Anaerobic biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by a facultative anaerobe Pseudomonas sp. JP1

Molecular and microbial insights towards anaerobic biodegradation of anionic polyacrylamide in oil sands tailings

Anionic polyacrylamide (A-PAM) is widely used as a flocculant in the management of oil sands tailings. Nevertheless, apprehensions arise regarding its potential biodegradation and environmental consequences within the context of oil sands tailings. Consequently, it is imperative to delve into the anaerobic biodegradation of A-PAM in oil sands tailings to gain a comprehensive understanding of its influence on tailings water quality. This work explored the dynamics of A-PAM biodegradation across concentrations: 50, 100, 250, 500, 1000, and 2000 mg/kg TS. The results showed a significant decrease in A-PAM concentration and molecular weight at lower concentrations (50 and 100 mg/kg TS) compared to higher ones, suggesting enhanced degradation efficiency. Likewise, the organic transformation and methane production exhibited dependency on A-PAM concentrations. The peak concentrations observed were 20.0 mg/L for volatile fatty acids (VFAs), 0.07 mg/L for acrylamide (AMD), and 8.9 mL for methane yield, with these maxima being recorded at 50 mg/kg TS. The biodegradation efficiency diminishes at higher concentrations of A-PAM, potentially due to the inhibitory effects of polyacrylic acid accumulation. A-PAM biodegradation under anaerobic condition did not contribute to acute toxicity or genotoxicity. SEM-EDS, FT-IR and XRD analyses further revealed that higher concentrations of A-PAM inhibited the biodegradation by altering floc structure and composition, thereby restricting the microbial activity. Major microorganisms, including Smithella, Candidatus_Cloacimonas, W5, XBB1006, and DMER64 were identified, highlighting A-PAM's dual role as a source of carbon and nitrogen under anaerobic conditions. The above findings from this research not only significantly advance understanding of A-PAM's environmental behavior but also contribute to the effective management practices in oil sands tailings.

Occurrence, removal, and risk assessment of polycyclic aromatic hydrocarbons and their derivatives in typical wastewater treatment plants

Wastewater treatment plants (WWTPs) have a certain removal capacity for polycyclic aromatic hydrocarbons (PAHs) and their derivatives, but some of them are discharged with effluent into the environment, which can affect the environment. Therefore, to understand the presence, sources, and potential risks of PAHs and their derivatives in WWTPs. Sixteen PAHs, three chlorinated polycyclic aromatic hydrocarbons (ClPAHs), three oxidized polycyclic aromatic hydrocarbons (OPAHs), and three methylated polycyclic aromatic hydrocarbons (MPAHs) were detected in the influent and effluent water of three WWTPs in China. The average concentrations of their influent ∑PAHs, ∑ClPAHs, ∑OPAHs, and ∑MPAHs ranged from 2682.50 to 2774.53 ng/L, 553.26-906.28 ng/L, 415.40-731.56 ng/L, and 534.04-969.83 ng/L, respectively, and the effluent concentrations ranged from 823.28 to 993.37 ng/L, 269.43-489.94 ng/L, 285.93-463.55 ng/L, and 376.25-512.34 ng/L, respectively. The growth of heat transport and industrial energy consumption in the region has a significant impact on the level of PAHs in WWTPs. According to the calculated removal efficiencies of PAHs and their derivatives in the three WWTPs (A, B, and C), the removal rates of PAHs and their derivatives were 69-72%, 62-71%, and 68-73%, respectively, and for the substituted polycyclic aromatic hydrocarbons (SPAHs), the removal rates were 41-49%, 31-40%, and 33-39%, respectively; moreover, the removal rates of PAHs were greater than those of SPAHs in the WWTPs. The results obtained via the ratio method indicated that the main sources of PAHs in the influent of WWTPs were the combustion of coal and biomass, and petroleum contamination was the secondary source. In risk evaluation, there were 5 compounds for which the risk quotient was considered high ecological risk. During chronic disease evaluation, there were 11 compounds with a risk quotient considered to indicate high risk. PAHs and SPAHs with high relative molecular masses in the effluent of WWTPs pose more serious environmental hazards than their PAHs counterparts.

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.

The discrepant metabolic pathways of PAHs by facultative anaerobic bacteria under aerobic and nitrate-reducing conditions

Studies regarding the facultative anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) were still in the initial stage. In this study, a facultative anaerobe which was identified as Bacillus Firmus and named as PheN7 was firstly isolated from the mixed petroleum-polluted soil samples using phenanthrene and nitrate as the solo carbon resource and electron acceptor under anaerobic condition. The degradation rates of PheN7 towards phenanthrene were detected as 33.17 μM/d, 13.81 μM/d and 7.11 μM/d at the initial phenanthrene concentration of 250.17 μM with oxygen, nitrate and sulfate as the electron acceptor, respectively. The metabolic pathways toward phenanthrene by PheN7 were deduced combining the metagenome analysis of PheN7 and intermediate metabolites of phenanthrene under aerobic and nitrate-reducing conditions. Dioxygenation and carboxylation were inferred as the initial activation reactions of phenanthrene degradation in these two pathways. This study highlighted the significance of facultative anaerobic bacteria in natural PAHs biodegradation, revealing the discrepant metabolic fates of PAHs by one solo bacteria under aerobic and anaerobic environments.

Effects of electron acceptors and donors on anaerobic biodegradation of PAHs in marine sediments

Polycyclic aromatic hydrocarbons (PAHs) are typical organic pollutants accumulated in the environment. PAHs' bioremediation in sediments can be promoted by adding electron acceptor (EA) and electron donor (ED). Bicarbonate and sulfate were chosen as two EAs, and acetate and lactate were selected as two EDs. Six groups of amendments were added into the sediments to access their role in the anaerobic biodegradation of five PAHs, containing phenanthrene, anthracene, fluoranthene, pyrene, and benzo[a]pyrene. The concentrations of PAHs, EAs and EDs, electron transport system activity, and microbial diversity were analyzed during 126-day biodegradation in serum bottles. The HA group (bicarbonate and acetate) achieved the maximum PAH degradation efficiency of 89.67 %, followed by the SL group (sulfate and lactate) with 87.10 %. As the main PAHs degrading bacteria, the abundance of Marinobacter in H group was 8.62 %, and the addition of acetate significantly increased the abundance of Marinobacter in the HA group by 75.65 %.

The negative effects of the excessive nitrite accumulation raised by anaerobic bioaugmentation on bioremediation of PAH-contaminated soil

Nitrite accumulation in anaerobic bioaugmentation and its side effects on remediation efficiency of polycyclic aromatic hydrocarbon (PAH)-contaminated soil were investigated in this study. Four gradient doses of PAH-degrading inoculum (10^4, 10^5, 10^6 and 10^7 cells/g soil) were separately supplied to the actual PAH-contaminated soil combining with nitrate as the biostimulant. Although bioaugmented with higher dose of inoculum could effectively improve the biodegradation efficiencies in the initial stage than sole nitrate addition but also accelerated the accumulation of nitrite in soil. The inhibition effects of nitrite swiftly occurred following the rapid accumulation of nitrite in each experiment group, restraining the PAH-degrading functionality by inhibiting the growth of total biomass and denitrifying functions in soil. This study revealed the side effects of nitrite accumulation raised by bioaugmentation on soil microorganisms, contributing to further improving the biodegrading efficiencies in the actual site restoration.

Degradation of Benzo[a]pyrene and 2,2',4,4'-Tebrabrominated Diphenyl Ether in Cultures Originated from an Agricultural Soil

Benzo[a]pyrene (BaP) and 2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) are common contaminants in the environment, posing a threat to the ecosystems and human health. Currently, information on the microbial metabolism of BaP and BDE-47 as well as the correlated bacteria is still limited. This research aimed to study the degradation of BaP and BDE-47 by enriched cultures originated from an agricultural soil in Tianjin (North China) and characterize the bacteria involved in the degradation. Two sets of experiments were set up with BaP and BDE-47 (2 mg/L) as the sole carbon source, respectively. The degradation of BaP and BDE-47 occurred at rate constants of 0.030 /d and 0.026 /d, respectively. For BaP, the degradation products included benzo[a]pyrene-9,10-dihydrodiol or its isomers, ben-zo(a)pyrene-7,8-dihydrodiol-9,10-epoxide, and cis-4 (8-hydroxypyrenyl-7)-2-oxo-3-butenoic acid. For BDE-47, the degradation products included 2,2',4-tribrominated diphenyl ether (BDE-17), 2,4-dibrominated diphenyl ether (BDE-7), and hydroxylated dibromodiphenyl ether. The bacterial community structures in the original soil, the BaP culture, and the BDE-47 culture were quite different. The richness and diversity of bacteria in the two cultures were much lower than that in the original soil, and the BaP culture had higher richness and diversity than the BDE-47 culture. In the BaP culture, multiple species such as Niabella (23.4%), Burkholderia-Caballeronia-Paraburkholderia (13.7%), Cupriavidus (8.3%), and Allorhizobi-um-Neorhizobium-Pararhizobium-Rhizobium (8.0%) were dominant. In the BDE-47 culture, an unassigned species in the Rhizobiaceae was dominant (82.3%). The results from this study provide a scientific basis for the risk assessment and bioremediation of BaP and/or BDE-47 in a contaminated environment.

Biodegradation of benzo[a]pyrene by a marine Chlorella vulgaris LH-1 with heterotrophic ability

In this study, a microalga, Chlorella vulgaris LH-1, with heterotrophic ability to degrade BaP was explored. The effect of BaP concentration on microalga growth was investigated, and the possible biodegradation mechanism of BaP was proposed. Results showed that low BaP concentration (<5 mg/L) had less negative influence on the growth of this microalga under mixotrophic condition, but high BaP concentration (>5 mg/L) had a significant inhibitory effect on its growth. During heterotrophic cultivation, low BaP concentration (<20 mg/L) promoted the growth of C. vulgaris LH-1, whereas high BaP concentration (>20 mg/L) inhibited its growth significantly. The degradation rates of mixotrophic and heterotrophic C. vulgaris LH-1 were 62.56 %-74.13 % and 52.07 %-71.67 %, respectively, when the BaP concentration ranged from 0.5 mg/L to 2 mg/L. The expression of functional enzyme genes of C. vulgaris LH-1 such as phenol 2-monooxygenase activity, protocatechuate 3,4-dioxygenase activity, catechol 1,2-dioxygenase activity, styrene degradation, and benzoate degradation were upregulated in the process of BaP degradation. C. vulgaris LH-1 may degrade BaP by monooxygenase and dioxygenase simultaneously. The degradation of BaP by this microalga under mixotrophic condition goes through the degradation pathway of phthalic acid, whereas it goes through the degradation pathway of benzoic acid under heterotrophic condition.

Cometabolic degradation of pyrene with phenanthrene as substrate: assisted by halophilic Pseudomonas stutzeri DJP1

At present, cometabolic degradation is an extensive method for the biological removal of high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) in the marine environment. However, due to the refractory to degradation and high toxicity, there are few studies on pyrene (PYR) cometabolic degradation with phenanthrene (PHE) as substrate. In this study, a Pseudomonas stutzeri DJP1 strain isolated from sediments was used in the cometabolic system of PHE and PYR. The biomass and the activity of key enzymes such as dehydrogenase and catechol 12 dioxygenase of strain were improved, but the enhancement of biotoxicity resulted in the inhibition of cometabolism simultaneously. Seven metabolites were identified respectively in PYR, PHE degradation cultures. It was speculated that the cometabolism of PHE and PYR had a common phthalic acid pathway, and the degradation pathway of PHE was included in the downstream pathway of PYR. The functional genes such as PhdF, NidD and CatA involved in DJP1 degradation were revealed by Genome analysis. This study provides a reference for the biodegradation of PYR and PHE in real marine environment.

Biodegradation mechanisms of polycyclic aromatic hydrocarbons: Combination of instrumental analysis and theoretical calculation

Polycyclic aromatic hydrocarbons (PAHs) are a common class of petroleum hydrocarbons, widely encountered in both environment and industrial pollution sources. Owing to their toxicity, environmental persistence, and potential bioaccumulation properties, a mounting interest has been kindled in addressing the remediation of PAHs. Biodegradation is widely employed for the removal and remediation of PAHs due to its low cost, lack of second-contamination and ease of operation. This paper reviews the degradation efficiency of degradation and the underlying mechanisms exhibited by algae, bacteria, and fungi in remediation. Additionally, it delved into the application of modern instrumental analysis techniques and theoretical investigations in the realm of PAH degradation. Advanced instrumental analysis methods such as mass spectrometry provide a powerful tool for identifying intermediates and metabolites throughout the degradation process. Meanwhile, theoretical calculations could guide the optimization of degradation processes by revealing the reaction mechanisms and energy changes in PAH degradation. The combined use of instrumental analysis and theoretical calculations allows for a comprehensive understanding of the degradation mechanisms of PAHs and provides new insights and approaches for the development of environmental remediation technologies.

Microbiome based approaches for the degradation of polycyclic aromatic hydrocarbons (PAHs): A current perception

Globally, polycyclic aromatic hydrocarbons (PAHs) pollution is primarily driven by their release into the air through various combustion processes, including burning fossil fuels such as coal, oil, and gas in motor vehicles, power plants, and industries, as well as burning organic matter like wood, tobacco, and food in fireplaces, cigarettes, and grills. Apart from anthropogenic pollution sources, PAHs also occur naturally in crude oil, and their potential release during oil extraction, refining processes, and combustion further contributes to contamination and pollution concerns. PAHs are resistant and persistent in the environment because of their inherent features, viz., heterocyclic aromatic ring configurations, hydrophobicity, and thermostability. A wide range of microorganisms have been found to be effective degraders of these recalcitrant contaminants. The presence of hydrocarbons as a result of numerous anthropogenic activities is one of the primary environmental concerns. PAHs are found in soil, water, and the air, making them ubiquitous in nature. The presence of PAHs in the environment creates a problem, as their presence has a detrimental effect on humans and animals. For a variety of life forms, PAH pollutants are reported to be toxic, carcinogenic, mutation-inducing, teratogenic, and immune toxicogenics. Degradation of PAHs via biological activity is an extensively used approach in which diverse microorganisms (fungal, algal, clitellate, and protozoan) and plant species and their derived composites are utilized as biocatalysts and biosurfactants. Some microbes have the ability to transform and degrade these PAHs, allowing them to be removed from the environment. The goal of this review is to provide a critical overview of the existing understanding of PAH biodegradation. It also examines current advances in diverse methodologies for PAH degradation in order to shed light on fundamental challenges and future potential.

Anaerobic biodegradation of pyrene and benzo[a]pyrene by a new sulfate-reducing Desulforamulus aquiferis strain DSA

The study of anaerobic high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) biodegradation under sulfate-reducing conditions by microorganisms, including microbial species responsible for biodegradation and relative metabolic processes, remains in its infancy. Here, we found that a new sulfate-reducer, designated as Desulforamulus aquiferis strain DSA, could biodegrade pyrene and benzo[a]pyrene (two kinds of HMW-PAHs) coupled with the reduction of sulfate to sulfide. Interestingly, strain DSA could simultaneously biodegrade pyrene and benzo[a]pyrene when they co-existed in culture. Additionally, the metabolic processes for anaerobic pyrene and benzo[a]pyrene biodegradation by strain DSA were newly proposed in this study based on the detection of intermediates, quantum chemical calculations and analyses of the genome and RTqPCR. The initial activation step for anaerobic pyrene and benzo[a]pyrene biodegradation by strain DSA was identified as the formation of pyrene-2-carboxylic acid and benzo[a]pyrene-11-carboxylic acid by carboxylation Thereafter, CoA ligase, ring reduction through hydrogenation, and ring cracking occurred, and short-chain fatty acids and carbon dioxide were identified as the final products. Additionally, DSA could also utilize benzene, naphthalene, anthracene, phenanthrene, and benz[a]anthracene as carbon sources. Our study can provide new guidance for the anaerobic HMW-PAHs biodegradation under sulfate-reducing conditions.

Microbial-assisted phytodegradation for the amelioration of pyrene-contaminated soil using Pseudomonas aeruginosa and Aspergillus oryzae with alfalfa and sunflower

Environmental pollution caused by polycyclic aromatic hydrocarbons (PAHs) jeopardizes nature. PAHs are the most toxic, mutagenic, and carcinogenic pollutants and their cleanup is important for the environment. In the current research, to assess and evaluate three remediation strategies for pyrene removal from the soil, a pot experiment was performed: (a) bioremediation with Pseudomonas aeruginosa and Aspergillus oryzae, (b) phytoremediation with sunflower (Helianthus annuus) and alfalfa (Medicago sativa L.) and (c) microbial-assisted phytoremediation for the treatment of pyrene (700 mg kg-1). Results depict that P. aeruginosa significantly promoted the growth and tolerance of taken plants and reduced pyrene concentration in soil. Compared with those planted in pyrene-contaminated soil without inoculation. The highest percentage of pyrene removal was observed in P. aeruginosa inoculated alfalfa (91%), alfalfa inoculated with A. oryzae (83.96%), and without inoculation (78.20%). Moreover, alfalfa planted in P. aeruginosa augmented soil had the highest dehydrogenase activity (37.83 μg TPF g-1 soil h-1), and fluorescein diacetate hydrolysis (91.67 μg fluorescein g-1 dry soil). DHA and FDA are the indicators of bioaugmentation influence on the indigenous microbial activity of contaminated soil. As a result of the findings, the rhizospheric association of plants and microbes is beneficial for pyrene removal. Therefore, P. aeruginosa-assisted phytodegradation might be a more successful remediation technique for pyrene-contaminated soil than bioremediation and phytodegradation solely.

Anaerobic biodegradation of polycyclic aromatic hydrocarbons

Although many anaerobic microorganisms that can degrade PAHs have been harnessed, there is still a large gap between laboratory achievements and practical applications. Here, we review the recent advances in the biodegradation of PAHs under anoxic conditions and highlight the mechanistic insights into the metabolic pathways and functional genes. Achievements of practical application and enhancing strategies of anaerobic PAHs bioremediation in soil were summarized. Based on the concerned issues during research, perspectives of further development were proposed including time-consuming enrichment, byproducts with unknown toxicity, and activity inhibition with low temperatures. In addition, meta-omics, synthetic biology and engineering microbiome of developing microbial inoculum for anaerobic bioremediation applications are discussed. We anticipate that integrating the theoretical research on PAHs anaerobic biodegradation and its successful application will advance the development of anaerobic bioremediation.

Biodegradation of benzo(a)pyrene by Pseudomonas strains, isolated from petroleum refinery effluent: Degradation, inhibition kinetics and metabolic pathway

Benzo(a)pyrene, a five-ring polyaromatic hydrocarbon, originating from coal tar, crude oil, tobacco, grilled foods, car exhaust etc, is highly persistent in the environment. It has been classified as a Group I carcinogen, as on its ingestion in human body, diol epoxide metabolites are generated, which bind to DNA causing mutations and eventual cancer. Among various removal methods, bioremediation is most preferred as it is a sustainable approach resulting in complete mineralization of benzo(a)pyrene. Therefore, in this study, biodegradation of benzo(a)pyrene was performed by two strains of Pseudomonas, i. e WDE11 and WD23, isolated from refinery effluent. Maximum benzo(a)pyrene tolerance was 250 mg/L and 225 mg/L against Pseudomonas sp. WD23 and Pseudomonas sp. WDE11 correspondingly. Degradation rate constants varied between 0.0468 and 0.0513/day at 50 mg/L with half-life values between 13.5 and 14.3 days as per first order kinetics, while for 100 mg/L, the respective values varied between 0.006 and 0.007 L/mg. day and 15.28-16.67 days, as per second order kinetics. The maximum specific growth rate of strains WDE11 and WD23 was 0.3512/day and 0.38/day accordingly, while concentrations over 75 mg/L had an inhibitory effect on growth. Major degradation metabolites were identified as dihydroxy-pyrene, naphthalene-1,2-dicarboxylic acid, salicylic acid, and oxalic acid, indicating benzo(a)pyrene was degraded via pyrene intermediates by salicylate pathway through catechol meta-cleavage. The substantial activity of the catechol 2,3 dioxygenase enzyme was noted during the benzo(a)pyrene metabolism by both strains with minimal catechol 1,2 dioxygenase activity. This study demonstrates the exceptional potential of indigenous Pseudomonas strains in complete metabolism of benzo(a)pyrene.

Nitrogen transformation promotes the anaerobic degradation of PAHs in water level fluctuation zone of the Three Gorges Reservoir in Yangtze River, China: Evidences derived from in-situ experiment

Polycyclic aromatic hydrocarbons (PAHs) pose a great threat to human health and ecological system safety. The interception of nitrogen is common found in the riparian zone. However, there is no evidence on how nitrogen addition affects the anaerobic degradation of PAHs in soil of the water-level-fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR) in Yangtze River, China. Here, we investigated the PAHs degradation rate, the variation of key functional genes and microbial communities after nitrogen addition in soil that experienced a flooding period of water-level-fluctuation. The results revealed that the ∑16PAHs were decreased 16.19 %-36.65 % and more 3-5-rings PAHs were biodegraded with nitrogen addition in WLFZ. The most genes involved in PAHs-anaerobic degradation and denitrification were up-regulated by nitrate addition, and phyla Firmicutes, Actinobacteria and Proteobacteria were more advantages in nitrogen addition groups. The Tax4Fun based genome function analysis revealed that the microbial activity of PAHs-degradation increased with nitrate addition. The co-occurrence network analysis indicated that nitrogen addition accelerated the metabolism of nitrogen and PAHs. It is the first time to provide the direct experimental evidences that nitrogen transformation in the WLFZ soil promotes anaerobic PAHs degradation. This work is of importance to understand the effect of nitrogen intercepted in the WLFZ soil of TGR in Yangtze River, China.

Novel synergistic metabolic processes for phenanthrene biodegradation by a nitrate-reducing phenanthrene-degrading culture and an anammox culture

The synergistic metabolism by anammox cultures and nitrate-reducers for anaerobic PAH biodegradation is largely unknown, including whether anammox culture and which kind of anammox bacterium can perform nitrogen metabolism in the anaerobic PAH biodegradation processes, the inhibitory effect of PAH on anammox activity and nitrite on PAH-degrading nitrate-reducers activity, and the synergistic metabolic processes. Herein, an anammox culture that can eliminate nitrite accumulation and decrease inorganic carbon emission during anaerobic phenanthrene (a model of PAH in this study) biodegradation, the synergistic mechanism for phenanthrene biodegradation by a nitrate-reducer and such anammox culture, and the inhibition effect of phenanthrene on such anammox culture and nitrite on a phenanthrene-degrading nitrate-reducer were newly discussed. The results showed that nitrite largely accumulated during anaerobic phenanthrene biodegradation (nitrate accumulation is a common phenomenon for the biodegradation of refractory matter, including PAHs, by nitrate-reducers) by a nitrate-reducer, PheN2, which mineralizes phenanthrene to inorganic carbon, and nitrite was verified as an inhibiting factor for further biodegradation. Anaerobic phenanthrene biodegradation rates and nitrite concentrations (0-7 mM) appeared to have a negative linear correlation. The anammox culture that mainly contained Candidatus Kuenenia was newly found to efficiently reduce nitrite accumulation and inorganic carbon emissions and significantly promote biodegradation efficiency by ∼1.94-fold. Our results showed that phenanthrene absorbed in and on anammox cells had a more direct relationship with the inhibitory effect on anammox activity than phenanthrene in the environment, and 15.2 mg/gVSS phenanthrene absorbed in and on the cells (4 mM concentration in the culture) showed nearly complete inhibition of anammox culture in this study. In addition, few (less than 2% abundance) anammox bacteria were found to be enough for the removal of nitrite produced from anaerobic phenanthrene biodegradation. In an ideal world, co-pollutants of ammonia, nitrate, phenanthrene, and nitrite could be converted to nitrogen gas and biomass by the synergistic metabolism of anammox cultures and nitrate reducers. Our study reveals a new synergistic process that may exist in our environments for PAH elimination by an anammox culture and a nitrate-reducer, which provides a new strategy for the bioremediation of PAH-polluted anoxic zones.

Coupling of Anammox Activity and PAH Biodegradation: Current Insights and Future Directions

Anaerobic ammonium oxidation (anammox) has shown success in past years for the treatment of municipal and industrial wastewater containing inorganic nutrients (i.e., nitrogen). However, the increase in polycyclic aromatic hydrocarbon (PAH)-contaminated matrices calls for new strategies for efficient and environmentally sustainable remediation. Therefore, the present review examined the literature on the connection between the anammox process and PAHs using VOSviewer to shed light on the mechanisms involved during PAH biodegradation and the key factors affecting anammox bacteria. The scientific literature thoroughly discussed here shows that PAHs can be involved in nitrogen removal by acting as electron donors, and their presence does not adversely affect the anammox bacteria. Anammox activity can be improved by regulating the operating parameters (e.g., organic load, dissolved oxygen, carbon-to-nitrogen ratio) and external supplementation (i.e., calcium nitrate) that promote changes in the microbial community (e.g., Candidatus Jettenia), favoring PAH degradation. The onset of a synergistic dissimilatory nitrate reduction to ammonium and partial denitrification can be beneficial for PAH and nitrogen removal.

Benzo[A]Pyrene Biodegradation by Multiple and Individual Mesophilic Bacteria under Axenic Conditions and in Soil Samples

To date, only a handful of bacterial strains that can independently degrade and utilize benzo[a]pyrene (BaP) as the sole carbon source has been isolated and characterized. Here, three new bacterial strains-JBZ1A, JBZ2B, and JBZ5E-were isolated from contaminated soil and, using 16S rRNA sequencing, were identified as Brad rhizobium japonicum, Micrococcus luteus, and Bacillus cereus, respectively. The growth ability of each individual strain and a consortium of all strains in the presence of BaP (4-400 µmol·L^-1, pH 7, 37 °C) was identified by the doubling time (dt). The results illustrate that dt decreased with increasing BaP concentrations for individual strains and the consortium. The optimum growth conditions of the consortium were 37 °C, 0.5% NaCl (w/v), and pH 7. Under these conditions, the degradation rate was 1.06 µmol·L^-1·day^-1, whereas that of individual strains ranged from 0.9 to 0.38 µmol·L^-1·day^-1. B. cereus had the strongest contribution to the consortium's activity, with a degradation rate of 0.9 µmol·L^-1·day^-1. The consortium could also remove BaP spiked with soil but at a lower rate (0.01 µmol L^-1.day^-1). High-performance liquid chromatography-high-resolution tandem mass spectrometry permitted the detection of the metabolites of these strains, and a biodegradation pathway is proposed.

The combined enhancement of RL, nZVI and AQDS on the microbial anaerobic-aerobic degradation of PAHs in soil

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous persistent organic pollutants in soil, which have carcinogenic, teratogenic and mutagenic hazards. The effects of rhamnolipid (RL), nano zero-valent iron (nZVI), and anthraquinone-2,6-disulfonic acid (AQDS) on the degradation of PAHs in soil were studied. It was found that the treatment of 5 mg·kg^-1RL + 1% nZVI +0.2 mmol·kg^-1AQDS had the highest degradation rate. The degradation rate of total PAHs and HMW-PAHs was 72.81% and 79.47% respectively after 90 days. High-throughput sequencing showed that in RL + nZVI + AQDS enhanced soil, Clostridium, Geobacter, Anaeromyxobacter and Sphingomonas were the dominant species for anaerobic degradation of PAHs. Rhodococcus, Nocardioides, and Microvirga are the dominant species for aerobic degradation of PAHs. The activities of methyltransferase, dehydrogenase and catechol 1,2-dioxygenase in the anaerobic-aerobic degradation process of PAHs were consistent with the degradation process of PAHs, indicating the role of these enzymes in the degradation of PAHs. RL, nZVI, and AQDS combined enhanced microbial anaerobic-aerobic degradation has great application potential in remediation of PAHs-contaminated soil.

Current and emerging trends in bioaugmentation of organic contaminated soils: A review

Organic contaminated soils constitute an important environmental problem, whereas field applicability of existing physical-chemical methods has encountered numerous obstacles, such as high chemical cost, large energy consumption, secondary pollution, and soil degradation. Bioaugmentation is an environmentally friendly and potentially economic technology that efficiently removes toxic pollutants from organic contaminated soils by microorganisms or their enzymes and bioremediation additives. This review attempted to explore the recent advances in bioaugmentation of organic contaminated soils and provided a comprehensive summary of various bioaugmentation methods, including bacterial, fungus, enzymes and bioremediation additives. The practical application of bioaugmentation is frequently limited by soil environmental conditions, microbial relationships, enzyme durability and remediation cycles. To tackle these problems, the future of bioaugmentation can be processed from sustainability of broad-spectrum bioremediation carriers, microbial/enzyme agents targeting combined contaminants, desorption of environmentally friendly additives and small molecular biological stimulants. Findings of this research are expected to provide new references for bioaugmentation methods that are practically feasible and economically potential.

Bioaugmentation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil with the nitrate-reducing bacterium PheN7 under anaerobic condition

The remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil under anaerobic condition is still a huge challenge. In this study, an anaerobic Bacillus firmus strain named PheN7 was firstly isolated from mixture of contaminated soil and sludge samples with phenanthrene as the sole carbon resource under nitrate reducing environment. The anaerobic strain was then inoculated combining with nitrate into the phenanthrene-spiked PAH-contaminated soil to investigate the remediation efficiency by anaerobic bioaugmentation (BA). Results showed that the synergy between PheN7 and indigenous degrading bacteria promoted the remediation efficiency of soil. The average removal efficiencies of phenanthrene in 56 days were 1.73 mg/kg soil·d in BA group, much higher than biostimulation group (sole nitrate addition) and natural degradation which achieved 1.48 mg/kg soil·d and 1.24 mg/kg soil·d of degradation rate, respectively. The outstanding adaptability of PheN7 made it become the dominant species in soil in the terminal period, but the invasion of PheN7 also resulted in the decline of diversity of the indigenous microbial community. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt 2) results showed that a series of functional genes encoding anaerobic phenanthrene degradation and nitrate reductase enzymes in soil were remarkably strengthened with the addition of PheN7. This study confirmed the contribution of PheN7 as the anaerobic inoculum in PAH-contaminated soil remediation, further evaluating the practical applicability of anaerobic bioaugmentation technology in on-site remediation of real PAH-contaminated sites.

Effect of terminal electron acceptors on the anaerobic biodegradation of PAHs in marine sediments

The existing polycyclic aromatic hydrocarbons (PAHs) in marine sediment has become a critical threat to biological security. Terminal electron acceptor (TEA) amendment has been applied as a potential strategy to accelerate bioremediation in sediment. HCO₃^-, NO₃^-, and SO₄^2- were separately added to anaerobic sediment system containing five kinds of PAH, namely, phenanthrene, anthracene, fluoranthene, pyrene and benzo(a)pyrene. PAH concentration, PAH metabolites, TEA concentration, and electron transport system (ETS) activity were investigated. The HCO₃^- amendment group achieved the max PAH degradation efficiency of 84.98 %. SO₄^2- group led to the highest benzo(a)pyrene removal rate of 69.26 %. NO₃^- had the lowest PAH degradation rate of 76.16 %. ETS activity test showed that NO₃^- significantly inhibited electron transport activity in the sediment. The identified PAH metabolites were the same in each group, including 4,5-dimethylphenanthrene, 3-acetylphenanthrene, 9,10-anthracenedione, pyrene-7-hydroxy-8-carboxylic acid, anthrone, and dibenzothiophene. After 126 d's anaerobic degradation at 25 °C, the utilization of HCO₃^- and SO₄^2- as selected TEAs promoted the PAH biodegradation performance better than the utilization of NO₃^-.

Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation

Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.

Exploration of the biotransformation of phenanthrene degradation coupled with methanogensis by metabolites and enzyme analyses

The ubiquitous environmental contaminants, polycyclic aromatic hydrocarbons (PAHs), can be aerobically biodegraded. Strategies for biodegradation of PAHs are needed for the persisted character of it in anoxic environments. In current study, we obtained a highly enriched anaerobic, PAHs-degrading co-culture DYM1, from petroleum-polluted soil. DYM1 significantly degrades a range of PAHs in 4 days without supplementary terminal electron acceptors. Co-culture DYM1 is consists of two microorganisms (a degrading bacterium Paracoccus sp. strain PheM1 and an aceticlastic methanogen Methanosaeta concilii.) that utilize different carbon sources in a syntrophic metabolic process of phenanthrene. About 93% of phenanthrene (104.5 μM) has been removed under methanogenic conditions after incubation with co-culture DYM1 for 4 d, and produced 33.68 μmol CH₄. Carboxylation, which is catalyzed by UbiD-like carboxylase, was proposed as the initial steps of methanogenic phenanthrene-degrading pathway based upon the detection of 2-phenanthroic acid and 4-phenanthrene acid. Reduction and hydration of the benzene rings were followed by the initial reaction. Hydrated phenanthroic acid metabolites were newly detected and characterized under anaerobic conditions. Anaerobic degradation of phenanthrene without terminal electron acceptor addition not only sheds light on a poorly understood and environmentally relevant biological process, but also supply a novel approach to recover the energy of toxic pollutant in forms of methane.

Microbe mediated remediation of dyes, explosive waste and polyaromatic hydrocarbons, pesticides and pharmaceuticals

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Environmental pollutants dyes, pesticides, pharmaceuticals, explosive waste and polyaromatic hydrocarbons.

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Environmental pollutants toxicity.

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Possible microbial biodegradation pathways of environmental pollutants.

Industrialization and human activities have led to serious effects on environment. With the progress taking place in the biodegradation field, it is important to summarize the latest advancement. In this review, we intend to provide insights on the recent progress on the biodegradation of environmental contaminants such as dyes, pesticides, pharmaceuticals, explosive waste and polyaromatic hydrocarbons by microorganisms. Along with the biodegradation of environmental contaminants, toxicity effects have also been discussed.

Fast biodegradation of long-alkanes by enhancing bacteria performance rate by per-oxidation

The long-alkanes biodegradation rate was generally found slow during widely used pre-oxidation combined with biodegradation for oil contamination treatment, resulting in long and unsustainable removal. In this study, different chitosan content was used to produce iron catalysts for pre-oxidation, and nutrients were added for the long-alkanes biodegradation experiment. Mechanism of Fenton pre-oxidation and improvement in the biodegradation rate of long-alkanes were studied by analyzing the change in organic matter and bacterial community structure, the amount and activity of bacteria in the biological stage, and the degradation amount long-alkanes hydrocarbon before and after pre-oxidation. Results showed that the destruction of bacteria greatly reduced when hydroxyl radical intensity decreased to 4.40 a.u.. Also, the proportion of humic acid-like was high (40.88%), and the community structure was slightly changed with the pre-oxidation for the fast biodegradation (FB) group. In the subsequent biodegradation, it was found that the degradation rate of each long-alkanes in the FB group increased significantly (C₃₀: 4.18-8.32 mg/(kg·d)) with the increase of the degradation of long-alkanes (10-50%). Further studies showed that the high nutrient dynamics (6.05 mg/(kg·d)) of the FB group resulted in high bacteria performance rate (0.53 mol CO₂ × log CFU/(10⁴ g² d)), which further accelerated the substrate transformation(41%). Therefore, the biodegradation rate of long-alkanes was increased (43.8 mg/(kg·d)) with the removal rate of long-alkanes of 76%. The half-life of long-alkanes for the FB group (64 d) was 33 d shorter than the slow biodegradation group (99 d). These results exhibited that pre-oxidation regulation can shorten the bioremediation cycle by improving the biodegradation rate of long-alkanes. This research has good engineering application value.

Performance and microbial community dynamics relationship within a step-feed anoxic/oxic/anoxic/oxic process (SF-A/O/A/O) for coking wastewater treatment

A step-feed anoxic/oxic/anoxic/oxic (SF-A/O/A/O) was developed and successfully applied to full-scale coking wastewater treatment. The performance and microbial community were evaluated and systematically compared with the anoxic/oxic/oxic (A/O/O) process. SF-A/OA/O process exhibited efficient removal of COD, NH₄⁺-N, TN, phenols, and cyanide with corresponding average effluent concentrations of 317.9, 1.8, 46.2, 1.1, and 0.2 mg·L^-1, respectively. In particular, the TN removal efficiency of A/O/O process was only 7.8%, with an effluent concentration of 300.6 mg·L^-1. Furthermore, polycyclic aromatic hydrocarbons with high molecular weight were the dominant compounds in raw coking wastewater, which were degraded to a greater extent in SF-A/OA/O. The abundance in Thiobacillus, SM1A02, and Thauera could be the main reason why SF-A/O/A/O was superior to A/O/O in treating TN. The microbial community structure of SF-A/O/A/O was similar among stages in system (P ≥ 0.05, Welch's t-test) and was less affected by environmental factors, which may have been one of the important factors in the system's strong stability.

Degradation of 2,4,6-Trinitrotoluene (TNT): Involvement of Protocatechuate 3,4-Dioxygenase (P34O) in Buttiauxella sp. S19-1

Extensive use and disposal of 2,4,6-trinitrotoluene (TNT), a primary constituent of explosives, pollutes the environment and causes severe damage to human health. Complete mineralization of TNT via bacterial degradation has recently gained research interest as an effective method for the restoration of contaminated sites. Here, screening for TNT degradation by six selected bacteria revealed that Buttiauxella sp. S19-1, possesses the strongest degrading ability. Moreover, BuP34O (a gene encoding for protocatechuate 3,4-dioxygenase—P34O, a key enzyme in the β-ketoadipate pathway) was upregulated during TNT degradation. A knockout of BuP34O in S19-1 to generate S-M1 mutant strain caused a marked reduction in TNT degradation efficiency compared to S19-1. Additionally, the EM1 mutant strain (Escherichia coli DH5α transfected with BuP34O) showed higher degradation efficiency than DH5α. Gas chromatography mass spectrometry (GC-MS) analysis of TNT degradation by S19-1 revealed 4-amino-2,6-dinitrotolune (ADNT) as the intermediate metabolite of TNT. Furthermore, the recombinant protein P34O (rP34O) expressed the activity of 2.46 µmol/min·mg. Our findings present the first report on the involvement of P34O in bacterial degradation of TNT and its metabolites, suggesting that P34O could catalyze downstream reactions in the TNT degradation pathway. In addition, the TNT-degrading ability of S19-1, a Gram-negative marine-derived bacterium, presents enormous potential for restoration of TNT-contaminated seas.

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.

Enhancing biomethane production and pyrene biodegradation by addition of bio-nano FeS or magnetic carbon during sludge anaerobic digestion

Pyrene exerts toxic effects on methanogens during anaerobic digestion of sludge, thus affecting the efficiency of sludge treatment. This study evaluated the facilitated direct interspecific electron transfer (DIET) between bacteria and methanogens when bio-nano FeS or magnetic carbon is added into anaerobic reactors. Results showed that adding 200 mg/L bio-nano FeS or magnetic carbon clearly reduced the accumulation of short-chain fatty acids and avoided acidification during 25 days of anaerobic digestion. The methane productions were 98.38 L/kg total solid (TS) and 73.69 L/kg TS in the bio-nano FeS and magnetic carbon systems, respectively, which accelerated methane production by 58.1% and 33.4%, respectively, compared with the control system (40.26 L/kg TS). The pyrene removal rates reached 77.5% and 72.1% in the bio-nano FeS and magnetic carbon systems, whereas it was only 40.8% in the control system. Analysis of microbial community structure revealed that methanogens (e.g. Methanosarcina and Methanosaeta) and extracellular electron-transfer bacteria (e.g. Pseudomonas, Cloastridia, and Synergistetes) were enriched in the reactors added with bio-nano FeS or magnetic carbon. This result indicates that the addition of bio-nano FeS or magnetic carbon may promote the activity and growth of microorganisms to improve the efficiency of methane production and pyrene degradation by enhancing DIET.

Aerobic and Anaerobic Bacterial and Fungal Degradation of Pyrene: Mechanism Pathway Including Biochemical Reaction and Catabolic Genes

Microbial biodegradation is one of the acceptable technologies to remediate and control the pollution by polycyclic aromatic hydrocarbon (PAH). Several bacteria, fungi, and cyanobacteria strains have been isolated and used for bioremediation purpose. This review paper is intended to provide key information on the various steps and actors involved in the bacterial and fungal aerobic and anaerobic degradation of pyrene, a high molecular weight PAH, including catabolic genes and enzymes, in order to expand our understanding on pyrene degradation. The aerobic degradation pathway by Mycobacterium vanbaalenii PRY-1 and Mycobactetrium sp. KMS and the anaerobic one, by the facultative bacteria anaerobe Pseudomonas sp. JP1 and Klebsiella sp. LZ6 are reviewed and presented, to describe the complete and integrated degradation mechanism pathway of pyrene. The different microbial strains with the ability to degrade pyrene are listed, and the degradation of pyrene by consortium is also discussed. The future studies on the anaerobic degradation of pyrene would be a great initiative to understand and address the degradation mechanism pathway, since, although some strains are identified to degrade pyrene in reduced or total absence of oxygen, the degradation pathway of more than 90% remains unclear and incomplete. Additionally, the present review recommends the use of the combination of various strains of anaerobic fungi and a fungi consortium and anaerobic bacteria to achieve maximum efficiency of the pyrene biodegradation mechanism.

Assessment of the Suitability of Melilotus officinalis for Phytoremediation of Soil Contaminated with Petroleum Hydrocarbons (TPH and PAH), Zn, Pb and Cd Based on Toxicological Tests

The article presents issues related to the possibility of using toxicological tests as a tool to monitor the progress of soil treatment contaminated with petroleum substances (TPH, PAH), Zn, Pb and Cd in bio-phytoremediation processes. In order to reduce the high content of petroleum pollutants (TPH = 56,371 mg kg⁻¹ dry mass, PAH = 139.3 mg kg⁻¹ dry mass), the technology of stepwise soil treatment was applied, including basic bioremediation and inoculation with biopreparations based of indigenous non-pathogenic species of bacteria, fungi and yeasts. As a result of basic bioremediation in laboratory conditions (ex-situ method), the reduction of petroleum pollutants TPH by 33.9% and PAH by 9.5% was achieved. The introduction of inoculation with biopraparation-1 prepared on the basis of non-pathogenic species of indigenous bacteria made it possible to reduce the TPH content by 86.3%, PAH by 40.3%. The use of a biopreparation-1 enriched with indigenous non-pathogenic species of fungi and yeasts in the third series of inoculation increased to an increase in the degree of biodegradation of aliphatic hydrocarbons with long carbon chains and PAH by a further 28.9%. In the next stage of soil treatment after biodegradation processes, which was characterized by an increased content of heavy metals (Zn, Pb, Cd) and naphthalene, chrysene, benzo(a)anthracene and benzo(ghi)perylene belonging to polycyclic aromatic hydrocarbons, phytoremediation with the use of Melilotus officinalis was applied. After the six-month phytoremediation process, the following was achieved: Zn content by 25.1%, Pb by 27.9%, Cd by 23.2% and TPH by 42.2% and PAH by 49.9%. The rate of removal of individual groups of hydrocarbons was in the decreasing order: C₁₂–C₁₈ > C₆–C₁₂ > C₁₈–C₂₅ > C₂₅–C₃₆. PAHs tended to be removed in the following order: chrysene > naphthalene > benzo(a)anthracene > benzo(ghi)perylene. The TF and BCF coefficients were calculated to assess the capacity of M. officinalis to accumulate metal in tissues, uptake from soil and transfer from roots to shoots. The values of TF translocation coefficients were, respectively, for Zn (0.44), Pb (0.12), Cd (0.40). The calculated BCF concentration factors (BCF_roots > BCF_shoots) show that heavy metals taken up by M. officinalis are mainly accumulated in the root tissues in the following order Zn > Pb > Cd, revealing a poor metal translocation from the root to the shoots. This process was carried out in laboratory conditions for a period of 6 months. The process of phytoremediation of contaminated soil using M. officinalis assisted with fertilization was monitored by means of toxicological tests: Microtox, Ostracodtoxkit F^TM, MARA and Phytotoxkit^TM. The performed phytotoxicity tests have indicated variable sensitivity of the tested plants on contaminants occurring in the studied soils, following the sequence: Lepidium sativum < Sorghum saccharatum < Sinapis alba. The sensitivity of toxicological tests was comparable and increased in the order: MARA < Ostracodtoxkit F^TM < Microtox. The results of the toxicological monitoring as a function of the time of soil treatment, together with chemical analyses determining the content of toxicants in soil and biomass M. officinalis, clearly confirmed the effectiveness of the applied concept of bioremediation of soils contaminated with zinc, lead and cadmium in the presence of petroleum hydrocarbons.

Anaerobic degradation of high-concentration polycyclic aromatic hydrocarbons (PAHs) in seawater sediments

Recurring oil spill accidents have been a global challenge and contribute to PAHs' heavy accumulation in marine sediments. The rapid bioremediation of PAHs with high concentrations in marine sediments has rarely been studied. In this study, four representative PAHs in crude oil were tested for fast anaerobic biodegradation. An efficient system for the anaerobic degradation of high-concentration PAHs was obtained using petroleum-acclimated marine sediments as inoculants in the treatment system. The degradation efficiencies of benzo[b]fluoranthene, benzo[a]pyrene, pyrene, and phenanthrene reached 0.21, 1.71, 3.89, and 4.10 mg/(L·d), respectively, which are 16, 2.8, 1.8, and 1.0 times higher than the reported values. Nitrate was preferred to sulfate as an electron acceptor. The acclimated sediment contains a high abundance of hydrocarbon-degrading bacteria. The number and diversity of species in the treatment system supplemented with PAHs decreased, but the abundance of some hydrocarbon-degrading bacteria and hydrocarbon-intermediate utilising bacteria increased, and ecological succession was observed.

Denitrification performance and bacterial flora analysis of immobilized denitrification filler in industrial wastewater

The study aimed at evaluating the nitrogen removal performance of the immobilized denitrification filler, and the influence of shock loading on the high-rate denitrification process. A pilot scale reactor was operated for treatment of aniline production wastewater. The nitrogen removal activity significantly increased in the continuous feed experiments, reaching 5.23 kg N m^-3 day^-1 on day 31 (30 °C) at Hydraulic Retention Time (HRT) = 10 h. In the impact experiment, the denitrification filler was inhibited by Free Nitrite Acid (FNA) when the shock load flowed 1.5 times into the bioreactor and recovered after the load was restored for 20 h. The high-throughput results demonstrated that the dominant position of the denitrifying bacteria further enhanced in a micro toxic and high-salinity environment, providing a basis for the dominance of the composite denitrifying bacteria and the efficacy of the immobilization technology.

Degradation of benzo[a]pyrene by halophilic bacterial strain Staphylococcus haemoliticus strain 10SBZ1A

The exploitation of petroleum oil generates a considerable amount of “produced water or petroleum waste effluent (PWE)” that is contaminated with polycyclic aromatic hydrocarbons (PAHs), including Benzo[a]pyrene (BaP). PWE is characterised by its high salinity, which can be as high as 30% NaCl, thus the exploitation of biodegradation to remove PAHs necessitates the use of active halophilic microbes. The strain 10SBZ1A was isolated from oil contaminated soils, by enrichment experiment in medium containing 10% NaCl (w/v). Homology analyses of 16S rRNA sequences identified 10SBZ1A as a Staphylococcus haemoliticus species, based on 99.99% homology (NCBI, accession number GI: MN388897). The strain could grow in the presence of 4–200 μmol l^-1 of BaP as the sole source of carbon, with a doubling time of 17–42 h. This strain optimum conditions for growth were 37 ^oC, 10% NaCl (w/v) and pH 7, and under these conditions, it degraded BaP at a rate of 0.8 μmol l^-1 per day. The strain 10SBZ1A actively degraded PAHs of lower molecular weights than that of BaP, including pyrene, phenanthrene, anthracene. This strain was also capable of removing 80% of BaP in the context of soil spiked with BaP (10 μmol l^-1 in 100 g of soil) within 30 days. Finally, a metabolic pathway of BaP was proposed, based on the identified metabolites using liquid chromatography-high resolution tandem mass spectrometry. To the best of our knowledge, this is the first report of a halophilic BaP degrading bacterial strain at salinity > 5% NaCl.

Occurrence and distribution of PAHs and microbial communities in nearshore sediments of the Knysna Estuary, South Africa

This study investigated the polycyclic aromatic hydrocarbons (PAHs) occurrence, and their impact on the microbial community and PAH-degrading genera and genes in the Knysna Estuary of South Africa. The results reveal that the estuary exhibits low PAH levels (114.1-356.0 ng g^-1). Ignavibacteriae and Deferribacteres, as well as Proteobacteria and Bacteroidetes, are keystone phyla. Among measured environmental factors, total organic carbon (TOC), nutrients such as nitrite and nitrate, metals as Al, Cr, Cu, Ni, Pb and Zn, and environmental properties (pH and salinity) are primary contributors to structuring the bacterial community assemblage. The abundance of alpha subunit genes of the PAH-ring hydroxylating dioxygenases (PAH-RHDα) of Gram-negative bacteria lies in the range of (2.0-4.2) × 10⁵ copies g^-1, while that of Gram-positive bacteria ranges from 3.0 × 10⁵ to 1.3 × 10⁷ copies g^-1. The PAH-degrading bacteria account for up to 0.1% of the bacterial community and respond mainly to nitrate, TOC and salinity, while PAHs at low concentration are not significant influencing factors. PAH degraders such as Xanthomonadales, Pseudomonas, and Mycobacterium, which play a central role in PAH-metabolization coupled with other biogeochemical processes (e.g. iron cycling), may contribute to maintaining a healthy estuarine ecosystem. These results are important for developing appropriate utilization and protection strategies for pristine estuaries worldwide.

Disentangling the Relative Roles of Vertical Transmission, Subsequent Colonizations, and Diet on Cockroach Microbiome Assembly

A multitude of factors affect the assemblies of complex microbial communities associated with animal hosts, with implications for community flexibility, resilience, and long-term stability; however, their relative effects have rarely been deduced. Here, we use a tractable lab model to quantify the relative and combined effects of parental transmission (egg case microbiome present/reduced), gut inocula (cockroach versus termite gut provisioned), and varying diets (matched or unmatched with gut inoculum source) on gut microbiota structure of hatchlings of the omnivorous cockroach Shelfordella lateralis using 16S rRNA gene (rDNA) amplicon sequencing. We show that the presence of a preexisting bacterial community via vertical transmission of microbes on egg cases reduces subsequent microbial invasion, suggesting priority effects that allow initial colonizers to take a strong hold and which stabilize the microbiome. However, subsequent inoculation sources more strongly affect ultimate community composition and their ecological networks, with distinct host-taxon-of-origin effects on which bacteria establish. While this is so, communities respond flexibly to specific diets in ways that consequently impact predicted community functions. In conclusion, our findings suggest that inoculations drive communities toward different stable states depending on colonization and extinction events, through ecological host-microbe relations and interactions with other gut bacteria, while diet in parallel shapes the functional capabilities of these microbiomes. These effects may lead to consistent microbial communities that maximize the extended phenotype that the microbiota provides the host, particularly if microbes spend most of their lives in host-associated environments.IMPORTANCE When host fitness is dependent on gut microbiota, microbial community flexibility and reproducibility enhance host fitness by allowing fine-tuned environmental tracking and sufficient stability for host traits to evolve. Our findings lend support to the importance of vertically transmitted early-life microbiota as stabilizers, through interactions with potential colonizers, which may contribute to ensuring that the microbiota aligns within host fitness-enhancing parameters. Subsequent colonizations are driven by microbial composition of the sources available, and we confirm that host-taxon-of-origin affects stable subsequent communities, while communities at the same time retain sufficient flexibility to shift in response to available diets. Microbiome structure is thus the result of the relative impact and combined effects of inocula and fluctuations driven by environment-specific microbial sources and digestive needs. These affect short-term community structure on an ecological time scale but could ultimately shape host species specificities in microbiomes across evolutionary time, if environmental conditions prevail.

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.

Microbial vanadate reduction coupled to co-metabolic phenanthrene biodegradation in groundwater

Vanadate [V(V)] and phenanthrene (PHE) commonly coexist in groundwater aquifer, posing potential threats to ecological environment and public health. However, little is known about the complicated biogeochemical processes involving microbial V(V) reduction coupled with co-metabolic PHE biodegradation. Herein we demonstrated that synchronous removal of V(V) and PHE could be realized under anaerobic condition. Complete V(V) removal and PHE degradation efficiency of 82.0 ± 0.8% were achieved in 7-d operation in batch experiment. 250-d continuous column experiment implied that hydrochemical condition affected V(V) and PHE removals. V(V) was reduced to insoluble vanadium (IV) and PHE was degraded into small molecule organics (e.g. salicylic acid). Geobacter and Acetobacterium used methanol and intermediates from PHE degradation as electron donors for V(V) reduction. PHE was decomposed by Mycobacterium and Clostridium with methanol as co-metabolic substrate and V(V) as electron acceptor. Genes encoding proteins for V(V) reduction (omcA, omcB and mtrC) and PHE degradation (phnAc) were upregulated. Cytochrome c and nicotinamide adenine dinucleotide promoted electron transfer for V(V) and PHE detoxification. Extracellular polymeric substances could bind V(V) and improve the bioavailability of PHE. Our findings provide a robust strategy for remediation of V(V) and PHE co-contaminated groundwater.

The Utility of Electrochemical Systems in Microbial Degradation of Polycyclic Aromatic Hydrocarbons: Discourse, Diversity and Design

Polycyclic aromatic hydrocarbons (PAHs), especially high molecular weight PAHs, are carcinogenic and mutagenic organic compounds that are difficult to degrade. Microbial remediation is a popular method for the PAH removal in diverse environments and yet it is limited by the lack of electron acceptors. An emerging solution is to use the microbial electrochemical system, in which the solid anode is used as an inexhaustible electron acceptor and the microbial activity is stimulated by biocurrent in situ to ensure the PAH removal and avoid the defects of bioremediation. Based on the extensive investigation of recent literatures, this paper summarizes and comments on the research progress of PAH removal by the microbial electrochemical system of diversified design, enhanced measures and functional microorganisms. First, the bioelectrochemical degradation of PAHs is reviewed in separate and mixed PAH degradation, and the removal performance of PAHs in different system configurations is compared with the anode modification, the enhancement of substrate and electron transfer, the addition of chemical reagents, and the combination with phytoremediation. Second, the key functional microbiota including PAH degrading microbes and exoelectrogens are overviewed as well as the reduced microbes without competitive advantage. Finally, the typical representations of electrochemical activity especially the internal resistance, power density and current density of systems and influence factors are reviewed with the correlation analysis between PAH removal and energy generation. Presently, most studies focused on the anode modification in the bioelectrochemical degradation of PAHs and actually more attentions need to be paid to enhance the mass transfer and thus larger remediation radius, and other smart designs are also proposed, especially that the combined use of phytoremediation could be an eco-friendly and sustainable approach. Additionally, exoelectrogens and PAH degraders are partially overlapping, but the exact functional mechanisms of interaction network are still elusive, which could be revealed with the aid of advanced bioinformatics technology. In order to optimize the efficacy of functional community, more advanced techniques such as omics technology, photoelectrocatalysis and nanotechnology should be considered in the future research to improve the energy generation and PAH biodegradation rate simultaneously.

Gas ebullition from petroleum hydrocarbons in aquatic sediments: A review

Gas ebullition in sediment results from biogenic gas production by mixtures of bacteria and archaea. It often occurs in organic-rich sediments that have been impacted by petroleum hydrocarbon (PHC) and other anthropogenic pollution. Ebullition occurs under a relatively narrow set of biological, chemical, and sediment geomechanical conditions. This process occurs in three phases: I) biogenic production of primarily methane and dissolved phase transport of the gases in the pore water to a bubble nucleation site, II) bubble growth and sediment fracture, and III) bubble rise to the surface. The rate of biogenic gas production in phase I and the resistance of the sediment to gas fracture in phase II play the most significant roles in ebullition kinetics. What is less understood is the role that substrate structure plays in the rate of methanogenesis that drives gas ebullition. It is well established that methanogens have a very restricted set of compounds that can serve as substrates, so any complex organic molecule must first be broken down to fermentable compounds. Given that most ebullition-active sediments are completely anaerobic, the well-known difficulty in degrading PHCs under anaerobic conditions suggests potential limitations on PHC-derived gas ebullition. To date, there are no studies that conclusively demonstrate that weathered PHCs can alone drive gas ebullition. This review consists of an overview of the factors affecting gas ebullition and the biochemistry of anaerobic PHC biodegradation and methanogenesis in sediment systems. We next compile results from the scholarly literature on PHCs serving as a source of methanogenesis. We combine these results to assess the potential for PHC-driven gas ebullition using energetics, kinetics, and sediment geomechanics analyses. The results suggest that short chain <C₁₀ alkanes are the only PHC class that alone may have the potential to drive ebullition, and that PHC-derived methanogenesis likely plays a minor part in driving gas ebullition in contaminated sediments compared to natural organic matter.

Anaerobic biodegradation of phenanthrene by a newly isolated nitrate-dependent Achromobacter denitrificans strain PheN1 and exploration of the biotransformation processes by metabolite and genome analyses

Polycyclic aromatic hydrocarbons (PAHs) are widespread and harmful contaminants and are more persistent under anaerobic conditions. The bioremediation of PAHs in anaerobic zones has been enhanced by treating the contamination with nitrate, which is thermodynamically favourable, cost-effective, and highly soluble. However, anaerobic PAHs biotransformation processes that employ nitrate as an electron acceptor have not been fully explored. In this study, we investigated the anaerobic biotransformation of PAHs by strain PheN1, a newly isolated phenanthrene-degrading denitrifier, using phenanthrene as a model compound. PheN1 is phylogenetically closely related to Achromobacter denitrificans and reduces nitrate to nitrite (not N₂ ) during the anaerobic phenanthrene degradation process. Phenanthrene biotransformation processes were detected using gas chromatography-mass spectrometry and were further examined by reverse transcription-quantitative PCR and genome analyses. Carboxylation and methylation were both found to be the initial steps in the phenanthrene degradation process. Downstream biotransformation processed benzene compounds and cyclohexane derivatives. This study describes the isolation of an anaerobic phenanthrene-degrading bacterium along with the pure-culture evidence of phenanthrene biotransformation processes with nitrate as an electron acceptor. The findings in this study can improve our understanding of anaerobic PAHs biodegradation processes and guide PAHs bioremediation by adding nitrate to anaerobic environments.

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.

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.

NarL, a Novel Repressor for CYP108j1 Expression during PAHs Degradation in Rhodococcus sp. P14

Rhodococcus sp. P14 was isolated from crude-oil-contaminated sediments, and a wide range of polycyclic aromatic hydrocarbons (PAHs) could be used as the sole source of carbon and energy. A key CYP450 gene, designated as cyp108j1 and involved in the degradation of PAHs, was identified and was able to hydroxylate various PAHs. However, the regulatory mechanism of the expression of cyp108j1 remains unknown. In this study, we found that the expression of cyp108j1 is negatively regulated by a LuxR (helix-turn-helix transcription factors in acyl-homoserine lactones-mediated quorum sensing) family regulator, NarL (nitrate-dependent two-component regulatory factor), which is located upstream of cyp108j1. Further analysis revealed that NarL can directly bind to the promoter region of cyp108j1. Mutational experiments demonstrated that the binding site between NarL and the cyp108j1 promoter was the palindromic sequence GAAAGTTG-CAACTTTC. Together, the finding reveal that NarL is a novel repressor for the expression of cyp108j1 during PAHs degradation.

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.

Application of independent immobilization in benzo[a]pyrene biodegradation by synthetic microbial consortium

Bioaugmentation is an effective approach to remove the benzo[a]pyrene (BaP) from the environment, while its effect depends on the functional stability of the inoculated microorganisms. The aim of this study is to develop an approach on reducing the mutual exclusion of bacteria in the synthetic consortium in BaP degradation. Eight BaP-degrading bacterial strains were isolated from an enrichment with BaP as the sole carbon source. Two strains of Cupriavidus spp. exhibited greater degradation capacity (3.02-3.30 mg L^-1 day^-1) and selected as the "good degraders" in the synthetic consortia. Because of the mutual exclusion, the BaP-degradation capacity was reduced (1.47-1.77 mg L^-1 day^-1) when the other strains were added into "good degraders" through directly mixing the inocula. This mutual exclusion was mitigated through independent immobilization, in which the strains were embedded in sodium alginate before constructing the consortium. The consortium constructed by independent immobilization exhibited comparable BaP-degradation capacity with the high efficient strains. Therefore, the independent immobilization can be an advanced approach in functional consortium synthesis.