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

Air-plant interaction and air-soil exchange of polycyclic aromatic hydrocarbons in a large human-influenced reservoir in southwest China

The Three Gorges Reservoir (TGR) is totally manmade, strongly influenced by anthropogenic activity, and lies on the upper reaches of Yangtze River. The periodic storage and discharge of water from the Three Gorges Dam could have altered the original air-plant/soil interactions of contaminants in TGR. Herein, paired atmospheric gas-particle, air-plant, and air-soil samples were collected to investigate the air-plant interaction and air-soil exchange of 16 USEPA priority polycyclic aromatic hydrocarbons (PAHs). The air-plant interaction based on McLachlan's framework to our datasets suggests that PAHs were absorbed via gaseous deposition that was restricted by the plant-gas dynamic equilibrium. The equilibrium indicates a dynamic balance between the gaseous phase and plant surface in PAH absorption. The main limiting factor influencing the PAH uptake was the plant species rather than the atmospheric PAH concentration. The air-soil exchange of PAHs exhibited a net volatilization flux of 16.71 ng/m2/d from the soil to the air based on annual average. There was more volatilization and less deposition in summer and more deposition and less volatilization in autumn and winter. The soil serves as a secondary source of atmospheric PAHs. As the first attempt on probing the multi-interface geochemical process of PAHs, this study highlights the influence of manual water level manipulation from the TGD and environmental factors (such as temperature, humidity, and soil properties) on the regional fate of PAHs in the TGR.

The promotion of the polycyclic aromatic hydrocarbons degradation mechanism by humic acid as electron mediator in a sediment microbial electrochemical system

To enhance the removal efficiencies of polycyclic aromatic hydrocarbons (PAHs) in sediments and to elucidate the mechanisms by which microbial electrochemical action aids in the degradation of PAHs, humic acid was used as an electron mediator in the microbial electrochemical system in this study. The results revealed that the addition of humic acids led to increases in the removal efficiencies of naphthalene, phenanthrene, and pyrene by 45.91%, 97.83%, and 85.56%, respectively, in areas remote from the anode, when compared to the control group. The investigation into the microbial community structure and functional attributes showed that the presence of humic acid did not significantly modify the microbial community composition or its functional expression at the anode. However, an examination of humic acid transformations demonstrated that humic acid extended the electron transfer range in sediment via the redox reactions of quinone and semiquinone groups, thereby facilitating the PAHs degradation within the sediment.

Spatial distribution of volatile organic compounds in contaminated soil and distinct microbial effect driven by aerobic and anaerobic conditions

The vertical distribution of 35 volatile organic compounds (VOCs) was investigated in soil columns from two obsolete industrial sites in Eastern China. The total concentrations of ΣVOCs in surface soils (0-20 cm) were 134-1664 ng g-1. Contamination of VOCs in surface soil exhibited remarkable variability, closely related to previous production activities at the sampling sites. Additionally, the concentrations of ΣVOCs varied with increasing soil depth from 0 to 10 m. Soils at depth of 2 m showed ΣVOCs concentrations of 127-47,389 ng g-1. Among the studied VOCs, xylene was the predominant contaminant in subsoils (2 m), with concentrations ranging from n.d. to 45,400 ng g-1. Chlorinated alkanes and olefins demonstrated a greater downward migration ability compared to monoaromatic hydrocarbons, likely due to their lower hydrophobicity. As a result, this vertical distribution of VOCs led to a high ecological risk in both the surface and deep soil. Notably, the risk quotient (RQ) of xylene in subsoil (2 m, RQ up to 319) was much higher than that in surface soil. Furthermore, distinct effects of VOCs on soil microbes were observed under aerobic and anaerobic conditions. Specifically, after the 30-d incubation of xylene-contaminated soil, Ilumatobacter was enriched under aerobic condition, whereas Anaerolineaceae was enriched under anaerobic condition. Moreover, xylene contamination significantly affected methylotrophy and methanol oxidation functions for aerobic soil (t-test, p < 0.05). However, aromatic compound degradation and ammonification were significantly enhanced by xylene in anaerobic soil (t-test, p < 0.05). These findings suggest that specific VOC compound has distinct microbial ecological effects under different oxygen content conditions in soil. Therefore, when conducting soil risk assessments of VOCs, it is crucial to consider their ecological effects at different soil depths.

Microbial community structure and metabolic profile of anthropized freshwater tributary channels from La Plata River, Argentina, to develop sustainable remediation strategies

Microbial communities from freshwater sediments are involved in biogeochemical cycles and they can be modified by physical and chemical changes in the environment. Linking the microbial community structure (MCS) with physicochemistry of freshwater courses allows a better understanding of its ecology and can be useful to assess the ecological impact generated by human activity. The MCS of tributary channels from La Plata River affected by oil refinery (C, D, and E) and one also by urban discharges (C) was studied. For this purpose, 16S rRNA metabarcoding analysis, in silico metagenome functional prediction, and the hydrocarbon degradation potential (in silico predictions of hydrocarbon-degrading genes and their quantification by qPCR) of the MCS were studied. Principal coordinate analysis revealed that the MCS was different between sites, and it was not structured by the hydrocarbon content. Site C showed physicochemical characteristics, bacterial taxa, and an in silico functional prediction related to fermentative/heterotrophic metabolism. Site D, despite having higher concentration of hydrocarbon, presented autotrophic, syntrophic, and methanogenic pathways commonly involved in natural processes in anoxic sediments. Site E showed and intermediate autotrophic/heterotrophic behavior. The hydrocarbon degradation potential showed no positive correlation between the hydrocarbon-degrading genes quantified and predicted. The results suggest that the hydrocarbon concentration in the sites was not enough selection pressure to structure the bacterial community composition. Understanding which is the variable that structures the bacterial community composition is essential for monitoring and designing of sustainable management strategies for contaminated freshwater ecosystems.

Interaction patterns and keystone taxa of bacterial and eukaryotic communities during sulfamethoxazole mineralization in lake sediment

Sulfamethoxazole (SMX) is a common antibiotic pollutant in aquatic environments, which is highly persistent under various conditions and significantly contributes to the spread of antibiotic resistance. Biodegradation is the major pathway to eliminate antibiotics in the natural environment. The roles of bacteria and eukaryotes in the biodegradation of antibiotics have received considerable attention; however, their successions and co-occurrence patterns during the biodegradation of antibiotics remain unexplored. In this study, 13C-labled SMX was amended to sediment samples from Zhushan Bay (ZS), West Shore (WS), and Gonghu Bay (GH) in Taihu Lake to explore the interplay of bacterial and eukaryotic communities during a 30-day incubation period. The cumulative SMX mineralization on day 30 ranged from 5.2 % to 19.3 %, which was the highest in WS and the lowest in GH. The bacterial community showed larger within-group interactions than between-group interactions, and the positive interactions decreased during incubation. However, the eukaryotic community displayed larger between-group interactions than within-group interactions, and the positive interactions increased during incubation. The proportion of negative interactions between bacteria and eukaryotes increased during incubation. Fifty genera (including 46 bacterial and 4 eukaryotic genera) were identified as the keystone taxa due to their dominance in the co-occurrence network and tolerance to SMX. The cumulative relative abundance of these keystone taxa significantly increased during incubation and was consistent with the SMX mineralization rate. These taxa closely cooperated and played vital roles in co-occurrence networks and microbial community interactions, signifying their crucial role in SMX mineralization. These findings broadened our understanding of the complex interactions of microorganisms under SMX exposure and their potential functions during SMX mineralization, providing valuable insights for in situ bioremediation.

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.

Magnetic loofah sponge biochar facilitates microbial interspecies cooperation in surface and subsurface sediments for enhanced PAH biodegradation

Magnetic biochar had been used for the bioremediation of polycyclic aromatic hydrocarbon (PAH)-contaminated sediments. However, the long-term remediation pattern of vertical stratification driven by the application of magnetic biochar and the assembly of microbes had received little attention. In this study, magnetic loofah sponge biochar (MagLsBC), magnetic iron oxide (MagOx) and magnetic coconut shell activated carbon (MagCoAC) were applied for the 900-day remediation of contaminated sediments. Significant (p < 0.05) PAH biodegradation was observed in both the surface and subsurface sediments with MagLsBC addition. However, enhanced PAH biodegradation was observed only in the surface sediments with MagOx and MagCoAC treatments. Magnetotactic bacteria (Magnetococcus) was dominant genera in surface sediments and indigenous PAH degradation bacteria were more abundant in subsurface sediments of MagLsBC relative to other bacterial communities. The network interaction between microbes in surface and subsurface sediments with MagLsBC treatments was a less complex and tighter than those with MagCoAC, MagOx or Control treatments. Long-distance electron transfer rates could be enhanced through cooperation between magnetotactic bacteria and indigenous degradation bacteria, thus accelerating PAH degradation in sediment with MagLsBC treatment, especially in the underlying sediment.

Effects of terminal electron acceptors on the biodegradation of waste motor oil using Chlorella vulgaris-Rhodococcus erythropolis consortia: Kinetic and thermodynamic windows of opportunity analysis

The Chlorella vulgaris-Rhodococcus erythropolis consortia was constructed for the biodegradation of waste motor oil (WMO), combined with thermodynamic calculations and stoichiometric analyses. The microalgae-bacteria consortium was constructed as C. vulgaris: R. erythropolis = 1:1 (biomass, cell/mL), pH = 7, 3 g/L WMO. Under the same condition, the terminal electron acceptors (TEAs) play a crucial role in the WMO biodegradation, which follows Fe3+ >SO42- > none. The biodegradation of WMO fitted well with the first-order kinetic model under experimental temperatures with different TEAs (R2 >0.98). The WMO biodegradation efficiency reached 99.2 % and 97.1 % with Fe3+ and SO42-as TEAs at 37 °C, respectively. Thermodynamic methanogenesis opportunity windows with Fe3+ as TEA are 2.72 times fold as large as those with SO42-. Microorganism metabolism equations demonstrated the viability of anabolism and catabolism on WMO. This work lays the groundwork for the implementation of WMO wastewater bioremediation and supports research into the biochemical process of WMO biotransformation.

New insights into enhanced biodegradation of 4-bromphenol in a nitrate-reducing system: Process performance and mechanism

Due to the recalcitrant nature of halogenated phenol, conventional anaerobic bioprocess is often limited by low removal efficiency and poor process stability. At the presence of electron acceptors such as nitrate, 4-bromophenol (4-BP) removal efficiency is significantly higher than that in the anaerobic control system, but the mechanism involved is still unclear. Therefore, an up-flow nitrate-reducing bioreactor (NRBR) was designed and consecutively performed for 215 days to explore the synergistic mechanism for BPs biodegradation and nitrate reduction. Complete 4-BP biodegradation could be obtained in NRBR at HRT and 4-BP loading rate of 24 h and 0.29 mol m - 3d - 1, while the TOC removal and nitrate reduction efficiencies were as high as 91.33±2.11% and 98.31±1.33%, respectively. Population evolution analyses revealed that the microorganisms involved in 4-BP debromination and biodegradation (Candidatus Peregrinibacteria, Denitratisoma, Anaerolineaceae and Ignavibacterium) as well as nitrate reduction (Denitratisoma, Anaerolineaceae, Limnobacter and Ignavibacterium) were significantly enriched in NRBR. Major intermediates during 4-BP biodegradation, including 4-bromocatechol, 4‑bromo-6-oxo-hexanoic acid and succinic acid were identified, while a distinct 4-BP biodegradation pathway via hydration, aromatic-ring cleavage, hydrolysis debromination and oxidation was expounded. Metagenomic analysis indicated that oxidation (had, pht4, boh, butA), hydrolysis debromination ((S)-2-haloacid dehalogenase) and bio-mineralization (gabD, sdhA) of 4-BP were largely enhanced in NRBR. Moreover, carbon, nitrogen, energy and amino acid metabolisms were significantly facilitated with the injection of nitrate in order to provide energy and electron, thus enhanced microbial activities and enzymatic reactions in NRBR. The proposed mechanism provides new insights into our mechanistic understanding of halogenated phenol biodegradation and the development of sustainable bioremediation strategies.

Insights into the reaction of anammox to exogenous pyridine: Long-term performance and micro mechanisms

Some industrial wastewaters contain high amounts of toxic nitrogen-containing heterocyclic compounds, which may inhibit the efficiency of biological treatment. This work systematically investigated how exogenous pyridine affected the anaerobic ammonia oxidation (anammox) system and discussed the microscopic response mechanisms based on genes and enzymes. The anammox efficiency was not seriously inhibited by pyridine less than 50 mg/L. Bacteria secreted more extracellular polymeric substances to resist pyridine stress. After 6 days stress with 80 mg/L pyridine, the nitrogen removal rate of anammox system lost 47.7%. Long-term stress of pyridine reduced anammox bacteria by 7.26% and the expression of functional genes by 45%. Pyridine could actively bind to hydrazine synthase and ammonium transporter. This work fills a research gap in the ongoing threat of pyridines to anammox, and has guiding value for the application of anammox process in the treatment of ammonia-rich wastewater containing pyridine.

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.

Distribution of microbial communities in seasonally frozen soil layers on the Tibetan Plateau and the driving environmental factors

Large stocks of carbon and nitrogen stored in permafrost regions can potentially feed back to global biogeochemical cycles under climate warming. To understand the response of microbial communities to environmental changes, this study investigated the spatial distribution of bacterial communities in the upper layers (0-10, 10-20, and 20-30 cm) of seasonally frozen soil on the Tibetan Plateau and their relationships with the environmental factors. A total of 135 soil samples were collected from the soils at depths of 0-10, 10-20, and 20-30 cm in the Lhasa River and Nyang River basins, and the diversity and composition of bacterial communities in them were identified by high-throughput 16S rRNA gene sequencing. Bacterial diversity changed significantly with soil depth in the Nyang River basin (p < 0.001), while no obvious change was found in the Lhasa River basin. The whole bacterial composition exhibited small variations across different soil layers (p > 0.05). The relative abundance of aerobic bacteria, Sphingomonas and Arthrobacter, decreased with soil depth, while that of the other aerobic, facultative anaerobic, and anaerobic bacteria did not exhibit this trend. Soil pH was the key driving edaphic factor of the whole bacterial composition in all three depth layers, while vegetation also had an important influence on bacterial composition. Arthrobacter, Bradyrhizobium, and Bacillus had obvious correlations with soil nutrients or vegetation, while the other species were not significantly correlated with any environmental factors. Structural equation modeling revealed that vegetation and mean annual temperature had a key direct impact on the bacterial diversity and composition, respectively. Climate also indirectly affected bacterial communities, mainly through shaping soil pH and vegetation. These results indicate that the soil depth has a different impact on the bacterial α-diversity, whole bacterial composition, and specific taxa in the 0-30-cm surface layers of seasonally frozen soil, which were mainly determined by various environmental factors.

Electron acceptors determine the BTEX degradation capacity of anaerobic microbiota via regulating the microbial community

Anaerobic degradation is the major pathway for microbial degradation of benzene, toluene, ethylbenzene, and xylenes (BTEX) under electron acceptor lacking conditions. However, how exogenous electron acceptors modulate BTEX degradation through shaping the microbial community structure remains poorly understood. Here, we investigated the effect of various exogenous electron acceptors on BTEX degradation as well as methane production in anaerobic microbiota, which were enriched from the same contaminated soil. It was found that the BTEX degradation capacities of the anaerobic microbiota gradually increased along with the increasing redox potentials of the exogenous electron acceptors supplemented (WE: Without exogenous electron acceptors < SS: Sulfate supplement < FS: Ferric iron supplement < NS: Nitrate supplement), while the complexity of the co-occurring networks (e.g., avgK and links) of the microbiota gradually decreased, showing that microbiota supplemented with higher redox potential electron acceptors were less dependent on the formation of complex microbial interactions to perform BTEX degradation. Microbiota NS showed the highest degrading capacity and the broadest substrate-spectrum for BTEX, and it could metabolize BTEX through multiple modules which not only contained fewer species but also different key microbial taxa (eg. Petrimonas, Achromobacter and Comamonas). Microbiota WE and FS, with the highest methanogenic capacities, shared common core species such as Sedimentibacter, Acetobacterium, Methanobacterium and Smithella/Syntrophus, which cooperated with Geobacter (microbiota WE) or Desulfoprunum (microbiota FS) to perform BTEX degradation and methane production. This study demonstrates that electron acceptors may alter microbial function by reshaping microbial community structure and regulating microbial interactions and provides guidelines for electron acceptor selection for bioremediation of aromatic pollutant-contaminated anaerobic sites.

Toxicity determination, pollution source delineation, and microbial diversity evaluation of PAHs-contaminated sediments for an urban river

The Feng-Sang River is a metropolitan river in Kaohsiung City, Taiwan. In this study, Feng-Sang River sediments were analyzed to investigate the distributions and sources of polycyclic aromatic hydrocarbons (PAHs). The Sediment Quality Guidelines (SQGs), potentially carcinogenic PAHs (TEQcarc ), and toxic equivalence quotient (TEQ) were applied to evaluate influences of PAHs on ecosystems and microbial diversities. Results indicate that PAHs concentrations varied between seasons and locations. The concentrations of ∑16 PAHs ranged from 73.6 to 603.8 ng/kg in dry seasons and from 2.3 to 199.3 ng/kg in wet seasons. This could be because of the flushing effect during wet seasons, which caused the movement and dilution of the PAH-contaminated sediments. Diagnostic ratio analysis infers that high PAHs levels were generated by combustion processes and vehicle traffic, and results from multivariate descriptive statistical analysis also demonstrate that the vehicular traffic pollution could be the major emission source of PAHs contamination. Comparisons of PAHs with SQGs indicate that PAHs concentrations in sediment were below the effects range low (ERL) values, and thus, the immediate threat to organisms might not be significant. The diagnostic ratio analyses are effective methods for PAH source appointment. The metagenomic assay results imply that sediments contained essential microbial species with eminent diversity. The detected PAH-degrading bacteria (Desulfatiglans, Dechloromonas, Sphingomonas, Methylobacterium, Rhodobacter, Clostridium, and Exiguobacterium) played a key role in PAHs biotransformation, and Dechloromonas and Rhodobacter had a higher relative abundance. Results of microbial diversity analyses indicate that the contaminated environment induced the changes of governing microbial groups in sediments. PRACTITIONER POINTS: Diagnostic ratio analyses are effective methods for PAHs source appointment. Microbial composition in sediments are highly affected by anthropogenic pollution. Combustion and vehicle traffic contribute to urban river sediments pollution by PAHs. Dechloromonas and Rhodobacter are dominant PAHs-degrading bacteria in sediments.

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^-.

Effects of pyrene on the structure and metabolic function of soil microbial communities

The widely detected pyrene (PYR) is prone to accumulate and pose risks to the soil ecosystem. In this study, an aerobic closed microcosm was constructed to assess the effects of PYR at the environmental concentration (12.09 mg kg^-1) on the structure, interactions, and metabolism of carbon sources of soil microbial communities. The results found that half-life of PYR was 37 d and its aerobic biodegradation was mainly implemented by both Gram-negative and Gram-positive bacteria as revealed by the quantitative results. High-throughput sequencing based on 16 S rRNA and ITS genes showed that PYR exposure interfered more significantly with the diversity and abundance of the bacterial community than that of the fungal community. For bacteria, rare species were sensitive to PYR, while Gemmatimonadota, Gaiellales, and Planococcaceae involved in organic pollutants detoxification and degradation were tolerant of PYR stress. Co-occurrence network analysis demonstrated that PYR enhanced the intraspecific cooperation within the bacterial community and altered the patterns of trophic interaction in the fungal community. Furthermore, the keystone taxa and their topological roles were altered, potentially inducing functionality changes. Function annotation suggested PYR inhibited the nitrogen fixation and ammonia oxidation processes but stimulated methylotrophy and methanol oxidation, especially on day 7. For the metabolism, microbial communities accelerated the metabolism of nitrogenous carbon sources (e.g. amine) to meet the physiological needs under PYR stress. This study clarifies the impacts of PYR on the structure, metabolism, and potential N and C cycling functions of soil microbial communities, deepening the knowledge of the environmental risks of PYR.

Efficient degradation of anthracene in soil by carbon-coated nZVI activated persulfate

The easy passivation defect of nano zero-valent iron (nZVI) greatly limits its application in site pollution remediation. Carbon coating can effectively inhibit the passivation of nZVI, but its effectiveness in the soil is still unknown. This study investigated the feasibility of carbon-coated nZVI (Fe⁰@C) as a persulfate (PS) activator to degrade anthracene (ANT) in soil. The results show that the Fe⁰@C/PS system can remove 51.6% of ANT in the soil after 0.5 h of reaction, and reach 76.4% after 12 h of reaction. Not only that, the Fe⁰@C/PS system shows a good removal effect on ANT within the initial pH range of 3-9. Free radical scavenging experiments show that superoxide radicals (O₂^•-) and singlet oxygen (¹O₂) are mainly responsible for the removal of ANT, while O₂^•- may be mainly used as a precursor for the generation of ¹O₂. The activation of PS by Fe⁰@C can generate a large number of free radicals, and soil components (such as β-MnO₂) can promote the conversion of O₂^•- to ¹O₂. Furthermore, the possible degradation pathway of ANT was also proposed. The findings are of great significance to fill up the knowledge gaps in the application of nZVI in soil remediation.

Per- and poly-fluoroalkyl substances in sediments from the water-level-fluctuation zone of the Three Gorges Reservoir, China: Contamination characteristics, source apportionment, and mass inventory and loadings

Sixteen paired surface sediment samples (0-5 cm, n = 32) covering upstream to downstream of water-level-fluctuation zone of Three Gorges Reservoir, China were collected in March 2018 (following six months of submergence) and September 2018 (after six months of exposure). Seventeen per- and poly-fluoroalkyl substances (PFASs) were quantified to evaluate contamination characteristics, apportion source categories and estimate mass inventory and loadings. The concentration of ΣPFASs ranged from 0.26 to 0.82 ng·g^-1 at high water-level (HWL) and 0.46-1.53 ng·g^-1 at low water-level (LWL). Perfluorooctanoic acid (PFOA, mean: 0.32 ng·g^-1) and perfluorooctane sulfonate (PFOS, mean: 0.12 ng·g^-1) dominated, accounting 44.9% and 16.3% of the total PFASs, respectively. The distribution of PFASs was more influenced by anthropogenic activities than physicochemical parameters of the sediments. Positive matrix factorization (PMF) identified PFOA-based products was the major sources (40.1% and 38.6%, respectively). Besides, the direct sources of PFOA-, PFOS-, PFNA-and PFBA-based products played the predominant role, while the indirect degradation of precursors contributed relatively little. The sediment (0-5 cm) mass inventory of PFASs at LWL (57.5 kg) was higher than HWL (39.3 kg). The annual mass loadings of the total PFASs, PFOA, PFOS, perfluoroundecanoic acid (PFUdA) and perfluorononanoic acid (PFNA) from the upstream to the middle-lower reaches of Yangtze River were 27.4 kg, 11.1 kg, 4.63 kg, 2.89 kg and 2.57 kg, respectively. This study could provide the basic datasets of PFASs in surface sediments of the TGR, and also indicate an important transport of PFASs from upstream to the lower reaches, which should be further studied as well.

A global survey reveals a divergent extradiol dioxygenase clade as a widespread complementary contributor to the biodegradation of mono- and polycyclic aromatic hydrocarbons

Extradiol dioxygenation is a key reaction in the microbial aerobic degradation of mono- and polycyclic aromatic hydrocarbon catecholic derivatives. It has been reported that many bacterial enzymes exhibiting such converging functions act on a wide range of catecholic substrates. The present study reports a new subfamily of extradiol dioxygenases (EXDOs) with broad substrate specificity, the HrbC EXDOs. The new clade belongs to the XII cluster within family 2 of the vicinal oxygen chelate superfamily (EXDO-VC2), which is typically characterized by a preference for bicyclic substrates. Coding hrbC orthologs were isolated by activity-based screening of fosmid metagenomic libraries from large DNA fragments derived from heavily PAH-contaminated soils. They occurred as solitary genes within conserved sequences encoding enzymes for amino acid metabolism and were stably maintained in the chromosomes of the Betaproteobacteria lineages harboring them. Analysis of contaminated aquifers revealed coexpression of hrbC as a polycistronic mRNA component. The predicted open reading frames were verified by cloning and heterologous expression, confirming the expected molecular mass and meta-cleavage activity of the recombinant enzymes. Evolutionary analysis of the HrbC protein sequences grouped them into a discrete cluster of 1,2-dihydroxynaphthalene dioxygenases represented by a cultured PAH degrader, Rugosibacter aromaticivorans strain Ca6. The ecological importance and relevance of the new EXDO genes were confirmed by PCR-based mapping in different biogeographical localities contaminated with a variety of mono- and polycyclic aromatic compounds. The cosmopolitan distribution of hrbC in PAH-contaminated aquifers supports our hypothesis about its auxiliary role in the degradation of toxic catecholic intermediates, contributing to the composite EXDO catabolic capacity of the world's microbiomes.

Temporal-spatial variations, source apportionment, and ecological risk of trace elements in sediments of water-level-fluctuation zone in the Three Gorges Reservoir, China

The Three Gorges Reservoir (TGR) plays a crucial role in providing electricity for mega-cities across China. However, since the impoundment was completed in 2006, attention to environmental concerns has also been intensive. In order to determine the distribution, sources, and pollution status of trace elements in the water fluctuation zone of the TGR following ten years of repeated "submergence" and "exposure", we systematically collected 16 paired surface sediment samples (n = 32) covering the entire main body of the TGR in March 2018 (following 6 months of submergence) and September 2018 (after 6 months of exposure), and quantitatively analyzed 13 elements (e.g., Mn, Fe, V, Cr, Ni, Cu, Zn, As, Sr, Y, Zr, Ba, and Pb) using X-ray fluorescence spectrophotometry (XRF). The results showed that, except for Sr, concentrations of trace metals following submergence were generally higher than those after exposure due to the less settling of suspended solids at the faster flow velocity during the drawdown period. Assessment using enrichment factors (EFs) and a geo-accumulation index (Igeo) both characterized a relatively serious anthropogenic pollution status of metals in the upper reaches of the TGR with respect to the middle-lower reaches. Source apportionment by positive matrix factorization (PMF) analysis indicated that agricultural activities (24.8 and 24.3%, respectively) and industrial emissions (24.5 and 22.9%, respectively) were the two major sources in these two periods, followed by natural sources, domestic sewage, and ore mining. Ecological risk assessment showed that metalloid arsenic (As) could be the main potential issue of risk to aquatic organisms and human health. A new source-specific risk assessment method (pRI) combined with PMF revealed that agricultural activities could be the major source of potential ecological risk and should be prioritized as the focus of metal/metalloid risk management in the TGR.

A comprehensive exploration on distribution, risk assessment, and source quantification of heavy metals in the multi-media environment from Shaying River Basin, China

Comprehensively understand the distribution of pollutants in the multi-media environment at basin scale is of major importance to the ecological risk assessment and pollution control. In this study, multi-media contamination characteristics of eight heavy metals in the water, soil, and sediment from the Shaying River Basin of China have been analyzed to probe their ecological risks and potential sources. Results revealed that heavy metal concentrations in pore water were higher than those in surface water. While the mean concentrations of most heavy metals increased follow the order of bankside soil (BS)<water-level-fluctuating zone soil (WLFZS)<sediment. The WLFZ was an important transition zone between the BS and sediment for pollutant exchange. The mean heavy metal concentrations in surface water were all below their corresponding water quality standards except Hg. Whereas the mean concentrations of Cr, Ni, Zn, Cd, and Hg in BS, WLFZS, and sediment exceeded their corresponding background values. The assessment results of pollution and risks indicated that Hg and Cd posed the highest potential risks in each medium. Furthermore, according to the factor analysis and PMF model, six potential sources were identified, in which agricultural, fuel combustion, and industrial sources were the dominant anthropogenic sources, accounting for 23.84%, 17.43%, and 14.25% of the total contribution.

Up-regulation of ribosomal and carbon metabolism proteins enhanced pyrene biodegradation in fulvic acid-induced biofilm system

The polycyclic aromatic hydrocarbons (PAHs) that enter the aqueous phase usually coexist with fulvic acid (FA). Therefore, we initiated this investigation to explore the influences of FA on bacterial biofilm formation and its potential to biodegrade pyrene (PYR), using electron microscopic techniques and isobaric tags for relative and absolute quantification (iTRAQ). Our results revealed that FA stimulated biofilm formation and enhanced the biodegradation of PYR. First, FA favored the three-dimensional proliferation of bacteria, with an OD590/OD600 value of up to 14.78, and the extracellular surfaces covered by a layer of biomaterials. Distinctive intracellular morphologies of texture and organization were accompanied by reduced inter-bacterial distances of less than 0.31 μm. The biofilms formed displayed interactions between FA and surficial proteins, as noted by band shifts for the C-O and CO groups. Strikingly, FA triggered the upregulation of 130 proteins that were either operational in biofilm formation or in metabolic adjustments; with the changes supported by the increasing intensity of free amino acids and the newly generated N-O bonds. The results above revealed that the enhanced biodegradation was related to the up-regulation of the proteins functioned for ribosomal and carbon metabolism, and the ultra-structural changes in FA-induced biofilm system.

Variation of the mangrove sediment microbiomes and their phenanthrene biodegradation rates during the dry and wet seasons

Mangrove sediment is a major sink for phenanthrene in natural environments. Consequently, this study investigated the effects of seasonal variation on the biodegradation rates of low (150 mg kg^-1), moderate (600 mg kg^-1), and high (1200 mg kg^-1) phenanthrene-contaminated mangrove sediments using a microcosm study and identified potential key phenanthrene-degrading bacteria using high throughput sequencing of 16 S rRNA gene and quantitative-PCR of the PAH-ring hydroxylating dioxygenase (PAH-RHD_α) genes. The biodegradation rates of phenanthrene in all treatments were higher in the wet-season sediments (11.58, 14.51, and 8.94 mg kg^-1 sediment day^-1) than in the dry-season sediments (3.51, 12.56, and 5.91 mg kg^-1 sediment day^-1) possibly due to higher nutrient accumulation caused by rainfall and higher diversity of potential phenanthrene-degrading bacteria. The results suggested that the mangrove sediment microbiome significantly clustered according to season. Although Gram-negative phenanthrene-degrading bacteria (i.e., Anaerolineaceae, Marinobacter, and Rhodobacteraceae) played a key role in both dry and wet seasons, distinctly different phenanthrene-degrading bacterial taxa were observed in each season. Halomonas and Porticoccus were potentially responsible for the degradation of phenanthrene in the dry and wet seasons, respectively. The knowledge gained from this study contributes to the development of effective and rationally designed microbiome innovations for oil removal.

Assembly of a Benthic Microbial Community in a Eutrophic Bay with a Long History of Oyster Culturing

The introduction of oysters to a waterbody is an efficient method for decreasing levels of eutrophication. Oysters affect sedimental environments and benthic microbes via their roles in nutrient cycling. However, little is known about how long-term oyster culturing affects benthic microbial community assembly. In the present study, top and bottom sediments from an oyster-culture area and non-culture area, in a eutrophic bay with a long history of oyster culturing, were obtained for environmental parameter measurement and microbe identification. Deterministic and stochastic processes in microbial community assembly were assessed. In particular, keystone species identification through network analysis was combined with measured environmental parameters to determine the factors related to community assembly processes. Our results suggest that oyster culturing relates to greater variation in both biological and non-biological sediment profiles. In benthic communities, Proteobacteria and Chloroflexi were the most abundant phyla, and community compositions were significantly different between sample groups. We also found that community assembly was more affected by deterministic factors than stochastic ones, when oysters were present. Moisture, or water content, and pH were identified as affecting deterministic and stochastic processes, respectively, but only water content was a driver associated with oyster culturing. Additionally, although keystone species presented a similar pattern of composition to peripheral species, they responded to their environments differently. Furthermore, model selection, fitting keystone species to community assembly processes, indicates their role in shaping microbial communities.

More rapid dechlorination of 2,4-dichlorophenol using acclimated bacteria

The key step for anaerobic biodegradation of 2,4-dichlorophenol (2,4-DCP) is an initial dechlorination reaction, but Cl in the para-position is more difficult to remove than Cl in the ortho-position using normal 2,4-DCP-acclimated bacteria. In this work, a bacterial community previously acclimated to biodegrading 2,4-DCP slowly dechlorinated 4-chlorophenol (4-CP Cl only in the para-position), which limited mineralization. That community was exposed to the selective pressure of having 4-CP as its only organic substrate in order to generate a 4-CP-dechlorinating community. When the 4-CP-dechlorinating community was challenged with 2,4-DCP, 4-CP hardly accumulated, although the kinetics for 2,4-DCP biodegradation were slower. When the community acclimated to 4-CP was mixed with the community acclimated to 2,4-DCP, the 2,4-DCP removal rate remained high, and 4-CP was more rapidly biodegraded. The genera Treponema, Blvii28, Dechloromonas, Nitrospira, and Thauera were significantly more abundant in the 4-CP-dechlorinating biomass and may have played roles in 2,4-DCP dechlorination and mineralization.

Nitric oxide-dependent biodegradation of phenanthrene and fluoranthene: The co-occurrence of anaerobic and intra-aerobic pathways

Polycyclic aromatic hydrocarbons (PAHs) pollution as well as the emissions of nitric oxide (NO) and greenhouse gas nitrous oxide (N₂O) in denitrification processes are currently two environmental issues of great concern. Although bioremediation of PAHs under denitrification is considered a promising approach, denitrification was an important contributor to N₂O and NO emissions. This long-term study confirmed for the first time that microorganisms could utilize NO to efficiently degrade phenanthrene and fluoranthene. When the two systems of NO-dependent phenanthrene and fluoranthene degradation were stable, the first-order rate constants of phenanthrene and fluoranthene in the two systems (0.1940 and 0.0825 day^-1, respectively) were close to those values (0.2290 and 0.1085 day^-1, respectively) observed at nitrate-reducing conditions. Further analysis of functional genes revealed that phenanthrene and fluoranthene might be degraded under the combined action of the anaerobic pathway mediated by NO reduction and intra-aerobic pathway mediated by NO dismutation. The genomic analysis showed that Nod genes had high diversity and most of them were similar to aquifer cluster group in the two systems. Microbial community structure analysis indicated that Pseudomonas and Ochrobactrum might be key participants in NO-dependent phenanthrene degradation system, and Azoarcus, Alicycliphilus and Moheibacter might play vital roles in NO-dependent fluoranthene degradation system. This study provides new perspective for anaerobic remediation of PAH pollution and simultaneously reducing NO and N₂O emissions during bioprocesses, which has important ecological significance for amending sediment and soil PAHs contamination and potential application for the removal of PAHs in flue gas.

New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era

The accumulation of petroleum hydrocarbons in the environment substantially endangers terrestrial and aquatic ecosystems. Many microbial strains have been recognized to utilize aliphatic and aromatic hydrocarbons under aerobic conditions. Nevertheless, most of these pollutants are transferred by natural processes, including rain, into the underground anaerobic zones where their degradation is much more problematic. In oxic zones, anaerobic microenvironments can be formed as a consequence of the intensive respiratory activities of (facultative) aerobic microbes. Even though aerobic bioremediation has been well-characterized over the past few decades, ample research is yet to be done in the field of anaerobic hydrocarbon biodegradation. With the emergence of high-throughput techniques, known as omics (e.g., genomics and metagenomics), the individual biodegraders, hydrocarbon-degrading microbial communities and metabolic pathways, interactions can be described at a contaminated site. Omics approaches provide the opportunity to examine single microorganisms or microbial communities at the system level and elucidate the metabolic networks, interspecies interactions during hydrocarbon mineralization. Metatranscriptomics and metaproteomics, for example, can shed light on the active genes and proteins and functional importance of the less abundant species. Moreover, novel unculturable hydrocarbon-degrading strains and enzymes can be discovered and fit into the metabolic networks of the community. Our objective is to review the anaerobic hydrocarbon biodegradation processes, the most important hydrocarbon degraders and their diverse metabolic pathways, including the use of various terminal electron acceptors and various electron transfer processes. The review primarily focuses on the achievements obtained by the current high-throughput (multi-omics) techniques which opened new perspectives in understanding the processes at the system level including the metabolic routes of individual strains, metabolic/electric interaction of the members of microbial communities. Based on the multi-omics techniques, novel metabolic blocks can be designed and used for the construction of microbial strains/consortia for efficient removal of hydrocarbons in anaerobic zones.