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The slow rate of natural attenuation of organic pollutants, together with unwanted environmental impacts of traditional remediation strategies, has necessitated the exploration of plant-microbe systems for enhanced bioremediation applications. The identification of microorganisms capable of promoting rhizoremediation through both plant growth-promoting and hydrocarbon-degrading processes is crucial to the success and adoption of plant-based remediation techniques. In this study, through successive enrichments of soil samples from a historic oil-contaminated site in Wietze, Germany, we isolated a plant growth-promoting and hydrocarbon-degrading bacterial consortium dominated by Alphaproteobacteria. In microcosm experiments involving Medicago sativa L. and the isolated bacterial consortium, we examined the ability of the consortium to enhance rhizoremediation of petroleum hydrocarbons. The inoculation of M. sativa with the consortium resulted in 66% increase in plant biomass, and achieved a 91% reduction in diesel fuel hydrocarbon concentrations in the soil within 60 days. Metagenome analysis led to the identification of genes and taxa putatively involved in these processes. The majority of the coding DNA sequences associated with plant growth promotion and hydrocarbon degradation in this study were affiliated to Acidocella aminolytica and Acidobacterium capsulatum indicating their potential for biotechnological applications in the rhizoremediation of sites contaminated by petroleum-derived organic pollutants.

Hydroxylamine, an intermediate product in the nitrification process, is widely found in nature. However, hydroxylamine accumulation can decrease the biological nitrogen removal efficiency by reducing the activities, inhibiting the reproductions, and even causing the death of microorganisms. In this study, a novel heterotrophic nitrification bacterium was separated from biogas digester and identified as Glutamicibacter arilaitensis EM-H8. Strain EM-H8 exhibited efficient hydroxylamine removal (93.75%). The optimal conditions for hydroxylamine removal were as follows: Carbon source, glucose; C/N ratio, 25; temperature, 20 °C; inoculum size, 0.53 × 108 CFU; and shaking speed, 150 rpm. The nitrogen balance results using strain EM-H8 showed that about 26.86% of the initial nitrogen was removed as nitrogenous gas, while 4.6% was converted into biomass under aerobic conditions, confirming that strain EM-H8 possessed the capacity for heterotrophic nitrification. Furthermore, the successful expression of hydroxylamine oxidase (0.065 U/mg protein) showed that strain EM-H8 had the ability to transform hydroxylamine from wastewater.

Fecal shedding of SARS-CoV-2 from COVID-19 patients and presence of the viral RNA in wastewater have extensively been reported. Some wastewater treatment plant (WWTP) processes generate aerosols which have the potential to transmit pathogenic microorganisms and present a health risk for exposed individuals. We analyzed the presence of viral RNA of SARS-CoV-2 in raw wastewater and air samples of WWTPs. The risk that may arise from exposure to virus-contaminated aerosols of wastewater was estimated by developing a quantitative microbial risk analysis (QMRA) method. SARS-CoV-2 was detected in 9 of 24 (37.5%) wastewater samples with a concentration about 104 genomic copies L−1. The viral RNA was also detected in 40% (6/15) of air samples. QMRA analysis showed a relatively high risk of SARS-CoV-2 infection for wastewater workers via exposure to the viral aerosols. The estimated annual infection risk ranged from 1.1 × 10−2 to 2.3 × 10−2 per person per year (PPPY) for wastewater workers which was higher than the reference level recommended by WHO (10−3 pppy). However, due to the lack of data on survival of SARS-CoV-2 in wastewater and its fate in aerosolized state, more research is needed to determine the importance of wastewater in transmission of COVID-19., Graphical abstract Image 1, Highlights • SARS-CoV-2 presence in wastewater raises the question regarding the transmission via wastewater. • SARS-CoV-2 was detected in wastewater aerosols at pumping station and activated sludge plants. • There was a relatively high risk of COVID-19 for wastewater workers through wastewater aerosols. • Role of wastewater in SARS-CoV-2 transmission is limited by knowledge gaps about its viability. • Molecular detection along with cell culture is needed to validate infectivity of the SARS-CoV-2.

Bioelectrochemical systems (BESs) are known to enhance the remediation of hydrocarbon-contaminated soil and sediments compared with natural attenuation, and the primary mechanism has been assumed as anaerobic degradation facilitated by electroactive bacteria (EAB) using the electrode as electron acceptor. However, known EAB were rarely found on the anodes of reported BESs, which challenged the fundamental mechanism of BESs although significant current generation was always observed during degradation of these recalcitrant substrates. This study however found the abundant EAB Geobacter (∼27.3%) in the anodic biofilms, which confirmed the role of electroactive bio-anode on the conversion of hydrocarbons into the current for the enhancement of remediation. Widespread occurrence of aerobic hydrocarbon-degrading bacteria (HDB) (e.g. ∼24.0% Parvibaculum and ∼30.6% Pseudomonas) was observed in soils with limited dissolved oxygen (∼0.4 mg/L). The higher abundance of dehydrogenase genes was found in the anode biofilms than that in soils, indicating anodic microorganisms may be mainly responsible for the removal of intermediates of aerobic hydrocarbons degradation in soils. High water saturation level and sandy soil texture showed positive impacts on bioelectrochemical remediation, while clay soil and unsaturation condition pose challenges in mass transfers in the matrix. The reactor performance was consistent with the phylogenetic molecular ecological network (pMENs) analysis, which showed that sandy soil BESs had tighter microbial network interactions than clay soil reactors.

Fipronil is a highly effective, broad-spectrum insecticide used to control pests, globally. The increased usage has led to contamination of soil, water, fruits, and vegetables. The wide and frequent usage of fipronil across the globe calls for attention regarding risk assessment of undesirable effects on non-target microorganisms. In this context, the present study was carried to understand the impact of fipronil on non-pathogenic Escherichia coli. The non-pathogenic E. coli are important commensal of the intestinal tract of humans and animals and are also indicator organisms in the environment. Our study indicates that exposure of E. coli to fipronil (100 μM concentration) leads to significant reactive oxygen species production, loss of membrane potential and viability. Further, we have witnessed the bioaccumulation and biotransformation of fipronil by E. coli at non-lethal concentrations. The bio-transformed products (fipronil sulfone and fipronil sulfide) are also the major metabolites (along with amide) reported in the feces of the mammals when exposed to fipronil. Thus, there is a possibility that the gut E. coli might play a role in the degradation and thereby removal of fipronil. In addition, the bioaccumulation of fipronil in bacteria is of concern and need to be further explored because it can lead to biomagnification in the higher trophic level and can disturb the ecological balance. In our knowledge, this is the first report on the determination of fipronil and its metabolites in bacteria through GC-MS/MS.

Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are the emerging contaminants leading to a serious worldwide health problem. Although disinfection like ultraviolet (UV) irradiation could remove part of ARB and ARGs, there still are residual ARB and ARGs in the effluent of wastewater treatment plants. Conjugative transfer is main concern of the risk of ARGs and little is known about the effects of UV disinfection on the transfer ability of the non-inactivated ARB in the effluent which will enter the environment. Hence the influences of UV irradiation and reactivation on ARB conjugative transfer ability were studied under laboratory condition, focusing on the survival bacteria from UV irradiation and the reactivated bacteria, as well as their descendants. The experimental results imply that even 1 mJ/cm2 UV disinfection can significantly decrease the conjugative transfer frequency of the survival bacteria. However, viable but not culturable state cells induced by UV can reactivate through both photoreactivation and dark repair and retain the same level of transfer ability as the untreated strains. This finding is essential for re-considering about the post safety of UV irradiated effluent and microbial safety control strategies were required.

Landfill treatment of municipal solid waste treatment produces a large amount of leachate, which has been an important hotspot of ARGs. This study aimed to investigate the ARGs removal potential, kinetics and mechanism from leachate in aerobic and anaerobic conditions. Simulated landfill reactors showed the efficacy in reducing ARGs, and the removal efficiencies depended on ARGs types and aerobic/anaerobic conditions. The ARGs tetQ and blaCTX-M were more likely to attenuate with the log-removal efficiencies of 1.50–3 order of magnitude. The ARGs removal kinetic was well fitted by modified Collins-Selleck model, and aerobic condition showed better removal capacities and kinetics than anaerobic condition. Among the ARGs with great removal performance, sul2, aadA1and blaCTX-M were eliminated from leachate and refuse simultaneously, but tetM, ermB, and mefA were removed from leachate but enriched in refuse. Aerobic/anaerobic states might drive the bacterial community shift of leachate and refuse, and topology property comparison of co-occurrence networks suggested that refuse had a closer non-random host relationship between ARGs and microbial taxa than leachate. Further module analyses revealed that ARGs removal efficiencies depended on the taxonomy of host bacteria in leachate, while the refuse taxa-ARGs correlation determined ARGs removal patterns. By selecting distinct bacteria cluster in different conditions, aerobic treatment benefited ARGs reduction in leachate and refuse, while anaerobic treatment enhanced the enrichment of ARGs in refuse. These findings can potentially foster the understanding of ARGs removal mechanism in biological treatment processes.

Riverbank filtration (RBF) as a barrier of pathogenic microorganisms and organic micropollutants recently has been proven capable of removing sulfonamides. However, the study about the effect of redox conditions on biodegradation of common and persistent sulfonamides in RBF is limited and the response of microbial communities to sulfonamides stress during RBF is unknown. In this study, two column set-ups (with residence time 5 days and 11 days respectively), simulating different redox conditions of riverbank filtration systems, were operated for seven months to investigate 1) the long-term effect of redox conditions on ng∙L−1 level sulfonamides (sulfapyridine, sulfadiazine, sulfamethoxazole, sulfamethazine, sulfaquinoxaline) removal, and 2) the microbial community evolution represented by the phylogenetic and metabolic function shift under non-lethal selective pressures of sulfonamides. The results showed that sulfonamides were more degradable under anoxic conditions than oxic and suboxic conditions. In the sulfonamides stressed community, the phylogenetic diversity increased slightly. Relative abundance of an intrinsic sulfonamides resistant bacteria Bacillus spp. increased, suggesting that sulfonamide resistance developed in specific bacteria under sulfonamides contamination pressure in RBF systems. At the same time, an activated transport function in the stressed microbial community was noticed. The predicted relative abundance of gene folP, which encodes dihydropteroate synthase, also increased significantly, indicating a detoxification mechanism and sulfonamides resistance potential under non-lethal selective pressures of sulfonamides in RBF systems.

Biocides, also referred to as 'microbicides' or 'inhibitors', are widely used in industrial processes (e.g. utility water in cooling towers) to control and/or eliminate the growth of microorganisms. Because of their inherent toxicity, their presence in various sources (e.g. river sediments, potable water) can negatively affect ecosystems. Currently available biocide detection techniques are not suitable for 'point-of-use' applications since they are tedious, complicated, and often require experienced personnel to operate. To address this concern, we sought to develop a simple-to-use toxicity bioassay based on a model microorganism (E. coli) after short (30 min) exposure to known biocides that can be stored at room temperature (preferably) or in the fridge. Based on recent work and our expertise in polymer-based preservation of biomolecules, we leveraged this knowledge to improve E. coli preservation for biocide detection purposes. A design-of-experiments strategy was used to evaluate 16 different preservation conditions from 5 process parameters (i.e. 2

Extensive studies on anaerobic fermentation of waste activated sludge (WAS) for volatile fatty acids (VFAs) production focused on the effects of operating parameters and pretreatment methods, and little information is available for those of organic pollutants which were absorbed on sludge. The influence of sulfadiazine (SDZ), a typical antibiotic pollutant in WAS, on VFAs production during anaerobic fermentation was investigated in this study. The accumulation of VFAs was remarkably affected in the presence of SDZ. When the content of SDZ was 50 mg per kilogram dry sludge the concentration of VFAs from sludge was 2032.8 mg COD/L, much higher than that of control (1540.2 mg COD/L). Mechanism investigation revealed that the content of extracellular polymeric substances (EPS) from sludge was increased due to the presence of SDZ, which provided more substrates, i.e., protein and carbohydrate, and created a favorable environment for anaerobes. The hydrolysis and acidification of WAS were stimulated by SDZ, and the functional microorganisms were advantageous to VFAs production. The activities of protease, α-glucosidase and acetate kinase were promoted when SDZ occurred, which were beneficial for hydrolysis and acidification. The effect of SDZ on pure strains further confirmed that the formation of VFAs during anaerobic fermentation was stimulated by SDZ.

In many environments, biofilms are a major mode and an emergent form of microbial life. Biofilms play crucial roles in biogeochemical cycling and invertebrate recruitment in marine environments. However, relatively little is known about how marine biofilms form on different substrata and about how these biofilms impact invertebrate recruitment. Here, we performed a comparative analysis of a 28-day-old biofilm community on non-coated (a control glass) and coated substrata (polyurethane (PU), epoxy resin (EP) and polydimethylsiloxane (PDMS)) and examined the settlement of Mytilus coruscus plantigrades on these biofilms. PU, EP and PDMS deterred the development of marine biofilms by reducing the biofilm biomass including the biofilm dry weight, cell density of the bacteria and diatoms and chlorophyll a concentrations. Further analysis of bacterial community revealed that EP altered the bacterial community composition compared with that on the glass substrata by reducing the relative abundance of Ruegeria (Alphaproteobacteria) and by increasing the relative abundance of Methylotenera (Betaproteobacteria) and Cyanobacteria in the biofilms. However, bacterial communities developed on PU and PDMS, as well as glass and PU, EP and PDMS did not exhibit differences from each other. The M. coruscus settlement rates on biofilms on PU, EP and PDMS were reduced by 20-41% compared with those on the glass after 28 days. Thus, the tested coatings impacted the development of marine biofilms by altering the biofilm biomass and/or the bacterial community composition. The mussel settlements decreased in the biofilms that formed on the coatings compared with those on non-coated glass.

Despite the number of studies that have investigated the fate of endocrine disrupting compounds (EDCs), to date results are still contradictory and more research is required to evaluate the contribution of the microbial communities present in different engineered treatment systems. Thus, autotrophic and heterotrophic types of biomass were here compared in terms of efficiency in the removal of estrone (E1), 17β-estradiol (E2), estriol (E3), 17α-ethynilestradiol (EE2) and bisphenol A (BPA). Experiments were performed with enriched nitrifying activated sludge (NAS) and enriched ammonia oxidizing bacteria (AOB) sludge cultivated at lab-scale, as well as with conventional activated sludge (CAS) from a full-scale wastewater treatment plant. Both enriched NAS and AOB demonstrated a negligible degrading capacity. In both cases, the studied EDCs exhibited low removals (14%) and showed no correlation with the increasing nitrification rates contradicting some of the hypothesis present in literature. Contrariwise, the biodegradation capabilities of the heterotrophic fraction of CAS were highlighted. E2 and E3 were removed by up to 100% and 78%, respectively. E1 was found to be the main transformation product of E2 (almost quantitative oxidation) and it was also highly eliminated. Finally, EE2 and BPA were more persistent biologically with removals ranging from 10% to 39%. For these two compounds similar removals were obtained during experiments with heat-inactivated biomass suggesting that sorption could be a relevant route of elimination.

Fluoxil-24 is a commercial herbicide based on oxyfluorfen (a hazardous non-soluble organochlorinated compound) and additional compounds used as solvents. The aim of this work is to study the biotreatability of this commercial herbicide in water through batch experiments performed at different temperatures (15, 20, 25 and 30 °C) and initial concentrations (85, 150, 300 and 500 mg L−1 of oxyfluorfen). Activated sludge from an oil refinery wastewater treatment plant was acclimated and used for biodegradation experiments. Two main mechanisms, volatilization and biodegradation, were observed to be responsible of the herbicide removal. Fluoxil-24 removal efficiencies between approximately 40% and 80% were reached after 70 h, depending on the conditions used, and oxyfluorfen was not completely removed. Regarding the influence of the temperature, thermal inhibition problems appeared at 30 °C, and the volatilization rate of solvents increased, causing oxyfluorfen to become unavailable for microorganisms. An increase of herbicide initial concentration did not clearly affect the herbicide removal efficiency, whereas it negatively affected the biological mechanism. The experimental results were fitted to a mathematical model that included both simultaneous mechanisms of volatilization and Monod biodegradation kinetics. The model was able to predict the experimental results, and the calculated model parameters confirmed the effect of the variables under study.

Soil contamination with total petroleum hydrocarbons (TPH) is widespread throughout the globe due tothe massive production of TPH anthropogenically and its occurrence in the soil. TPH is toxic to beneficialsoil organisms and humans and thus has become a serious concern among the public. Traditionally TPHtoxicity in the soil is estimated based on chemical fractions and a range of bioassays including plants,invertebrates and microorganisms. There is a large inconsistency among ecotoxicology data using theseassays due to the nature of TPH and their weathering. Therefore, in this article, we critically reviewed theweathered conditions of TPH, the potential fate in soil and the bioindicators for the assessment of theecotoxicity. Based on the current research and the state-of-the-art problem, we also highlighted key recommendations for future research scope for the real-world solution of the ecotoxicological studies ofhydrocarbons. Refereed/Peer-reviewed

Micro-aerobic condition has proven to be effective in enhancing sulfide oxidation to elemental sulfur (S0) during integrated simultaneous desulfurization and denitrification process (ISDD). In this study we investigated and compared the performance and microbial community of ISDD process operating under initially anoxic, then micro-aerobic and finally switch back to anoxic condition. For all the three tested scenarios, comparable bioreactor performance in terms of sulfate (95.0 ± 4.4%, 90.6 ± 3.8%, 89.8 ± 3.5%) and nitrate (∼100%) removal was achieved. However, a shift of ISDD bioreactor from micro-aerobic to anoxic environment clearly increased the S0 production (30.6%), relative to that at initial anoxic condition (14.2%). Further anoxic bioreactor operation with different influent nitrate concentrations also obtained satisfactory performance particularly in terms of S0 production. Microbial community analysis results showed that functional microorganisms selectively enriched at micro-aerobic condition, particularly sulfide-oxidizing bacteria (SOB), could also function well and enhance S0 production when bioreactor switching from micro-aerobic to anoxic environment. We proposed that micro-aerobic strategy could function as a bio-selector and provide a new idea in functional microorganisms selectively enrichment for wastewater treatment.

The effluent produced in refineries is in the form of an oil/water emulsion that must be treated. These emulsions are often stable and a suitable method must be used to separate the oil from the emulsion. Recently, biosurfactants or biodemulsifiers have received much attention to reduce the interfacial tension between two liquids. Biodemulsifiers are produced by microorganisms and have several benefits over chemical demulsifiers such as low-toxic, biodegradability, eco-friendly and easy synthesis. They can eliminate two phases by changing the interfacial forces between the water and oil molecules. Biosurfactants are categorized based on the molecular weight of their compounds (low or high molecular weight). Sophorolipids, lipopeptides rhamnolipids, trehalolipids, glycolipid, lipoproteins, lichenysin, surfactin, and polymeric biosurfactants are several types of biosurfactants, which are produced by bacteria or fungi. This review study provides a deep evaluation of biosurfactants in the demulsification process. To this end, different types of biosurfactants, the synthesis method of various biosurfactants using various microorganisms, features of biosurfactants, and the role of biodemulsifiers in the demulsification process are thoroughly discussed. Also, the impact of various efficient factors like pH, microorganism type, temperature, the oil content in the emulsion, and gravity on biodemulsificaion was studied. Finally, the mechanism of the demulsification process was discussed. According to previous studies, rhamnolipid biodemulsifier showed the highest biodemulsification efficiency (100%) in the removal of oil from an emulsion.

The ultraviolet (UV)-based advanced oxidation process (AOP) is a powerful technology for removing pathogenic microorganisms and contaminants of emerging concern (CECs) from water. AOP in potable water reuse has been predominantly based on traditional low-pressure mercury (LP-Hg) lamps at 254 nm wavelength, supplemented by hydrogen peroxide addition. In this review, we assessed the potential of unconventional UV wavelengths (UV–B, 280–315 nm and UV-C, 100–280 nm) compared to conventional one (254 nm) in achieving the attenuation of pathogens and CECs. At the same UV doses, conventional 254 nm LP-Hg lamps and other sources such as, 222 nm KrCl lamps and 265 nm UV-LEDs, showed similar disinfection capability for viruses, protozoa, and bacteria, and the effect of hydrogen peroxide (H2O2) addition on disinfection remained unclear. The attenuation levels of key CECs in potable water reuse (N-nitrosodimethylamine and 1,4-dioxane) by 185 + 254 nm LP-Hg or 222 nm KrCl lamps were generally greater than those by conventional 254 nm LP-Hg and other UV lamps. CEC degradation was generally enhanced by H2O2 addition. Overall, our review suggests that 222 nm KrCl or 185 + 254 nm LP-Hg lamps with the addition of H2O2 would be the best alternative to conventional 254 nm LP-Hg lamps for achieving target removal levels of both pathogens and CECs in potable water reuse.

In recent years, various phosphate nanoparticles (PNPs) have been synthesized and applied for in situ Pb remediation in laboratory investigations. Here, three kinds of PNPs, CMC-nClAP (carboxymethyl cellulose stabilized nano-chlorapatite), SDS-nClAP (sodium dodecyl sulfate stabilized nano-chlorapatite) and Rha-nClAP (rhamnolipid stabilized nano-chlorapatite) were used to investigate the influence of PNPs on Pb bioavailability, enzyme activities and bacterial community in Pb polluted sediment. Pb bioavailability can be reduced by the application of CMC-nClAP, SDS-nClAP and Rha-nClAP with the maximum increases of residual fraction to 57.2 %, 58.3 % and 61.4 %, respectively. Alternatively, catalase activity, urease activity and protease activity also changed with the remediation of PNPs. Microbes responded quickly to PNPs in different ways: bacterial richness was all increased while bacterial diversity was only increased with the application of SDS-nClAP. Three dominant species, Proteobacteria, Firmicutes and Bacteroidetes were redistributed differentially during the treatment of PNPs. Interestingly, PNPs didn't significantly change the bacterial community structure in treated samples and CMC-nClAP induced fewer changes in microbial activity and community as compared with SDS-nClAP and Rha-nClAP. Overall, our findings suggested that long-term exposure to PNPs would decrease Pb bioavailability, regulate enzyme activities and affect bacterial community in sediments. The Pb bioavailability, physical-chemical properties of PNPs and properties of chemical/bio-surfactant may determine the response of microorganisms to PNPs in Pb polluted sediment.

Polyhydroxyalkanoates (PHAs) are bioplastic substitutes for petroleum-derived plastics that may help to reduce the increasing environmental impact of plastic pollution. Among them, polyhydroxybutyrate (PHB) is a promising biopolymer, incentivizing many researchers to search for PHB-producing and PHB-degrading bacteria for improved PHB utilization. Many novel PHB-producing microorganisms have been discovered; however, relatively few PHB-degrading bacteria have been identified. Six PHB-degrading bacteria were found in marine soil and investigated their PHB-degrading abilities under various temperature and salinity conditions using solid-media based culture. Finally, thermotolerant and halotolerant PHB-degrader Bacillus sp. JY14 was selected. PHB degradation was confirmed by monitoring changes in the physical and chemical properties of PHB films incubated with Bacillus sp. JY14 using scanning electron microscopy, Fourier-transform infrared spectroscopy, and gel permeation chromatography. Further, PHB degradation ability of Bacillus sp. JY14 was measured in liquid culture by gas chromatography. After 14 days of cultivation with PHB film, Bacillus sp. JY14 achieved approximately 98% PHB degradation. Applying various bioplastics to assess the bacteria's biodegradation capabilities, the result showed that Bacillus sp. JY14 could also degrade P(3HB-co-4HB) and P(3HB-co-3HV). Overall, this study identified a thermotolerant and halotolerant bacteria capable of PHB degradation under solid and liquid conditions. These results suggest that this bacteria could be utilized to degrade various PHAs.

The increase in global population size over the past 100 decades has doubled the requirements for energy resources. To mitigate the limited fossil fuel available, new clean energy sources being environmental sustainable for replacement of traditional energy sources are explored to supplement the current scarcity. Biomass containing lignin and cellulose is the main raw material to replace fossil energy given its abundance and lower emission of greenhouse gases and NOx when transformed into energy. Bacteria, fungi and algae decompose lignocellulose leading to generation of hydrogen, methane, bioethanol and biodiesel being the clean energy used for heating, power generation and the automobile industry. Microbial Fuel Cell (MFC) uses microorganisms to decompose biomass in wastewater to generate electricity and remove heavy metals in wastewater. Biomass contains cellulose, hemicellulose, lignin and other biomacromolecules which need hydrolyzation for conversion into small molecules by corresponding enzymes in order to be utilized by microorganisms. This paper discusses microbial decomposition of biomass into clean energy and the five major ways of clean energy production, and its economic benefits for future renewable energy security.

Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.

Strains of the genus Mucilaginibacter, belonging to the phylum Bacteroidetes, have been noted for exhibiting high genome plasticity and for the vigorous production of extracellular polymeric substances (EPS). Here we analyzed the composition and properties of EPS generated by M. rubeus P2, isolated from a gold-copper mine and exhibiting extremely high resistance to multiple heavy metals. Production of EPS increased significantly upon exposure to elevated concentrations of Cu(II) and Zn(II), but not Au(III). In addition, the EPS produced by M. rubeus P2 displayed extremely high bio-adsorption of As(III), Cu(II) and Au(III), but not of Zn(II). Moreover, EPS production in Mucilaginibacter rubeus P2 exposed to 1 mM of Cu(II) was 8.5 times higher than EPS production in the same strain without metal (loid)-exposure. These findings constitute the basis for a future use of these EPS-overproducing bacteria in bioremediation of heavy metal contaminated environments. The functional groups, especially –SH, C O, and N–H/C–N in the fingerprint zone of glutathione (GSH) and polysaccharides-like components of EPS, were the main components of EPS involved in both Zn(II) and Cu(II) binding and removal. Around 31.22% and 5.74% of Cu(II)-treated EPS was shown to exist as (C O) structures and these structures were converted into C–OH and O–C–O upon exposure to Cu(II), respectively. In contrast, (C–OH/C–O–C/P–O–C) groups in EPS were observed to be positively correlated to increasing concentrations of Zn(II) in strain P2. Furthermore, the complete genome of M. rubeus P2 helped us to identify 350 genes involved in carbohydrate metabolism, some of which are predicted to be involved in EPS production and modification. This work describes the first detailed biochemical and biophysical analysis of EPS from any strain of Mucilaginibacter with unique heavy metal binding properties. The results will be useful for a better understanding of how microorganisms such as M. rubeus P2 adapt to heavy metal polluted environments and how this knowledge can potentially be harnessed in biotechnological applications such as industrial waste water purification, bioremediation of heavy metal contaminated soil and beneficial plant microbe interactions. The toolbox provided in this paper will provide a valuable basis for future studies.

Denitrification can be enhanced in the Integrated Fixed Film Activated System (IFAS) system by integrating media into the anoxic or aerobic zone. The simultaneous nitrification and denitrification (SND) in the biofilm layers has been reported in the aerobic zone of the IFAS system. In this study, two IFAS systems with Bioweb® media installed in the anoxic or aerobic reactor were operated in parallel to evaluate both anoxic denitrification or aerobic SND in the biofilm layers enhanced by fixed film media at three different nitrite and nitrate recirculation (NR) ratios of 75%, 100%, and 125%. The results revealed that both IFAS systems achieved the same organic and nitrogen removal efficiencies without statistically significant difference. The NR ratio of 125% enhanced slightly the denitrification in the anoxic zones of both systems. The media increased the anoxic denitrification at the NR ratio of 100%. The SND in the biofilm was found insignificant in both systems. It was evident that suspended-growth microorganisms stored substrates internally in the cells under anoxic conditions due to insufficient retention time. The aerobic denitrifiers including Chryseobacterium sp., Klebsiella pneumonia, and Pseudomonas aeruginosa were abundant in both IFAS systems providing aerobic denitrification with storage products as carbon sources. In summary, the denitrification in the anoxic zone and SND in the biofilm of the aerobic zone, both were enhanced by the fixed film media, did not contribute significantly to the IFAS system for the biological nitrogen removal because of microbial storage products and aerobic denitrification of several aerobic denitrifiers.

The residual ozone played an important role in enhancing the organics removal by stimulate subsequent biological processes. However, how the residual ozone affects the biological process is not well studied. In this work, a pilot scale integrated O3-BAF, ordinary BAF and separated O3-BAF were compared in advanced treatment of real bio-treated petrochemical wastewater. Results showed that residual ozone with 0.05–0.10 mg L−1 in the BAF demonstrated relatively high chemical oxygen demand (COD) removal efficiency of 48.4%, which was 1.5-fold higher than that obtained by separated O3-BAF and 3-fold higher than that obtained by ordinary BAF. The stimulative effect of low dosage of O3 on biological treatment additionally donated 33.9% of the COD removal in the BAF. The COD removal amount per dosage of ozone reached 5.30 mg-COD/mg-O3. The biofilm thickness in the integrated O3-BAF was reduced by 30–50% while the dehydrogenase activity (DHA) was improved by 500%, indicating the stimulate effect on the bioactivity. Additionally, Illumina HiSeq sequencing of 16S rRNA gene amplicons demonstrated significant microbial diversity decreasing. Specially, Gemmatimonadetes and Bacteroidetes are the dominate microorganism in the integrated O3-BAF, having a positive correlation with the proper residual ozone, and increased by 5.4% and 4.2% in comparison with the separated O3-BAF, respectively. The residual ozone higher than 0.22 mg L−1 showed inhibition effect on the bioactivity. In summary, the control of residual ozone introduced to BAF was crucial for stimulative effects and manager the microbial community in the integrated O3-BAF, which still need further detail research.

Glycerol is a biodiesel byproduct. In the present study, glycerol was used as a co-substrate during biodegradation of dibenzothiophene (DBT) by Paraburkholderia sp. C3. Polycyclic aromatic hydrocarbons (PAHs) are a group of persistent, ubiquitous and carcinogenic chemicals found in the environment. DBT is a major sulfur-containing PAH. The chemical properties of DBT make it an ideal model pollutant for examining the bioremediation of higher molecular weight PAHs. Bioremediation uses microbial catalysis for removal of environmental pollutants. Environmental microorganisms that encounter aromatic substrates such as heterocyclic PAHs develop unique characteristics that allow the uptake and assimilation of these cytotoxic substrates. Microbial adaptations include changes in membrane lipid composition, secretion of surface-active compounds and accumulation of lipid granules to withstand chemical toxicity. Biostimulation using more readily metabolized substrates can increase the biodegradation rate of PAHs, but the molecular mechanisms are not well understood. We analyzed the DBT biodegradation kinetics in C3, proteome changes and TEM micrographs in different culturing conditions. We utilized 2-bromoalkanoic lipid metabolic inhibitors to establish a correlation between polyhydroxyalkanoate (PHA) granule formation and the enhancement of DBT biodegradation induced by glycerol. This is the first description linking PHA biosynthesis, DBT biodegradation and 2-bromoalkanoic acids in a Paraburkholderia species.

Poly-3-hydroxyalkanoates (PHA) are biodegradable and compostable polyesters. This review is aimed to provide a unique approach that can help think tanks to frame strategies aiming for clean technology by utilizing cutting edge biotechnological advances to convert fruit and vegetable waste to biopolymer. A PHA manufacturing method based on watermelon waste residue that does not require extensive pretreatment provides a more environmentally friendly and sustainable approach that utilizes an agricultural waste stream. Incorporating fruit processing industry by-products and water, and other resource conservation methods would not only make the manufacturing of microbial bio-plastics like PHA more eco-friendly, but will also help our sector transition to a bioeconomy with circular product streams. The final and most critical element of this review is an in-depth examination of the several hazards inherent in PHA manufacturing.

To overcome the easy loss of microorganism, the mass production of sludge and the consumption of aeration energy during biological treatment of anaerobically digested swine wastewater, this study used chitosan–sodium alginate composite carrier to prepare immobilized bacteria pellets. The heterotrophic bacteria tolerant to high concentrations of ammonia nitrogen were isolated and the conditions for immobilizing bacteria were optimized. The performance of immobilized bacteria pellets to remove ammonia nitrogen from ADSW was determined and the corresponding mechanism was investigated. Results showed that the isolated bacteria were Bacillus subtilis, and the optimal conditions to prepare the immobilized bacteria pellets by response surface methodology tests were sodium alginate of 0.84% (m/V), chitosan of 0.22% (m/V), embedding time of 32 min and embedding amount of 15% (V/V). In ADSW treatment, at pH 6, 20 g/L of the immobilized bacteria pellets removed 96.5% of ammonia nitrogen. Both adsorption and microbial action contributed to ammonia nitrogen removal, and their contributions were 54.3% and 42.2%, respectively. Compared with the immobilized bacteria pellets using chitosan–sodium alginate as carrier, the one using mono alginate as carrier had a weaker ability to remove ammonia nitrogen, with a removal efficiency of 67.4%. The main mechanism was the formation of polyelectrolyte membrane by the connection between amino groups of chitosan and carboxyl groups of sodium alginate, which stabilized the immobilized bacteria pellets and prolonged their service life. To sum up, the immobilized bacteria pellets using chitosan–sodium alginate as an embedding agent have a promising prospect in ammonia nitrogen removal from wastewater.

Nitrification and denitrification are crucial processes in the nitrogen cycle, a vital microbially driven biogeochemical cycle. N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) is widespread in bacteria and plays a key role in their physiological status. Recently, there has been an increase in research into how the AHL-mediated QS system is involved in nitrification and denitrification. Consequentially, the AHL-mediated QS system has been considered a promising regulatory approach in nitrogen metabolism processes, with high potential for real-world applications. In this review, the universal presence of QS in nitrifiers and denitrifiers is summarized. Many microorganisms taking part in nitrification and denitrification harbor QS genes, and they may produce AHLs with different chain lengths. The phenotypes and processes affected by QS in real-world applications are also reviewed. In wastewater bioreactors, QS could affect nitrogen metabolism efficiency, granule aggregation, and biofilm formation. Furthermore, methods commonly used to identify the existence and functions of QS, including physiological tests, genetic manipulation and omics analyses are discussed.

The identification of dominant microbes in anaerobic mercury (Hg) methylation, methylmercury (MeHg) demethylation, and methane oxidation as sulfate-reducing bacteria, methanogens or, probably, anaerobic methanotrophic archaea (ANMEs) is of great interest. To date, however, the interrelationship of bacteria and archaea involved in these processes remains unclear. Here, we demonstrated the dynamics of microorganisms participating in these processes. Anaerobic fixed-bed reactors were operated with swine manure and sludge to produce methane stably, and then, sulfate (reactor C), sulfate and Hg(II) (reactor H), and sulfate and MeHg (reactor M) were added, and the reactors were operated for 120 d, divided equally into four periods, P1–P4. The bacterial compositions changed nonsignificantly, whereas Methanosaeta in reactors H and M decreased significantly, revealing that it was irrelevant for Hg transformation. The abundances of Syntrophomonadaceae, Methanoculleus, Candidatus Methanogranum and Candidatus Methanoplasma increased continuously with time; these species probably functioned in these processes, but further evidence is needed. Desulfocella and Desulfobacterium dominated first but eventually almost vanished, while the dominant archaeal genera Methanogenium, Methanoculleus and Methanocorpusculum were closely related to ANME–1 and ANME–2. PLS-DA results indicated that both bacteria and archaea in different periods in the three reactors were clustered separately, implying that the microbial compositions in the same periods were similar and changed markedly with time.

Cyanobacteria are photosynthetic microorganisms with widespread diversity and extensive global distribution. They produce a wide variety of bioactive substances (e.g., lipopeptides, fatty acids, toxins, carotenoids, vitamins and plant growth regulators) that are released into culture media. In this study, the capability of a cyanobacterial strain of Planktothricoides raciborskii to produce intra- and extracellular auxins was investigated. The filamentous cyanobacterial P. raciborskii strain was isolated from a river in Vietnam, and it was cultivated in the laboratory under the optimum conditions of the BG11 culture medium and a pH of 7.0. The auxins were identified and quantified by the Salkowski colorimetric method and high-performance liquid chromatography coupled with mass spectrometry (HPLC–MS). Colorimetric analysis revealed that P. raciborskii produces extracellular indole-3-acetic acid (IAA) in the absence and presence of l -tryptophan. The maximum extracellular IAA concentration of the culture reached 118 ± 2 μg mL−1, which was supplemented with 900 μg mL−1 of l -tryptophan. HPLC–MS analysis revealed that the isolated cyanobacteria accumulate other plant-growth-promoting hormones besides IAA, such as indole-3-carboxylic acid (ICA), indole-3 butyric acid (IBA) and indole propionic acid (IPA). This is the first report on the production of auxins in an isolated strain of cyanobacteria Planktothricoides from a polluted river. The capability of producing auxins makes the P. raciborskii strain an appropriate candidate for the formulation of a biofertilizer.

International audience; Mining and smelting activities have introduced severe potentially toxic metals (PTMs) contamination into surrounding soil settings. Influences of PTMs on microbial diversity have been widely studied. However, variations of microbial communities, network structures and community functions in different levels of PTMs contaminated soils adjacent to mining and smelting aera are still poorly investigated. In this study, microbial communities of soils around different levels of PTMs contamination were comprehensively studied by 16S rRNA gene amplicons high-throughput sequencing. Microbial interactions and module functions were also exploited to ascertain the discrepancies of PTMs concentration levels on microbial ecological functions. Results indicated that the microbial community composition was significantly distinct attributed to the phylum Protebacteria (p = 0.002) dominating in soil with high level PTMs contents but Actinobacteria (p = 0.002) in low level of PTMs-contaminated soil. Microbial α diversity was not significantly influenced by different levels of PTMs contaminations. Microorganisms proactively responded to PTMs content levels by means of strengthening network complexities and modularities among microbe-microbe interactions. The functions of main network modules were predicted associating membrane transport, amino acid metabolism, energy metabolism and carbohydrate metabolism. The PTMs detoxification and anti-oxidation were significantly strengthened at the high level of PTMs contamination. The present study demonstrated that modification of microbial community by the adaptive adjustment of microbial compositions and strengthening their network complexity and modularity.

Large amounts of lignocellulosic biomass are discarded, whereas the carbon source of sewage is deficient. This situation greatly impairs the efficiency of wastewater treatment. To address this concern, we evaluate the feasibility of using hydrochar as a potential carbon source by systematically investigating the effects of hydrothermal carbonization (HTC) conditions on the composition, content, and chemical structure of dissolved organic matter (DOM) released from hydrochar. Results show that the most important factor that affects the properties of hydrochar and DOM is temperature, followed by heating rate. Under optimal HTC conditions, the growth of Bacillus subtilis increased by 18.32% in hydrochar aqueous solution in comparison with the 6.64% growth of the untreated biomass group. Excitation emission matrix-parallel factor analysis and UV-vis analyses confirm that the DOM released by hydrochar produced at a low temperature mainly contains protein substances, which promote the growth of microorganisms. The DOM released by hydrochar at a high temperature mainly contains humic substances with an aromatic structure; such substances are toxic to microorganisms. This study demonstrates that hydrochar obtained under optimized conditions can be a potential carbon source of wastewater treatment plants.

The mechanisms of struvite production through biomineralisation were investigated for five microorganisms (Bacillus pumilus, Brevibacterium antiquum, Myxococcus xanthus, Halobacterium salinarum and Idiomarina loihiensis). After 72–96 h of incubation, the microbial strains tested increased the solution pH from 7.5 to 7.7 to 8.4–8.7, and removed ortho-phosphate (63–71%) and magnesium (94–99%) by biomineralisation. The minerals formed were identified as struvite (i.e. bio-struvite). Within the initial 24 h of incubation, microbial growth rates of 0.16–0.28 1/h were measured, and bio-struvite production was observed when the solution supersaturation index with respect to struvite achieved 0.6–0.8 units. The crystals produced by B. pumilus, H. salinarum and M. xanthus were thin trapezoidal-platy shaped and presented a gap size about 200 μm for intervals between cumulative volume undersize distribution at 50% and 90%. While B. antiquum and I. loihiensis produced crystals of coffin-lid/long-bar shape and a narrow size gap around 100 μm for intervals between cumulative volume percentage of 50% and 90%, indicating homogeneous crystal size distribution. Intracellular supersaturation of struvite phase was achieved within B. antiquum and I. loihiensis cells, corresponding to observation of intracellular vesicle-like structures occupied with electron-dense granules/materials. This study suggests that B. antiquum and I. loihiensis produced bio-struvite through biologically controlled mineralisation. This mechanism is the preferred for recovering nutrients from streams such as wastewater because it allows a link between manipulation of microbial growth conditions and bio-struvite production, even in highly complex streams like wastewater.

Disinfectant-containing wastewaters have been generated from many places, including marine industries. The synthetic NaClO-containing wastewaters have been effectively treated in a saline MBBR-MBR (moving bed biofilm reactor & membrane bioreactor) system containing marine microorganisms. A low concentration of NaCl (below 100 mg/L) is not enough to kill the microorganisms, but can affect their bioactivity and induce membrane biofouling. A linear relationship has been obtained for the half-life of membrane biofouling as a function of the NaClO concentration (10–100 mg/L): [half-life] = 25–0.12 × [NaClO concentration]. The COD and NH3–N removals are the highest at a salinity of 30 g/L for the marine bioreactors. The behaviour of the typical biofoulants, measured real-timely by fluorescence spectroscopy, can indicate the levels of membrane biofouling and microbial activity, responding to the NaClO and NaCl influences. Based on the behaviour of biofoulants, this work has also proposed a novel strategy of biofoulants monitoring for membrane antifouling, where antifouling responses can be carried out when the concentration of biofoulants significantly increases., Graphical abstract Image 1, Highlights • The NaClO-containing wastewaters were treated in a saline MBBR-MBR system. • The synergistic toxicity from NaClO and NaCl was observed to the microorganisms. • The behaviour of biofoulants showed the levels of fouling and biodegradability. • A novel strategy of biofoulants monitoring was proposed for membrane antifouling.

The environment is contaminated by synthetic contaminants owing to their extensive applications globally. Hence, the removal of synthetic pollutants (SPs) from the environment has received widespread attention. Different remediation technologies have been investigated for their abilities to eliminate SPs from the ecosystem; these include photocatalysis, sonochemical techniques, nanoremediation, and bioremediation. SPs, which can be organic or inorganic, can be degraded by microbial metabolism at contaminated sites. Owing to their diverse metabolisms, microbes can adapt to a wide variety of environments. Several microbial strains have been reported for their bioremediation potential concerning synthetic chemical compounds. The selection of potential strains for large-scale removal of organic pollutants is an important research priority. Additionally, novel microbial consortia have been found to be capable of efficient degradation owing to their combined and co-metabolic activities. Microbial engineering is one of the most prominent and promising techniques for providing new opportunities to develop proficient microorganisms for various biological processes; here, we have targeted the SP-degrading mechanisms of microorganisms. This review provides an in-depth discussion of microbial engineering techniques that are used to enhance the removal of both organic and inorganic pollutants from different contaminated environments and under different conditions. The degradation of these pollutants is investigated using abiotic and biotic approaches; interestingly, biotic approaches based on microbial methods are preferable owing to their high potential for pollutant removal and cost-effectiveness.