Anaerobic degradation of non-substituted aromatic hydrocarbons

Differential degradation of petroleum hydrocarbons by Shewanella putrefaciens under aerobic and anaerobic conditions

The complexity of crude oil composition, combined with the fluctuating oxygen level in contaminated environments, poses challenges for the bioremediation of oil pollutants, because of compound-specific microbial degradation of petroleum hydrocarbons under certain conditions. As a result, facultative bacteria capable of breaking down petroleum hydrocarbons under both aerobic and anaerobic conditions are presumably effective, however, this hypothesis has not been directly tested. In the current investigation, Shewanella putrefaciens CN32, a facultative anaerobic bacterium, was used to degrade petroleum hydrocarbons aerobically (using O2 as an electron acceptor) and anaerobically (using Fe(III) as an electron acceptor). Under aerobic conditions, CN32 degraded more saturates (65.65 ± 0.01%) than aromatics (43.86 ± 0.03%), with the following order of degradation: dibenzofurans > n-alkanes > biphenyls > fluorenes > naphthalenes > alkylcyclohexanes > dibenzothiophenes > phenanthrenes. In contrast, under anaerobic conditions, CN32 exhibited a higher degradation of aromatics (53.94 ± 0.02%) than saturates (23.36 ± 0.01%), with the following order of degradation: dibenzofurans > fluorenes > biphenyls > naphthalenes > dibenzothiophenes > phenanthrenes > n-alkanes > alkylcyclohexanes. The upregulation of 4-hydroxy-3-polyprenylbenzoate decarboxylase (ubiD), which plays a crucial role in breaking down resistant aromatic compounds, was correlated with the anaerobic degradation of aromatics. At the molecular level, CN32 exhibited a higher efficiency in degrading n-alkanes with low and high carbon numbers relative to those with medium carbon chain lengths. In addition, the degradation of polycyclic aromatic hydrocarbons (PAHs) under both aerobic and anaerobic conditions became increasingly difficult with increased numbers of benzene rings and methyl groups. This study offers a potential solution for the development of targeted remediation of pollutants under oscillating redox conditions.

Progress of Crude Oil Gasification Technology Assisted by Microorganisms in Reservoirs

Crude oil gasification bacteria, including fermenting bacteria, hydrocarbon-oxidizing bacteria, reducing bacteria, and methanogenic bacteria, participate in multi-step reactions involving initial activation, intermediate metabolism, and the methanogenesis of crude oil hydrocarbons. These bacteria degrade crude oil into smaller molecules such as hydrogen, carbon dioxide, acetic acid, and formic acid. Ultimately, they convert it into methane, which can be utilized or stored as a strategic resource. However, the current challenges in crude oil gasification include long production cycles and low efficiency. This paper provides a summary of the microbial flora involved in crude oil gasification, the gasification metabolism pathways within reservoirs, and other relevant information. It specifically focuses on analyzing the factors that affect the efficiency of crude oil gasification metabolism and proposes suggestions for improving this efficiency. These studies deepen our understanding of the potential of reservoir ecosystems and provide valuable insights for future reservoir development and management.

Microbial functional heterogeneity induced in a petroleum-polluted soil profile

Microbial taxonomic diversity declines with increasing stress caused by petroleum pollution. However, few studies have tested whether functional diversities vary similarly to taxonomic diversity along the stress gradient. Here, we investigated soil microbial communities in a petrochemically polluted site in China. Total petroleum hydrocarbon (TPH) concentrations were higher in the middle (2-3 m) and deep soil layer (3-5 m) than in the surface soil layer (0-2 m). Accordingly, microbial taxonomic α-diversity was decreased by 44% (p < 0.001) in the middle and deep soil layers, compared to the surface soil layer. In contrast, functional α-diversity decreased by 3% (p < 0.001), showing a much better buffering capacity to environmental stress. Differences in microbial taxonomic and functional β-diversities were enlarged in the middle and deep soil layers, extending the Anna Karenina Principle (AKP) that a community adapts to stressful environments in its own way. Consistent with the stress gradient hypothesis, we revealed a higher degree of network connectivity among microbial species and genes in the middle and deep soil layers compared to the surface soil layer. Together, we demonstrate that microbial functionality is more tolerant to stress than taxonomy, both of which were amenable to AKP and the stress gradient hypothesis.

Overview of enhancing biological treatment of coal chemical wastewater: New strategies and future directions

Coal chemical wastewater (CCW) is a type of refractory industrial wastewater, and its treatment has become the main bottleneck restricting the sustainable development of novel coal chemical industry. Biological treatment is considered as an economical, effective and environmentally friendly technology for CCW treatment. However, conventional biological process is difficult to achieve the efficient removal of refractory organics because of CCW with the characteristics of composition complexity and high toxicity. Therefore, seeking the novel enhancement strategy appears to be a favorable solution for enhancing biological treatment efficiency of CCW. This review focuses on presenting a comprehensive picture about the exogenous enhancement strategies for CCW biological treatment. The performance and potential application of exogenous enhancement strategies, including co-metabolic substrate enhancement, biofilm filler enhancement, adsorption material enhancement and conductive mediator enhancement, were expounded. Meanwhile, the enhancing mechanisms of different strategies were comprehensively discussed from a biological perspective. Furthermore, the prospects of enhancement strategies based on the engineering performance, economic cost and environmental impact (3E) evaluation were introduced. And novel enhancement strategy based on "low carbon emissions", "resource recycling" and "water environment security" in the context of carbon neutrality was proposed. Taken together, this review provides technical reference and new direction to facilitate the regulation and optimization of typical industrial wastewater biological treatment.

Microbial remediation of oil-contaminated shorelines: a review

Frequent marine oil spills have led to increasingly serious oil pollution along shorelines. Microbial remediation has become a research hotspot of intertidal oil pollution remediation because of its high efficiency, low cost, environmental friendliness, and simple operation. Many microorganisms are able to convert oil pollutants into non-toxic substances through their growth and metabolism. Microorganisms use enzymes' catalytic activities to degrade oil pollutants. However, microbial remediation efficiency is affected by the properties of the oil pollutants, microbial community, and environmental conditions. Feasible field microbial remediation technologies for oil spill pollution in the shorelines mainly include the addition of high-efficiency oil degrading bacteria (immobilized bacteria), nutrients, biosurfactants, and enzymes. Limitations to the field application of microbial remediation technology mainly include slow start-up, rapid failure, long remediation time, and uncontrolled environmental impact. Improving the environmental adaptability of microbial remediation technology and developing sustainable microbial remediation technology will be the focus of future research. The feasibility of microbial remediation techniques should also be evaluated comprehensively.

Chemical characterization and anaerobic treatment of bitumen fume condensate using a membrane bioreactor

Bitumen fume condensate (BFC) is a hazardous wastewater generated at asphalt reclamation and production sites. BFC contains a wide variety of potentially toxic organic pollutants that negatively affect anaerobic processes. In this study, we chemically characterized BFC produced at an industrial site and evaluated its degradation under anaerobic conditions. Analyses identified about 900 compounds including acetate, polycyclic aromatic hydrocarbons, phenolic compounds, and metal ions. We estimated the half maximal inhibitory concentrations (IC₅₀) of methanogenesis of 120, 224, and 990 mgCOD·L^-1 for three types of anaerobic biomass, which indicated the enrichment and adaptation potentials of methanogenic biomass to the wastewater constituents. We operated an AnMBR (7.0 L, 35 °C) for 188 days with a mixture of BFC, phenol, acetate, and nutrients. The reactor showed a maximum average COD removal efficiency of 87.7 ± 7.0 %, that corresponded to an organic conversion rate of 286 ± 71 mgCOD^-1·L^-1d^-1. The microbial characterization of the reactor's biomass showed the acetoclastic methanogen Methanosaeta as the most abundant microorganism (43 %), whereas the aromatic and phenol degrader Syntrophorhabdus was continuously present with abundances up to 11.5 %. The obtained results offer the possibility for the application of AnMBRs for the treatment of BFC or other petrochemical wastewater.

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.

Response of methanogenic system to long-term polycyclic aromatic hydrocarbon exposure: Adsorption and biodegradation, performance variation, and microbial function assessment

Phenanthrene (PHE) as a typical polycyclic aromatic hydrocarbon (PAH) is prevalent and harmful to organisms in petroleum-polluted sites. The effects of PHE concentration levels on performance, microbial community and functions in methanogenic system were comprehensively investigated by an operation of UASB reactor (198 days) and a series of batch tests. The results found that PHE was prone to accumulate in reactor by sludge adsorption (Final concentration = 12.53 mg/g TS Sludge), which posed significant influences on methanogenic system. The removal of chemical oxygen demand (COD), NH₄⁺-N and volatile fatty acids (VFAs) in reactor were reduced with PHE accumulation. Meanwhile, microbes with higher ATPase secrete more EPS activity to self-protect against PHE toxicity. Sequencing analysis showed that PHE interfered significantly diversity and structure of microbial community. For bacteria, PHE was toxic to Bacteroidetes and Latescibacteria, while syntrophs (f_Syntrophaceae, Syntrophorhabdus, etc.) involved in VFAs oxidation and aromatic organics degradation were tolerant of PHE stress. For archaea, acetoclastic methanogens (Methanosaeta) abundance was continuously diminished by 45.1% under long-term PHE exposure. Further functions analysis suggested that microbial community accelerated amino acid metabolism, energy metabolism and xenobiotics biodegradation & metabolism to satisfy physiological demanding under PHE stress. Combining batch tests of methanogenic metabolism proved that acetoclastic methanogenesis was negatively affected by PHE due to inhibition of functional enzymes (acetate kinase, phosphate acetyltransferase, etc.) expression. These findings may provide the basis for enhancing bioremediation of PAH pollution in anaerobic environment.

Microbial Communities of Seawater and Coastal Soil of Russian Arctic Region and Their Potential for Bioremediation from Hydrocarbon Pollutants

The development of Arctic regions leads to pollution of marine and coastal environments with oil and petroleum products. The purpose of this work was to determine the diversity of microbial communities in seawater, as well as in littoral and coastal soil, and the potential ability of their members to degrade hydrocarbons degradation and to isolate oil-degrading bacteria. Using high-throughput sequencing of the V4 region of the 16S rRNA gene, the dominance of bacteria in polar communities was shown, the proportion of archaea did not exceed 2% (of the total number of sequences in the libraries). Archaea inhabiting the seawater belonged to the genera Nitrosopumilus and Nitrosoarchaeum and to the Nitrososphaeraceae family. In the polluted samples, members of the Gammaproteobacteria, Alphaproteobacteria, and Actinomycetes classes predominated; bacteria of the classes Bacteroidia, Clostridia, Acidimicrobiia, Planctomycetia, and Deltaproteobacteria were less represented. Using the iVikodak program and KEGG database, the potential functional characteristics of the studied prokaryotic communities were predicted. Bacteria were potentially involved in nitrogen and sulfur cycles, in degradation of benzoate, terephthalate, fatty acids, and alkanes. A total of 19 strains of bacteria of the genera Pseudomonas, Aeromonas, Oceanisphaera, Shewanella, Paeniglutamicibacter, and Rhodococcus were isolated from the studied samples. Among them were psychrotolerant and psychrophilic bacteria growing in seawater and utilizing crude oil, diesel fuel, and motor oils. The data obtained suggest that the studied microbial communities could participate in the removal of hydrocarbons from arctic seawater and coastal soils and suggested the possibility of the application of the isolates for the bioaugmentation of oil-contaminated polar environments.

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.

Polycyclic aromatic hydrocarbon contamination in soils and sediments: Sustainable approaches for extraction and remediation

Polycyclic aromatic hydrocarbons (PAHs) are carcinogenic environmental pollutants that are extremely hydrophobic in nature and resistant to biological degradation. Extraction of PAHs from environmental matrices is the first and most crucial step in PAH quantification. Extraction followed by quantification is essential to understand the extent of contamination prior to the application of remediation approaches. Due to their non-polar structures, PAHs can be adsorbed tightly to the organic matter in soils and sediments, making them more difficult to be extracted. Extraction of PAHs can be achieved by a variety of methods. Techniques such as supercritical and subcritical fluid extraction, microwave-assisted solvent extraction, plant oil-assisted extraction and some microextraction techniques provide faster PAH extraction using less organic solvents, while providing a more environmentally friendly and safer process with minimum matrix interferences. More recently, more environmentally friendly methods for soil and sediment remediation have been explored. This often involves using natural chemicals, such as biosurfactants, to solubilize PAHs in contaminated soils and sediments to allow subsequent microbial degradation. Vermiremediation and microbial enzyme-mediated remediation are emerging approaches, which require further development. The following summarises the existing literature on traditional PAH extraction and bioremediation methods and contrasts them to newer, more environmentally friendly ways.

Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics

Environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams with high- and low-sulfate levels. An advanced subsurface environmental sampler allowed the establishment of coal-associated microbial communities under in situ conditions for metagenomic analyses from environmental and translationally active populations. Metagenomic sequencing demonstrated that biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways were present in active populations across the sampled coal seams. In particular, results suggested the importance of anaerobic degradation pathways under high-sulfate conditions with an emphasis on fumarate addition. Under low-sulfate conditions, a mixture of both aerobic and anaerobic pathways was observed but with a predominance of aerobic dioxygenases. The putative low-molecular-weight biosurfactant, lichysein, appeared to play a more important role compared to rhamnolipids. The methods used in this study—subsurface environmental samplers in combination with metagenomic sequencing of both total and translationally active metagenomes—offer a deeper and environmentally relevant perspective on community genetic potential from coal seams poised at different redox conditions broadening the understanding of degradation strategies for subsurface carbon.

Characterization of microbial communities and functions in shale gas wastewaters and sludge: Implications for pretreatment

As hydraulic fracturing (HF) practices keep expanding in China, a comparative understanding of biological characteristics of flowback and produced waters (FPW) and sludge in impoundments for FPW reserve will help propose appropriate treatment strategies. Therefore, in this study, the microbial communities and functions in impoundments that collected wastewaters from dozens of wells were characterized. The results showed that microbial richness and diversity were significantly increased in sludge compared with those in FPW. The vast majority of microorganisms found in FPW and sludge are organic degraders, providing the possibility of using these indigenous microorganisms to biodegrade organic compounds. Our laboratory findings first show that wastewater pretreatment using these microorganisms was effective, and organic compounds in FPW from different shale formations were removed by 35-68% within 72 h in a wide temperature range (8 - 30 ℃). Meanwhile, highly toxic compounds such as phthalate esters (PAEs), polycyclic aromatic hydrocarbons (PAHs), and petroleum hydrocarbons were effectively eliminated in reactors. The main microorganisms, key functional genes, and putative pathways for alkanes, PAHs, and PAEs degradation were also identified.

Definition of the Metagenomic Profile of Ocean Water Samples From the Gulf of Mexico Based on Comparison With Reference Samples From Sites Worldwide

Computational and statistical analysis of shotgun metagenomes can predict gene abundance and is helpful for elucidating the functional and taxonomic compositions of environmental samples. Gene products are compared against physicochemical conditions or perturbations to shed light on the functions performed by the microbial community of an environmental sample; however, this information is not always available. The present study proposes a method for inferring the metabolic potential of metagenome samples by constructing a reference based on determining the probability distribution of the counts of each enzyme annotated. To test the methodology, we used marine water samples distributed worldwide as references. Then, the references were utilized to compare the annotated enzymes of two different water samples extracted from the Gulf of Mexico (GoM) to distinguish those enzymes with atypical behavior. The enzymes whose annotation counts presented frequencies significantly different from those of the reference were used to perform metabolic reconstruction, which naturally identified pathways. We found that several of the enzymes were involved in the biodegradation of petroleum, which is consistent with the impact of human hydrocarbon extraction activity and its ubiquitous presence in the GoM. The examination of other reconstructed pathways revealed significant enzymes indicating the presence of microbial communities characterizing each ocean depth and ocean cycle, providing a fingerprint of each sampled site.

A review on the enzymes and metabolites identified by mass spectrometry from bacteria and microalgae involved in the degradation of high molecular weight PAHs

High molecular weight PAHs (HMW PAHs) are dangerous pollutants widely distributed in the environment. The use of microorganisms represents an important tool for HMW PAHs bioremediation, so, the understanding of their biochemical pathways facilitates the development of biodegradation strategies. For this reason, the potential role of species of microalgae, bacteria, and microalga-bacteria consortia in the degradation of HMW PAHs is discussed. The identification of their metabolites, mostly by GC-MS and LC-MS, allows a better approach to the enzymes involved in the key steps of the metabolic pathways of HMW PAHs biodegradation. So, this review intends to address the proteomic research on enzyme activities and their involvement in regulating essential biochemical functions that help bacteria and microalgae in the biodegradation processes of HMW PAHs. It is noteworthy that, given that to the best of our knowledge, this is the first review focused on the mass spectrometry identification of the HMW PAHs metabolites; whereby and due to the great concern of the presence of HMW PAHs in the environment, this material could help the urgency of developing new bioremediation methods. The elucidation of the metabolic pathways of persistent pollutant degrading microorganisms should lead to a better knowledge of the enzymes involved, which could contribute to a very ecological route to the control of environmental contamination in the future.

Anaerobic phenanthrene biodegradation by a newly isolated sulfate-reducer, strain PheS1, and exploration of the biotransformation pathway

Phenanthrene is a widespread and harmful polycyclic aromatic hydrocarbon that is difficult to anaerobically biodegrade. Current challenges in anaerobic phenanthrene bioremediation are a lack of degrading cultures and limited knowledge of biotransformation pathways. Under sulfate-reducing conditions, pure-cultures and biotransformation processes for anaerobic phenanthrene biodegradation are poorly understood. In this study, strain PheS1, which is phylogenetically closely related to Desulfotomaculum, was found to be a sulfate-reducing phenanthrene-degrading bacterium. Anaerobic phenanthrene biodegradation using PheS1 was proposed based on metabolite and genome analyses, and the initial step was identified as carboxylation based on the detection of 2-phenanthroic acid, [¹³C]-2-phenanthroic acid, and [D9]-2- phenanthroic acid when phenanthrene+HCO₃^-, phenanthrene+H¹³CO₃^-, and [D10]-phenanthrene+HCO₃^- were used as the substrate, respectively. PheS1 genome ubiD gene encoding of carboxylase putatively involved in the biodegradation was performed. Next, benzene ring reduction and cleavage that produced benzene compounds and cyclohexane derivative were reported to occur in the downstream biotransformation processes. Additionally, benzene, naphthalene, benz[a]anthracene, and anthracene can be utilised by PheS1, whereas pyrene and benz[a]pyrene cannot. We discovered a new phenanthrene-degrading sulfate-reducer and provided the anaerobic phenanthrene biotransformation pathway under sulfate-reducing conditions, which can act as a reference for practical applications in bioremediation and for studying the molecular mechanisms of phenanthrene in anaerobic zones.

Co-metabolic Effect of Glucose on Methane Production and Phenanthrene Removal in an Enriched Phenanthrene-Degrading Consortium Under Methanogenesis

Anaerobic digestion is used to treat diverse waste classes, and polycyclic aromatic hydrocarbons (PAHs) are a class of refractory compounds that common in wastes treated using anaerobic digestion. In this study, a microbial consortium with the ability to degrade phenanthrene under methanogenesis was enriched from paddy soil to investigate the cometabolic effect of glucose on methane (CH₄) production and phenanthrene (a representative PAH) degradation under methanogenic conditions. The addition of glucose enhanced the CH₄ production rate (from 0.37 to 2.25mg⋅L^-1⋅d^-1) but had no influence on the degradation rate of phenanthrene. Moreover, glucose addition significantly decreased the microbial α-diversity (from 2.59 to 1.30) of the enriched consortium but showed no significant effect on the microbial community (R ²=0.39, p=0.10), archaeal community (R ²=0.48, p=0.10), or functional profile (R ²=0.48, p=0.10). The relative abundance of genes involved in the degradation of aromatic compounds showed a decreasing tendency with the addition of glucose, whereas that of genes related to CH₄ synthesis was not affected. Additionally, the abundance of genes related to the acetate pathway was the highest among the four types of CH₄ synthesis pathways detected in the enriched consortium, which averagely accounted for 48.24% of the total CH₄ synthesis pathway, indicating that the acetate pathway is dominant in this phenanthrene-degrading system during methanogenesis. Our results reveal that achieving an ideal effect is diffcult via co-metabolism in a single-stage digestion system of PAH under methanogenesis; thus, other anaerobic systems with higher PAH removal efficiency should be combined with methanogenic digestion, assembling a multistage pattern to enhance the PAH removal rate and CH₄ production in anaerobic digestion.

Microbial community structure and co-occurrence are essential for methanogenesis and its contribution to phenanthrene degradation in paddy soil

Although polycyclic aromatic hydrocarbons (PAHs) degradation under methanogenesis is an ideal approach to remediating PAH-polluted soil, the contribution of methanogenesis to soil PAH elimination and the relationships between microbial ecological characteristics and PAH degradation during this process remain unclear. Here, we conducted a short-term (60 days) incubation using a paddy soil amended with phenanthrene and examined the effects of a specific methanogenic inhibitor (2-bromoethanesulfonate, BES) on this process. As treatment assessments, the methane production activity (MPA), phenanthrene degradation rate (PDR), and microbial ecological characteristics were determined. The results indicated that BES significantly inhibited both soil MPA and PDR, and we detected a positive relationship between MPA and PDR. Furthermore, BES significantly altered the soil microbial community structure, and it was the microbial community structure but not α-diversity was significantly correlated with soil MPA and PDR. BES decentralized the co-occurrence of bacterial genera but intensified the co-occurrence of methanogens. Moreover, certain bacterial taxa, including Bacteroidetes-vadinHA17, Gemmatimonas, and Sporomusaceae, were responsible for the MPA and PDR in this paddy soil. Collectively, these findings confirm the role of methanogenesis in PAH elimination from paddy soil, and reveal the importance of microbial co-occurrence characteristics in the determination of soil MPA and pollutant metabolism.

Efficient anaerobic bioremediation of high-concentration benzo[a]pyrene in marine environments

Benzo[a]pyrene (BaP), a persistent organic pollutant that may accumulate in sea sediments after oil spill or BaP chemical leakage accidents, considerably harms marine ecosystems and human health. Previous studies have been predominantly focused on its degradation at low concentrations, while the remediation of BaP pollution with high concentrations was neglected. Additionally, the metabolic pathways associated with its anaerobic degradation remain unclear. As a first attempt, super-efficient systems for BaP anaerobic degradation were established, and the corresponding metabolic pathways were elucidated in this study. The results showed that the BaP removal rate in BaP-only system with initial concentrations of 200 mg/L reached 3.09 mg/(L·d) within 45 days. Co-solvent, acetone promoted anaerobic BaP degradation (4.252 mg/(L·d)), while dichloromethane showed a newly-discovered co-metabolic effect. In the system with 500 mg/L of BaP and dichloromethane addition, the removal rate increased drastically (14.64 mg/(L·d)) at 400 mg/L turn point of BaP. Additionally, the corresponding microbial community-level metabolic network was firstly proposed.

Biodegradation potential of polycyclic aromatic hydrocarbons in Taihu Lake sediments

ABSTRACTTo assess the biodegradation potential of polycyclic aromatic hydrocarbons (PAHs) in sediments, sediment microcosms were constructed with sediments collected from six lake zones with different trophic statuses in Taihu Lake. The presence and concentration of PAH-degrading bacteria (PDB) were estimated by the most probable number (MPN) method. After 85 d of aerobic and anaerobic incubation, spiked PAHs (phenanthrene, pyrene, and benzo[a]pyrene) were partially degraded by indigenous sediment microorganisms. Large differences in PAH degradation were observed depending on the molecular size of the PAHs. The PAH removal efficiency in sediments under aerobic conditions was higher than that under anaerobic conditions. MPN analyses showed a higher abundance of degrading microflora in the high PAH-contaminated sites than in the low PAH-contaminated sites. Moreover, the anaerobic PDB populations in the sediments from the six different sites were much higher than those of aerobic PDB. The PAH biodegradation capability in sediments was associated with the geochemical conditions and bacterial populations. PDB showed a broad spatial distribution, thereby implying that they played an important role in the natural attenuation and cycling of PAHs in Taihu Lake. This work indicates that PAHs remain a concern in Taihu Lake sediments and can provide useful information for further bioremediation of PAH-contaminated sediments.

Understanding the fundamentals of microbial remediation with emphasize on metabolomics

The post-genomic tool metabolomics is a great advancement in science and technology which acquires novel strategies and pathways to analyze various biological compounds. Metabolomics aids in retrieving the qualitative and quantitative data from the various biological system. The current review is focused on the application of metabolomics in bioremediation and helps to focus on the xenobiotic compounds which are discharged into the environment and have long term impact. The microbial based biodegradation can be effectively used along with the combination of metabolomic approach for a better understanding of the breakdown of certain recalcitrant. Additionally, this review also discusses the candidate gene approach which helps to comprehend the functional analysis of microbial genes in response to different contaminants. Therefore, this review intends to discuss the metabolomics in bioremediation by studying the complete set of metabolites involved during the process of degradation and their interaction with the environment.

Investigation of anaerobic biodegradation of phenanthrene by a sulfate-dependent Geobacter sulfurreducens strain PheS2

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous and harmful contaminants, which can be degraded aerobically. However, the persistence of PAHs in anoxic environments indicates that anaerobic biodegradation of PAHs should also be investigated. Pure-culture and biotransformation processes for anaerobic phenanthrene biodegradation with sulfate as a terminal electron acceptor remains in its infancy. In this study, we investigated anaerobic biodegradation of PAHs by PheS2, an isolated phenanthrene-utilizing sulfate-reducer, using phenanthrene as a model compound. PheS2 was phylogenetically closely related to Geobacter sulfurreducens and reduced sulfate to sulfide during anaerobic phenanthrene biodegradation. Phenanthrene biodegradation processes were detected using gas chromatography-mass spectrometry, genome, and reverse transcription quantitative PCR analyses. Carboxylation was the initial step of anaerobic phenanthrene biodegradation based upon detection of 2- and 4-phenanthroic acid, its isotopically labeled analogs when using ¹³C-labeled bicarbonate and fully deuterated-phenanthrene (C14D10), and genes encoding enzymes putatively involved in the biodegradation. Further, ring-system reducing and cleavage occurred, and substituted benzene series and cyclohexane derivatives were detected in downstream biotransformation metabolites. Additionally, PheS2 can degrade benzene, naphthalene, anthracene, and benz[a]anthracene, but not pyrene and benz[a]pyrene. This study describes the isolation of an anaerobic phenanthrene-degrading sulfate-reducer, the first pure-culture evidence of phenanthrene biotransformation processes with sulfate as an electron acceptor.

Potential applications of halophilic microorganisms for biological treatment of industrial process brines contaminated with aromatics

Saline wastewater contaminated with aromatic compounds can be frequently found in various industrial sectors. Those compounds need to be degraded before reuse of wastewater in other process steps or release to the environment. Halophiles have been reported to efficiently degrade aromatics, but their application to treat industrial wastewater is rare. Halophilic processes for industrial wastewater treatment need to satisfy certain requirements: a continuous process mode, low operational expenditures, suitable reactor systems and a monitoring and control strategy. The aim of this review is to provide an overview of halophilic microorganisms, principles of aromatic biodegradation, and sources of saline wastewater containing aromatics and other contaminants. Finally, process examples for halophilic wastewater treatment and potential process monitoring strategies are discussed. To further illustrate the significant potential of halophiles for saline wastewater treatment and to facilitate development of ready-to-implement processes, future research should focus on scale-up and innovative process monitoring and control strategies.

Biocatalytic Reduction Reactions from a Chemist's Perspective

Reductions play a key role in organic synthesis, producing chiral products with new functionalities. Enzymes can catalyse such reactions with exquisite stereo-, regio- and chemoselectivity, leading the way to alternative shorter classical synthetic routes towards not only high-added-value compounds but also bulk chemicals. In this review we describe the synthetic state-of-the-art and potential of enzymes that catalyse reductions, ranging from carbonyl, enone and aromatic reductions to reductive aminations.

A Review and Bibliometric Analysis on Applications of Microbial Degradation of Hydrocarbon Contaminants in Arctic Marine Environment at Metagenomic and Enzymatic Levels

The globe is presently reliant on natural resources, fossil fuels, and crude oil to support the world’s energy requirements. Human exploration for oil resources is always associated with irreversible effects. Primary sources of hydrocarbon pollution are instigated through oil exploration, extraction, and transportation in the Arctic region. To address the state of pollution, it is necessary to understand the mechanisms and processes of the bioremediation of hydrocarbons. The application of various microbial communities originated from the Arctic can provide a better interpretation on the mechanisms of specific microbes in the biodegradation process. The composition of oil and consequences of hydrocarbon pollutants to the various marine environments are also discussed in this paper. An overview of emerging trends on literature or research publications published in the last decade was compiled via bibliometric analysis in relation to the topic of interest, which is the microbial community present in the Arctic and Antarctic marine environments. This review also presents the hydrocarbon-degrading microbial community present in the Arctic, biodegradation metabolic pathways (enzymatic level), and capacity of microbial degradation from the perspective of metagenomics. The limitations are stated and recommendations are proposed for future research prospects on biodegradation of oil contaminants by microbial community at the low temperature regions of the Arctic.

Exploration of the biotransformation processes in the biodegradation of phenanthrene by a facultative anaerobe, strain PheF2, with Fe(III) or O2 as an electron acceptor

The study of biodegradation of polycyclic aromatic hydrocarbons (PAHs) with metal ions as electron acceptors is still in its infancy. Here, a pure culture of PheF2 sharing 99.79% 16S rRNA-sequence similarity with Trichococcus alkaliphilus, which was recently reported to degrade PAHs, was isolated and found to degrade PAHs with Fe (III) or O₂ reduction. Phenanthrene was selected as a model of PAH to study the biodegradation process by PheF2 with Fe (III) or O₂ as an electron acceptor. PheF2 exhibited nearly 100%, 37.1%, and 28.5% anaerobic biodegradation of phenanthrene at initial concentrations of 280.7 μM, 280.6 μM, and 281.3 μM, respectively, within 10 days under anaerobic conditions with XAD-7 as a carrier, heptamethylnonane (HMN) as a solution, and nothing, respectively. PheF2 could degrade nearly 100% of the initial phenanthrene concentration of 283.4 μM under aerobic conditions within three days. The initial step of phenanthrene biodegradation by PheF2 involved carboxylation and dioxygenation under anaerobic and aerobic conditions, respectively. The biotransformation processes of phenanthrene degradation by PheF2 with Fe(III) or O₂ as an electron acceptor were explored by metabolite and genome analysis. These findings provide an important theoretical support for evaluation of PAHs fate and for PAHs pollution control or remediation in anaerobic and aerobic environments.

An underappreciated DIET for anaerobic petroleum hydrocarbon-degrading microbial communities

Direct interspecies electron transfer (DIET) via electrically conductive minerals can play a role in the anaerobic oxidation of petroleum hydrocarbons in contaminated sites and can be exploited for the development of new, more effective bioremediation approaches.

Nitrate-assisted biodegradation of polycyclic aromatic hydrocarbons (PAHs) in the water-level-fluctuation zone of the three Gorges Reservoir, China: Insights from in situ microbial interaction analyses and a microcosmic experiment

An increase in polycyclic aromatic hydrocarbon (PAH) pollution poses significant challenges to human and ecosystem health in the Three Gorges Reservoir (TGR) of the Yangtze River. Based on the combination of PAH analysis with qPCR and high-throughput sequencing of bacteria, 32 topsoil samples collected from 16 sites along the TGR were used to investigate the distribution and biodegradation pathways of PAHs in the water-level-fluctuation zone (WLFZ). The results indicated that the concentrations of PAHs were 43.8-228.2 and 30.8-206.3 ng/g soil (dry weight) under the high- and low-water-level (HWL and LWL) conditions, respectively. The PAH concentration in urban areas was higher than that in rural areas. Under both the HWL and LWL conditions, the abundance of the bamA gene, a biomarker of anaerobic PAH biodegradation, was significantly higher than that of the ring-hydroxylating-dioxygenase (RHD) gene, a biomarker of aerobic PAH biodegradation. The abundance of the bamA gene was significantly positively correlated with PAHs (R² = 0.8), and the biodegradation percentage of PAHs incubated anaerobically was greater than that in the aerobically incubated microcosm experiments. These data implicated a key role of the anaerobic pathway in PAH biodegradation. Co-occurrence network analysis suggested that anaerobic Anaerolineaceae, Dechloromonas, Bacteroidetes_vadin HA17 and Geobacter were key participants in the biodegradation of PAHs. The diversity analysis of functional bacteria based on the bamA gene and microcosm experiments further demonstrated that nitrate was the primary electron acceptor for PAH biodegradation. These findings provide a new perspective on the mechanism of PAH biodegradation in the TGR and knowledge that can be used to develop strategies for environmental management.

Current Status of and Future Perspectives in Bacterial Degradation of Benzo[a]pyrene

Benzo[a]pyrene (BaP) is one the main pollutants belonging to the high-molecular-weight PAHs (HMW-PAHs) class and its degradation by microorganisms remains an important strategy for its removal from the environment. Extensive studies have been carried out on the isolation and characterisation of microorganisms that can actively degrade low-molecular-weight PAHs (LMW-PAHs), and to a certain extent, the HMW-PAH pyrene. However, so far, limited work has been carried out on BaP biodegradation. BaP consists of five fused aromatic rings, which confers this compound a high chemical stability, rendering it less amenable to biodegradation. The current review summarizes the emerging reports on BaP biodegradation. More specifically, work carried out on BaP bacterial degradation and current knowledge gaps that limit our understanding of BaP degradation are highlighted. Moreover, new avenues of research on BaP degradation are proposed, specifically in the context of the development of "omics" approaches.

The 5,6,7,8-Tetrahydro-2-Naphthoyl-Coenzyme A Reductase Reaction in the Anaerobic Degradation of Naphthalene and Identification of Downstream Metabolites

Anaerobic degradation of polycyclic aromatic hydrocarbons has been investigated mostly with naphthalene as a model compound. Naphthalene degradation by sulfate-reducing bacteria proceeds via carboxylation to 2-naphthoic acid, formation of a coenzyme A thioester, and subsequent reduction to 5,6,7,8-tetrahydro-2-naphthoyl-coenzyme A (THNCoA), which is further reduced to hexahydro-2-naphthoyl-CoA (HHNCoA) by tetrahydronaphthoyl-CoA reductase (THNCoA reductase), an enzyme similar to class I benzoyl-CoA reductases. When analyzing THNCoA reductase assays with crude cell extracts and NADH as electron donor via liquid chromatography-mass spectrometry (LC-MS), scanning for putative metabolites, we found that small amounts of the product of an HHNCoA hydratase were formed in the assays, but the downstream conversion by an NAD+-dependent β-hydroxyacyl-CoA dehydrogenase was prevented by the excess of NADH in those assays. Experiments with alternative electron donors indicated that 2-oxoglutarate can serve as an indirect electron donor for the THNCoA-reducing system via a 2-oxoglutarate:ferredoxin oxidoreductase. With 2-oxoglutarate as electron donor, THNCoA was completely converted and further metabolites resulting from subsequent β-oxidation-like reactions and hydrolytic ring cleavage were detected. These metabolites indicate a downstream pathway with water addition to HHNCoA and ring fission via a hydrolase acting on a β'-hydroxy-β-oxo-decahydro-2-naphthoyl-CoA intermediate. Formation of the downstream intermediate cis-2-carboxycyclohexylacetyl-CoA, which is the substrate for the previously described lower degradation pathway leading to the central metabolism, completes the anaerobic degradation pathway of naphthalene.IMPORTANCE Anaerobic degradation of polycyclic aromatic hydrocarbons is poorly investigated despite its significance in anoxic sediments. Using alternative electron donors for the 5,6,7,8-tetrahydro-2-naphthoyl-CoA reductase reaction, we observed intermediary metabolites of anaerobic naphthalene degradation via in vitro enzyme assays with cell extracts of anaerobic naphthalene degraders. The identified metabolites provide evidence that ring reduction terminates at the stage of hexahydro-2-naphthoyl-CoA and a sequence of β-oxidation-like degradation reactions starts with a hydratase acting on this intermediate. The final product of this reaction sequence was identified as cis-2-carboxycyclohexylacetyl-CoA, a compound for which a further downstream degradation pathway has recently been published (P. Weyrauch, A. V. Zaytsev, S. Stephan, L. Kocks, et al., Environ Microbiol 19:2819-2830, 2017, https://doi.org/10.1111/1462-2920.13806). Our study reveals the first ring-cleaving reaction in the anaerobic naphthalene degradation pathway. It closes the gap between the reduction of the first ring of 2-naphthoyl-CoA by 2-napthoyl-CoA reductase and the lower degradation pathway starting from cis-2-carboxycyclohexylacetyl-CoA, where the second ring cleavage takes place.

Investigation of hydrolysis acidification process during anaerobic treatment of coal gasification wastewater (CGW): Evolution of dissolved organic matter and biotoxicity

Coal gasification wastewater (CGW) contains several types of aromatic pollutants, which impart high biotoxicity and reduce the quality of anaerobic treatment. Two types of hydrolysis acidification processes, namely microaerobic hybrid reactor (HA-1) and upflow anaerobic sludge blanket reactor (HA-2), were developed for pre-treatment before the anaerobic treatment. The changes in the dissolved organic matter and biotoxicity were investigated to comprehensively understand the degradation process. The results showed that HA-2 coupled with an anaerobic reactor achieved a 12.3% and 13.4% higher removal efficiency for chemical oxygen demand and total phenols, respectively, compared with the coupled process with HA-1. Furthermore, HA-2 could transform macromolecules into small molecules more efficiently and produce fewer intermediates. The coupled process with HA-2 preferentially removed complex aromatic substances with absorption wavelengths of 285 and 254 nm, according to the sequential orders interpreted from two-dimensional correlation spectroscopy. In addition, the results of fluorescence excitation-emission-matrix with regional integration analysis revealed that the contents of typical cyclic compounds in CGW, such as phenolic, heterocyclic, and polycyclic aromatic compounds were remarkably reduced by HA-2. In addition, HA-2 reduced the toxic unit value of CGW by 67.5% and increased the resazurin dehydrogenase activity of the sludge by 37.5% during CGW treatment, thus improving the biotoxicity removal and biodegradability. However, the coupled process with HA-2 did not significantly affect the "indirect estrogenic activity" of CGW. A Pearson correlation analysis indicated that spectral indicators, such as UV₂₅₄ and Φ_T,n, presented a high positive correlation with the reduction of acute toxicity and organics.

Anaerobic biodegradation of pyrene by Klebsiella sp. LZ6 and its proposed metabolic pathway

Pyrene is one of the polycyclic aromatic hydrocarbons, which are a potential threat to ecosystems due to their mutagenicity, carcinogenicity, and teratogenicity. In this study, several bacteria were isolated from oil contaminated sludge and their capacity to biodegrade pyrene was investigated. Of these bacteria, the monoculture strain LZ6 showed the highest pyrene anaerobic biodegradation rate of 33% after 30 days when the initial concentration was 50 mg/L, and was identified as Klebsiella sp. LZ6 by morphological observation, the GENIII technology of Biolog, and 16S rDNA gene sequence analysis. The influence of various culture parameters on the biodegradation of pyrene were evaluated, and Klebsiella sp. LZ6 all showed the high degradation rate at an inoculum of 10-20% (v/v), pH 6.0-8.4, temperature 30-38°C, and initial pyrene concentration of 50-150 mg/L. The intermediate metabolites of the anaerobic biodegradation were analyzed by GC-MS. Several metabolites were identified, such as pyrene, 4,5-dihydro-, phenanthrene, dibenzo-p-dioxin, and 4-hydroxycinnamate acid. The anaerobic metabolic pathway for the degradation of pyrene was inferred by the products. It seems that pyrene was first reduced to pyrene,4,5-dihydro- by the adding of two hydrogen atoms, and then the carbon-carbon bond cleavage at saturated carbon atoms generated phenanthrene.

Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis

Natural attenuation represents all processes that govern contaminant mass removal, which mainly occurs via microbial degradation in the environment. Although this process is intrinsic its rate and efficiency depend on multiple factors. This study aimed to characterize the microbial taxonomic and functional diversity in different aquifer sediments collected in the saturated zone and in situ microcosms (BACTRAP®s) amended with hydrocarbons (¹³C-labeled and non-labeled benzene, toluene and naphthalene) using 16S rRNA gene and "shotgun" Illumina high throughput sequencing at a jet-fuel contaminated site. The BACTRAP®s were installed to assess hydrocarbon metabolism by native bacteria. Results indicated that Proteobacteria, Actinobacteria and Firmicutes were the most dominant phyla (~98%) in the aquifer sediment samples. Meanwhile, in the benzene- and toluene-amended BACTRAP®s the phyla Firmicutes and Proteobacteria accounted for about 90% of total community. In the naphthalene-amended BACTRAP®, members of the SR-FBR-L83 family (Order Ignavibacteriales) accounted for almost 80% of bacterial community. Functional annotation of metagenomes showed that only the sediment sample located at the source zone border and with the lowest BTEX concentration, has metabolic potential to degrade hydrocarbons aerobically. On the other hand, in situ BACTRAP®s allowed enrichment of hydrocarbon-degrading bacteria. Metagenomic data suggest that fumarate addition is the main mechanism for hydrocarbon activation of toluene. Also, indications for methylation, hydroxylation and carboxylation as activation mechanisms for benzene anaerobic conversion were found. After 120 days of exposure in the contaminated groundwater, the isotopic analysis of fatty acids extracted from BACTRAP®s demonstrated the assimilation of isotopic labeled compounds in the cells of microbes expressed by strong isotopic enrichment. We propose that the microbiota in this jet-fuel contaminated site has metabolic potential to degrade benzene and toluene by a syntrophic process, between members of the families Geobacteraceae and Peptococcaceae (genus Pelotomaculum), coupled to nitrate, iron and/or sulfate reduction.

Investigation of anaerobic phenanthrene biodegradation by a highly enriched co-culture, PheN9, with nitrate as an electron acceptor

In this study, we developed a highly enriched phenanthrene-degrading co-culture, PheN9, which uses nitrate as an electron acceptor under anaerobic conditions, and the processes mediating biodegradation were proposed. The dominant bacteria populations included Pseudomonas stutzeri (91.7% relative abundance), which shared 98% 16S rRNA-sequence similarity with the naphthalene-degrading, nitrate-reducing strain NAP-3-1, and Candidatus_Kuenenia (2.3% relative abundance), which is a type of anammox bacteria. Enrichment transformed 54% of the added phenanthrene, reduced nitrate, and generated significant amounts of nitrite. Enrichment also result in partial consumption of the produced nitrite by the anammox bacteria. The key initial steps of anaerobic phenanthrene biodegradation by PheN9 were methylation and carboxylation, which were identified for detection of metabolic products, as well as carboxylase and methyltransferase activities. The methylation product was then oxidized to 2-naphthoic acid and then underwent sequential biodegradation steps. Then, ring-system reducing occurred, and the metabolic products were identified as dihydro-, tetrahydro-, hexahydro-, and octahydro-2-phenanthroic acid. Downstream degradation proceeded via a substituted benzene series and cyclohexane derivatives. This study employed anaerobic phenanthrene-biodegradation processes with nitrate as an electron acceptor. These findings can improve our understanding of anaerobic polycyclic aromatic hydrocarbon (PAH) biodegradation processes and guide PAH bioremediation by adding nitrate to anaerobic environments.

Highly efficient anaerobic co-degradation of complex persistent polycyclic aromatic hydrocarbons by a bioelectrochemical system

Polycyclic aromatic hydrocarbons (PAHs) that undergo long-distance migration and have strong biological toxicity are a great threat to the health of ecosystems. In this study, the biodegradation characteristics and combined effects of mixed PAHs in bioelectrochemical systems (BESs) were studied. The results showed that, compared with a mono-carbon source, low-molecular-weight PAHs (LMW PAHs)-naphthalene (NAP) served as the co-substrate to promote the degradation of phenanthrene (PHE) and pyrene (PYR). The maximum degradation rates of PHE and PYR were 89.20% and 51.40% at 0.2500 mg/L in NAP-PHE and NAP-PYR at the degradation time of 120 h, respectively. Intermediate products were also detected, which indicated that the appending of relatively LMW PAHs had different effects on the metabolism of high-molecular-weight PAHs (HMW PAHs). The microbe species under different substrates (NAP-B, PHE-B, PYR-B, NAP-PHE, NAP-PYR, PHE-PYR) are highly similar, although the structure of the microbial community changed on the anode in the BES. In this study, the degradation regularity of mixed PAHs in BES was studied and provided theoretical guidance for the effective co-degradation of PAHs in the environment.

Anaerobic Microbial Degradation of Polycyclic Aromatic Hydrocarbons: A Comprehensive Review

Polycyclic aromatic hydrocarbons (PAHs) are a class of hazardous organic contaminants that are widely distributed in nature, and many of them are potentially toxic to humans and other living organisms. Biodegradation is the major route of detoxification and removal of PAHs from the environment. Aerobic biodegradation of PAHs has been the subject of extensive research; however, reports on anaerobic biodegradation of PAHs are so far limited. Microbial degradation of PAHs under anaerobic conditions is difficult because of the slow growth rate of anaerobes and low energy yield in the metabolic processes. Despite the limitations, some anaerobic bacteria degrade PAHs under nitrate-reducing, sulfate-reducing, iron-reducing, and methanogenic conditions. Anaerobic biodegradation, though relatively slow, is a significant process of natural attenuation of PAHs from the impacted anoxic environments such as sediments, subsurface soils, and aquifers. This review is intended to provide comprehensive details on microbial degradation of PAHs under various reducing conditions, to describe the degradation mechanisms, and to identify the areas that should receive due attention in further investigations.

Co-occurrence patterns of the microbial community in polycyclic aromatic hydrocarbon-contaminated riverine sediments

Understanding environmental and spatial gradient influences on sediment microbial communities, especially the communities of highly contaminated subsurface sediments, has received great attention with respect to natural attenuation and bioremediation. Here, we investigated the spatial variation and the co-occurrence patterns of microbial communities in polycyclic aromatic hydrocarbon (PAH)-contaminated riverine sediments by using spatial-series 16S rRNA gene data. The results showed that species from the surface and subsurface sediment samples tended to show greater co-occurrence patterns and facilitative interactions in the sediment microbial community as environmental severity increased. Microorganisms in the heavier PAH-contaminated sediment have stronger relationships and are more centrally clustered within the network compared to microorganisms in the lower PAH-contaminated sediment. The core communities harbored the keystone species (Dechloromonas, Crenothrix, Desulfuromonadales, Xanthomonadales, Anaerolineaceae and Dehalococcoidales), which responded to changes in the environmental and spatial gradients. The sediment PAH concentrations, ferrous iron and vertical distance were identified as the main drivers in determining the bacterial community assembly. The keystone species were linked to PAHs biodegradation coupled with iron cycling in sediments and could orchestrate core communities to perform ecosystem processes. Overall, these findings provide new insight into microbial community assembly and contribute to harnessing their functions in ecosystems for bioremediation.

Anaerobic bioaugmentation hydrolysis of selected nitrogen heterocyclic compound in coal gasification wastewater

Anaerobic bottle experiments were conducted in parallel for 120 consecutive days to perform the bioaugmentation hydrolysis of selected nitrogen heterocyclic compounds (NHCs) in coal gasification wastewater. Due to enhancement with PAC and Fe(OH)₃@PAC, quinoline, pyridine, and indole were hydrolyzed more effectively. The addition of PAC and Fe(OH)₃@PAC improved the coagulation capacity of microorganisms, which laid a solid foundation for the removal of selected NHCs and the adverse environmental conditions. Anaerobic degradation of the NHCs occurred first through hydrogenation, then through the opening of the nitrogen heterocycles, followed by the release of ammonia nitrogen and finally the opening of the benzene rings. Enriched Acinetobacter, Levilinea, Comamonas, and Longilinea were the main functional groups responsible for the anaerobic biodegradation of the selected NHCs.

Enhanced Anaerobic Biodegradation of Benzoate Under Sulfate-Reducing Conditions With Conductive Iron-Oxides in Sediment of Pearl River Estuary

Anaerobic biodegradation of aromatic compounds under sulfate-reducing conditions is important to marine sediments. Sulfate respiration by a single bacterial strain and syntrophic metabolism by a syntrophic bacterial consortium are primary strategies for sulfate-dependent biodegradation of aromatic compounds. The objective of this study was to investigate the potential of conductive iron oxides to facilitate the degradation of aromatic compounds under sulfate-reducing conditions in marine sediments, using benzoate as a model aromatic compound. Here, in anaerobic incubations of sediments from the Pearl River Estuary, the addition of hematite or magnetite (20 mM as Fe atom) enhanced the rates of sulfate-dependent benzoate degradation by 81.8 and 91.5%, respectively, compared with control incubations without iron oxides. Further experiments demonstrated that the rate of sulfate-dependent benzoate degradation accelerated with increased magnetite concentration (5, 10, and 20 mM). The detection of acetate as an intermediate product implied syntrophic benzoate degradation pathway, which was also supported by the abundance of putative acetate- or/and H₂-utilizing sulfate reducers from microbial community analysis. Microbial reduction of iron oxides under sulfate-reducing conditions only accounted for 2–11% of electrons produced by benzoate oxidation, thus the stimulatory effect of conductive iron oxides on sulfate-dependent benzoate degradation was not mainly due to an increased pool of terminal electron acceptors. The enhanced rates of syntrophic benzoate degradation by the presence of conductive iron oxides probably resulted from the establishment of a direct interspecies electron transfer (DIET) between syntrophic partners. In the presence of magnetite, Bacteroidetes and Desulfobulbaceae with potential function of extracellular electron transfer might be involved in syntrophic benzoate degradation. Results from this study will contribute to the development of new strategies for in situ bioremediation of anaerobic sediments contaminated with aromatic compounds, and provide a new perspective for the natural attenuation of aromatic compounds in iron-rich marine sediments.

Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment

To advance understanding of the fate of hydrocarbons released from the Deepwater Horizon oil spill and deposited in marine sediments, this study characterized the microbial populations capable of anaerobic hydrocarbon degradation coupled with sulfate reduction in non-seep sediments of the northern Gulf of Mexico. Anaerobic, sediment-free enrichment cultures were obtained with either hexadecane or phenanthrene as sole carbon source and sulfate as a terminal electron acceptor. Phylogenetic analysis revealed that enriched microbial populations differed by hydrocarbon substrate, with abundant SSU rRNA gene amplicon sequences from hexadecane cultures showing high sequence identity (up to 98%) to Desulfatibacillum alkenivorans (family Desulfobacteraceae), while phenanthrene-enriched populations were most closely related to Desulfatiglans spp. (up to 95% sequence identity; family Desulfarculaceae). Assuming complete oxidation to CO₂, observed stoichiometric ratios closely resembled the theoretical ratios of 12.25:1 for hexadecane and 8.25:1 for phenanthrene degradation coupled to sulfate reduction. Phenanthrene carboxylic acid was detected in the phenanthrene-degrading enrichment cultures, providing evidence to indicate carboxylation as an activation mechanism for phenanthrene degradation. Metagenome-assembled genomes (MAGs) revealed that phenanthrene degradation is likely mediated by novel genera or families of sulfate-reducing bacteria along with their fermentative syntrophic partners, and candidate genes linked to the degradation of aromatic hydrocarbons were detected for future study.

Aerobic and anaerobic enrichment cultures highlight the pivotal role of facultative anaerobes in soil hydrocarbon degradation

Aliphatic and aromatic hydrocarbons are ubiquitous in the environment due to natural and anthropogenic processes. Under aerobic conditions hydrocarbons can be rapidly biodegraded but oxygenated environments often quickly become anaerobic when microbial respiration is coupled to contaminant oxidation. Most studies in literature usually focus on the initial microbial diversity of the hydrocarbon impacted environment and examine either aerobic or anaerobic conditions for enrichment. Hence, the aim of the present study was to enrich bacterial consortiums from two diesel impacted soil samples under both these conditions to assess the enrichment diversities and hydrocarbon degradation potentials. This would shed light upon how an environmental population shift would correlate to oxygen intrusion and depletion and still continue hydrocarbon degradation. Analysis of the 16S rRNA gene sequences showcases the different microbial populations that could emerge as the environmental factors change, resulting in different populations that are still capable of hydrocarbon degradation. Microbial diversity analysis also highlights the role of facultative anaerobic bacteria like Pseudomonas spp. and Citrobacter spp. in maintaining hydrocarbon degradation. This study shows that microorganisms capable of surviving under both oxic and anoxic (aerobic and anaerobic) conditions are the most crucial to the long term degradation of hydrocarbons in the environment.

Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation

Despite the significance of biogenic methane generation in coal beds, there has never been a systematic long-term evaluation of the ecological response to biostimulation for enhanced methanogenesis in situ. Biostimulation tests in a gas-free coal seam were analysed over 1.5 years encompassing methane production, cell abundance, planktonic and surface associated community composition and chemical parameters of the coal formation water. Evidence is presented that sulfate reducing bacteria are energy limited whilst methanogenic archaea are nutrient limited. Methane production was highest in a nutrient amended well after an oxic preincubation phase to enhance coal biofragmentation (calcium peroxide amendment). Compound-specific isotope analyses indicated the predominance of acetoclastic methanogenesis. Acetoclastic methanogenic archaea of the Methanosaeta and Methanosarcina genera increased with methane concentration. Acetate was the main precursor for methanogenesis, however more acetate was consumed than methane produced in an acetate amended well. DNA stable isotope probing showed incorporation of ¹³C-labelled acetate into methanogenic archaea, Geobacter species and sulfate reducing bacteria. Community characterisation of coal surfaces confirmed that methanogenic archaea make up a substantial proportion of coal associated biofilm communities. Ultimately, methane production from a gas-free subbituminous coal seam was stimulated despite high concentrations of sulfate and sulfate-reducing bacteria in the coal formation water. These findings provide a new conceptual framework for understanding the coal reservoir biosphere.

Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons under anaerobic conditions: Overview of studies, proposed pathways and future perspectives

The biodegradation of low- and high-molecular-weight polycyclic aromatic hydrocarbons (PAHs) (LWM-PAHs and HMW-PAHs, respectively) has been studied extensively under aerobic conditions. Molecular O₂ plays 2 critical roles in this biodegradation process. O₂ activates the aromatic rings through hydroxylation prior to ring opening and serves as a terminal electron acceptor (TEA). However, several microorganisms have devised ways of activating aromatic rings, leading to ring opening (and thus biodegradation) when TEAs other than O₂ are used (under anoxic conditions). These microorganisms belong to the sulfate-, nitrate-, and metal-ion-reducing bacteria and the methanogens. Although the anaerobic biodegradation of monocyclic aromatic hydrocarbons and LWM-PAH naphthalene have been studied, little information is available about the biodegradation of HMW-PAHs. This manuscript reviews studies of the anaerobic biodegradation of HMW-PAHs and identifies gaps that limit both our understanding and the efficiency of this biodegradation process. Strategies that can be employed to overcome these limitations are also discussed.

Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture

Polycyclic aromatic hydrocarbons (PAH) such as naphthalene are widespread, recalcitrant pollutants in anoxic and methanogenic environments. A mechanism catalyzing PAH activation under methanogenic conditions has yet to be discovered, and the microbial communities coordinating their metabolism are largely unknown. This is primarily due to the difficulty of cultivating PAH degraders, requiring lengthy incubations to yield sufficient biomass for biochemical analysis. Here, we sought to characterize a new methanogenic naphthalene-degrading enrichment culture using DNA-based stable isotope probing (SIP) and metagenomic analyses. 16S rRNA gene sequencing of fractionated DNA pinpointed an unclassified Clostridiaceae species as a putative naphthalene degrader after two months of SIP incubation. This finding was supported by metabolite and metagenomic evidence of genes predicted to encode for enzymes facilitating naphthalene carboxylic acid CoA-thioesterification and degradation of an unknown arylcarboxyl-CoA structure. Our findings also suggest a possible but unknown role for Desulfuromonadales in naphthalene degradation. This is the first reported functional evidence of PAH biodegradation by a methanogenic consortium, and we envision that this approach could be used to assess carbon flow through other slow growing enrichment cultures and environmental samples.

Sulfate-Reducing Naphthalene Degraders Are Picky Eaters

Polycyclic aromatic hydrocarbons (PAHs) are common organic contaminants found in anoxic environments. The capacity for PAH biodegradation in unimpacted environments, however, has been understudied. Here we investigate the enrichment, selection, and sustainability of a microbial community from a pristine environment on naphthalene as the only amended carbon source. Pristine coastal sediments were obtained from the Jacques Cousteau National Estuarine Research Reserve in Tuckerton, New Jersey, an ecological reserve which has no direct input or source of hydrocarbons. After an initial exposure to naphthalene, primary anaerobic transfer cultures completely degraded 500 µM naphthalene within 139 days. Subsequent transfer cultures mineralized naphthalene within 21 days with stoichiometric sulfate loss. Enriched cultures efficiently utilized only naphthalene and 2-methylnaphthalene from the hydrocarbon mixtures in crude oil. To determine the microorganisms responsible for naphthalene degradation, stable isotope probing was utilized on cultures amended with fully labeled ¹³C-naphthalene as substrate. Three organisms were found to unambiguously synthesize ¹³C-DNA from ¹³C-naphthalene within 7 days. Phylogenetic analysis revealed that 16S rRNA genes from two of these organisms are closely related to the known naphthalene degrading isolates NaphS2 and NaphS3 from PAH-contaminated sites. A third 16S rRNA gene was only distantly related to its closest relative and may represent a novel naphthalene degrading microbe from this environment.

Oxygenic denitrification for nitrogen removal with less greenhouse gas emissions: Microbiology and potential applications

Nitrogen pollution is a worldwide problem and has been extensively treated by canonical denitrification (CDN) process. However, the CDN process generates several issues such as intensive greenhouse gas (GHG) emissions. In the past years, a novel biological nitrogen removal (BNR) process of oxygenic denitrification (O2DN) has been proposed as a promising alternative to the CDN process. The classic denitrification four steps are simplified to three steps by O2DN bacteria without producing and releasing the intermediate nitrous oxide (N₂O), a potent GHG. In this article, we summarized the findings in previous literatures as well as our results, including involved microorganisms and metabolic mechanisms, functional genes and microbial detection, kinetics and influencing factors and their potential applications in wastewater treatment. Based on our knowledge and experience, the benefits and limitations of the current O2DN process were analyzed. Since O2DN is a new field in wastewater treatment, more research and application is required, especially the development of integrated processes and the quantitative assessment of the contribution of O2DN process in natural habitats and engineered systems.