyticus could provide a basis for future research on the complex network system that regulates the formation of bacterial biofilms.

Response of electroactive biofilms from real wastewater to metal ion shock in bioelectrochemical systems

The electrochemical activity of bioelectrochemical systems (BESs) was proven to be dependent on the stability of electroactive biofilms (EABs), but the response of EABs based on real wastewater to external disturbances is not fully known. Herein, we used real wastewater (beer brewery wastewater) as a substrate for culturing EABs and found that current generation, biomass, redox activity and extracellular polymeric substances (EPS) content in those EABs were lower as compared to EABs cultured with synthetic wastewaters (acetate and glucose). However, the EABs from the beer brewery wastewater showed moderate anti-shock resistance capability. The proteins and humic acid in loosely bound EPS (LB-EPS) exhibited a positive linear relationship with current recovery after Ag⁺ shock, indicating the importance of LB-EPS for protecting the EABs. Fluorescence and Fourier transform infrared spectroscopy integrated with two-dimensional correlation spectroscopy verified that the spectra of the protein-like region of LB-EPS changed considerably under the interference of Ag⁺ concentration and the CO group of humic acid or proteins was mainly responsible for binding with Ag⁺ to attenuate its toxicity to the EABs. This is the first study revealing the underlying molecular mechanism of EABs cultured with real wastewater against external heavy metal shock and provides useful insights into enhancing the application of BESs in future water treatment.

Role of Exopolysaccharides of Pseudomonas in Heavy Metal Removal and Other Remediation Strategies

Pseudomonas biofilms have been studied intensively for several decades and research outcomes have been successfully implemented in various medical and agricultural applications. Research on biofilm synthesis and composition has also overlapped with the objectives of environmental sciences, since biofilm components show exceptional physicochemical properties applicable to remediation techniques. Especially, exopolysaccharides (ExPs) have been at the center of scientific interest, indicating their potential in solving the environmental issues of heavy metal land and water contamination via sorptive interactions and flocculation. Since exposure to heavy metal via contaminated water or soil poses an imminent risk to the environment and human health, ExPs provide an interesting and viable solution to this issue, alongside other effective and green remedial techniques (e.g., phytostabilization, implementation of biosolids, and biosorption using agricultural wastes) aiming to restore contaminated sites to their natural, pollution-free state, or to ameliorate the negative impact of heavy metals on the environment. Thus, we discuss the plausible role and performance of Pseudomonas ExPs in remediation techniques, aiming to provide the relevant available and comprehensive information on ExPs’ biosynthesis and their usage in heavy metal remediation or other environmental applications, such as wastewater treatment via bioflocculation and soil remediation.

Integrative chemical and omics analyses reveal copper biosorption and tolerance mechanisms of Bacillus cereus strain T6

A comprehensive understanding of the cellular response of microbes to metal stress is necessary for the rational development of microbe-based biosorbents for metal removal. The present study investigated the copper (Cu) sorption and resistance mechanism of Bacillus cereus strain T6, a newly isolated Cu-resistant bacterium, by integrative analyses of physiochemistry, genomics, transcriptomics, and metabolomics. The growth inhibition assay and biosorption determination showed that this bacterium exhibited high tolerance to Cu, with a minimum inhibitory concentration of 4.0 mM, and accumulated Cu by both extracellular adsorption and intracellular binding. SEM microscopic images and FTIR spectra showed significant cellular surface changes at the high Cu level but not at low, and the involvement of surface functional groups in the biosorption of Cu, respectively. Transcriptomic and untargeted metabolomic analyses detected 362 differentially expressed genes and 60 significantly altered metabolites, respectively. Integrative omics analyses revealed that Cu exposure dramatically induced a broad spectrum of genes involved in Cu transport and iron homeostasis, and suppressed the denitrification pathway, leading to significant accumulation of metabolites for metal transporter synthesis, membrane remolding, and antioxidant activities. The results presented here provide a new perspective on the intricate regulatory network of Cu homeostasis in bacteria.

Extracellular Polymeric Substances and Biocorrosion/Biofouling: Recent Advances and Future Perspectives

Microbial cells secrete extracellular polymeric substances (EPS) to adhere to material surfaces, if they get in contact with solid materials such as metals. After phase equilibrium, microorganisms can adhere firmly to the metal surfaces causing metal dissolution and corrosion. Attachment and adhesion of microorganisms via EPS increase the possibility and the rate of metal corrosion. Many components of EPS are electrochemical and redox active, making them closely related to metal corrosion. Functional groups in EPS have specific adsorption ability, causing them to play a key role in biocorrosion. This review emphasizes EPS properties related to metal corrosion and protection and the underlying microbially influenced corrosion (MIC) mechanisms. Future perspectives regarding a comprehensive study of MIC mechanisms and green methodologies for corrosion protection are provided.

Biofilm formation and extracellular polymeric substance (EPS) production by Bacillus haynesii and influence of hexavalent chromium

Biofilm-forming bacteria play a key role in the removal of heavy metals including hexavalent chromium [Cr(VI)] from contaminated sites. In this study, biofilm-forming B. haynesii was examined for extracellular polymeric substances (EPS) production and hexavalent chromium [Cr(VI)] reduction potential. Exposure of B. haynesii with Cr(VI) (12.5-100 mg L^-1) for 48 h enhanced pellicle dry weight (20-24%), cell-size (5.1-23.2%) and cell granularity (8.5-19.2%). Also, EPS production was increased by 10-35% by promoting the synthesis of protein (94-119%) and polysaccharide (2-33%) components in EPS. Further, the reduction (27.7 %) and distribution (15.87%) of Cr(VI) were mainly mediated by EPS than the other cellular fractions. Findings of the study suggest that the EPS from B. haynesii was efficiently reduced to Cr(VI) present in aqueous medium and the potential of the organism can be further explored for the mitigation of Cr(VI) contamination.

Role of extracellular polymeric substances in the immobilization of hexavalent chromium by Shewanella putrefaciens CN32 unsaturated biofilms

Microbial remediation provides a promising avenue for the management and restoration of heavy metal-contaminated soils. Microorganisms in soils usually exist within unsaturated biofilms, however, their response to heavy metals is still limited compared to saturated biofilms. This work investigated the Cr(VI) immobilization by Shewanella putrefaciens CN32 unsaturated biofilms, and explored the underlying mechanisms of Cr(VI) complexation. Results reveal a dose-dependent toxicity of Cr(VI) to the growth of the unsaturated biofilms. During the early growth stage, the Cr(VI) addition stimulated more extracellular polymeric substances (EPS) production. In the meantime, the EPS were demonstrated to be the primary components for Cr(VI) immobilization, which accounted for more than 60% of the total adsorbed Cr(VI). The Fourier transform infrared spectra and X-ray photoelectron spectra corroborated that the binding sites for immobilizing Cr(VI) were hydroxyl, carboxyl, phosphoryl and amino functional groups of the proteins and polysaccharides in EPS. However, for the starved unsaturated biofilms, EPS were depleted and the EPS-bound Cr(VI) were released, which caused approximately 60% of the adsorbed Cr(VI) onto cell components and further aggravated the Cr(VI) stress to cells. This work extends our understanding about the Cr(VI) immobilization by unsaturated biofilms, and provides useful information for remediation of heavy metal-contaminated soils.

Variable metal resistance of P. putida CZ1 biofilms in different environments suggests its remediation application scope

Pseudomonas putida is potentially used in the bioremediation of heavy metals (HMs). Its response to different HMs in different environments is still not fully understood. This study investigated resistance against 12 kinds of metals by P. putida CZ1 planktonic cells and its biofilm in LB and mineral medium (MM). P. putida CZ1 biofilms have high resistance and accumulation capacity for Cu²⁺, Zn²⁺, Pb²⁺, Fe³⁺, Mn²⁺, Al³⁺ and Ni²⁺, but less resistance to Co²⁺, Cd²⁺, Cr₂O₇^2-, Ag⁺ and Hg²⁺. Biofilms were 2-8 times more resistant to Cu²⁺ and Zn²⁺ than planktonic cells. There was a strong correlation between the P content and the accumulation of Cu²⁺, Zn²⁺, Fe³⁺, Mn²⁺, Pb²⁺, Ni²⁺and Al³⁺ respectively. Confocal laser scanning microscopy (CLSM) combined with live/dead staining study found that cells in the biofilms can keep viable after 36 h under MIC of Cu²⁺ or Zn²⁺ both in LB and MM. When the metal concentration increased, cells can be killed gradually. For Cu²⁺, Zn²⁺, Fe³⁺, Mn²⁺, Pb²⁺ and Ni²⁺, higher resistance was found in MM (2-4 times higher) than in LB and higher accumulation of these metals were also found in MM. P. putida CZ1 biofilm cultured in MM with citric acid as carbon source had stronger resistance and accumulation ability to Cu²⁺, Zn²⁺, Pb²⁺, Fe³⁺, Mn²⁺, and Ni²⁺. This suggested that P. putida CZ1 had greater remediation potential for these metals in organic acid rich environments.

Plasmid-mediated catabolism for the removal of xenobiotics from the environment

The large-scale application of xenobiotics adversely affects the environment. The genes that are present in the chromosome of the bacteria are considered nonmobile, whereas the genes present on the plasmids are considered mobile genetic elements. Plasmids are considered indispensable for xenobiotic degradation into the contaminated environment. In the contaminated sites, bacteria with plasmids can transfer the mobile genetic element into another strain. This mechanism helps in spreading the catabolic genes into the bacterial population at the contaminated sites. The indigenous microbial strains with such degradative plasmids are important for the bioremediation of xenobiotics. Environmental factors play a critical role in the conjugation efficiency, which is involved in the bioremediation of the xenobiotics at the contaminated sites. However, there is still a need for more research to fill in the gaps regarding plasmids and their impact on bioremediation. This review explores the role of bacterial plasmids in the bioremediation of xenobiotics from contaminated environments.

Role of intertidal microbial communities in carbon dioxide sequestration and pollutant removal: A review

Intertidal microbial communities occur as biofilms or microphytobenthos (MPB) which are sediment-attached assemblages of bacteria, protozoa, fungi, algae, diatoms embedded in extracellular polymeric substances. Despite their global occurrence, they have not been reviewed in light of their structural and functional characteristics. This paper reviews the importance of such microbial communities and their importance in carbon dioxide sequestration as well as pollutant bioremediation. Global annual benthic microalgal productivity was 500 million tons of carbon, 50% of which contributed towards the autochthonous carbon fixation in the estuaries. Primary production by MPB was 27-234 gCm^-2y^-1 in the estuaries of Asia, Europe and the United States. Mechanisms of heavy metal removal remain to be tested in intertidal communities. Cyanobacteria facilitate hydrocarbon degradation in intertidal biofilms and microbial mats by supporting the associated sulfate-reducing bacteria and aerobic heterotrophs. Physiological cooperation between the microorganisms in intertidal communities imparts enhanced ability to utilize polycyclic aromatic hydrocarbon pollutants by these microorganisms than mono-species communities. Future research may be focused on biochemical characteristics of intertidal mats and biofilms, pollutant-microbial interactions and ecosystem influences.

Removal of perfluoroalkyl acids (PFAAs) in constructed wetlands: Considerable contributions of submerged macrophytes and the microbial community

The broad application of perfluoroalkyl acids (PFAAs) has attracted global concern regarding their adverse environmental effects. The possible removal processes of PFAAs in constructed wetlands were excavated and quantified using two typical submerged macrophytes (rooted Potamogeton wrightii and rootless Ceratophyllum demersum). Our results showed that 33.59-88.99% of PFAAs could be removed via not only sediment sorption or phytoextraction but also by the bioaccumulation of microbiota. The sediment acts as a vital sink for PFAAs, preloading 23.51-50.09% and 16.65-52.18% of PFAAs in treatments with P. wrightii (Pw1) and C. demersum (Cd1), respectively. C. demersum showed a better capacity to accumulate PFAAs (0.91-32.03%) than P. wrightii (<10%). Considerable PFAAs were observed to be distributed in microbes, underlining the non-negligible role of microbiota in bioaccumulating PFAAs. The contributions of planktonic microbes, biofilm microbes, and extracellular polymeric substances in biofilms were 0.39-20.96%, 0.03-7.95%, and 0.39-14.15% in Pw1 and 0.23-15.68%, 0.01-15.68%, and 0.53-26.77% in Cd1, respectively. The adsorption/uptake was significantly correlated with the perfluoroalkyl chain length (p<0.05), except for the uptake of biofilms in C. demersum. Furthermore, PFAAs and submerged macrophytes could decrease the richness of microbiota but increase the relative abundance of some strains in Betaproteobacteriales, Sphingomonadales, and Cytophagales. Our results were helpful for understanding the removal processes of PFAAs in constructed wetlands and their linkages with PFAA properties, thus further providing insight into the management and removal of emerging organic contaminants.

Kinetic modelling of the uranium biosorption by Deinococcus radiodurans biofilm

Increasing number of reports on uranium contamination in groundwater bodies is a growing concern. Deinococcus radiodurans biofilm-based U(VI) bioremediation has great potential to provide solution. This study focuses on the kinetic modelling of uranium biosorption by D. radiodurans biofilm biomass and identification of the functional groups involved in the sequestration process. The effect of temperature, pH and amount of biofilm dry mass were studied using two uranyl ion concentrations (100 and 1000 mg/L). D. radiodurans dry biomass showed good affinity for uranyl ion adsorption. The kinetic experiments revealed that the biosorption process was spontaneous and exothermic in nature. The modelling of kinetic adsorption data revealed that U(VI) sorption by D. radiodurans biofilm biomass follows a pseudo-second-order reaction. Mechanism of U(VI) sorption was suggested to follow an intra-particle diffusion model, which includes covalent bonding between U(VI) and functional groups present on the surface of biofilm biomass, and diffusional barrier acts as a rate limiting step. External mass transfer was the rate-limiting step as evident from Boyd and Elovich plot. Chemical modifications in surface functional groups of biofilm biomass, confirmed the involvement of carboxyl, phosphate, and hydroxyl groups in uranium binding as a significant loss in U(VI) sorption capacity was recorded in these chemically modified biomasses. XRD data indicated the formation of metal deposits, predominantly as uranyl phosphates.

Trace Metal Contamination Impacts Predicted Functions More Than Structure of Marine Prokaryotic Biofilm Communities in an Anthropized Coastal Area

Trace metal (TM) contamination in marine coastal areas is a worldwide threat for aquatic communities. However, little is known about the influence of a multi-chemical contamination on both marine biofilm communities' structure and functioning. To determine how TM contamination potentially impacted microbial biofilms' structure and their functions, polycarbonate (PC) plates were immerged in both surface and bottom of the seawater column, at five sites, along strong TM contamination gradients, in Toulon Bay. The PC plates were incubated during 4 weeks to enable colonization by biofilm-forming microorganisms on artificial surfaces. Biofilms from the PC plates, as well as surrounding seawaters, were collected and analyzed by 16S rRNA amplicon gene sequencing to describe prokaryotic community diversity, structure and functions, and to determine the relationships between bacterioplankton and biofilm communities. Our results showed that prokaryotic biofilm structure was not significantly affected by the measured environmental variables, while the functional profiles of biofilms were significantly impacted by Cu, Mn, Zn, and salinity. Biofilms from the contaminated sites were dominated by tolerant taxa to contaminants and specialized hydrocarbon-degrading microorganisms. Functions related to major xenobiotics biodegradation and metabolism, such as methane metabolism, degradation of aromatic compounds, and benzoate degradation, as well as functions involved in quorum sensing signaling, extracellular polymeric substances (EPS) matrix, and biofilm formation were significantly over-represented in the contaminated site relative to the uncontaminated one. Taken together, our results suggest that biofilms may be able to survive to strong multi-chemical contamination because of the presence of tolerant taxa in biofilms, as well as the functional responses of biofilm communities. Moreover, biofilm communities exhibited significant variations of structure and functional profiles along the seawater column, potentially explained by the contribution of taxa from surrounding sediments. Finally, we found that both structure and functions were significantly distinct between the biofilm and bacterioplankton, highlighting major differences between the both lifestyles, and the divergence of their responses facing to a multi-chemical contamination.

Copper Surfaces in Biofilm Control

Biofilms are structures comprising microorganisms associated to surfaces and enclosed by an extracellular polymeric matrix produced by the colonizer cells. These structures protect microorganisms from adverse environmental conditions. Biofilms are typically associated with several negative impacts for health and industries and no effective strategy for their complete control/eradication has been identified so far. The antimicrobial properties of copper are well recognized among the scientific community, which increased their interest for the use of these materials in different applications. In this review the use of different copper materials (copper, copper alloys, nanoparticles and copper-based coatings) in medical settings, industrial equipment and plumbing systems will be discussed considering their potential to prevent and control biofilm formation. Particular attention is given to the mode of action of copper materials. The putative impact of copper materials in the health and/or products quality is reviewed taking into account their main use and the possible effects on the spread of antimicrobial resistance.

Degradation of subµ-sized bioplastics by clinically important bacteria under sediment and seawater conditions: Impact on the bacteria responses

In this study, we investigated the interaction of submicron-sized bioplastics with environmentally and clinically important bacteria under seawater and sediment conditions. To examine the relationship between submicron-sized bioplastics and bacteria in seawater and sediment, we focused on the bacterial activation and their biochemical key events toward the protein, carbohydrate, lipid, and antioxidant response. In addition, culture-dependent biofilm formation on submicron-sized bioplastics and their characterization was performed. The results indicated that selected bacteria increased their viability both in seawater and sediment with the submicron-sized bioplastics in that the bioplastics decreased their mass at the level of 10-23%. However, the activation level and mechanism affected the polymer type, bacteria, and environmental media, and submicron-sized bioplastics promoted biofilm formation with enhancing basophilic characteristics of biofilms.

Kerr P, Ali S, Sultana N, Jia Z. Multifunctional Periphytic Biofilms: Polyethylene Degradation and Cd2+ and Pb2+ Bioremediation under High Methane Scenario

Priority pollutants such as polyethylene (PE) microplastic, lead (Pb²⁺), and cadmium (Cd²⁺) have attracted the interest of environmentalists due to their ubiquitous nature and toxicity to all forms of life. In this study, periphytic biofilms (epiphyton and epixylon) were used to bioremediate heavy metals (HMs) and to biodegrade PE under high (120,000 ppm) methane (CH₄) doses. Both periphytic biofilms were actively involved in methane oxidation, HMs accumulation and PE degradation. Epiphyton and epixylon both completely removed Pb²⁺ and Cd²⁺ at concentrations of 2 mg L⁻¹ and 50 mg L⁻¹, respectively, but only partially removed these HMs at a relatively higher concentration (100 mg L⁻¹). Treatment containing 12% ¹³CH₄ proved to be most effective for biodegradation of PE. A synergistic effect of HMs and PE drastically changed microbial biota and methanotrophic communities. High-throughput 16S rRNA gene sequencing revealed that Cyanobacteria was the most abundant class, followed by Gammaproteobacteria and Alphaproteobacteria in all high-methane-dose treatments. DNA stable-isotope probing was used to label ¹³C in a methanotrophic community. A biomarker for methane-oxidizing bacteria, pmoA gene sequence of a ¹³C-labeled fraction, revealed that Methylobacter was most abundant in all high-methane-dose treatments compared to near atmospheric methane (NAM) treatment, followed by Methylococcus. Methylomonas, Methylocystis, Methylosinus, and Methylocella were also found to be increased by high doses of methane compared to NAM treatment. Overall, Cd⁺² had a more determinantal effect on methanotrophic activity than Pb²⁺. Epiphyton proved to be more effective than epixylon in HMs removal and PE biodegradation. The findings proved that both epiphyton and epixylon can be used to bioremediate HMs and biodegrade PE as an efficient ecofriendly technique under high methane concentrations.