Biofilm-mediated bioremediation is a powerful tool for the removal of environmental pollutants

Evaluation of antibiofilm activity of metal oxides nanoparticles and carbon nanotubes coated styrofoam on the bacterium Jeotgalicoccus huakuii

The co-existence of metal oxide nanoparticles (MONPs), carbon-based nanomaterials and microplastics (MPs) in the natural environment are expected to be of growing global concern due to their increasing abundance and persistence in the environment worldwide. Knowledge of the interaction of the above compounds particularly under light irradiation in water remains limited. In the present study, the possible individual and combined toxic effects of MONPs, carbon nanotubes (CNTs) through styrofoam (SF) on the environmental bacterium Jeotaglicoccus huakuii were systematically investigated. The fabricated MONPs and CNTs were characterized using the following techniques: FT-IR (functional groups), XRD (crystallinity), SEM, and EDX (topological morphology). The objective of this study was to investigate and identify naturally occurring bacteria capable of mitigating and detoxifying toxic pollutants under adverse conditions. Moreover, the assessment of minimum inhibitory concentration (MIC) was made through an agar well plate method, resazurin (ELISA measurement), growth kinetics and bacterial viability were assessed employing live and dead assay and biofilm combating ability was analyzed using an antibiofilm assay. Further, the biotransformation of f-MWCNTs by J. huakuii was evaluated employing RT-PCR and SEM analysis. The results demonstrated that the toxicity of Pb3O4@f-MWCNTs was comparatively higher than the remaining Pb3O4 NPs and SF coated NPs.. Interestingly, J. huakuii showed resistance against f-MWCNTs at very high concentrations and able to utilize f-MWCNTs as a sole carbon source suggesting J. huakuii as a suitable aquatic bioremediation tool for both MONPs and CNTs transfer via MPs. The results also enhanced our understanding of the affinity of MPs towards MONPs and CNTs under extreme environmental conditions.

Nonlinear responses of biofilm bacteria to alkyl-chain length of parabens by DFT calculation

Parabens can particularly raise significant concerns regarding the disruption of microbial ecology due to their antimicrobial properties. However, the responses of biofilm bacteria to diverse parabens with different alkyl-chain length remains unclear. Here, theoretical calculations and bioinformatic analysis were performed to decipher the influence of parabens varying alkyl-chain lengths on the biofilm bacteria. Our results showed that the disturbances in bacterial community did not linearly response to the alkyl-chain length of parabens, and propylparaben (PrP), with median chain length, had more severe impact on bacterial community. Despite the fact that paraben lethality linearly increased with chain length, the PrP had a higher chemical reactions potential than parabens with shorter or longer alkyl-chain. The chemical reactions potential was critical in the nonlinear responses of bacterial community to alkyl-chain length of parabens. PrP could impose selective pressure to disturb the bacterial community, because it had a more profound contribution to deterministic assembly process. Furthermore, N-acyl-homoserine lactones was also significantly promoted under PrP exposure, confirming that PrP could affect the bacterial community by influencing the quorum-sensing system. Overall, our study reveals the nonlinear responses of bacterial communities to the alkyl-chain lengths of parabens and provides insightful perspectives for the better regulation of parabens. ENVIRONMENTAL IMPLICATION: Parabens are recognized as emerging organic pollutants, which specially raise great concerns due to their antimicrobial properties disturbing microbial ecology. However, few study have addressed the relationship between bacterial community responses and the molecular structural features of parabens with different alkyl-chain length. This investigation revealed nonlinear responses of the bacterial community to the alkyl-chain length of parabens through DFT calculation and bioinformatic analysis and identified the critical roles of chemical reactions potential in nonlinear responses of bacterial community. Our results benefit the precise evaluation of ecological hazards posed by parabens and provide useful insights for better regulation of parabens.

The effect of quorum sensing on cadmium- and lead-containing wastewater treatment using activated sludge: Removal efficiency, enzyme activity, and microbial community

Quorum sensing (QS) is prevalent in activated sludge processes; however, its essential role in the treatment of heavy metal wastewater has rarely been studied. Therefore, in this study, acyl homoserine lactone (AHL)-mediated QS was used to regulate the removal performance, enzyme activity, and microbial community of Cd- and Pb-containing wastewater in a sequencing batch reactor (SBR) over 30 cycles. The results showed that exogenous AHL strengthened the removal of Cd(II) and Pb(II) in their coexistence wastewater during the entire period. The removal of NH4+-N, total phosphorus, and chemical oxygen demand (COD) was also enhanced by the addition of AHL despite the coexistence of Cd(II) and Pb(II). Meanwhile, the protein content of extracellular polymeric substances was elevated and the microbial metabolism and antioxidative response were stimulated by the addition of AHL, which was beneficial for resistance to heavy metal stress and promoted pollutant removal by activated sludge. Microbial sequencing indicated that AHL optimized the microbial community structure, with the abundance of dominant taxa Proteobacteria and Unclassified_f_Enterobacteriaceae increasing by 73.9% and 59.2% maximally, respectively. This study offers valuable insights into the mechanisms underlying Cd(II) and Pb(II) removal as well as microbial community succession under AHL availability in industrial wastewater.

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.

Oxidative stress responses in biofilms

Oxidizing agents are low-molecular-weight molecules that oxidize other substances by accepting electrons from them. They include reactive oxygen species (ROS), such as superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (HO-), and reactive chlorine species (RCS) including sodium hypochlorite (NaOCl) and its active ingredient hypochlorous acid (HOCl), and chloramines. Bacteria encounter oxidizing agents in many different environments and from diverse sources. Among them, they can be produced endogenously by aerobic respiration or exogenously by the use of disinfectants and cleaning agents, as well as by the mammalian immune system. Furthermore, human activities like industrial effluent pollution, agricultural runoff, and environmental activities like volcanic eruptions and photosynthesis are also sources of oxidants. Despite their antimicrobial effects, bacteria have developed many mechanisms to resist the damage caused by these toxic molecules. Previous research has demonstrated that growing as a biofilm particularly enhances bacterial survival against oxidizing agents. This review aims to summarize the current knowledge on the resistance mechanisms employed by bacterial biofilms against ROS and RCS, focussing on the most important mechanisms, including the formation of biofilms in response to oxidative stressors, the biofilm matrix as a protective barrier, the importance of detoxifying enzymes, and increased protection within multi-species biofilm communities. Understanding the complexity of bacterial responses against oxidative stress will provide valuable insights for potential therapeutic interventions and biofilm control strategies in diverse bacterial species.

Environmental stressor assessment of hydrocarbonoclastic bacteria biofilms from a marine oil spill

The environmental and economic impact of an oil spill can be significant. Biotechnologies applied during a marine oil spill involve bioaugmentation with immobilised or encapsulated indigenous hydrocarbonoclastic species selected under laboratory conditions to improve degradation rates. The environmental factors that act as stressors and impact the effectiveness of hydrocarbon removal are one of the challenges associated with these applications. Understanding how native microbes react to environmental stresses is necessary for effective bioaugmentation. Herein, Micrococcus luteus and M. yunnanensis isolated from a marine oil spill mooring system showed hydrocarbonoclastic activity on Maya crude oil in a short time by means of total petroleum hydrocarbons (TPH) at 144 h: M. luteus up to 98.79 % and M. yunnanensis 97.77 % removal. The assessment of Micrococcus biofilms at different temperature (30 °C and 50 °C), pH (5, 6, 7, 8, 9), salinity (30, 50, 60, 70, 80 g/L), and crude oil concentration (1, 5, 15, 25, 35 %) showed different response to the stressors depending on the strain. According to response surface analysis, the main effect was temperature > salinity > hydrocarbon concentration. The hydrocarbonoclastic biofilm architecture was characterised using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Subtle but significant differences were observed: pili in M. luteus by SEM and the topographical differences measured by AFM Power Spectral Density (PSD) analysis, roughness was higher in M. luteus than in M. yunnanensis. In all three domains of life, the Universal Stress Protein (Usp) is crucial for stress adaptation. Herein, the uspA gene expression was analysed in Micrococcus biofilm under environmental stressors. The uspA expression increased up to 2.5-fold in M. luteus biofilms at 30 °C, and 1.3-fold at 50 °C. The highest uspA expression was recorded in M. yunnanensis biofilms at 50 °C with 2.5 and 3-fold with salinities of 50, 60, and 80 g/L at hydrocarbon concentrations of 15, 25, and 35 %. M. yunnanensis biofilms showed greater resilience than M. luteus biofilms when exposed to harsh environmental stressors. M. yunnanensis biofilms were thicker than M. luteus biofilms. Both biofilm responses to environmental stressors through uspA gene expression were consistent with the behaviours observed in the response surface analyses. The uspA gene is a suitable biomarker for assessing environmental stressors of potential microorganisms for bioremediation of marine oil spills and for biosensing the ecophysiological status of native microbiota in a marine petroleum environment.

Innovative remediation strategies for persistent organic pollutants in soil and water: A comprehensive review

Persistent organic pollutants (POPs) provide a serious threat to human health and the environment in soil and water ecosystems. This thorough analysis explores creative remediation techniques meant to address POP pollution. Persistent organic pollutants are harmful substances that may withstand natural degradation processes and remain in the environment for long periods of time. Examples of these pollutants include dioxins, insecticides, and polychlorinated biphenyls (PCBs). Because of their extensive existence, cutting-edge and environmentally friendly eradication strategies must be investigated. The most recent advancements in POP clean-up technology for soil and water are evaluated critically in this article. It encompasses a wide range of techniques, such as nanotechnology, phytoremediation, enhanced oxidation processes, and bioremediation. The effectiveness, cost-effectiveness, and environmental sustainability of each method are assessed. Case studies from different parts of the world show the difficulties and effective uses of these novel techniques. The study also addresses new developments in POP regulation and monitoring, highlighting the need of all-encompassing approaches that include risk assessment and management. In order to combat POP pollution, the integration of diverse remediation strategies, hybrid approaches, and the function of natural attenuation are also examined. Researchers, legislators, and environmental professionals tackling the urgent problem of persistent organic pollutants (POPs) in soil and water should benefit greatly from this study, which offers a complete overview of the many approaches available for remediating POPs in soil and water.

Beneficial applications of biofilms

Many microorganisms live in the form of a biofilm. Although they are feared in the medical sector, biofilms that are composed of non-pathogenic organisms can be highly beneficial in many applications, including the production of bulk and fine chemicals. Biofilm systems are natural retentostats in which the biocatalysts can adapt and optimize their metabolism to different conditions over time. The adherent nature of biofilms allows them to be used in continuous systems in which the hydraulic retention time is much shorter than the doubling time of the biocatalysts. Moreover, the resilience of organisms growing in biofilms, together with the potential of uncoupling growth from catalytic activity, offers a wide range of opportunities. The ability to work with continuous systems using a potentially self-advancing whole-cell biocatalyst is attracting interest from a range of disciplines, from applied microbiology to materials science and from bioengineering to process engineering. The field of beneficial biofilms is rapidly evolving, with an increasing number of applications being explored, and the surge in demand for sustainable and biobased solutions and processes is accelerating advances in the field. This Review provides an overview of the research topics, challenges, applications and future directions in beneficial and applied biofilm research.

Delignified porous wood as biofilm support for 1,4-dioxane-degrading bacterial consortium

Delignified porous wood samples were used as carriers for biofilm formation of a bacterial consortium with the ability to degrade 1,4-dioxane (DX). The delignification treatment of the natural wood resulted in higher porosity, formation of macropores, increase in surface roughness and hydrophilicity of the treated wood pieces. These superior properties of two types of treated carriers (respectively, A and B) compared to the untreated wood resulted in 2.19 ± 0.52- and 2.66 ± 0.23-fold higher growth of biofilm. Moreover, analysis of the fatty acid profiles indicated an increase in proportion of the saturated fatty acids during the biofilm formation, characterising an enhancement in rigidity and hydrophobicity of the biofilms. DX initial concentration of 100 mg/L was completely degraded (detection limit 0.01 mg/L) in 24 and 32 h using the treated A and B woods, while only 25.84 ± 5.95% was removed after 32 h using the untreated wood. However, fitting the DX biodegradation data to the Monod model showed a lower maximum specific growth rate for biofilm (0.0276 ± 0.0018 1/h) versus planktonic (0.0382 ± 0.0024 1/h), because of gradual accumulation of inactive cells in the biofilm. Findings of this study can contribute to the knowledge of biofilm formation regarding the physical/chemical properties of biofilm carriers and be helpful to the ongoing research on bioremediation of DX.

Multitasking functions of bacterial extracellular DNA in biofilms

Bacterial biofilms are intricate ecosystems of microbial communities that adhere to various surfaces and are enveloped by an extracellular matrix composed of polymeric substances. Within the context of bacterial biofilms, extracellular DNA (eDNA) originates from cell lysis or is actively secreted, where it exerts a significant influence on the formation, stability, and resistance of biofilms to environmental stressors. The exploration of eDNA within bacterial biofilms holds paramount importance in research, with far-reaching implications for both human health and the environment. An enhanced understanding of the functions of eDNA in biofilm formation and antibiotic resistance could inspire the development of strategies to combat biofilm-related infections and improve the management of antibiotic resistance. This comprehensive review encapsulates the latest discoveries concerning eDNA, encompassing its origins, functions within bacterial biofilms, and significance in bacterial pathogenesis.

Revealing the characteristics of biofilms on different polypropylene plastic products: Comparison between disposable masks and takeaway boxes

The increasingly severe plastic pollution issue was intensified by the enormous plastic emissions into ecosystems during the Covid-19 pandemic. Plastic wastes entering the environment were swiftly exposed to microorganisms and colonized by biofilms, and the plastic-biofilm combined effects further influenced the ecosystem. However, the non-woven structure of disposable masks discarded carelessly during the COVID-19 pandemic was different from those of plastics with flat surface. To reveal the potential effects of plastic structure on colonized biofilms, white disposable surgical masks (DM) and transparent takeaway boxes (TB), both made of polyethylene, were selected for the incubation of organic conditioning films and biofilms. The results indicated that the non-woven structure of disposable mask was destroyed by the influence of water infiltration and biofilm colonization. The influence of surface structure on conditioning films led to a relatively higher proportion of tryptophan-like substances on DM than those on TB samples. Therefore, biofilms with significantly higher microbial biomass and carbon metabolic capacity were formed on DM than those on TB samples owing to the combined effects of their differences in surface structure and conditioning films. Moreover, abundant functional microorganisms associated with stress tolerance, carbon metabolism and biofilm formation were observed in biofilms on disposable mask. Combining with the results of partial least squares regression analysis, the selective colonization of functional microorganisms on disposable masks with uneven surface longitudinal fluctuation was revealed. Although the predicted functions of biofilms on disposable masks and takeaway boxes showed more similarity to each other than to those of free-living aquatic microorganisms owing to the existence of the plastisphere, biofilms on disposable masks may potentially trigger environmental risks different from those of takeaway boxes by unique carbon metabolism and abundant biomass.

Biodegradation of atrazine with biochar-mediated functional bacterial biofilm: Construction, characterization and mechanisms

The abuse and residue of herbicides in the black soil area had seriously affected the soil structure, function and crop growth, posing severe threats to agricultural soil environment and public health. Given the limitation of routine microbial remediation, innovative and eco-friendly functional bacterial biofilm which could adapt under adverse conditions was developed on the biochar to investigate its enhanced bioremediation and metabolic characteristics of typical herbicide atrazine. Results revealed that the atrazine degrading strain Acinetobacter lwoffii had competitive advantage in soil indigenous microorganisms and formed dense biofilms on the biochar which was beneficial to cell viability maintenance and aggregations. Metatranscriptomics and RT-qPCR analysis demonstrated that the biochar-mediated biofilm improved the frequency of intercellular communications through quorum sensing and two-component signal regulation systems, and enhanced the atrazine biodegradation efficiency through horizontal gene transfer in co-metabolism mode, providing important scientific basis for the biological remediation of farmland soil non-point source pollution.

Biofilm formation by selected microbial strains isolated from wastewater and their consortia: mercury resistance and removal potential

Wastewater often contains an increased amount of mercury and, at the same time, resistant microorganisms. During wastewater treatment, a biofilm of indigenous microorganisms is often unavoidable. Therefore, the objective of this research is to isolate and identify microorganisms from wastewater and investigate their ability to form biofilms for possible application in mercury removal processes. The resistance of planktonic cells and their biofilms to the effects of mercury was investigated using Minimum Biofilm Eradication Concentration-High Throughput Plates. The formation of biofilms and the degree of resistance to mercury were confirmed in polystyrene microtiter plates with 96 wells. Biofilm on AMB Media carriers (Assisting Moving Bad Media) was quantified using the Bradford protein assay. The removal of mercury ions by biofilms formed on AMB Media carriers of selected isolates and their consortia was determined by a removal test in Erlenmeyer flasks simulating MBBR. All isolates in planktonic form showed some degree of resistance to mercury. The most resistant microorganisms (Enterobacter cloacae, Klebsiella oxytoca, Serratia odorifera, and Saccharomyces cerevisiae) were tested for their ability to form biofilms in the presence and absence of mercury, both in polystyrene plates and on ABM carriers. The results showed that among planktonic forms, K. oxytoca was the most resistant. A biofilm of the same microorganisms was more than 10-fold resistant. Most consortia biofilms had MBEC values > 100,000 μg/mL. Among individual biofilms, E. cloacae showed the highest mercury removal efficiency (97.81% for 10 days). Biofilm consortia composed of three species showed the best ability to remove mercury (96.64%-99.03% for 10 days). This study points to the importance of consortia of different types of wastewater microorganisms in the form of biofilms and suggests that they can be used to remove mercury in wastewater treatment bioreactors.

Enhanced exopolysaccharide production in gamma irradiated Bacillus subtilis: A biofilm-mediated strategy for ZnO nanoparticles removal

Biofilm-mediated strategy was studied for ZnO nanoparticle removal from aqueous media. Bacillus subtilis isolated from the soil rhizosphere was selected based on its high viscosity (133 Pa/s) of the cultivated culture and biofilm formation. The bacterium was exposed to gamma-irradiation to enhance EPS production along with its cultivation in EPS-producing media. The results show an increase in viscosity that reached 160 Pa/s at 2 kGy. EPS production increased from 4.45 to 7.95 mg/mL and the protein/carbohydrate ratio increased from 3 to 4.4 which reflects the stickiness of EPS. Thermal Gravimetric Analysis (TGA) showed 2 phase weight loss for gamma irradiated EPS and defined protein peaks when characterized using Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF). Native and gamma-irradiated Bacillus subtilis cells with their enhanced EPS were grown as a biofilm on sterile waste gauze fabric, Scanning Electron Microscopy (SEM) showed an increased biofilm attachment in gamma-irradiated samples. The latter was used for the removal of ZnO NP from aqueous media. Energy dispersive X-ray (EDX) mapping confirms that ZnO NPs were entrapped within the carbon and oxygen elements forming the biofilm with net intensities of 14.04, 1713, and 1190, respectively. The results confirm that biofilm-mediated strategy is effective in nanoparticles removal.

Microbial and Monosaccharide Composition of Biofilms Developing on Sandy Loams from an Aquifer Contaminated with Liquid Radioactive Waste

The development of microbial biofilms increases the survival of microorganisms in the extreme conditions of ecosystems contaminated with components of liquid radioactive waste (LRW) and may contribute to the successful bioremediation of groundwater. The purpose of this work was to compare the composition of the microorganisms and the exopolysaccharide matrix of the biofilms formed on sandy loams collected at the aquifer from a clean zone and from a zone with nitrate and radionuclide contamination. The aquifer is polluted from the nearby surface repository for liquid radioactive waste (Russia). The phylogenetic diversity of prokaryotes forming biofilms on the sandy loams' surface was determined during 100 days using high-throughput sequencing of the V4 region of the 16S rRNA genes. Scanning electron microscopy was used to study the development of microbial biofilms on the sandy loams. The ratio of proteins and carbohydrates in the biofilms changed in the course of their development, and the diversity of monosaccharides decreased, depending on the contamination of the sites from which the rocks were selected. The presence of pollution affects biofilm formation and EPS composition along with the dominant taxa of microorganisms and their activity. Biofilms establish a concentration gradient of the pollutant and allow the microorganisms involved to effectively participate in the reduction of nitrate and sulfate; they decrease the risk of nitrite accumulation during denitrification and suppress the migration of radionuclides. These biofilms can serve as an important barrier in underground water sources, preventing the spread of pollution. Pure cultures of microorganisms capable of forming a polysaccharide matrix and reducing nitrate, chromate, uranyl, and pertechnetate ions were isolated from the biofilms, which confirmed the possibility of their participation in the bioremediation of the aquifer from nonradioactive waste components and the decrease in the radionuclides' migration.

Three dimensional printed biofilms: Fabrication, design and future biomedical and environmental applications

Three dimensional printing has emerged as a widely acceptable strategy for the fabrication of mammalian cell laden constructs with complex microenvironments for tissue engineering and regenerative medicine. More recently 3D printed living materials containing microorganisms have been developed and matured into living biofilms. The potential for engineered 3D biofilms as in vitro models for biomedical applications, such as antimicrobial susceptibility testing, and environmental applications, such as bioleaching, bioremediation, and wastewater purification, is extensive but the need for an in-depth understanding of the structure-function relationship between the complex construct and the microorganism response still exists. This review discusses 3D printing fabrication methods for engineered biofilms with specific structural features. Next, it highlights the importance of bioink compositions and 3D bioarchitecture design. Finally, a brief overview of current and potential applications of 3D printed biofilms in environmental and biomedical fields is discussed.

Biofilm formation in xenobiotic-degrading microorganisms

The increased presence of xenobiotics affects living organisms and the environment at large on a global scale. Microbial degradation is effective for the removal of xenobiotics from the ecosystem. In natural habitats, biofilms are formed by single or multiple populations attached to biotic/abiotic surfaces and interfaces. The attachment of microbial cells to these surfaces is possible via the matrix of extracellular polymeric substances (EPSs). However, the molecular machinery underlying the development of biofilms differs depending on the microbial species. Biofilms act as biocatalysts and degrade xenobiotic compounds, thereby removing them from the environment. Quorum sensing (QS) helps with biofilm formation and is linked to the development of biofilms in natural contaminated sites. To date, scant information is available about the biofilm-mediated degradation of toxic chemicals from the environment. Therefore, we review novel insights into the impact of microbial biofilms in xenobiotic contamination remediation, the regulation of biofilms in contaminated sites, and the implications for large-scale xenobiotic compound treatment.

Genomic Insights into the Microbial Agent Streptomyces albidoflavus MGMM6 for Various Biotechnology Applications

Microbial biotechnology plays a crucial role in improving industrial processes, particularly in the production of compounds with diverse applications. In this study, we used bioinformatic approaches to analyze the genomic architecture of Streptomyces albidoflavus MGMM6 and identify genes involved in various metabolic pathways that have significant biotechnological potential. Genome mining revealed that MGMM6 consists of a linear chromosome of 6,932,303 bp, with a high G+C content of 73.5%, lacking any plasmid contigs. Among the annotated genes, several are predicted to encode enzymes such as dye peroxidase, aromatic ring-opening dioxygenase, multicopper oxidase, cytochrome P450 monooxygenase, and aromatic ring hydroxylating dioxygenases which are responsible for the biodegradation of numerous endogenous and xenobiotic pollutants. In addition, we identified genes associated with heavy metal resistance, such as arsenic, cadmium, mercury, chromium, tellurium, antimony, and bismuth, suggesting the potential of MGMM6 for environmental remediation purposes. The analysis of secondary metabolites revealed the presence of multiple biosynthesis gene clusters responsible for producing compounds with potent antimicrobial and metal-chelating activities. Furthermore, laboratory tests conducted under controlled conditions demonstrated the effectiveness of MGMM6 in inhibiting phytopathogenic microbes, decolorizing and degrading aromatic triphenylmethane dyes, particularly Blue Brilliant G250, from wastewater by up to 98 ± 0.15%. Overall, the results of our study highlight the promising biotechnological potential of S. albidoflavus MGMM6.

The aggregated biofilm dominated by Delftia tsuruhatensis enhances the removal efficiency of 2,4-dichlorophenol in a bioelectrochemical system

Bioelectrochemical system is a prospective strategy in organic-contaminated groundwater treatment, while few studies clearly distinguish the mechanisms of adsorption or biodegradation in this process, especially when dense biofilm is formed. This study employed a single chamber microbial electrolysis cell (MEC) with two three-dimensional electrodes for removing a typical organic contaminant, 2,4-dichlorophenol (DCP) from groundwater, which inoculated with anaerobic bacteria derived from sewage treatment plant. Compared with the single biodegradation system without electrodes, the three-dimensional electrodes with a high surface enabled an increase of alpha diversity of the microbial community (increased by 52.6% in Shannon index), and provided adaptive ecological niche for more bacteria. The application of weak voltage (0.6 V) furtherly optimized the microbial community structure, and promoted the aggregation of microorganisms with the formation of dense biofilm. Desorption experiment proved that the contaminants were removed from the groundwater mainly via adsorption by the biofilm rather than biodegradation, and compared with the reactor without electricity, the bioelectrochemical system increased the adsorption capacity from 50.0% to 74.5%. The aggregated bacteria on the surface of electrodes were mainly dominated by Delftia tsuruhatensis (85.0%), which could secrete extracellular polymers and has a high adsorption capacity (0.30 mg/g electrode material) for the contaminants. We found that a bioelectrochemical system with a three-dimensional electrode could stimulate the formation of dense biofilm and remove the organic contaminants as well as their possible more toxic degradation intermediates via adsorption. This study provides important guidance for applying bioelectrochemical system in groundwater or wastewater treatment.

Dibenzothiophene removal by environmental bacteria with differential accumulation of intracellular inorganic polyphosphate

Dibenzothiophene (DBT), which belongs to the group of polycyclic aromatic heterocycles of sulfur, is a model substance to study the removal of sulfur compounds from oil due to its recalcitrance to traditional and specific removal processes. The aim of this work was to evaluate DBT bioremoval by environmental bacteria and its relationship with polyphosphate (polyP) accumulation, cell surface characteristics and bioemulsifying activity. Pseudomonas sp. P26 achieved the highest DBT removal percentage (48%) after 7 days of incubation. Moreover, positive correlations were estimated between DBT removal and bioemulsifying activity and biofilm formation. A strain-dependent relationship between the content of intracellular polyP and the presence of DBT in the culture medium was also demonstrated. The study of these bacterial characteristics, which could promote DBT transformation, is a first approach to select DBT-removing bacteria, in order to develop bioformulations that are able to contribute to desulfurization processes of petroleum-derived pollutants in the future.

Regulation of cadmium-induced biofilm formation by artificial polysaccharide-binding proteins for enhanced phytoremediation

Phytoremediation is an economic way to attenuate soil heavy metal pollution, but is frequently limited by its low pollutant-removing efficiency. Recently, we revealed the close relation between polysaccharide-based biofilm formation and cadmium removal. In this study, for improving the phytoremediation efficiency, an artificial polysaccharide-binding protein was designed by synthetic biology techniques to regulate biofilm formation. The artificial protein Syn contained two polysaccharide-binding domains from the Ruminococcus flavefaciens CttA and the Clostridium cellulolyticum CipC, preferentially binding polysaccharides exposed on both cadmium-treated bacteria and plant roots. Under cadmium stress, Syn remarkably promoted bacterial polysaccharide production from 99 mg/L to 237 mg/L, leading to 1.23-fold higher biofilm biomass. During treatment of the remediation plants with exogenous cadmium-capturing bacteria, Syn improved root biofilm formation, with the root surface polysaccharide contents increasing by 79%, and the Log10 CFU/g root increasing from 7.01 to 7.80. Meanwhile, Syn remodeled the rhizosphere microbiome, especially increasing the abundance of the bacterial groups involved in biofilm formation and stress tolerance, e.g., Pseudomonas, Enterobacter, etc. Consequently, Syn promoted plant cadmium adsorption, with the cadmium-removing efficiency increasing from 17.2% to 33.8%. This study sheds light on synthetic biology-based regulation of biofilm formation for enhanced phytoremediation.

Iron-Nitrogen Amendment Reduced Perfluoroalkyl Acids' Phyto-Uptake in the Wheat-Soil Ecosystem: Contributions of Dissolved Organic Matters in Soil Solution and Root Extracellular Polymeric Substances

Understanding the mechanisms underlying perfluoroalkyl acids (PFAAs) translocation, distribution, and accumulation in wheat-soil ecosystems is essential for agricultural soil pollution control and crop ecological risk assessment. This study systematically investigated the translocation of 13 PFAAs under different iron and nitrogen fertilization conditions in a wheat-soil ecosystem. Short-chain PFAAs including PFBA, PFPeA, PFHxA, and PFBS mostly accumulated in soil solution (10.43-55.33%) and soluble extracellular polymeric substances (S-EPS) (11.39-14.77%) by the adsorption to amino- (-NH2) and hydroxyl (-OH) groups in dissolved organic matter (DOM). Other PFAAs with longer carbon chain lengths were mostly distributed on the soil particle surface by hydrophobic actions (74.63-94.24%). Iron-nitrogen amendments triggered (p < 0.05) soil iron-nitrogen cycling, rhizospheric reactive oxygen species fluctuations, and the concentration increases of -NH2 and -OH in the DOM structure. Thus, the accumulation capacity of PFAAs in soil solution and root EPS was increased. In sum, PFAAs' translocation from soil particles to wheat root was synergistically reduced by iron and nitrogen fertilization through increased adsorption of soil particles (p < 0.05) and the retention of soil solution and root EPSs. This study highlights the potential of iron-nitrogen amendments in decreasing the crop ecological risks to PFAAs' pollution.

Microbial degradation as a powerful weapon in the removal of sulfonylurea herbicides

Sulfonylurea herbicides have been widely used worldwide and play a significant role in modern agricultural production. However, these herbicides have adverse biological effects that can damage the ecosystems and harm human health. As such, rapid and effective techniques that remove sulfonylurea residues from the environment are urgently required. Attempts have been made to remove sulfonylurea residues from environment using various techniques such as incineration, adsorption, photolysis, ozonation, and microbial degradation. Among them, biodegradation is regarded as a practical and environmentally responsible way to eliminate pesticide residues. Microbial strains such as Talaromyces flavus LZM1, Methylopila sp. SD-1, Ochrobactrum sp. ZWS16, Staphylococcus cohnii ZWS13, Enterobacter ludwigii sp. CE-1, Phlebia sp. 606, and Bacillus subtilis LXL-7 can almost completely degrade sulfonylureas. The degradation mechanism of the strains is such that sulfonylureas can be catalyzed by bridge hydrolysis to produce sulfonamides and heterocyclic compounds, which deactivate sulfonylureas. The molecular mechanisms associated with microbial degradation of sulfonylureas are relatively poorly studied, with hydrolase, oxidase, dehydrogenase and esterase currently known to play a pivotal role in the catabolic pathways of sulfonylureas. Till date, there are no reports specifically on the microbial degrading species and biochemical mechanisms of sulfonylureas. Hence, in this article, the degradation strains, metabolic pathways, and biochemical mechanisms of sulfonylurea biodegradation, along with its toxic effects on aquatic and terrestrial animals, are discussed in depth in order to provide new ideas for remediation of soil and sediments polluted by sulfonylurea herbicides.

Host-derived peptide signals regulate Pseudomonas aeruginosa virulence stress via the ParRS and CprRS two-component systems

Pseudomonas aeruginosa, a versatile bacterium, has dual significance because of its beneficial roles in environmental soil processes and its detrimental effects as a nosocomial pathogen that causes clinical infections. Understanding adaptability to environmental stress is essential. This investigation delves into the complex interplay of two-component system (TCS), specifically ParRS and CprRS, as P. aeruginosa interprets host signals and navigates stress challenges. In this study, through phenotypic and proteomic analyses, the nuanced contributions of ParRS and CprRS to the pathogenesis and resilience mechanisms were elucidated. Furthermore, the indispensable roles of the ParS and CprS extracellular sensor domains in orchestrating signal perception remain unknown. Structural revelations imply a remarkable convergence of TCS sensors in interacting with host peptides, suggesting evolutionary strategies for bacterial adaptation. This pioneering work not only established links between cationic antimicrobial peptide (CAMP) resistance-associated TCSs and virulence modulation in nosocomial bacteria, but also transcended conventional boundaries. These implications extend beyond clinical resistance, permeating into the realm of soil revitalization and environmental guardianship. As it unveils P. aeruginosa intricacies, this study assumes a mantle of guiding strategies to mitigate clinical hazards, harness environmental advantages, and propel sustainable solutions forward.

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.

A graphene microelectrode array based microfluidic device for in situ continuous monitoring of biofilms

In situ continuous monitoring of bacterial biofilms has been a challenging job so far, but it is fundamental to the screening of novel anti-biofilm reagents. In this work, a microfluidic system utilizing a graphene-modified microelectrode array sensor was proposed to realize the dynamic state of bacterial biofilm monitoring by electrochemical impedance. The results illustrated that the observation window period of the biofilm state is significantly prolonged due to the increment of bacterial cell load on the sensing interface, thereby greatly improving the sensing signal quality. Simulation of anti-biofilm drug screening demonstrated that the performance of this method manifestly exceeded that of its endpoint counterparts.

In Vitro Biofilm-Mediated Biodegradation of Pesticides and Dye-Contaminated Effluents Using Bacterial Biofilms

Overuse of pesticides in agricultural soil and dye-polluted effluents severely contaminates the environment and is toxic to animals and humans making their removal from the environment essential. The present study aimed to assess the biodegradation of pesticides (cypermethrin (CYP) and imidacloprid (IMI)), and dyes (malachite green (MG) and Congo red (CR)) using biofilms of bacteria isolated from pesticide-contaminated soil and dye effluents. Biofilms of indigenous bacteria, i.e., Bacillus thuringiensis 2A (OP554568), Enterobacter hormaechei 4A (OP723332), Bacillus sp. 5A (OP586601), and Bacillus cereus 6B (OP586602) individually and in mixed culture were tested against CYP and IMI. Biofilms of indigenous bacteria i.e., Lysinibacillus sphaericus AF1 (OP589134), Bacillus sp. CF3 (OP589135) and Bacillus sp. DF4 (OP589136) individually and in mixed culture were tested for their ability to degrade dyes. The biofilm of a mixed culture of B. thuringiensis + Bacillus sp. (P7) showed 46.2% degradation of CYP compared to the biofilm of a mixed culture of B. thuringiensis + E. hormaechei + Bacillus sp. + B. cereus (P11), which showed significantly high degradation (70.0%) of IMI. Regarding dye biodegradation, a mixed culture biofilm of Bacillus sp. + Bacillus sp. (D6) showed 86.76% degradation of MG, which was significantly high compared to a mixed culture biofilm of L. sphaericus + Bacillus sp. (D4) that degraded only 30.78% of CR. UV-VIS spectroscopy revealed major peaks at 224 nm, 263 nm, 581 nm and 436 nm for CYP, IMI, MG and CR, respectively, which completely disappeared after treatment with bacterial biofilms. Fourier transform infrared (FTIR) analysis showed the appearance of new peaks in degraded metabolites and disappearance of a peak in the control spectrum after biofilm treatment. Thin layer chromatography (TLC) analysis also confirmed the degradation of CYP, IMI, MG and CR into several metabolites compared to the control. The present study demonstrates the biodegradation potential of biofilm-forming bacteria isolated from pesticide-polluted soil and dye effluents against pesticides and dyes. This is the first report demonstrating biofilm-mediated bio-degradation of CYP, IMI, MG and CR utilizing soil and effluent bacterial flora from Multan and Sheikhupura, Punjab, Pakistan.

Factors Influencing Pseudomonas aeruginosa Initial Adhesion and Evolution at the Dodecane-Water Interface

Bacterial adhesion and evolution at the oil-water interface are important for a broad range of applications such as food manufacturing and microbial-enhanced oil recovery, etc. However, our understanding on bacterial interfacial adhesion and evolution, particularly at the single-cell level, is still far from complete. In this work, by employing Pseudomonas aeruginosa PAO1 at the dodecane-water interface as a model system, we have studied the effects of different factors on bacterial interfacial adhesion and the dynamic evolution of bacterial interfacial behavior at the single-cell level. The results show that PAO1 cells displayed a chemotactic behavior toward dodecane. Among the tested factors, bacterial initial interfacial attachment showed a negative correlation with the secreted cell-surface associated lipopolysaccharide and Psl while a positive correlation with type IV pili. Adding nonbiological surfactant Pluronic F-127, as expected, greatly reduced the cell interfacial adhesion. More importantly, the dynamics analysis of cell attachment/detachment at the dodecane-water interface over a long-time scale revealed a reversible to irreversible attachment transition of cells. This transition is accompanied with the interface aging resulting from bacterial activities, which led to an increase of the interfacial viscoelasticity with time and finally the formation of the gel-like interface. Further analysis demonstrated the important role of exopolysaccharides in the latter process. Our findings provide more details of bacterial oil-water interfacial behavior at the single-cell level and may shed light on developing new strategies for controlling bacterial colonization at the oil-water interface.

Effect of quorum quenching on biofouling control and microbial community in membrane bioreactors by Brucella sp. ZJ1

Quorum quenching (QQ) has been demonstrated to be a novel technique for controlling biofouling in membrane bioreactors (MBRs), as it can significantly inhibit biofilm formation by disrupting quorum sensing (QS). The exploration of new QQ bacterial strains and the evaluation of their performance in mitigating membrane fouling in MBR systems is significant. In this study, an efficient QQ strain, Brucella sp. ZJ1 was encapsulated in alginate beads and evaluated for its ability to mitigate biofouling. The findings revealed that MBR with QQ beads extended the operation time by 2-3 times without affecting pollutant degradation. QQ beads maintained approximately 50% QQ activity after more than 50 days operation, indicating a long-lasting and endurable QQ effect. The QQ effect reduced extracellular polymeric substance (EPS) production especially in terms of polysaccharide and protein by more than 40%. QQ beads in the MBR also reduced the cake resistance and the irreversible resistance of membrane biofouling. Metagenomic sequencing suggests that QQ beads suppressed the QS effect and increased the abundance of QQ enzyme genes, ultimately inducing efficient membrane biofouling control.

Adaptive Evolution Laws of Biofilm under Emerging Pollutant-Induced Stress: Community Assembly-Driven Structure Response

The widely used biofilm process in advanced wastewater treatment is currently challenged by numerous exotic emerging pollutants (EPs), and the underlying principle of the challenge is the adaptive evolution laws of biofilm under EP stress. However, there is still a knowledge gap in exploration of the biofilm adaptive evolution theory. Herein, we comprehensively analyzed the morphological variation, community succession, and assembly mechanism of biofilms to report the mechanism underlying their adaptive evolution under sulfamethoxazole and carbamazepine stress for the first time. The ecological role of the dominant species was driven as a pioneer and assembly hub by EP stress, and the deterministic processes indicated the functional basis of the transformation. In addition, the characteristic responses of dispersal limitation and homogenizing dispersal adequately revealed the assembly pathways in adaptive evolution and the resulting structural variation. Therefore, the "interfacial exposure-structural variation-mass transfer feedback" mechanism was inferred to underly the adaptive evolution process of biofilms. Overall, this study highlighted the internal drivers of the adaptive evolution of the biofilm at the phylogenetic level and deepened our understanding of the mechanism of biofilm development under EP stress in advanced wastewater purification.

Insights into the metabolic pathways and biodegradation mechanisms of chloroacetamide herbicides

Chloroacetamide herbicides are widely used around the world due to their high efficiency, resulting in increasing levels of their residues in the environment. Residual chloroacetamides and their metabolites have been frequently detected in soil, water and organisms and shown to have toxic effects on non-target organisms, posing a serious threat to the ecosystem. As such, rapid and efficient techniques that eliminate chloroacetamide residues from the ecosystem are urgently needed. Degradation of these herbicides in the environment mainly occurs through microbial metabolism. Microbial strains such as Acinetobacter baumannii DT, Bacillus altitudinis A16, Pseudomonas aeruginosa JD115, Sphingobium baderi DE-13, Catellibacterium caeni DCA-1, Stenotrophomonas acidaminiphila JS-1, Klebsiella variicola B2, and Paecilomyces marquandii can effectively degrade chloroacetamide herbicides. The degradation pathway of chloroacetamide herbicides in aerobic bacteria is mainly initiated by an N/C-dealkylation reaction, followed by aromatic ring hydroxylation and cleavage processes, whereas dechlorination is the initial reaction in anaerobic bacteria. The molecular mechanisms associated with bacterial degradation of chloroacetamide herbicides have been explored, with amidase, hydrolase, reductase, ferredoxin and cytochrome P450 oxygenase currently known to play a pivotal role in the catabolic pathways of chloroacetamides. The fungal pathway for the degradation of these herbicides is more complex with more diversified products, and the degradation enzymes and genes involved remain to be discovered. However, there are few reviews specifically summarizing the microbial degrading species and biochemical mechanisms of chloroacetamide herbicides. Here, we briefly summarize the latest progress resulting from research on microbial strain resources and enzymes involved in degradation of these herbicides and their corresponding genes. Furthermore, we explore the biochemical pathways and molecular mechanisms for biodegradation of chloroacetamide herbicides in depth, thereby providing a reference for further research on the bioremediation of such herbicides.

New insights into the bioremediation of petroleum contaminants: A systematic review

Petroleum product is an essential resource for energy, that has been exploited by wide range of industries and regular life. A carbonaceous contamination of marine and terrestrial environments caused by errant runoffs of consequential petroleum-derived contaminants. Additionally, petroleum hydrocarbons can have adverse effects on human health and global ecosystems and also have negative demographic consequences in petroleum industries. Key contaminants of petroleum products, primarily includes aliphatic hydrocarbons, benzene, toluene, ethylbenzene, and xylene (BTEX), polycyclic aromatic hydrocarbons (PAHs), resins, and asphaltenes. On environmental interaction, these pollutants result in ecotoxicity as well as human toxicity. Oxidative stress, mitochondrial damage, DNA mutations, and protein dysfunction are a few key causative mechanisms behind the toxic impacts. Henceforth, it becomes very evident to have certain remedial strategies which could help on eliminating these xenobiotics from the environment. This brings the efficacious application of bioremediation to remove or degrade pollutants from the ecosystems. In the recent scenario, extensive research and experimentation have been implemented towards bio-benign remediation of these petroleum-based pollutants, aiming to reduce the load of these toxic molecules in the environment. This review gives a detailed overview of petroleum pollutants, and their toxicity. Methods used for degrading them in the environment using microbes, periphytes, phyto-microbial interactions, genetically modified organisms, and nano-microbial remediation. All of these methods could have a significant impact on environmental management.

Current insights into the microbial degradation of nicosulfuron: Strains, metabolic pathways, and molecular mechanisms

Nicosulfuron is among the sulfonylurea herbicides that are widely used to control annual and perennial grass weeds in cornfields. However, nicosulfuron residues in the environment are likely to cause long-lasting harmful environmental and biological effects. Nicosulfuron degrades via photo-degradation, chemical hydrolysis, and microbial degradation. The latter is crucial for pesticide degradation and has become an essential strategy to remove nicosulfuron residues from the environment. Most previous studies have focused on the screening, degradation characteristics, and degradation pathways of biodegrader microorganisms. The isolated nicosulfuron-degrading strains include Bacillus, Pseudomonas, Klebsiella, Alcaligenes, Rhodopseudomonas, Ochrobactrum, Micrococcus, Serratia, Penicillium, Aspergillus, among others, all of which have good degradation efficiency. Two main intermediates, 2-amino-4,6-dimethoxypyrimidine (ADMP) and 2-aminosulfonyl-N,N-dimethylnicotinamide (ASDM), are produced during microbial degradation and are derived from the C-N, C-S, and S-N bond breaks on the sulfonylurea bridge, covering almost every bacterial degradation pathway. In addition, enzymes related to the degradation of nicosulfuron have been identified successively, including the manganese ABC transporter (hydrolase), Flavin-containing monooxygenase (oxidase), and E3 (esterase). Further in-depth studies based on molecular biology and genetics are needed to elaborate on their role in the evolution of novel catabolic pathways and the microbial degradation of nicosulfuron. To date, few reviews have focused on the microbial degradation and degradation mechanisms of nicosulfuron. This review summarizes recent advances in nicosulfuron degradation and comprehensively discusses the potential of nicosulfuron-degrading microorganisms for bioremediating contaminated environments, providing a reference for further research development on nicosulfuron biodegradation in the future.

Biotechnological applications of biofilms formed by osmotolerant and halotolerant yeasts

Many microorganisms are capable of developing biofilms under adverse conditions usually related to nutrient limitation. They are complex structures in which cells (in many cases of different species) are embedded in the material that they secrete, the extracellular matrix (ECM), which is composed of proteins, carbohydrates, lipids, and nucleic acids. The ECM has several functions including adhesion, cellular communication, nutrient distribution, and increased community resistance, this being the main drawback when these microorganisms are pathogenic. However, these structures have also proven useful in many biotechnological applications. Until now, the most interest shown in these regards has focused on bacterial biofilms, and the literature describing yeast biofilms is scarce, except for pathological strains. Oceans and other saline reservoirs are full of microorganisms adapted to extreme conditions, and the discovery and knowledge of their properties can be very interesting to explore new uses. Halotolerant and osmotolerant biofilm-forming yeasts have been employed for many years in the food and wine industry, with very few applications in other areas. The experience gained in bioremediation, food production and biocatalysis with bacterial biofilms can be inspiring to find new uses for halotolerant yeast biofilms. In this review, we focus on the biofilms formed by halotolerant and osmotolerant yeasts such as those belonging to Candida, Saccharomyces flor yeasts, Schwannyomyces or Debaryomyces, and their actual or potential biotechnological applications. KEY POINTS: • Biofilm formation by halotolerant and osmotolerant yeasts is reviewed. • Yeasts biofilms have been widely used in food and wine production. • The use of bacterial biofilms in bioremediation can be expanded to halotolerant yeast counterparts.

Impact of historical legacy pesticides on achieving legislative goals in Europe

Pesticides are widely used in agriculture to optimise food production. However, the movement of pesticides into water bodies negatively impacts aquatic environments. The European Union (EU) aims to make food systems fair, healthy and environmentally friendly through its current Farm to Fork strategy. As part of this strategy, the EU plans to reduce the overall use and risk of chemical pesticides by 50 % by 2030. The attainment of this target may be compromised by the prevalence of legacy pesticides arising from historical applications to land, which can persist in the environment for several decades. The current EU Farm to Fork policy overlooks the potential challenges of legacy pesticides and requirements for their remediation. In this review, the current knowledge regarding pesticide use in Europe, as well as pathways of pesticide movement to waterways, are investigated. The issues of legacy pesticides, including exceedances, are examined, and existing and emerging methods of pesticide remediation, particularly of legacy pesticides, are discussed. The fact that some legacy pesticides can be detected in water samples, more than twenty-five years after they were prohibited, highlights the need for improved EU strategies and policies aimed at targeting legacy pesticides in order to meet future targets.

Co-assembled nanocomplexes comprising epigallocatechin gallate and berberine for enhanced antibacterial activity against multidrug resistant Staphylococcus aureus

Berberine (BBR), a major alkaloid in Coptis chinensis, and (-)-epigallocatechin-3-gallate (EGCG), a major catechin in green tea, are two common phytochemicals with numerous health benefits, including antibacterial efficacy. However, the limited bioavailability restricts their application. Advancement in the co-assembly technology to form nanocomposite nanoparticles precisely controls the morphology, electrical charge, and functionalities of the nanomaterials. Here, we have reported a simple one-step method for preparing a novel nanocomposite BBR-EGCG nanoparticles (BBR-EGCG NPs). These BBR-EGCG NPs exhibit improved biocompatibility and greater antibacterial effects both in vitro and in vivo relative to free-BBR and first-line antibiotics (i.e., benzylpenicillin potassium and ciprofloxacin). Furthermore, we demonstrated a synergistic bactericidal effect for BBR when combined with EGCG. We also evaluated the antibacterial activity of BBR and the possible synergism with EGCG in MRSA-infected wounds. A potential mechanism for synergism between S. aureus and MRSA was also explored through ATP determination, the interaction between nanoparticles and bacteria, and, then, transcription analysis. Furthermore, our experiments on S. aureus and MRSA confirmed the biofilm-scavenging effect of BBR-EGCG NPs. More importantly, toxicity analysis revealed that the BBR-EGCG NPs had no toxic effects on the major organs of mice. Finally, we proposed a green method for the fabrication of BBR-EGCG combinations, which may provide an alternative approach to treating infections with MRSA without using antibiotics.

Phosphorus-rich biochar modified with Alcaligenes faecalis to promote U(VI) removal from wastewater: Interfacial adsorption behavior and mechanism

Phosphorus-rich biochar (PBC) has been extensively studied due to its significant adsorption effect on U(VI). However, the release of phosphorus from PBC into solution decreases its adsorption performance and reusability and causes phosphorus pollution of water. In this study, Alcaligenes faecalis (A. faecalis) was loaded on PBC to produce a novel biocomposite (A/PBC). After adsorption equilibrium, phosphorus released into solution from PBC was 2.32 mg/L, while it decreased to 0.34 mg/L from A/PBC (p < 0.05). The U(VI) removal ratio of A/PBC reached nearly 100%, which is 13.08% higher than that of PBC (p < 0.05), and it decreased only by 1.98% after 5 cycles. When preparing A/PBC, A. faecalis converted soluble phosphate into insoluble metaphosphate minerals and extracellular polymeric substances (EPS). And A. faecalis cells accumulated through these metabolites and formed biofilm attached to the PBC surface. The adsorption of metal cations on phosphate further contributed to phosphorus fixation in the biofilm. During U(VI) adsorption by A/PBC, A. faecalis synthesize EPS and metaphosphate minerals by using the internal components of PBC, thus increasing the abundance of acidic functional groups and promoting U(VI) adsorption. Hence, A/PBC can be a green and sustainable material for U(VI) removal from wastewater.

Core Species Derived from Multispecies Interactions Facilitate the Immobilization of Cadmium

Microbial consortia have opened new avenues for heavy-metal remediation. However, the limited understanding of the overall effect of interspecific interactions on remediation efficacy hinders its application. Here, the effects of multispecies growth and biofilm formation on Cd immobilization were explored from direct and multiple interactions through random combinations of two or three rhizosphere bacteria. In monocultures, Cd stress resulted in an average decrease in planktonic biomass of 26%, but through cooperation, the decrease was attenuated in dual (21%) and triple cultures (13%), possibly involving an increase in surface polysaccharides. More than 65% of the co-cultures exhibited induction of biofilm formation under Cd stress, which further enhanced the role of biofilms in Cd immobilization. Notably, excellent biofilm-forming ability or extensive social induction makes Pseudomonas putida and Brevundimonas diminuta stand out in multispecies biofilm formation and Cd immobilization. These two core species significantly increase the colonization of soil microorganisms on rice roots compared to the control, resulting in a 40% decrease in Cd uptake by rice. Our study enhances the understanding of bacterial interactions under Cd stress and provides a novel strategy for adjusting beneficial soil consortia for heavy-metal remediation.

The role of microorganisms in petroleum degradation: Current development and prospects

Petroleum hydrocarbon compounds are persistent organic pollutants, which can cause permanent damage to ecosystems due to their biomagnification. Bioremediation of oil is currently the main solution for the remediation of petroleum hydrocarbon pollutants in ecosystems. Despite several lab studies on oil microbial biodegradation efficiency, still there are various challenges for microorganisms to perform efficiently in outside environments. Herewith, investigating efficient biodegradation technologies through discovering new microorganisms, biodegradation pathways modification, and new bioremediations technologies are in great demand. The degradation of petroleum pollutants by microorganisms and the remediation of contaminated soils are achieved through their key enzymes and metabolic pathways. Although, several challenges hinder the effective biodegradation processes such as the toxic environment, long chains and versatility of petroleum hydrocarbons and the existence of the full metabolism pathways in a single microorganism. There are several developed oil biodegradation strategies by microorganisms such as synthetic biology, biofilm, recombinant technology and microbial consortia. Herewith, the application of multi-omics technology to discover oil-contaminated environments microbial communities, synthetic biology, microbial consortia, and other technologies would help improve the efficiency of microbial remediation.

Significance of microbial genome in environmental remediation

Environmental pollutants seriously threaten the ecosystem and health of various life forms, particularly with the rapid industrialization and emerging population. Conventionally physical and chemical strategies are being opted for the removal of these pollutants. Bioremediation, through several advancements, has been a boon to combat the existing threat faced today. Microbes with enzymes degrade various pollutants and utilize them as a carbon and energy source. With the existing demand and through several research explorations, Genetically Engineered Microorganisms (GEMs) have paved to be a successful approach to abate pollution through bioremediation. The genome of the microbe determines its biodegradative nature. Thus, methods including pure culture techniques and metagenomics are used for analyzing the genome of microbes, which provides information about catabolic genes. The information obtained along with the aid of biotechnology helps to construct GEMs that are cost-effective and safer thereby exhibiting higher degradation of pollutants. The present review focuses on the role of microbes in the degradation of environmental pollutants, role of evolution in habitat and adaptation of microbes, microbial degenerative genes, their pathways, and the efficacy of recombinant DNA (rDNA) technology for creating GEMs for bioremediation. The present review also provides a gist of existing GEMs for bioremediation and their limitations, thereby providing a future scope of implementation of these GEMs for a sustainable environment.

Ultraviolet control of bacterial biofilms in microfluidic chips

Polydimethylsiloxane (PDMS) microfluidic systems have been instrumental in better understanding couplings between physical mechanisms and bacterial biofilm processes, such as hydrodynamic effects. However, precise control of the growth conditions, for example, the initial distribution of cells on the substrate or the boundary conditions in a flow system, has remained challenging. Furthermore, undesired bacterial colonization in crucial parts of the systems, in particular, in mixing zones or tubing, is an important factor that strongly limits the duration of the experiments and, therefore, impedes our ability to study the biophysics of biofilm evolving over long periods of time, as found in the environment, in engineering, or in medicine. Here, we develop a new approach that uses ultraviolet-C (UV-C) light-emitting diodes (LEDs) to confine bacterial development to specific zones of interest in the flow channels. The LEDs are integrated into a 3D printed light guide that is positioned upon the chip and used to irradiate germicidal UV-C directly through the PDMS. We first demonstrate that this system is successful in controlling undesired growth of Pseudomonas aeruginosa biofilm in inlet and outlet mixing zones during 48 h. We further illustrate how this can be used to define the initial distribution of bacteria to perturb already formed biofilms during an experiment and to control colonization for seven days-and possibly longer periods of time-therefore opening the way toward long-term biofilm experiments in microfluidic devices. Our approach is easily generalizable to existing devices at low cost and may, thus, become a standard in biofilm experiments in PDMS microfluidics.

Bioremediation of heavy metals polluted environment and decolourization of black liquor using microbial biofilms

BACKGROUND

With increased urbanization and industrialization, modern life has led to an anthropogenic impact on the biosphere. Heavy metals pollution and pollutants from black liquor (BL) have caused severe effects on environment and living organisms. Bacterial biofilm has potential to remediate heavy metals and remove BL from the environment. Hence, this study was planned to investigate the potential of microbial biofilms for the bioremediation of heavy metals and BL polluted environments.

METHODS AND RESULTS

Eleven biofilm forming bacterial strains (SB1, SB2, SC1, AF1, 5A, BC-1, BC-2, BC-3, BC-4, BC-5 and BC-6) were isolated and identified upto species level via 16S rRNA gene sequencing. Biofilm strains belonging to Bacillus and Lysinibacillus sphaericus were used to remediate heavy metals (Pb, Ni, Mn, Zn, Cu, and Co). Atomic absorption spectroscopy showed significantly high (P ≤ 0.05) bioremediation potential by L. sphaericus biofilm (1462.0 ± 0.67 µgmL^-1) against zinc (Zn). Similarly, Pseudomonas putida biofilm significantly (P ≤ 0.05) decolourized (65.1%) BL. Fourier transform infrared (FTIR) analysis of treated heavy metals showed the shifting of major peaks (1637 & 1629-1647, 1633 & 1635-1643, and 1638-1633 cm^-1) corresponding to specific amide groups due to C = O stretching.

CONCLUSION

The study suggested that biofilm of the microbial flora from tanneries and pulp paper effluents possesses a strong potential for heavy metals bioremediation and BL decolourization. To our knowledge, this is the first report showing promising biofilm remediation potential of bacterial flora of tanneries and pulp-paper effluent from Kasur and Sheikhupura, Punjab, Pakistan, against heavy metals and BL.

Horizontal Gene Transfer of Antibiotic Resistance Genes in Biofilms

Most bacteria attach to biotic or abiotic surfaces and are embedded in a complex matrix which is known as biofilm. Biofilm formation is especially worrisome in clinical settings as it hinders the treatment of infections with antibiotics due to the facilitated acquisition of antibiotic resistance genes (ARGs). Environmental settings are now considered as pivotal for driving biofilm formation, biofilm-mediated antibiotic resistance development and dissemination. Several studies have demonstrated that environmental biofilms can be hotspots for the dissemination of ARGs. These genes can be encoded on mobile genetic elements (MGEs) such as conjugative and mobilizable plasmids or integrative and conjugative elements (ICEs). ARGs can be rapidly transferred through horizontal gene transfer (HGT) which has been shown to occur more frequently in biofilms than in planktonic cultures. Biofilm models are promising tools to mimic natural biofilms to study the dissemination of ARGs via HGT. This review summarizes the state-of-the-art of biofilm studies and the techniques that visualize the three main HGT mechanisms in biofilms: transformation, transduction, and conjugation.

Environmental occurrence, toxicity concerns, and biodegradation of neonicotinoid insecticides

Neonicotinoids (NEOs) are fourth generation pesticides, which emerged after organophosphates, pyrethroids, and carbamates and they are widely used in vegetables, fruits, cotton, rice, and other industrial crops to control insect pests. NEOs are considered ideal substitutes for highly toxic pesticides. Multiple studies have reported NEOs have harmful impacts on non-target biological targets, such as bees, aquatic animals, birds, and mammals. Thus, the remediation of neonicotinoid-sullied environments has gradually become a concern. Microbial degradation is a key natural method for eliminating neonicotinoid insecticides, as biodegradation is an effective, practical, and environmentally friendly strategy for the removal of pesticide residues. To date, several neonicotinoid-degrading strains have been isolated from the environment, including Stenotrophomonas maltophilia, Bacillus thuringiensis, Ensifer meliloti, Pseudomonas stutzeri, Variovorax boronicumulans, and Fusarium sp., and their degradation properties have been investigated. Furthermore, the metabolism and degradation pathways of neonicotinoids have been broadly detailed. Imidacloprid can form 6-chloronicotinic acid via the oxidative cleavage of guanidine residues, and it is then finally converted to non-toxic carbon dioxide. Acetamiprid can also be demethylated to remove cyanoimine (=N-CN) to form a less toxic intermediate metabolite. A few studies have discussed the neonicotinoid toxicity and microbial degradation in contaminated environments. This review is focused on providing an in-depth understanding of neonicotinoid toxicity, microbial degradation, catabolic pathways, and information related to the remediation process of NEOs. Future research directions are also proposed to provide a scientific basis for the risk assessment and removal of these pesticides.

Direct Z-scheme heterojunction Bi/Bi2S3/α-MoO3 photoelectrocatalytic degradation of tetracycline under visible light

A hot research topic in visible-light-driven photoelectrocatalytic (PEC) oxidation technology is the development of superior photoanode materials. The design of the photoanode system with a direct Z-scheme charge transfer mechanism is crucial to achieving effective charge separation for sustainable photoelectrocatalysis. Here, a novel Bi/Bi2S3/α-MoO3 heterostructure was successfully assembled by a simple and feasible strategy. The direct Z-scheme heterogeneous formed between Bi2S3 and α-MoO3 has the advantages of low resistance, high optical response current and the surface plasmon resonance (SPR) effect of Bi nanoparticles (Bi NPs). Thus, the efficiency of photogenerated carrier separation and transfer is further enhanced, and the catalytic activity is significantly improved. It is impressive that the unique photoanode has achieved a maximum removal efficiency of 85.8% of tetracycline (TC) pollutants under visible light irradiation within 60 min and has excellent stability, which is expected to degrade antibiotics efficiently and environmentally in harsh environments. These characteristics give Bi/Bi2S3/α-MoO3 promising candidates for practical applications in antibiotic degradation.

Instrumental role of bioreactors in nitrate/nitrite-dependent anaerobic methane oxidation-based biotechnologies for wastewater treatment: A review

Recently, the nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) processes have become a research hotspot in the field of wastewater treatment. The n-DAMO processes could not only mitigate direct and indirect carbon emissions from wastewater treatment plants but also strengthen biological nitrogen removal. However, the applications of n-DAMO-based biotechnologies face practical difficulties mainly caused by the distinctive properties of n-DAMO microorganisms and the limited/availability of methane with poor solubility. In this sense, the choice of bioreactors will play important roles that influence the growth and functioning of n-DAMO microorganisms, thus enabling dedicated development of the n-DAMO processes and efficient applications of n-DAMO-based biotechnologies. Therefore, this paper aims to discuss the three commonly-applied types of bioreactors, covering the individual working principle and state-of-the-art removal performance of nitrogen as well as dissolved methane observed when adopted for n-DAMO-based biotechnologies. With noted limitations for each bioreactor type, several key perspectives were proposed which hopefully would inspire future investigation and practical applications of the n-DAMO processes.

Innovative microbial disease biocontrol strategies mediated by quorum quenching and their multifaceted applications: A review

With the increasing resistance exhibited by undesirable bacteria to traditional antibiotics, the need to discover alternative (or, at least, supplementary) treatments to combat chemically resistant bacteria is becoming urgent. Quorum sensing (QS) refers to a novel bacterial communication system for monitoring cell density and regulation of a network of gene expression that is mediated by a group of signaling molecules called autoinducers (AIs). QS-regulated multicellular behaviors include biofilm formation, horizontal gene transfer, and antibiotic synthesis, which are demonstrating increasing pathogenicity to plants and aquacultural animals as well as contamination of wastewater treatment devices. To inhibit QS-regulated microbial behaviors, the strategy of quorum quenching (QQ) has been developed. Different quorum quenchers interfere with QS through different mechanisms, such as competitively inhibiting AI perception (e.g., by QS inhibitors) and AI degradation (e.g., by QQ enzymes). In this review, we first introduce different signaling molecules, including diffusible signal factor (DSF) and acyl homoserine lactones (AHLs) for Gram-negative bacteria, AIPs for Gram-positive bacteria, and AI-2 for interspecies communication, thus demonstrating the mode of action of the QS system. We next exemplify the QQ mechanisms of various quorum quenchers, such as chemical QS inhibitors, and the physical/enzymatic degradation of QS signals. We devote special attention to AHL-degrading enzymes, which are categorized in detail according to their diverse catalytic mechanisms and enzymatic properties. In the final part, the applications and advantages of quorum quenchers (especially QQ enzymes and bacteria) are summarized in the context of agricultural/aquacultural pathogen biocontrol, membrane bioreactors for wastewater treatment, and the attenuation of human pathogenic bacteria. Taken together, we present the state-of-the-art in research considering QS and QQ, providing theoretical evidence and support for wider application of this promising environmentally friendly biocontrol strategy.

Inhibitory effects of hexanal on acylated homoserine lactones (AHLs) production to disrupt biofilm formation and enzymes activity in Erwinia carotovora and Pseudomonas fluorescens

Erwinia carotovora and Pseudomonas fluorescens were two bacteria commonly caused the spoilage of vegetables through biofilm formation and secretion of extracellular enzymes. In this study, N-(3-oxohexanoyl)-L-homoserine lactone (3-oxo-C6-HSL) and N-Octanoyl-L-homoserine lactone (C8-HSL) were confirmed as acylated homoserine lactones (AHLs) signal molecule produced by E. carotovora and P. fluorescens, respectively. In addition, quorum sensing inhibitory (QSI) effects of hexanal on AHLs production were evaluated. Hexanal at 1/2 minimum inhibitory concentration (MIC) was achieved 76.27% inhibitory rate of 3-oxo-C6-HSL production in E. carotovora and a inhibitory rate of C8-HSL (60.78%) in P. fluorescens. The amount of biofilm formation and activity of extracellular enzymes treated with 1/2 MIC of hexanal were restored with different concentrations (10 ng/mL, 50 ng/mL, 100 ng/mL) of exogenous AHLs (P < 0.05), which verified QSI effect of hexanal on biofilm and extracellular enzymes were due to its inhibition on AHLs production. Molecular docking analysis showed that hexanal could interact with EcbI and PcoI protein to disrupt AHLs production. Furthermore, results showed that sub-MICs of hexanal could suppress expressions of ecbI and pcoI genes in AHL-mediated QS system of E. carotovora and P. fluorescens. This study provides theoretical support for the application of essential oils as QS inhibitors in the preservation of vegetables.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-022-05624-9.

Latest eco-friendly approaches for pesticides decontamination using microorganisms and consortia microalgae: A comprehensive insights, challenges, and perspectives

Pesticides are chemical compounds that are considered toxic to many organisms, including humans. Their elimination from polluted sites attracted the attention of Scientifics in the last decade; Among the various methods used to decontaminate pesticides from the environment, the microbial-algae consortium is a promising bioremediation technology, which implies several advantages as an eco-friendly process that generate biomass produced that could be valorized in the form of bioenergy, In this review, we will discuss the latest eco-friendly approaches using microorganisms to remediate sites contaminated by pesticides, and shows the ability of microbial, algae and their consortium to remove pesticides and the role of different enzymes in degradation processes.

Insights into the microbial degradation and resistance mechanisms of glyphosate

Glyphosate, as one of the broad-spectrum herbicides for controlling annual and perennial weeds, is widely distributed in various environments and seriously threatens the safety of human beings and ecology. Glyphosate is currently degraded by abiotic and biotic methods, such as adsorption, photolysis, ozone oxidation, and microbial degradation. Of these, microbial degradation has become the most promising method to treat glyphosate because of its high efficiency and environmental protection. Microorganisms are capable of using glyphosate as a phosphorus, nitrogen, or carbon source and subsequently degrade glyphosate into harmless products by cleaving C-N and C-P bonds, in which enzymes and functional genes related to glyphosate degradation play an indispensable role. There have been many studies on the abiotic and biotic treatment technologies, microbial degradation pathways and intermediate products of glyphosate, but the related enzymes and functional genes involved in the glyphosate degradation pathways have not been further discussed. There is little information on the resistance mechanisms of bacteria and fungi to glyphosate, and previous investigations of resistance mechanisms have mainly focused on how bacteria resist glyphosate damage. Therefore, this review explores the microorganisms, enzymes and functional genes related to the microbial degradation of glyphosate and discusses the pathways of microbial degradation and the resistance mechanisms of microorganisms to glyphosate. This review is expected to provide reference for the application and improvement of the microbial degradation of glyphosate in microbial remediation.