Biodegradation: Updating the concepts of control for microbial cleanup in contaminated aquifers

Co-migration behavior of toluene coupled with trichloroethylene and the response of the pristine groundwater ecosystems - A mesoscale indoor experiment

Experimental scale and sampling precision are the main factors limiting the accuracy of migration and transformation assessments of complex petroleum-based contaminants in groundwater. In this study, a mesoscale indoor aquifer device with high environmental fidelity and monitoring accuracy was constructed, in which dissolved toluene and trichloroethylene were used as typical contaminants in a 1.5-year contaminant migration experiment. The process was divided into five stages, namely, pristine, injection, accumulation, decrease, and recovery, and characteristics such as differences in contaminant migration, the responsiveness of environmental factors, and changes in microbial communities were investigated. The results demonstrated that the mutual dissolution properties of the contaminants increased the spread of the plume and confirmed that toluene possessed greater mobility and natural attenuation than trichloroethylene. Attenuation of the contaminant plume proceeded through aerobic degradation, nitrate reduction, and sulfate reduction phases, accompanied by negative feedback from characteristic ion concentrations, dissolved oxygen content, the oxidation-reduction potential and microbial community structure of the groundwater. This research evaluated the migration and transformation characteristics of typical petroleum-based pollutants, revealed the response mechanism of the ecosystem to pollutant, provided a theoretical basis for predicting pollutant migration and formulating control strategies.

Sulfamethoxazole is Metabolized and Mineralized at Extremely Low Concentrations

The presence of organic micropollutants in water and sediments motivates investigation of their biotransformation at environmentally low concentrations, usually in the range of μg L-1. Many are biotransformed by cometabolic mechanisms; however, there is scarce information concerning their direct metabolization in this concentration range. Threshold concentrations for microbial assimilation have been reported in both pure and mixed cultures from different origins. The literature suggests a range value for bacterial growth of 1-100 μg L-1 for isolated aerobic heterotrophs in the presence of a single substrate. We aimed to investigate, as a model case, the threshold level for sulfamethoxazole (SMX) metabolization in pure cultures of Microbacterium strain BR1. Previous research with this strain has covered the milligram L-1 range. In this study, acclimated cultures were exposed to concentrations from 0.1 to 25 μg L-1 of 14C-labeled SMX, and the 14C-CO2 produced was trapped and quantified over 24 h. Interestingly, SMX removal was rapid, with 98% removed within 2 h. In contrast, mineralization was slower, with a consistent percentage of 60.0 ± 0.7% found at all concentrations. Mineralization rates increased with rising concentrations. Therefore, this study shows that bacteria are capable of the direct metabolization of organic micropollutants at extremely low concentrations (sub μg L-1).

Bioaugmentation has temporary effect on anaerobic pesticide biodegradation in simulated groundwater systems

Groundwater is the most important source for drinking water in The Netherlands. Groundwater quality is threatened by the presence of pesticides, and biodegradation is a natural process that can contribute to pesticide removal. Groundwater conditions are oligotrophic and thus biodegradation can be limited by the presence and development of microbial communities capable of biodegrading pesticides. For that reason, bioremediation technologies such as bioaugmentation (BA) can help to enhance pesticide biodegradation. We studied the effect of BA using enriched mixed inocula in two column bioreactors that simulate groundwater systems at naturally occurring redox conditions (iron and sulfate-reducing conditions). Columns were operated for around 800 days, and two BA inoculations (BA1 and BA2) were conducted in each column. Inocula were enriched from different wastewater treatment plants (WWTPs) under different redox-conditions. We observed a temporary effect of BA1, reaching 100% removal efficiency of the pesticide 2,4-D after 100 days in both columns. In the iron-reducing column, 2,4-D removal was in general higher than under sulfate-reducing conditions demonstrating the influence of redox conditions on overall biodegradation. We observed a temporary shift in microbial communities after BA1 that is relatable to the increase in 2,4-D removal efficiency. After BA2 under sulfate-reducing conditions, 2,4-D removal efficiency decreased, but no change in the column microbial communities was observed. The present study demonstrates that BA with a mixed inoculum can be a valuable technique for improving biodegradation in anoxic groundwater systems at different redox-conditions.

Different oxygen affinities of methanotrophs and Comammox Nitrospira inform an electrically induced symbiosis for nitrogen loss

Aerobic methanotrophs establish a symbiotic association with denitrifiers to facilitate the process of aerobic methane oxidation coupled with denitrification (AME-D). However, the symbiosis has been frequently observed in hypoxic conditions continuing to pose an enigma. The present study has firstly characterized an electrically induced symbiosis primarily governed by Methylosarcina and Hyphomicrobium for the AME-D process in a hypoxic niche caused by Comammox Nitrospira. The kinetic analysis revealed that Comammox Nitrospira exhibited a higher apparent oxygen affinity compared to Methylosarcina. While the coexistence of comammox and AME-D resulted in an increase in methane oxidation and nitrogen loss rates, from 0.82 ± 0.10 to 1.72 ± 0.09 mmol CH4 d-1 and from 0.59 ± 0.04 to 1.30 ± 0.15 mmol N2 d-1, respectively. Furthermore, the constructed microbial fuel cells demonstrated a pronounced dependence of the biocurrents on AME-D due to oxygen competition, suggesting the involvement of direct interspecies electron transfer in the AME-D process under hypoxic conditions. Metagenomic and metatranscriptomic analysis revealed that Methylosarcina efficiently oxidized methane to formaldehyde, subsequently generating abundant NAD(P)H for nitrate reduction by Hyphomicrobium through the dissimilatory RuMP pathway, leading to CO2 production. This study challenges the conventional understanding of survival mechanism employed by AME-D symbionts, thereby contributing to the characterization responsible for limiting methane emissions and promoting nitrogen removal in hypoxic regions.

The comprehensive evaluation of nitrate origin and transformation pathways in the oxic alluvial aquifer in Serbia

Accurate pollution source identification is essential for establishing adequate water management strategies, particularly in groundwater with slow flow and prolonged recharge process allowing long-term pollution retention. An integrated study based on hydrogeochemical, dual isotopic (δ15NNO3 and δ18ONO3), and microbiological approaches (DN, IRB, and SRB BART tests) along with the statistical data processing was conducted to determine nitrate origin and fate in oxic alluvial groundwater source Ključ in Serbia. The findings from a comprehensive investigation, encompassing 20 groundwater sampling locations during the period 2010-2019, delineated three distinct zones - the hinterland (anthropogenic impact area-untreated sewage inflow), the middle zone (area of mixed influence from fertilizer application, accompanied by a mitigated anthropogenic impact), and the zone of riparian denitrification. Significant linear relationship between anthropogenic impact parameters (Na, Cl, B, NO3-, NH4+, and electrical conductivity) along with the isotopic signatures (δ15N-NO3- ranking from + 10.01 to + 11.18‰ and δ18O-NO3- ranking from + 1.15 to + 6.24‰) and grouped sampling objects by cluster analysis indicated that hinterland is burdened by the nitrates originating from anthropogenic impact. The cross-section of groundwater flow data, concurrent increase of NH4+, and pH levels, along with the highest values of δ15N-NO3- (+ 12.90‰) and δ18O-NO3- (+ 9.70‰), indicated area of fertilizers (urea) impact. BART test results, pH increase, and low oxygen concentration, along with the groundwater flow data in riparian zone, indicated the unfolding of denitrification process. Presented research emphasizes the importance, necessities, and advantages of simultaneous and complementary use of hydrogeochemical, microbiological, and isotopic data.

Natural attenuation of sulfonamides and metabolites in contaminated groundwater - Review, advantages and challenges of current documentation techniques

Sulfonamides are applied worldwide as antibiotics. They are emerging contaminants of concern, as their presence in the environment may lead to the spread of antibiotic resistance genes. Sulfonamides are present in groundwater systems, which suggest their persistence under certain conditions, highlighting the importance of understanding natural attenuation processes in groundwater. Biodegradation is an essential process, as degradation of sulfonamides reduces the risk of antibiotic resistance spreading. In this review, natural attenuation, and in particular assessment of biodegradation, is evaluated for sulfonamides in groundwater systems. The current knowledge level on biodegradation is reviewed, and a scientific foundation is built based on sulfonamide degradation processes, pathways, metabolites and toxicity. An overview of bacterial species and related metabolites is provided. The main research effort has focused on aerobic conditions while investigations under anaerobic conditions are lacking. The level of implementation in research is laboratory scale; here we strived to bridge towards field application and assessment, by assessing approaches commonly used in monitored natural attenuation. Methods to document contaminant mass loss are assessed to be applicable for sulfonamides, while the approach is limited by a lack of reference standards for metabolites. Furthermore, additional information is required on relevant metabolites in order to improve risk assessments. Based on the current knowledge on biodegradation, it is suggested to use the presence of substituent-containing metabolites from breakage of the sulfonamide bridge as specific indicators of degradation. Microbial approaches are currently available for assessment of microbial community's capacities, however, more knowledge is required on indigenous bacteria capable of degrading sulfonamides and on the impact of environmental conditions on biodegradation. Compound specific stable isotope analysis shows great potential as an additional in situ method, but further developments are required to analyse for sulfonamides at environmentally relevant levels. Finally, in a monitored natural attenuation scheme it is assessed that approaches are available that can uncover some processes related to the fate of sulfonamides in groundwater systems. Nevertheless, there are still unknowns related to relevant bacteria and metabolites for risk assessment as well as the effect of environmental settings such as redox conditions. Alongside, uncovering the fate of sulfonamides in future research, the applicability of the natural attenuation documentation approaches will advance, and provide a step towards in situ remedial concepts for the frequently detected sulfonamides.

Influence of heavy Canadian crude oil on pristine freshwater boreal lake ecosystems in an experimental oil spill

The overall impact of a crude oil spill into a pristine freshwater environment in Canada is largely unknown. To evaluate the impact on the native microbial community, a large-scale in situ model experimental spill was conducted to assess the potential role of the natural community to attenuate hydrocarbons. A small volume of conventional heavy crude oil (CHV) was introduced within contained mesocosm enclosures deployed on the shoreline of a freshwater lake. The oil was left to interact with the shoreline for 72 h and then free-floating oil was recovered using common oil spill response methods (i.e. freshwater flushing and capture on oleophilic absorptive media). Residual polycyclic aromatic hydrocarbon (PAH) concentrations returned to near preoiling concentrations within 2 months, while the microbial community composition across the water, soil, and sediment matrices of the enclosed oligotrophic freshwater ecosystems did not shift significantly over this period. Metagenomic analysis revealed key polycyclic aromatic and alkane degradation mechanisms also did not change in their relative abundance over the monitoring period. These trends suggest that for small spills (<2 l of oil per 15 m2 of surface freshwater), physical oil recovery reduces polycyclic aromatic hydrocarbon concentrations to levels tolerated by the native microbial community. Additionally, the native microbial community present in the monitored pristine freshwater ecosystem possesses the appropriate hydrocarbon degradation mechanisms without prior challenge by hydrocarbon substrates. This study corroborated trends found previously (Kharey et al. 2024) toward freshwater hydrocarbon degradation in an environmentally relevant scale and conditions on the tolerance of residual hydrocarbons in situ.

Enhancing in situ biodegradation in groundwater using pump and treat remediation: a proof of concept and modelling analysis of controlling variables

A remediation approach which uses pump and treatment (PAT) to enhance the biodegradation of organic contaminants by increasing dispersive mixing between plumes and groundwater was evaluated for a phenol-contaminated aquifer, using a reactive transport model which simulates kinetic reactions between an electron donor (ED) in the plume and electron acceptor (EA) in the groundwater. The influence of system design and operation was examined in six modelling scenarios. Injection or extraction of groundwater increases biodegradation above no action and the location, pumping rate, and distance between well(s) are important variables which influence biodegradation. An increase in pumping rate, distance of the wells from the plume centreline, and changing the flow direction increase dispersive mixing between the plume and groundwater. This increases plume spreading and the plume fringe interface, providing a greater flux of dissolved EAs for biodegradation. In general, injection of groundwater containing natural EAs enhances biodegradation more than extraction. The enhancement of biodegradation is sensitive to the relative fluxes of ED and EA, as controlled by the arrangement of the wells. In the best performing scenario, biodegradation was enhanced by 128%, compared with no action.

Cable bacteria: Living electrical conduits for biogeochemical cycling and water environment restoration

Since the discovery of multicellular cable bacteria in marine sediments in 2012, they have attracted widespread attention and interest due to their unprecedented ability to generate and transport electrical currents over centimeter-scale long-range distances. The cosmopolitan distribution of cable bacteria in both marine and freshwater systems, along with their substantial impact on local biogeochemistry, has uncovered their important role in element cycling and ecosystem functioning of aquatic environments. Considerable research efforts have been devoted to the potential utilization of cable bacteria for various water management purposes during the past few years. However, there lacks a critical summary on the advances and contributions of cable bacteria to biogeochemical cycles and water environment restoration. This review aims to provide an up-to-date and comprehensive overview of the current research on cable bacteria, with a particular view on their participation in aquatic biogeochemical cycles and promising applications in water environment restoration. It systematically analyzes (i) the global distribution of cable bacteria in aquatic ecosystems and the major environmental factors affecting their survival, diversity, and composition, (ii) the interactive associations between cable bacteria and other microorganisms as well as aquatic plants and infauna, (iii) the underlying role of cable bacteria in sedimentary biogeochemical cycling of essential elements including but not limited to sulfur, iron, phosphorus, and nitrogen, (iv) the practical explorations of cable bacteria for water pollution control, greenhouse gas emission reduction, aquatic ecological environment restoration, as well as possible combinations with other water remediation technologies. It is believed to give a step-by-step introduction to progress on cable bacteria, highlight key findings, opportunities and challenges of using cable bacteria for water environment restoration, and propose directions for further exploration.

Natural attenuation of BTEX and chlorobenzenes in a formerly contaminated pesticide site in China: Examining kinetics, mechanisms, and isotopes analysis

Groundwater contamination from abandoned pesticide sites is a prevalent issue in China. To address this problem, natural attenuation (NA) of pollutants has been increasingly employed as a management strategy for abandoned pesticide sites. However, limited studies have focused on the long-term NA process of co-existing organic pollutants in abandoned pesticide sites by an integrated approach. In this study, the NA of benzene, toluene, ethylbenzene, and xylene (BTEX), and chlorobenzenes (CBs) in groundwater of a retired industry in China was systematically investigated during the monitoring period from June 2016 to December 2021. The findings revealed that concentrations of BTEX and CBs were effectively reduced, and their NA followed first-order kinetics with different rate constants. The sulfate-reducing bacteria, nitrate-reducing bacteria, fermenting bacteria, aromatic hydrocarbon metabolizing bacteria, and reductive dechlorinating bacteria were detected in groundwater. It was observed that distinct environmental parameters played a role in shaping both overall and key bacterial communities. ORP (14.72%) and BTEX (12.89%) were the main drivers for variations of the whole and key functional microbial community, respectively. Moreover, BTEX accelerated reductive dechlorination. Furthermore, BTEX and CBs exhibited significant enrichment of 13C, ranging from +2.9 to +27.3‰, demonstrating their significance in situ biodegradation. This study provides a scientific basis for site management.

Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season

Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe2+ (6.65-17.1 mg/L), NH4+ (0.57-3.98 mg/L), total organic carbon (1.02-1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe2+ remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.

Responses of microbial communities subjected to hydrodynamically induced disturbances in an organic contaminated site

Organic contaminated sites have gained significant attention as a prominent contributor to shallow groundwater contamination. However, limited knowledge exists regarding the impact of hydrodynamic effects on microbially mediated contaminant degradation at such sites. In this study, we investigated the distribution characteristics and community structure of prokaryotic microorganisms at the selected site during both wet and dry seasons, with a particular focus on their environmental adaptations. The results revealed significant seasonal variations (P < 0.05) in the α-diversity of prokaryotes within groundwater. The dry season showed more exclusive OTUs than the wet season. The response of prokaryotic metabolism to organic pollution pressure in different seasons was explored by PICRUSt2, and enzymes associated with the degradation of organic pollutants were identified based on the predicted functions. The results showed that hormesis was considered as an adaptive response of microbial communities under pollution stress. In addition, structural equation models demonstrated that groundwater level fluctuations can, directly and indirectly, affect the abundance and diversity of prokaryotes through other factors such as oxidation reduction potential (ORP), dissolved oxygen (DO), and naphthalene (Nap). Overall, our findings imply that the taxonomic composition and functional properties of prokaryotes in groundwater in organic contaminated sites is influenced by the interaction between seasonal variations and characteristics of organic pollution. The results provide new insights into microbiological processes in groundwater systems in organic contaminated sites.

Adaptive characteristics of indigenous microflora in an organically contaminated high salinity groundwater

Salinity, a critical factor, could directly or indirectly affect the microbial community structure and diversity. Changes in salinity levels act as environmental filters that influence the transformation of key microbial species. This study investigates the adaptive characteristics of indigenous microflora in groundwater in relation to external organic pollutants under high salinity stress. A highly mineralized shallow groundwater in Northwest China was conducted as the study area, and six representative sampling points were chosen to explore the response of groundwater hydrochemical parameters and microflora, as well as to identify the tolerance mechanisms of indigenous microflora to combined pollution. The results revealed that the dominant genera found in high salinity groundwater contaminated with organic pollutants possess the remarkable ability to degrade such pollutants even under challenging high salinity conditions, including Halomonas, Pseudomonas, Halothiobacillus, Sphingomonas, Lutibacter, Aquabacterium, Thiomicrospira, Aequorivita, etc. The hydrochemical factors, including total dissolved solids (TDS), sulfide, nitrite, nitrate, oxidation reduction potential (ORP), NH3-N, Na, Fe, benzene series, phenols, and halogenated hydrocarbons, demonstrated a significant influence on microflora. High levels of sulphate and sulfide in groundwater can exhibit dual effects on microflora. On one hand, these compounds can inhibit the growth and metabolism of microorganisms. On the other hand, they can also serve as effective electron donors/receptors during the microbial degradation of organic pollutants. Microorganisms exhibit resilience to the inhibitory effects of high salinity and organic pollutants via a series of tolerance mechanisms, such as strengthening the extracellular membrane barrier, enhancing the synthesis of relevant enzymes, initiating novel biochemical reactions, improving cellular self-healing capabilities, responding to unfavorable environmental conditions by migration, and enhancing the S cycle for the microbial metabolism of organic pollutants.

Rapid Consumption of Dihydrogen Injected into a Shallow Aquifer by Ecophysiologically Different Microbes

The envisaged future dihydrogen (H2) economy requires a H2 gas grid as well as large deep underground stores. However, the consequences of an unintended spread of H2 through leaky pipes, wells, or subterranean gas migrations on groundwater resources and their ecosystems are poorly understood. Therefore, we emulated a short-term leakage incident by injecting gaseous H2 into a shallow aquifer at the TestUM test site and monitored the subsequent biogeochemical processes in the groundwater system. At elevated H2 concentrations, an increase in acetate concentrations and a decrease in microbial α-diversity with a concomitant change in microbial β-diversity were observed. Additionally, microbial H2 oxidation was indicated by temporally higher abundances of taxa known for aerobic or anaerobic H2 oxidation. After H2 concentrations diminished below the detection limit, α- and β-diversity approached baseline values. In summary, the emulated H2 leakage resulted in a temporally limited change of the groundwater microbiome and associated geochemical conditions due to the intermediate growth of H2 consumers. The results confirm the general assumption that H2, being an excellent energy and electron source for many microorganisms, is quickly microbiologically consumed in the environment after a leakage.

A multi-omics approach to unravelling the coupling mechanism of nitrogen metabolism and phenanthrene biodegradation in soil amended with biochar

The presence of polycyclic aromatic hydrocarbons (PAHs) in soil negatively affects the environment and the degradation of these contaminants is influenced by nitrogen metabolism. However, the mechanisms underlying the interrelationships between the functional genes involved in nitrogen metabolism and phenanthrene (PHE) biodegradation, as well as the effects of biochar on these mechanisms, require further study. Therefore, this study utilised metabolomic and metagenomic analysis to investigate primary nitrogen processes, associated functional soil enzymes and functional genes, and differential soil metabolites in PHE-contaminated soil with and without biochar amendment over a 45-day incubation period. Results showed that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were the dominant nitrogen metabolism processes in PHE-contaminated soil. The addition of biochar enhanced nitrogen modules, exhibiting discernible temporal fluctuations in denitrification and DNRA proportions. Co-occurrence networks and correlation heatmap analysis revealed potential interactions among functional genes and enzymes responsible for PHE biodegradation and nitrogen metabolism. Notably, enzymes associated with denitrification and DNRA displayed significant positive correlation with enzymes involved in downstream phenanthrene degradation. Of particular interest was stronger correlation observed with the addition of biochar. However, biochar amendment inhibited the 9-phenanthrol degradation pathway, resulting in elevated levels of glutathione (GSH) in response to environmental stress. These findings provide new insights into the interactions between nitrogen metabolism and PHE biodegradation in soil and highlight the dual effects of biochar on these processes.

Machine Learning Modeling Based on Microbial Community for Prediction of Natural Attenuation in Groundwater

Natural attenuation is widely adopted as a remediation strategy, and the attenuation potential is crucial to evaluate whether remediation goals can be achieved within the specified time. In this work, long-term monitoring of indigenous microbial communities as well as benzene, toluene, ethylbenzene, and xylene (BTEX) and chlorinated aliphatic hydrocarbons (CAHs) in groundwater was conducted at a historic pesticide manufacturing site. A machine learning approach for natural attenuation prediction was developed with random forest classification (RFC) followed by either random forest regression (RFR) or artificial neural networks (ANNs), utilizing microbiological information and contaminant attenuation rates for model training and cross-validation. Results showed that the RFC could accurately predict the feasibility of natural attenuation for both BTEX and CAHs, and it could successfully identify the key genera. The RFR model was sufficient for the BTEX natural attenuation rate prediction but unreliable for CAHs. The ANN model showed better performance in the prediction of the attenuation rates for both BTEX and CAHs. Based on the assessments, a composite modeling method of RFC and ANN was proposed, which could reduce the mean absolute percentage errors. This study reveals that the combined machine learning approach under the synergistic use of field microbial data has promising potential for predicting natural attenuation.

A biodegradable chitosan-based polymer for sustained nutrient release to stimulate groundwater hydrocarbon-degrading microflora

Petroleum hydrocarbon-contaminated groundwater often has a low indigenous microorganism population and lacks the necessary nutrient substrates for biodegradation reaction, resulting in a weak natural remediation ability within the groundwater ecosystem. In this paper, we utilized the principle of petroleum hydrocarbon degradation by microorganisms to identify effective nutrients (NaH2PO4, K2HPO4, NH4NO3, CaCl2, MgSO4·7H2O, FeSO4·7H2O, and VB12) and optimize nutrient substrate allocation through a combination of actual surveys of petroleum hydrocarbon-contaminated sites and microcosm experiments. Building on this, combining biostimulation and controlled-release technology, we developed a biodegradable chitosan-based encapsulated targeted biostimulant (i.e., YZ-1) characterized by easy uptake, good stability, controllable slow-release migration, and longevity to stimulate indigenous microflora in groundwater to efficiently degrade petroleum hydrocarbon. Results showed that YZ-1 extended the active duration of nutrient components by 5-6 times, with a sustainable release time exceeding 2 months. Under YZ-1 stimulation, microorganisms grew rapidly, increasing the degradation rate of petroleum hydrocarbon (10 mg L-1) by indigenous microorganisms from 43.03% to 79.80% within 7 d. YZ-1 can easily adapt to varying concentrations of petroleum hydrocarbon-contaminated groundwater. Specifically, in the range of 2-20 mg L-1 of petroleum hydrocarbon, the indigenous microflora was able to degrade 71.73-80.54% of the petroleum hydrocarbon within a mere 7 d. YZ-1 injection facilitated the delivery of nutrient components into the underground environment, improved the conversion ability of inorganic electron donors/receptors in the indigenous microbial community system, and strengthened the co-metabolism mechanism among microorganisms, achieving the goal of efficient petroleum hydrocarbon degradation.

Heterogeneous distribution of carbofuran shaped by Pseudomonas stutzeri biofilms enhances biodegradation of agrochemicals

Biodegradation, harnessing the metabolic versatility of microorganisms to reduce agrochemical contaminations, is commonly studied with enriched planktonic cells but overlooking the dominant lifestyle of microorganisms is to form biofilms, which compromises the efficiency of biodegradation in natural environment. Here, we employed a carbofuran-degrading bacterium Pseudomonas stutzeri PS21 to investigate how the bacterial biofilms formed and responded to agrochemicals. First, the PS21 biofilms formed with a core of bacterial cells enclosing with extracellular polymeric substances (EPSs), and the biofilms were active and resilient when exposed to carbofuran (up to 50 mg L^-1). The formation was regulated by the second messenger bis-(3'-5')-cyclic di-guanosine monophosphate signaling, which strengthened the structural resistance and metabolic basis of biofilms to remain the degrading efficiency as comparable as the planktonic cells. Second, carbofuran distributed heterogeneously in the near-biofilm microenvironment via the covalent adsorption of biofilms, which provided a spontaneous force that enhanced the combination of carbofuran with biofilms to maintain high degrading activity. Additionally, we elucidated the biodegradation was driven by the integrated metabolic system of biofilms involving the extracellular enzymes located in the EPSs. This study exhibited the structural and metabolic advantages of microbial biofilms, highlighting the attractive potentials of exploring biofilm-based strategies to facilitate the in-situ bioremediation of organic contaminations.

Nitrogen species and microbial community coevolution along groundwater flowpath in the southwest of Poyang Lake area, China

Nitrate and ammonia overload in groundwater can lead to eutrophication of surface water in areas where surface water is recharged by groundwater. However, this process remained elusive due to the complicated groundwater N cycling, which is governed by the co-evolution of hydrogeochemical conditions and N-cycling microbial communities. Herein, this process was studied along a generalized groundwater flowpath in Ganjing Delta, Poyang Lake area, China. From groundwater recharge to the discharge area near the lake, oxidation-reduction potential (ORP), NO₃-N, and NO₂-N decreased progressively, while NH₃-N, total organic carbon (TOC), Fe²⁺, sulfide, and TOC/NO₃^- ratio accumulated in the lakeside samples. The anthropogenic influences such as sewage and agricultural activities drove the nitrate distribution, as observed by Cl^- vs. NO₃^-/Cl^- ratio and isotopic composition of nitrate. The hydrogeochemical evolution was intimately coupled with the changes in microbial communities. Variations in microbial community structures was significantly explained by Fe²⁺, NH₃-N, and sulfide, while TOC/NO₃^- controlled the distribution of predicted N cycling gene. The absence of NH₃-N in groundwater upstream was accompanied by the enrichment in Acinetobacter capable of nitrification and aerobic denitrification. These two processes were also supported by Ca²⁺ + Mg²⁺ vs. HCO₃^- ratio and isotopic composition of NO₃^-. The DNRA process downstream was revealed by both the presence of DNRA-capable microbes such as Arthrobacter and the isotopic composition of NH₄⁺ in environments with high concentrations of NH₃-N, TOC/NO₃^-, Fe²⁺, and sulfide. This coupled evolution of N cycling and microbial community sheds new light on the N biogeochemical cycle in areas where surface water is recharged by groundwater.

Electroactive microorganism-assisted remediation of groundwater contamination: Advances and challenges

Groundwater contamination has become increasingly prominent, therefore, the development of efficient remediation technology is crucial for improving groundwater quality. Bioremediation is cost-effective and environmentally friendly, while coexisting pollutant stress can affect microbial processes, and the heterogeneous character of groundwater medium can induce bioavailability limitations and electron donor/acceptor imbalances. Electroactive microorganisms (EAMs) are advantageous in contaminated groundwater because of their unique bidirectional electron transfer mechanism, which allows them to use solid electrodes as electron donors/acceptors. However, the relatively low-conductivity groundwater environment is unfavorable for electron transfer, which becomes a bottleneck problem that limits the remediation efficiency of EAMs. Therefore, this study reviews the recent advances and challenges of EAMs applied in the groundwater environment with complex coexisting ions, heterogeneity, and low conductivity and proposes corresponding future directions.

A supervised machine learning approach to discriminate the effect of carcass leachate on shallow groundwater quality around on-farm livestock mortality burial sites

The evaluation of leachate leakage at livestock mortality burial sites is challenging, particularly when groundwater is previously contaminated by agro-livestock farming. Supervised machine learning was applied to discriminate the impacts of carcass leachate from pervasive groundwater contamination in the following order: data labeling, feature selection, synthetic data generation, and classification. Physicochemical data of 359 water samples were collected from burial pits (LC), monitoring wells near pits (MW), pre-existing shallow household wells (HW), and background wells with pervasive contamination (BG). A linear classification model was built using two representative groups (LC and BG) affected by different pollution sources as labeled data. A classifier was then applied to assess the impact of leachate leakage in MW and HW. As a result, leachate impacts were observed in 40% of MW samples, which indicates improper construction and management of some burial pits. Leachate impacts were also detected in six HW samples, up to 120 m downgradient, within one year. The quantitative decision-making tool to diagnose groundwater contamination with leachate leakage can contribute to ensuring timely responses to leakage. The proposed machine learning approach can also be used to improve the environmental impact assessment of water pollution by improper disposal of organic waste.

N/S element transformation modulating lithospheric microbial communities by single-species manipulation

BACKGROUND

The lithospheric microbiome plays a vital role in global biogeochemical cycling, yet their mutual modulation mechanisms remain largely uncharted. Petroleum reservoirs are important lithosphere ecosystems that provide desirable resources for understanding microbial roles in element cycling. However, the strategy and mechanism of modulating indigenous microbial communities for the optimization of community structures and functions are underexplored, despite its significance in energy recovery and environmental remediation.

RESULTS

Here we proposed a novel selective stimulation of indigenous functional microbes by driving nitrogen and sulfur cycling in petroleum reservoirs using injections of an exogenous heterocycle-degrading strain of Pseudomonas. We defined such bacteria capable of removing and releasing organically bound sulfur and nitrogen from heterocycles as "bioredox triggers". High-throughput 16S rRNA amplicon sequencing, metagenomic, and gene transcription-level analyses of extensive production water and sandstone core samples spanning the whole oil production process clarified the microbiome dynamics following the intervention. These efforts demonstrated the feasibility of in situ N/S element release and electron acceptor generation during heterocycle degradation, shifting microbiome structures and functions and increasing phylogenetic diversity and genera engaged in sulfur and nitrogen cycling, such as Desulfovibrio, Shewanella, and Sulfurospirillum. The metabolic potentials of sulfur- and nitrogen-cycling processes, particularly dissimilatory sulfate reduction and dissimilatory nitrate reduction, were elevated in reservoir microbiomes. The relative expression of genes involved in sulfate reduction (dsrA, dsrB) and nitrate reduction (napA) was upregulated by 85, 28, and 22 folds, respectively. Field trials showed significant improvements in oil properties, with a decline in asphaltenes and aromatics, hetero-element contents, and viscosity, hence facilitating the effective exploitation of heavy oil.

CONCLUSIONS

The interactions between microbiomes and element cycling elucidated in this study will contribute to a better understanding of microbial metabolic involvement in, and response to, biogeochemical processes in the lithosphere. The presented findings demonstrated the immense potential of our microbial modulation strategy for green and enhanced heavy oil recovery. Video Abstract.

Naphthalene Carboxylation in the Sulfate-Reducing Enrichment Culture N47 Is Proposed to Proceed via 1,3-Dipolar Cycloaddition to the Cofactor Prenylated Flavin Mononucleotide

Polycyclic aromatic hydrocarbons are persistent pollutants of anthropogenic or natural origin in the environment and accumulate in anoxic habitats. In this study, we investigated the mechanism of the enzyme naphthalene carboxylase as a model reaction for polycyclic aromatic hydrocarbon activation by carboxylation. An enzyme assay was established with cell extracts of the highly enriched culture N47. In assays without addition of ATP, naphthalene carboxylase catalyzed a stable isotope exchange of the carboxyl group of naphthoate with 13C-labeled bicarbonate buffer, which can only occur via a partial backwards reaction of the naphthalene carboxylase reaction to an intermediate that does not include the carboxyl group. Hence, a new carboxyl group from the labeled bicarbonate is added upon forward reaction to the naphthoate. This indicates that the reaction mechanism consists of two or more steps and that at least the latter steps are reversible and ATP independent. Naphthalene carboxylation assays were carried out in deuterated buffer and revealed the incorporation of 0, 1, 2, or 3 deuterium atoms in the final product naphthoyl-coenzyme A, indicating that the reaction is fully reversible. Putative reaction mechanisms were tested by quantum mechanical calculations. The proposed mechanism of the reaction consists of three steps: the activation of the naphthalene by 1,3-dipolar cycloaddition of the cofactor prFMN to naphthalene, release of a proton and rearomatization producing a stable intermediate, and a carboxylation with a reverse 1,3-dipolar cycloaddition and cleavage of the bond to the cofactor producing 2-naphthoate. IMPORTANCE Pollution with polycyclic aromatic hydrocarbons poses a great hazard to humans and animals, with considerable long-term effects. The anaerobic degradation of polycyclic aromatic hydrocarbons in anoxic zones and anaerobic growth of such organisms is very slow, leading to only poor investigation of the degradation pathways, so far. In this work, we elucidated the mechanism of naphthalene carboxylase, a key enzyme in anaerobic naphthalene degradation. This is the first mechanism proposed for a carboxylase targeting nonsubstituted (polycyclic) aromatic compounds and can serve as a model for the initial activation reaction in the anaerobic degradation of benzene or nonsubstituted polycyclic aromatic hydrocarbons, as well as similar enzymatic reactions from the expanding class of UbiD-like (de)carboxylases.

Reactive transport of micropollutants in laboratory aquifers undergoing transient exposure periods

Groundwater quality is of increasing concern due to the ubiquitous occurrence of micropollutant mixtures. Stream-groundwater interactions near agricultural and urban areas represent an important entry pathway of micropollutants into shallow aquifers. Here, we evaluated the biotransformation of a micropollutant mixture (i.e., caffeine, metformin, atrazine, terbutryn, S-metolachlor and metalaxyl) during lateral stream water flow to adjacent groundwater. We used an integrative approach combining concentrations and transformation products (TPs) of the micropollutants, compound-specific isotope analysis (δ¹³C and δ¹⁵N), sequencing of 16S rRNA gene amplicons and reactive transport modeling. Duplicate laboratory aquifers (160 cm × 80 cm × 7 cm) were fed with stream water and subjected over 140 d to three successive periods of micropollutant exposures as pulse-like (6000 μg L^-1) and constant (600 μg L^-1) injections under steady-state conditions. Atrazine, terbutryn, S-metolachlor and metalaxyl persisted in both aquifers during all periods (<10 % attenuation). Metformin attenuation (up to 14 %) was only observed from 90 d onwards, suggesting enhanced degradation over time. In contrast, caffeine dissipated during all injection periods (>90 %), agreeing with fast degradation rates (t_1/2 < 3 d) in parallel microcosm experiments and detection of TPs (theobromine and xanthine). Significant stable carbon isotope fractionation (Δδ¹³C ≥ 6.6 ‰) was observed for caffeine in both aquifers, whereas no enrichment in ¹⁵N occurred. A concentration dependence of caffeine biotransformation in the aquifers was further suggested by model simulations following Michaelis-Menten kinetics. Changes in bacterial community composition reflected long-term bacterial adaptation to micropollutant exposures. Altogether, the use of an integrative approach can help to understand the interplay of subsurface hydrochemistry, bacterial adaptations and micropollutants biotransformation during stream-groundwater interactions.

Comparing the indigenous microorganism system in typical petroleum-contaminated groundwater

The environmental conditions at a contaminated site will impact on the indigenous microbial communities, with implications for the removal of pollutants. An analysis of the characteristics of microbial communities in petroleum-contaminated groundwater can give insights into the relationships between microbial community and environmental factors, and provide guidance about how microbes can be used to remediate and regulate petroleum-contaminated groundwater. This study focuses on two petroleum-contaminated sites in northeast China, the physico-chemical-biological changes in petroleum-contaminated groundwater were analyzed, the response relationship between hydro-chemical indicators and microbial communities was characterized, and the bioindicator that can reflect the petroleum contamination status were established for environmental monitoring and management. The results showed that Proteobacteria was the dominant bacteria in petroleum-contaminated groundwater, with a relative abundance of 42.45%-91.19%. pH, TDS, DO, NO3-, NO2-, SO42-, NH4+, Al, and Mn have significant effects on microbial community. The effect of petroleum pollutants on microbial communities is not only related to the concentration and composition of the pollutants themselves, but also could indirectly affect microbial communities by changing the content of inorganic electron acceptor components such as iron, manganese, sulfate and nitrate in groundwater, and this indirect effect is significantly greater than the direct impact of pollutants on microbial communities. In petroleum-contaminated groundwater, the dominant genera (Polaromonas, Caulobacter) and microbial metabolic functions (methanol oxidation, methylotrophy, ureolysis, and reductive biosynthesis) of the indigenous microbial community can be used as bioindicators to indicate petroleum contamination status. The higher abundance of these bioindicators in petroleum-contaminated groundwater, the more serious petroleum pollution in groundwater.

Simulating degradation of organic compounds accounting for the growth of microorganisms (Monod kinetics) in a fully Lagrangian framework

Biologically mediated degradation of organic compounds in porous media is a complex mathematical problem, described by a non-linear differential equation. The organic compound gets in contact with the biomass, and an enzyme-catalysed reaction takes place. The net result is that part of the parent compound degrades into some daughter product, while some of the organic carbon is used for microbial growth. The rate of biomass growth in the presence of a limiting nutrient supply is usually modelled with the experimentally derived Monod equation, i.e., it is proportional to the actual existing biomass multiplied by a factor that is non-linear in terms of available organic matter. This non-linearity in the degradation equation implies a strong difficulty in directly implementing a numerical solution within a fully Lagrangian framework, and thus, numerical solutions have traditionally been sought in either an Eulerian, or else an Eulerian-Lagrangian framework. Here we pursue a fully Lagrangian solution to the problem. First, the Monod empirical equation is formulated as the outcome of a two-step reaction; while the approach is less general than other derivations existing in the literature based on a full understanding of the thermodynamics of the process, it allows two things: 1) providing some physical meaning to the actual parameters in the Monod equation, and more interestingly, 2) formulating a methodology for the solution of the degradation equation incorporating Monod kinetics by means of a particle tracking formulation. For the latter purpose, both reactants and biomass are represented by particles, and their location at any given time is represented by a kernel that accounts for the uncertainty in the actual physical location. By solving the reaction equation in a kernel framework, we can reproduce the Monod kinetics and, as a particular result in the case no biomass growth is allowed, the Michaelis-Menten kinetics. The methodology proposed is then successfully applied to reproduce two studies of microbially induced degradation of organic compounds in porous media, first, the observed kinetics of Pseudomonas putida F1 in batch reactors while growing on benzene, toluene and phenol, and second, the column study of carbon tetrachloride biodegradation by the denitrifying bacterium Pseudomonas Stutzeri KC.

A starch-based controlled-release targeted nutrient agent to stimulate the activity of volatile chlorinated hydrocarbon-degrading indigenous microflora present in groundwater

Volatile chlorinated hydrocarbons (VCHs) contaminated groundwater has a low indigenous microorganism population, and lack of nutrient substrates involved in degradation reactions, resulting in a weak natural remediation ability of groundwater ecosystems. In this study, based on the principle of degradation of VCHs by indigenous microorganisms in groundwater, and combined with biostimulation and controlled-release technology, we developed a starch-based encapsulated targeted bionutrient (YH-1) with easy uptake, good stability, controllable slow-release migration, and long timeliness for the remediation of groundwater contaminated by VCHs by indigenous microorganisms. The results showed that YH-1 is easily absorbed by microorganisms and can rapidly initiate itself to stimulate the microbial degradation of VCHs, and the degradation rate of various VCH components within 7 days was 82.38-92.38 %. The release rate of nutrient components in YH-1 increases with increasing VCH concentrations in groundwater; this could effectively prolong the action time of nutrient components, while also improving the degradation efficiency of pollutants with a sustained effect of more than 15 days. Simultaneously, owing to the fluidity, water solubility, and biodegradability of YH-1 in lithologic media, YH-1 injection did not cause blockage of the lithologic media in the aquifer. Through YH-1 stimulation, indigenous microorganisms grew rapidly in the underground environment, the diversity of microbial communities and the total number of species increased, and the correlation between genera strengthened. Simultaneously, YH-1 improved the ability of microbial community to convert inorganic electron donors/acceptors, thereby strengthening the co-metabolic mechanism between microorganisms. Additionally, there was a significant increase in the percentage of many microorganisms (e.g., Sphingomonas, Janthinobacterium, Duganella, etc.) that mediated the reductive dechlorination process and were redox inorganic electron donors/acceptors. This was conducive to the reductive dechlorination process of VCHs and achieved the efficient degradation of VCHs.

Polycyclic aromatic hydrocarbon removal from subsurface soil mediated by bacteria and archaea under methanogenic conditions: Performance and mechanisms

In situ anoxic bioremediation is an easy-to-use technology to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated soil. Degradation of PAHs mediated by soil bacteria and archaea using CO₂ as the electron acceptor is an important process for eliminating PAHs under methanogenic conditions; however, knowledge of the performance and mechanisms involved is poorly unveiled. In this study, the effectiveness and efficiency of NaHCO₃ (CO₂) as an electron acceptor to stimulate the degradation of PAHs by bacteria and archaea in highly contaminated soil were investigated. The results showed that CO₂ addition (EC2000) promoted PAH degradation compared to soil without added CO₂ (EC0), with 4.18%, 9.01%-8.05%, and 6.19%-12.45% increases for 2-, 3- and 4-ring PAHs after 250 days of incubation, respectively. Soil bacterial abundances increased with increasing incubation time, especially for EC2000 (2.90 × 10⁸ g^-1 soil higher than EC0, p < 0.05). Different succession patterns of the soil bacterial and archaeal communities during PAH degradation were observed. According to the PCoA and ANOSIM results, the soil bacterial communities were greatly (ANOSIM: R = 0.7232, P = 0.001) impacted by electron acceptors, whereas significant differences in the archaeal communities were not observed (ANOSIM: R = 0.553, P = 0.001). Soil bacterial and archaeal co-occurrence network analyses showed that positive correlations outnumbered the negative correlations throughout the incubation period for both treatments (e.g., EC0 and EC2000), suggesting the prevalence of coexistence/cooperation within and between these two domains rather than competition. The higher complexity, connectance, edge, and node numbers in EC2000 revealed stronger linkage and a more stable co-occurrence network compared to EC0. The results of this study could improve the knowledge on the removal of PAHs and the responses of soil bacteria and archaea to CO₂ application, as well as a scientific basis for the in situ anoxic bioremediation of PAH-contaminated industrial sites.

Trichloroethylene remediation using zero-valent iron with kaolin clay, activated carbon and bacteria

Nanoscale particles of zero-valent iron were used to form a permeable reactive barrier whose performance in dechlorinating a solution of trichloroethylene was compared with that of a barrier formed from limestone. The iron was combined with kaolin by calcination. The test liquid contained sewage sludge, and also added NH₄Cl and KH₂PO₄. The average removal rates of trichloroethylene and phosphorus over 365 days both exceeded 94%. Chemical oxygen demand was reduced by 92% and ammonium nitrogen by 43.6%. All were significantly greater than the removals with the limestone barrier. The ceramsite barrier retained 85% of its effectiveness even after 365 days of use. Dechloromonas sp. was the main dechlorinating bacterium, but its removal ability is limited. The removal of trichloroethylene in such a barrier mainly depends on reduction by the zero-valent iron and biodegradation. The results show that the prepared ceramsite is stable and effective in removing trichloroethylene from water. It is a promising in-situ remediation material for groundwater.

Escherichia coli chemotaxis to competing stimuli in a microfluidic device with a constant gradient

In natural systems bacteria are exposed to many chemical stimulants; some attract chemotactic bacteria as they promote survival, while others repel bacteria because they inhibit survival. When faced with a mixture of chemoeffectors, it is not obvious which direction the population will migrate. Predicting this direction requires an understanding of how bacteria process information about their surroundings. We used a multiscale mathematical model to relate molecular level details of their two-component signaling system to the probability that an individual cell changes its swimming direction to the chemotactic velocity of a bacterial population. We used a microfluidic device designed to maintain a constant chemical gradient to compare model predictions to experimental observations. We obtained parameter values for the multiscale model of Escherichia coli chemotaxis to individual stimuli, α-methylaspartate and nickel ion, separately. Then without any additional fitting parameters, we predicted bacteria response to chemoeffector mixtures. Migration of E. coli toward α-methylaspartate was modulated by adding increasing concentrations of nickel ion. Thus, the migration direction was controlled by the relative concentrations of competing chemoeffectors in a predictable way. This study demonstrated the utility of a multiscale model to predict the migration direction of bacteria in the presence of competing chemoeffectors. This article is protected by copyright. All rights reserved.

Coordination of bacterial biomarkers with the dominant microbes enhances triclosan biodegradation in soil amended with food waste compost and cow dung compost

Increasing concerns regarding the micropollutant triclosan (TCS) derive from its potential threats to human health and ecological security. Compost addition have been verified to be effective in soil remediation, however, the biodegradation of TCS under compost amendment in soil remain unclear. This study investigated the removal of TCS in soils amended with food waste compost (FS), cow dung compost (CS) and sludge compost (SS), respectively, explored the key TCS-degraders and biological mechanisms of TCS removal. Compost addition significantly enhanced the removal of TCS (p < 0.05) in the order of FS > CS > SS. The dosage of 20% (w/w) was the most efficient one and the ultimate concentrations of TCS were decreased by 76.67%, 67.90% and 56.79% compared with CK, respectively. The abundance of key dominant bacterial genus (7 in FS and 4 in CS) and fungal genus (3 in FS and CS) was stimulated due to the increase of soil nutrient factors (including dissolved organic carbon, DOC; soil organic matter, SOM; ammonium nitrogen, NH₄⁺; nitrate nitrogen, NO₃^-) and the decrease of pH. A negative correlation between these dominant microbes and TCS concentration indicated their potential effect on TCS degradation. A total of four bacterial biomarkers, namely Saccharomonospora, Aequorivita, Bacillaceae and Fodinicurvataceae (both at family level) were the key TCS-degraders. Structural equation model (SEM) indicated that the improvement of soil nutrient factors in FS and CS promoted TCS biodegradation by improving the activity of bacterial biomarkers, as while, the key dominant microbes showed good tolerance to TCS stress. However, there were no significant biological effects on TCS in SS group. Network analysis further confirmed that it was the coordination of bacterial biomarkers with the dominant microbes that enhanced TCS biodegradation in soil amended with food waste compost and cow dung compost.

Combining reverse osmosis and microbial degradation for remediation of drinking water contaminated with recalcitrant pesticide residue

Groundwater contamination by recalcitrant organic micropollutants such as pesticide residues poses a great threat to the quality of drinking water. One way to remediate drinking water containing micropollutants is to bioaugment with specific pollutant degrading bacteria. Previous attempts to augment sand filters with the 2,6-dichlorobenzamide (BAM) degrading bacterium Aminobacter niigataensis MSH1 to remediate BAM-polluted drinking water initially worked well, but the efficiency rapidly decreased due to loss of degrader bacteria. Here, we use pilot-scale augmented sand filters to treat retentate of reverse osmosis treatment, thus increasing residence time in the biofilters and potentially nutrient availability. In a first pilot-scale experiment, BAM and most of the measured nutrients were concentrated 5-10 times in the retentate. This did not adversely affect the abundances of inoculated bacteria and the general prokaryotic community of the sand filter presented only minor differences. On the other hand, the high degradation activity was not prolonged compared to the filter receiving non-concentrated water at the same residence time. Using laboratory columns, it was shown that efficient BAM degradation could be achieved for >100 days by increasing the residence time in the sand filter. A slower flow may have practical implications for the treatment of large volumes of water, however this can be circumvented when treating only the retentate water equalling 10-15% of the volume of inlet water. We therefore conducted a second pilot-scale experiment with two inoculated sand filters receiving membrane retentate operated with different residence times (22 versus 133 min) for 65 days. While the number of MSH1 in the biofilters was not affected, the effect on degradation was significant. In the filter with short residence time, BAM degradation decreased from 86% to a stable level of 10-30% degradation within the first two weeks. The filter with the long residence time initially showed >97% BAM degradation, which only slightly decreased with time (88% at day 65). Our study demonstrates the advantage of combining membrane filtration with bioaugmented filters in cases where flow rate is of high importance.

Anaerobic degradation of benzene and other aromatic hydrocarbons in a tar-derived plume: Nitrate versus iron reducing conditions

The anaerobic degradation of aromatic hydrocarbons in a plume originating from a Pintsch gas tar-DNAPL zone was investigated using molecular, isotopic- and microbial analyses. Benzene concentrations diminished at the relatively small meter scale dimensions of the nitrate reducing plume fringe. The ratio of benzene to toluene, ethylbenzene, xylenes and naphthalene (BTEXN) in the fringe zone compared to the plume zone, indicated relatively more loss of benzene in the fringe zone than TEXN. This was substantiated by changes in relative concentrations of BTEXN, and multi-element compound specific isotope analysis for δ²H and δ¹³C. This was supported by the presence of (abcA) genes, indicating the presumed benzene carboxylase enzyme in the nitrate-reducing plume fringe. Biodegradation of most hydrocarbon contaminants at iron reducing conditions in the plume core, appears to be quantitatively of greater significance due to the large volume of the plume core, rather than relatively faster biodegradation under nitrate reducing conditions at the smaller volume of the plume fringe. Contaminant concentration reductions by biodegradation processes were shown to vary distinctively between the source, plume (both iron-reducing) and fringe (nitrate-reducing) zones of the plume. High anaerobic microbial activity was detected in the plume zone as well as in the dense non aqueous phase liquid (DNAPL) containing source zone. Biodegradation of most, if not all, other water-soluble Pintsch gas tar aromatic hydrocarbon contaminants occur at the relatively large dimensions of the anoxic plume core. The highest diversity and concentrations of metabolites were detected in the iron-reducing plume core, where the sum of parent compounds of aromatic hydrocarbons was greater than 10 mg/L. The relatively high concentrations of metabolites suggest a hot spot for anaerobic degradation in the core of the plume downgradient but relatively close to the DNAPL containing source zone.

Microbial compositional and functional traits of BTEX and salinity co-contaminated shallow groundwater by produced water

Intrusion of salinity and petroleum hydrocarbons (e.g., benzene, toluene, ethylbenzene, and xylenes, BTEX) into shallow groundwater by so-called 'produced water' (the water associated with oil and gas production) has recently drawn much attention. However, how this co-contamination affects the groundwater microbial community remains unknown. Herein, geochemical methods (e.g., ion ratios) and high-throughput sequencing (amplicon and shotgun metagenomic) were used to study the contaminant source, hydrogeochemical conditions, microbial community and function in salinity and BTEX co-contaminated shallow groundwater in an oil field, northwest China. The desulfurization coefficient (100rSO₄^2-/rCl^-), coefficient of sodium and chloride (rNa⁺/rCl^-), and coefficient of magnesium and chloride (rMg²⁺/rCl^-) revealed an intrusion of produced water into groundwater, resulting in elevated levels of salinity and BTEX. The consumption of terminal electron acceptors (e.g., NO₃^-, Fe³⁺, and SO₄^2-) was likely coupled with BTEX degradation. Relative to the bacteria, decreased archaeal diversity and enriched community in produced water-contaminated groundwater suggested that archaea were more susceptible to elevated BTEX and salinity. Relative to the nitrate and sulfate reduction genes, the abundance of marker genes encoding fermentation (acetate and hydrogen production) and methanogenesis (aceticlastic and methylotrophic) was more proportional to BTEX concentration. The produced water intrusion significantly enriched the salt-tolerant anaerobic fermentative heterotroph Woesearchaeia in shallow groundwater, and its co-occurrence with BTEX-degrading bacteria and methanogen Methanomicrobia suggested mutualistic interactions among the archaeal and bacterial communities to couple BTEX degradation with fermentation and methanogenesis. This study offers a first insight into the microbial community and function in groundwater contaminated by produced water.

Selective pressure on microbial communities in a drinking water aquifer - Geochemical parameters vs. micropollutants

Groundwater quality is crucial for drinking water production, but groundwater resources are increasingly threatened by contamination with pesticides. As pesticides often occur at micropollutant concentrations, they are unattractive carbon sources for microorganisms and typically remain recalcitrant. Exploring microbial communities in aquifers used for drinking water production is an essential first step towards understanding the fate of micropollutants in groundwater. In this study, we investigated the interaction between groundwater geochemistry, pesticide presence, and microbial communities in an aquifer used for drinking water production. Two groundwater monitoring wells in The Netherlands were sampled in 2014, 2015, and 2016. In both wells, water was sampled from five discrete depths ranging from 13 to 54 m and was analyzed for geochemical parameters, pesticide concentrations and microbial community composition using 16S rRNA gene sequencing and qPCR. Groundwater geochemistry was stable throughout the study period and pesticides were heterogeneously distributed at low concentrations (μg L^-1 range). Microbial community composition was also stable throughout the sampling period. Integration of a unique dataset of chemical and microbial data showed that geochemical parameters and to a lesser extent pesticides exerted selective pressure on microbial communities. Microbial communities in both wells showed similar composition in the deeper aquifer, where pumping results in horizontal flow. This study provides insight into groundwater parameters that shape microbial community composition. This information can contribute to the future implementation of remediation technologies to guarantee safe drinking water production.

Tracing long-distance electron transfer and cable bacteria in freshwater sediments by agar pillar gradient columns

Cable bacteria (CB) perform electrogenic sulphur oxidation (e-SOX) by spatially separating redox-half-reactions over cm-distances. For freshwater systems, the ecology of CB is not yet well understood, partly because they proved difficult to cultivate. This study introduces a new "agar pillar" approach to selectively enrich and investigate CB-populations. Within sediment columns, a central agar pillar is embedded, providing a sediment-free gradient-system in equilibrium with the surrounding sediment. We incubated freshwater sediments from a streambed, a sulfidic lake, and a hydrocarbon polluted aquifer in such agar pillar columns. Microprofiling revealed typical patterns of e-SOx, such as the development of a suboxic zone and the establishment of electric potentials. The bacterial communities in the sediments and agar pillars were analysed over depth by PacBio near-full-length 16S rRNA gene amplicon sequencing, allowing for a precise phylogenetic placement of taxa detected. The selective niche of the agar pillar was preferentially colonized by CB related to Candidatus Electronema for surface-water sediments, including several potentially novel species, but not for putative groundwater CB affiliated with Desulfurivibrio spp. The presence of CB was seemingly linked to co-enriched fermenters, hinting at a possible role of e-SOx-populations as an electron sink for heterotrophic microbes. These findings add to our current understanding of the diversity and ecology of CB in freshwater systems, and to a discrimination of CB from surface and groundwater sediments. The agar pillar approach provides a new strategy that may facilitate the cultivation of redox gradient-dependent microorganisms, including previously unrecognized CB populations.

Toward Improved Bioremediation Strategies: Response of BAM-Degradation Activity to Concentration and Flow Changes in an Inoculated Bench-Scale Sediment Tank

Compound-specific isotope analysis (CSIA) can reveal mass-transfer limitations during biodegradation of organic pollutants by enabling the detection of masked isotope fractionation. Here, we applied CSIA to monitor the adaptive response of bacterial degradation in inoculated sediment to low contaminant concentrations over time. We characterized Aminobacter sp. MSH1 activity in a flow-through sediment tank in response to a transient supply of elevated 2,6-dichlorobenzamide (BAM) concentrations as a priming strategy and took advantage of an inadvertent intermittence to investigate the effect of short-term flow fluctuations. Priming and flow fluctuations yielded improved biodegradation performance and increased biodegradation capacity, as evaluated from bacterial activity and residual concentration time series. However, changes in isotope ratios in space and over time evidenced that mass transfer became increasingly limiting for degradation of BAM at low concentrations under such stimulated conditions, and that activity decreased further due to bacterial adaptation at low BAM (μg/L) levels. Isotope ratios, in conjunction with residual substrate concentrations, therefore helped identifying underlying limitations of biodegradation in such a stimulated system, offering important insight for future optimization of remediation schemes.

Innovative Bacterial Removal Technique Using Green Synthetic Nano Curcumin Zinc (II) Complex for Sustainable Water Resource Management

Sustainable management of water resources is a daunting challenge, especially with respect to microbes. This study primarily focused on the development of a novel application for the removal of specific bacterial groups in different water types using a green synthetic nano Cur-Zn(II) complex. The results of UV and FT-IR spectroscopic techniques suggested the formation of a chelation complex. Proton NMR showed that the main enolic proton peak with a chemical shift of 16.45 nm identified in curcumin was missed, indicating the contribution of carbonyl oxygen of enol in the formation of the complex. The crystalline nature of the complex and Wurtzite structure of annealed products was inferred from the XRD analysis data. SEM results confirmed the complex’s morphology as spherical and clustered with a rough surface, having an average particle size of 68.2 nm. In addition, the complex was observed to be stable up to 300 °C without any decomposition from STA. Being acidic in nature with a pH of 5.36, the complex penetrates into the cell membrane and inhibit microbial growth. Intrinsically, no studies have been reported for the removal of microbes from water using natural materials embedded with inorganic metals, particularly in nano form. Therefore, the study is the first, innovative, eco-friendly, and economical method to use nano Cur-Zn(II) for removing targeted bacteria in real water samples with 100% efficiency by using optimized amounts (0.025–0.2 g/L) of the complex at a contact time interval between 4 and 24 h. The complex developed is toxic-free and can be applied in situ.

Management of large dilute plumes of chloroethenes and 1,4-dioxane via monitored natural attenuation (MNA) and MNA augmentation

Management of large, dilute groundwater plumes of comingled chlorinated volatile organic compounds (CVOCs) and 1,4-dioxane (dioxane) is problematic due to chemical, hydrogeologic and economic concerns. The US Environmental Protection Agency (US EPA) has conducted research on the management of CVOC plumes for many years, and more recently dioxane. US EPA research on monitored natural attenuation (MNA) of CVOC plumes was reviewed by a science advisory board in 2001. Specific additional research was recommended and has been addressed in a series of US EPA reports produced over almost two decades. These reports are summarized in this document along with supporting information including evidence of biological degradation of dioxane. Based on the summarized reports, US EPA work documented elsewhere, and the work of others, under appropriate conditions MNA or augmented MNA remain viable management options for these plumes. Unlike MNA of plumes containing only CVOCs, however, MNA of large dilute comingled plumes should be expected to occur by cometabolic oxidation rather than direct metabolic processes.

Bacterial community profile of the crude oil-contaminated saline soil in the Yellow River Delta Natural Reserve, China

Crude oil contamination greatly influence soil bacterial community. Proliferative microbes in the crude oil-contaminated soil are closely related to the living conditions. Oil wells in the Yellow River Delta Natural Reserve (YRDNR) region is an ideal site for investigating the bacterial community of crude oil-contaminated saline soil. In the present study, 18 soil samples were collected from the depths of 0-20 cm and 20-40 cm around the oil wells in the YRDNR. The bacterial community profile was analyzed through high-throughput sequencing to trace the oil-degrading aerobic and anaerobic bacteria. The results indicated that C₁₅-C₂₈ and C₂₉-C₃₈ were the main fractions of total petroleum hydrocarbon (TPH) in the sampled soil. These TPH fractions had a significant negative effect on bacterial biodiversity (Shannon, Simpson, and Chao1 indices), which led to the proliferation of hydrocarbon-degrading bacteria. A comprehensive analysis between the environmental factors and soil microbial community structure showed that Streptococcus, Bacillus, Sphingomonas, and Arthrobacter were the aerobic hydrocarbon-degrading bacteria; unidentified Rhodobacteraceae and Porticoccus were considered to be the possible facultative anaerobic bacteria with hydrocarbon biodegradation ability; Acidithiobacillus, SAR324 clade, and Nitrosarchaeum were predicted to be the anaerobic hydrocarbon-degrading bacteria in the sub-surface soil. Furthermore, large amount of carbon sources derived from TPH was found to cause depletion of bioavailable nitrogen in the soil. The bacteria associated with nitrogen transformation, such as Solirubrobacter, Candidatus Udaeobacter, Lysinibacillus, Bradyrhizobium, Sphingomonas, Mycobacterium, and Acidithiobacillus, were highly abundant; these bacteria may possess the ability to increase nitrogen availability in the crude oil-contaminated soil. The bacterial community functions were significantly different between the surface and the sub-surface soil, and the dissolved oxygen concentration in soil was considered to be potential influencing factor. Our results could provide useful information for the bioremediation of crude oil-contaminated saline soil.

Response of environmental factors to attenuation of toluene in vadose zone

Contaminated groundwater migrates in reverse direction under capillary force in vadose zone, and the attenuation process of pollutant adsorption and microbial degradation changes the environment of vadose zone. In this study, the response of toluene to environmental factors during reverse migration and attenuation of toluene from aquifer to vadose zone was studied by column experiment and experimental data analysis. The changes of environmental factors, including potential of hydrogen (pH), dissolved oxygen (DO), and oxidation-reduction potential (ORP), and toluene concentration were monitored by soil column experiment under sterilized and non-sterilized conditions. The 16S rRNA molecular biological detection technology was used to quantitatively analyze the impact of microbial degradation on the environment. Finally, the correlation between environmental factors and concentration in the attenuation process of toluene in the vadose zone was quantitatively studied by Pearson Correlation Coefficient (PCC) and multivariate statistical equation. The results showed that pH was primarily affected by microbial degradation, and DO and ORP were primarily affected by both adsorption and microbial degradation. The attenuation of toluene was divided into two stages: adsorption dominated (0~26 d) and microbial degradation dominated (26~55 d). The degradation amounts of microorganisms at each position in the non-sterilized column from bottom to top were 9.37%, 55.34%, 68.64%, 75.70%, 66.03% and 42.50%. At the same time, the article proposes for the first time that there is an obvious functional relationship between environmental factors (DO, ORP, pH), time (t) and concentration (C_Toluene):C_Toluene=C₀+A100t+Bα+Cβ+D100γ, (α,β,γ are the pH, DO and ORP of capillary water, respectively; A, B, C and D are all undetermined coefficients), R² > 0.95. The results of this study may facilitate the use of simple and easy-to-obtain environmental factors to characterize the dynamic process of pollutant concentration changes.

Sulfidic acetate mineralization at 45°C by an aquifer microbial community: key players and effects of heat changes on activity and community structure

High-Temperature Aquifer Thermal Energy Storage (HT-ATES) is a sustainable approach for integrating thermal energy from various sources into complex energy systems. Temperatures ≥45°C, which are relevant in impact zones of HT-ATES systems, may dramatically influence the structure and activities of indigenous aquifer microbial communities. Here, we characterized an acetate-mineralizing, sulfate-reducing microbial community derived from an aquifer and adapted to 45°C. Acetate mineralization was strongly inhibited at temperatures ≤25°C and 60°C. Prolonged incubation at 12°C and 25°C resulted in acetate mineralization recovery after 40-80 days whereas acetate was not mineralized at 60°C within 100 days. Cultures pre-grown at 45°C and inhibited for 28 days by incubation at 12°C, 25°C, or 60°C recovered quickly after changing the temperature back to 45°C. Phylotypes affiliated to the order Spirochaetales and to endospore-forming sulfate reducers of the order Clostridiales were highly abundant in microcosms being active at 45°C highlighting their key role. In summary, prolonged incubation at 45°C resulted in active microbial communities mainly consisting of organisms adapted to temperatures between the typical temperature range of mesophiles and thermophiles and being resilient to temporary heat changes.

Beneficial effects of dynamic groundwater flow and redox conditions on Natural Attenuation of mono-, poly-, and NSO-heterocyclic hydrocarbons

Natural Attenuation (NA) processes have been demonstrated to reduce pollutant loads at different contaminated groundwater sites world-wide and are increasingly considered in contaminated site management concepts. However, data are mainly available for steady state groundwater flow and stable redox conditions as well as pollutants listed in standard regulatory schemes. In this study, the influence of transient groundwater flow and redox conditions on NA was examined at a former gas works site near the river Rhine in Germany. The investigated 78 pollutants included 40 mono- and polyaromatic hydrocarbons (MAHs, PAHs) and 38 NSO-heterocyclic aromatic hydrocarbons (NSO-HET). In the highly polluted areas, the MAHs benzene, indene and indane, the PAHs naphthalene, acenaphthene, 1- and 2-methylnaphthalene and the NSO-HET 2-methylquinoline, carbazole, benzothiophene, dibenzofuran and benzofuran were predominant. Pollutant concentrations decreased with increasing distance from the sources of contamination. At the plume fringes, the MAHs benzene and indane, the PAH acenaphthene, the NSO-HET carbazole, 5-methylbenzothiophene, 2- and 3-methylbenzofuran and 2-methyldibenzofuran were predominant, indicating low retention and slow intrinsic biodegradation of these compounds. The influence of surface water on groundwater level, pollutant concentrations, and redox conditions in the monitoring wells was observed with a permanently installed groundwater sensor. The temporary availability of oxygen was observed at the plume fringes, resulting in aerobic and ferric iron reducing biodegradation processes. Field and laboratory data were used to set-up a groundwater flow and reactive transport model used for quantification of the field mass transfer rates. In conclusion, the study demonstrates that NA is effective under transient flow and redox conditions. A conceptual model and reactive transport simulation can facilitate the interpretation of pronounced fluctuations of pollutant concentration in monitoring wells. Based on the analysis of 78 pollutants, indane, indene and several NSO-HET like carbazole, benzothiophene and 2-methyldibenzofuran are recommended for monitoring at tar oil polluted sites, besides EPA-PAHs and BTEX.

Factors Influencing the Bacterial Bioremediation of Hydrocarbon Contaminants in the Soil: Mechanisms and Impacts

The discharge of hydrocarbons and their derivatives to environments due to human and/or natural activities cause environmental pollution (soil, water, and air) and affect the natural functioning of an ecosystem. To minimize or eradicate environmental pollution by hydrocarbon contaminants, studies showed strategies including physical, chemical, and biological approaches. Among those strategies, the use of biological techniques (especially bacterial biodegradation) is critically important to remove hydrocarbon contaminants. The current review discusses the insights of major factors that enhance or hinder the bacterial bioremediation of hydrocarbon contaminants (aliphatic, aromatic, and polyaromatic hydrocarbons) in the soil. The key factors limiting the overall hydrocarbon biodegradation are generally categorized as biotic factors and abiotic factors. Among various environmental factors, temperature range from 30 to 40°C, pH range from 5 to 8, moisture availability range from 30 to 90%, carbon/nitrogen/phosphorous (C/N/P; 100:20:1) ratio, and 10–40% of oxygen for aerobic degradation are the key factors that show positive correlation for greatest hydrocarbon biodegradation rate by altering the activities of the microbial and degradative enzymes in soil. In addition, the formation of biofilm and production of biosurfactants in hydrocarbon-polluted soil environments increase microbial adaptation to low bioavailability of hydrophobic compounds, and genes that encode for hydrocarbon degradative enzymes are critical for the potential of microbes to bioremediate soils contaminated with hydrocarbon pollutants. Therefore, this review works on the identification of factors for effective hydrocarbon biodegradation, understanding, and optimization of those factors that are essential and critical.

Structural diversity, functional aspects and future therapeutic applications of human gut microbiome

The research on human gut microbiome, regarded as the black box of the human body, is still at the stage of infancy as the functional properties of the complex gut microbiome have not yet been understood. Ongoing metagenomic studies have deciphered that the predominant microbial communities belong to eubacterial phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Cyanobacteria, Verrucomicrobia and archaebacterial phylum Euryarchaeota. The indigenous commensal microbial flora prevents opportunistic pathogenic infection and play undeniable roles in digestion, metabolite and signaling molecule production and controlling host's cellular health, immunity and neuropsychiatric behavior. Besides maintaining intestinal health via short-chain fatty acid (SCFA) production, gut microbes also aid in neuro-immuno-endocrine modulatory molecule production, immune cell differentiation and glucose and lipid metabolism. Interdependence of diet and intestinal microbial diversity suggests the effectiveness of pre- and pro-biotics in maintenance of gut and systemic health. Several companies worldwide have started potentially exploiting the microbial contribution to human health and have translated their use in disease management and therapeutic applications. The present review discusses the vast diversity of microorganisms playing intricate roles in human metabolism. The contribution of the intestinal microbiota to regulate systemic activities including gut-brain-immunity crosstalk has been focused. To the best of our knowledge, this review is the first of its kind to collate and discuss the companies worldwide translating the multi-therapeutic potential of human intestinal microbiota, based on the multi-omics studies, i.e. metagenomics and metabolomics, as ready solutions for several metabolic and systemic disorders.

K-strategy species plays a pivotal role in the natural attenuation of petroleum hydrocarbon pollution in aquifers

The natural attenuation of petroleum hydrocarbons is inseparable from the action of microorganisms, while the degradation methods and ecological strategies of microorganisms in petroleum-contaminated aquifers are still under debate. In the present study, 16 S rRNA sequencing and quantitative real-time polymerase chain reaction were used to assess the potential microbial degradation of petroleum hydrocarbons, and the ecological strategy of microorganisms under petroleum stress was analyzed through a co-occurrence network. The results showed that the microbial community in sediments exhibit higher efficiency and stability and stronger ecological function than that in groundwater. Keystone species coordinated with the community to execute ecosystem processes and tended to choose a K-strategy to survive, with the aquifer sediment being the main site of petroleum hydrocarbon degradation. Under natural conditions, the presence of petroleum hydrocarbons at concentrations higher than 126 μg kg^-1 and 5557 μg kg^-1 was not conducive to the microbial degradation of polycyclic aromatic hydrocarbons and alkanes, respectively. These results can be used as a reference for an enhanced bioremediation of contaminated groundwater. Overall, these findings provide support to managers for developing environmental management strategies.

Biostimulation is a valuable tool to assess pesticide biodegradation capacity of groundwater microorganisms

Groundwater is the main source for drinking water production globally. Groundwater unfortunately can contain micropollutants (MPs) such as pesticides and/or pesticide metabolites. Biological remediation of MPs in groundwater requires an understanding of natural biodegradation capacity and the conditions required to stimulate biodegradation activity. Thus, biostimulation experiments are a valuable tool to assess pesticide biodegradation capacity of field microorganisms. To this end, groundwater samples were collected at a drinking water abstraction aquifer at two locations, five different depths. Biodegradation of the MPs BAM, MCPP and 2,4-D was assessed in microcosms with groundwater samples, either without amendment, or amended with electron acceptor (nitrate or oxygen) and/or carbon substrate (dissolved organic carbon (DOC)). Oxygen + DOC was the most successful amendment resulting in complete biodegradation of 2,4-D in all microcosms after 42 days. DOC was most likely used as a growth substrate that enhanced co-metabolic 2,4-D degradation with oxygen as electron acceptor. Different biodegradation rates were observed per groundwater sample. Overall, microorganisms from the shallow aquifer had faster biodegradation rates than those from the deep aquifer. Higher microbial activity was also observed in terms of CO₂ production in the microcosms with shallow groundwater. Our results seem to indicate that shallow groundwater contains more active microorganisms, possibly due to their exposure to higher concentrations of both DOC and MPs. Understanding field biodegradation capacity is a key step towards developing further bioremediation-based technologies. Our results show that biostimulation has real potential as a technology for remediating MPs in aquifers in order to ensure safe drinking production.

Optimized Cultivation and Syntrophic Relationship of Anaerobic Benzene-Degrading Enrichment Cultures under Methanogenic Conditions

Current challenges in the anaerobic bioremediation of benzene are the lack of capable cultures and limited knowledge on the biodegradation pathway. Under methanogenic conditions, benzene may be mineralized by syntrophic interactions between microorganisms, which are poorly understood. The present study developed an optimized formula for anoxic medium to successfully promote the growth of the putative benzene degrader Deltaproteobacterium Hasda-A and enhance the benzene degradation activity of methanogenic enrichment cultures. Within 70‍ ‍d of incubation, the benzene degradation activity and relative abundance of Hasda-A in cultures in the new defined medium increased from 0.5 to >3‍ ‍mg L^–1 d^–1 and from 2.5% to >17%, respectively. Together with Hasda-A, we found a strong positive relationship between the abundances of superphylum OD1 bacteria, three methanogens (Methanoregula, Methanolinea, and Methanosaeta) and benzene degradation activity. The syntrophic relationship between these microbial taxa and Hasda-A was then demonstrated in a correlation analysis of longitudinal data. The involvement of methanogenesis in anaerobic benzene mineralization was confirmed by inhibition experiments. The high benzene degradation activity and growth of Hasda-A were quickly recovered in successive dilutions of enrichment cultures, proving the feasibility of using the medium developed in the present study to produce highly capable cultures. The present results will facilitate practical applications in bioremediation and research on the molecular mechanisms underlying benzene activation and syntrophic interactions in benzene mineralization.