Autochthonous Bioaugmentation-Modified Bacterial Diversity of Phenanthrene Degraders in PAH-Contaminated Wastewater as Revealed by DNA-Stable Isotope Probing

The effect of the 13C abundance of soil microbial DNA on identifying labelled fractions after ultracentrifugation

DNA-based stable isotope probing (DNA-SIP) technology has been widely employed to trace microbes assimilating target substrates. However, the fractions with labelled universal genes are sometimes difficult to distinguish when detected by quantitative real-time PCR. In this experiment, three paddy soils (AQ, CZ, and NB) were amended with 0.1% glucose containing 13C at six levels, and DNA was then extracted after a 7-day incubation and subjected to isopycnic gradient centrifugation. The results showed that the amount of labelled DNA was notably related to the 13C-glucose percentage, while the separation spans of 18S rRNA and 16S rRNA genes between labelled and unlabelled treatments became notably clearer when the δ13C values of the total DNA were 90.9, 61.6, and 38.9‰ and 256.2, 104.5 and 126.1‰ in the AQ, CZ, and NB soils, respectively. Moreover, fractionated DNA was also labelled by determining the δ13C values while adding only 5 atom% 13C-glucose to the soil. The results suggest that the optimal labelling fractions were not always those fractions with the maximal gene abundance, and detecting the δ13C values of the total and fractionated DNA was beneficial in estimating the results of DNA-SIP. KEY POINTS: • Appropriate 13C-DNA amount was needed for DNA-SIP. • Detecting the 13C ratio of fractionated DNA directly was an assistant method for identifying the labelled fractions. • Fractions with the maximal 18S or 16S rRNA gene abundance always were not labelled.

Controllable chemical redox reactions to couple microbial degradation for organic contaminated sites remediation: A review

Global environmental concern over organic contaminated sites has been progressively conspicuous during the process of urbanization and industrial restructuring. While traditional physical or chemical remediation technologies may significantly destroy the soil structure and function, coupling moderate chemical degradation with microbial remediation becomes a potential way for the green, economic, and efficient remediation of contaminated sites. Hence, this work systematically elucidates why and how to couple chemical technology with microbial remediation, mainly focused on the controllable redox reactions of organic contaminants. The rational design of materials structure, selective generation of reactive oxygen species, and estimation of degradation pathway are described for chemical oxidation. Meanwhile, current progress on efficient and selective reductions of organic contaminants (i.e., dechlorination, defluorination, -NO2 reduction) is introduced. Combined with the microbial remediation of contaminated sites, several consideration factors of how to couple chemical and microbial remediation are proposed based on both fundamental and practical points of view. This review will advance the understanding and development of chemical-microbial coupled remediation for organic contaminated sites.

Using Network Analysis and Predictive Functional Analysis to Explore the Fluorotelomer Biotransformation Potential of Soil Microbial Communities

Microbial transformation of per- and polyfluoroalkyl substances (PFAS), including fluorotelomer-derived PFAS, by native microbial communities in the environment has been widely documented. However, few studies have identified the key microorganisms and their roles during the PFAS biotransformation processes. This study was undertaken to gain more insight into the structure and function of soil microbial communities that are relevant to PFAS biotransformation. We collected 16S rRNA gene sequencing data from 8:2 fluorotelomer alcohol and 6:2 fluorotelomer sulfonate biotransformation studies conducted in soil microcosms under various redox conditions. Through co-occurrence network analysis, several genera, including Variovorax, Rhodococcus, and Cupriavidus, were found to likely play important roles in the biotransformation of fluorotelomers. Additionally, a metagenomic prediction approach (PICRUSt2) identified functional genes, including 6-oxocyclohex-1-ene-carbonyl-CoA hydrolase, cyclohexa-1,5-dienecarbonyl-CoA hydratase, and a fluoride-proton antiporter gene, that may be involved in defluorination. This study pioneers the application of these bioinformatics tools in the analysis of PFAS biotransformation-related sequencing data. Our findings serve as a foundational reference for investigating enzymatic mechanisms of microbial defluorination that may facilitate the development of efficient microbial consortia and/or pure microbial strains for PFAS biotransformation.

A novel mycelial pellet applied to remove polycyclic aromatic hydrocarbons: High adsorption performance & its mechanisms

Mycelial pellets formed by Penicillium thomii ZJJ were applied as efficient biosorbents for the removal of polycyclic aromatic hydrocarbons (PAHs), which are a type of ubiquitous harmful hydrophobic pollutants. The live mycelial pellets were able to remove 93.48 % of pyrene at a concentration of 100 mg/L within 48 h, demonstrating a maximum adsorption capacity of 285.63 mg/g. Meanwhile, the heat-killed one also achieved a removal rate of 65.01 %. Among the six typical PAHs (pyrene, phenanthrene, fluorene, anthracene, fluoranthene, benzo[a]pyrene), the mycelial pellets preferentially adsorbed the high molecular weight PAHs, which also have higher toxicity, resulting in higher removal efficiency. The experimental results showed that the biosorption of mycelial pellets was mainly a spontaneous physical adsorption process that occurred as a monolayer on a homogeneous surface, with mass transfer being the key rate-limiting step. The main adsorption sites on the surface of mycelia were carboxyl and N-containing groups. Extracellular polymeric substances (EPS) produced by mycelial pellets could enhance adsorption, and its coupling with dead mycelia could achieve basically the same removal effect to that of living one. It can be concluded that biosorption by mycelial pellets occurred due to the influence of electrostatic and hydrophobic interactions, consisting of five steps. Furthermore, the potential applicability of mycelial pellets has been investigated considering diverse factors. The mycelia showed high environmental tolerance, which could effectively remove pyrene across a wide range of pH and salt concentration. And pellets diameters and humic acid concentration had a significant effect on microbial adsorption effect. Based on a cost-effectiveness analysis, mycelium pellets were found to be a low-cost adsorbent. The research outcomes facilitate a thorough comprehension of the adsorption process of pyrene by mycelial pellets and their relevant applications, proposing a cost-effective method without potential environmental issues (heat-killed mycelial pellets plus EPS) to removal PAHs.

Identification, degradation characteristics, and application of a newly isolated pyridine-degrading Paracidovorax sp. BN6-4

The Paracidovorax sp. BN6-4 capable of degrading high concentrations of pyridine was isolated from the coking sludge. The removal rate of BN6-4 to 1,000 mg/L pyridine during 48 h was 97.49 ±1.59%. The primary intermediate metabolites of pyridine degradation by strain BN6-4 were identified by gas chromatography-mass spectrometry (GC-MS), including N-Ethylurea, acetamidoacetaldehyde, and N-Hydroxymethylacetamide, etc. Subsequently, two different biodegradation pathways of pyridine were proposed. First, the hydroxylation of pyridine to form the intermediates pyridin-2(1H)-one and 5,6-dihydropyridine-2,5-diol, the former undergoing oxidative ring opening and the latter oxidative ring opening via N-C2 and C2-C3 ring opening to ammonia and carbon dioxide. Furthermore, the organic matter was greatly degraded by the bioremediation of real coking wastewater using BN6-4. This study enriched the microbial resource for pyridine degradation and provided new insights about the biodegradation pathway of pyridine, which is of great significance for the pyridine pollution control and coking wastewater treatment.

Unveiling the synergistic mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation for enhanced phenanthrene degradation in oil-contaminated soils

Autochthonous bioaugmentation and nutrient biostimulation are promising bioremediation methods for polycyclic aromatic hydrocarbons (PAHs) in contaminated agricultural soils, but little is known about their combined working mechanism. In this study, a microcosm trial was conducted to explore the combined mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation, using DNA stable-isotope-probing (DNA-SIP) and microbial network analysis. Both treatments significantly improved phenanthrene (PHE) removal, with their combined application producing the best results. The microbial community composition was notably altered by all bioremediation treatments, particularly the PHE-degrading bacterial and fungal taxa. Fungal bioaugmentation removed PAHs through extracellular enzyme secretion but reduced soil microbial diversity and ecological stability, while nitrogen biostimulation promoted PAH dissipation by stimulating indigenous soil degrading microbes, including fungi and key bacteria in the soil co-occurrence networks, ensuring the ecological diversity of soil microorganisms. The combination of both approaches proved to be the most effective strategy, maintaining a high degradation efficiency and relatively stable soil biodiversity through the secretion of lignin hydrolytic enzymes by fungi, and stimulating the reproduction of soil native degrading microbes, especially the key degraders in the co-occurrence networks. Our findings provide a fresh perspective of the synergy between fungal bioaugmentation and nitrogen biostimulation, highlighting the potential of this combined bioremediation approach for in situ PAH-contaminated soils.

New insights into bioaugmented removal of sulfamethoxazole in sediment microcosms: degradation efficiency, ecological risk and microbial mechanisms

BACKGROUND

Bioaugmentation has the potential to enhance the ability of ecological technology to treat sulfonamide-containing wastewater, but the low viability of the exogenous degraders limits their practical application. Understanding the mechanism is important to enhance and optimize performance of the bioaugmentation, which requires a multifaceted analysis of the microbial communities. Here, DNA-stable isotope probing (DNA-SIP) and metagenomic analysis were conducted to decipher the bioaugmentation mechanisms in stabilization pond sediment microcosms inoculated with sulfamethoxazole (SMX)-degrading bacteria (Pseudomonas sp. M2 or Paenarthrobacter sp. R1).

RESULTS

The bioaugmentation with both strains M2 and R1, especially strain R1, significantly improved the biodegradation rate of SMX, and its biodegradation capacity was sustainable within a certain cycle (subjected to three repeated SMX additions). The removal strategy using exogenous degrading bacteria also significantly abated the accumulation and transmission risk of antibiotic resistance genes (ARGs). Strain M2 inoculation significantly lowered bacterial diversity and altered the sediment bacterial community, while strain R1 inoculation had a slight effect on the bacterial community and was closely associated with indigenous microorganisms. Paenarthrobacter was identified as the primary SMX-assimilating bacteria in both bioaugmentation systems based on DNA-SIP analysis. Combining genomic information with pure culture evidence, strain R1 enhanced SMX removal by directly participating in SMX degradation, while strain M2 did it by both participating in SMX degradation and stimulating SMX-degrading activity of indigenous microorganisms (Paenarthrobacter) in the community.

CONCLUSIONS

Our findings demonstrate that bioaugmentation using SMX-degrading bacteria was a feasible strategy for SMX clean-up in terms of the degradation efficiency of SMX, the risk of ARG transmission, as well as the impact on the bacterial community, and the advantage of bioaugmentation with Paenarthrobacter sp. R1 was also highlighted. Video Abstract.

Effects of short and long-term thermal exposure on microbial compositions in soils contaminated with mixed benzene and benzo[a]pyrene: A short communication

Polycyclic aromatic hydrocarbons (PAHs) and benzene, toluene, ethylbenzene, and xylene (BTEX) are the most persistent and toxic organic contaminants often found co-contaminated in anthropogenic and petrochemical industrial sites. Therefore, an experiment was performed for the safe biodegradation of benzene and benzo[a]pyrene (BaP) through thermally-enhanced biodegradation, and to explore the influence of elevated thermal treatments on microbial diversity and composition. The results revealed that elevated thermal treatments (15 to 45 °C) significantly enhanced the diversity of both bacteria and fungi. The composition analysis revealed that short-term and long-term elevated temperature conditions can directly enhance the specificity of microorganisms that play a crucial role in the biodegradation of benzene and BaP co-contaminated soil. Moreover, the indirect role of elevated temperature conditions on microbial compositions was through the fluctuations of soil properties, especially soil pH, moisture, TOC, potassium, phosphorous, total Fe, Fe(II), and Fe(III). In addition, the correlation analyses revealed that thermal exposure enhances the synergistic association (fungal-fungal, fungal-bacterial, bacterial-bacterial) of microbes to degrade the toxic contaminants and to cope with harsh environmental conditions. These results concluded that the biodegradation of benzene and BaP co-contamination was efficiently enhanced under the thermally-enhanced biodegradation approach and the elevation of temperature can affect the microbial compositions directly via microbial specificity or indirectly by influencing the soil properties.

Community pattern of potential phenanthrene (PHE) degrading bacteria in PHE contaminated soil revealed by 13C-DNA stable isotope probing

Quantification of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil and identification of potential PAH degraders are essential for comprehending their environmental fate and conducting bioremediation. However, the microbial population responsible for the breakdown of phenanthrene (PHE) in polluted soil environments is frequently disregarded. In this study, via DNA-stable-isotope probing (DNA-SIP), we found that soil microbiota likely plays a crucial part in the PHE degradation. The PHE removal rates were 98% and 99%, in 13C-PHE and 12C-PHE microcosmic incubations, respectively. 13CO2 was produced along with the degradation of 13C-PHE. According to the analysis of 16S rRNA gene, there was a relatively higher presence of unidentified bacteria in the 'heavy' DNA fractions treated with 13C-PHE. Genus of Enterobacteriales, Acidobacteria, Alphaproteobacteria, Paenibacillaceae, Flavobacteriia, Chloroflexi, Cyanobacteria, Caldilineae, Latescibacteria, Armatimonadetes and Blastocatellia were succseesfully labeled during the degradation of 13C-PHE, indicating their capacity of utilizing PHE. Co-occurrence network of 13C-heavy fractions exhibited greater complexity compared with that of 12C-heavy fractions, revealling an enhancement of bacterial interspecies interactions. Collectivley, this study eluidated the soil microbes involed in the PHE degradation and offered fresh perspectives on the community pattern of potential PHE degrading bacteria.

In Situ Discrimination and Cultivation of Active Degraders in Soils by Genome-Directed Cultivation Assisted by SIP-Raman-Activated Cell Sorting

The identification and in situ cultivation of functional yet uncultivable microorganisms are important to confirm inferences regarding their ecological functions. Here, we developed a new method that couples Raman-activated cell sorting (RACS), stable-isotope probing (SIP), and genome-directed cultivation (GDC)─namely, RACS-SIP-GDC─to identify, sort, and cultivate the active toluene degraders from a complex microbial community in petroleum-contaminated soil. Using SIP, we successfully identified the active toluene degrader Pigmentiphaga, the single cells of which were subsequently sorted and isolated by RACS. We further successfully assembled the genome of Pigmentiphaga based on the metagenomic sequencing of 13C-DNA and genomic sequencing of sorted cells, which was confirmed by gyrB gene comparison and average nucleotide identity determination. Additionally, the genotypes and phenotypes of this degrader were directly linked at the single-cell level, and its complete toluene metabolic pathways in petroleum-contaminated soil were reconstructed. Based on its unique metabolic properties uncovered by genome sequencing, we modified the traditional cultivation medium with antibiotics, amino acids, carbon sources, and growth factors (e.g., vitamins and metals), achieving the successful cultivation of RACS-sorted active degrader Pigmentiphaga sp. Our results implied that RACS-SIP-GDC is a state-of-the-art approach for the precise identification, targeted isolation, and cultivation of functional microbes from complex communities in natural habitats. RACS-SIP-GDC can be used to explore specific and targeted organic-pollution-degrading microorganisms at the single-cell level and provide new insights into their biodegradation mechanisms.

Uncovering the metabolic pathway of novel Burkholderia sp. for efficient triclosan degradation and implication: Insight from exogenous bioaugmentation and toxicity pressure

Triclosan (TCS), a synthetic and broad-spectrum antimicrobial agent, is frequently detected in various environmental matrices. A novel TCS degrading bacterial strain, Burkholderia sp. L303, was isolated from local activated sludge. The strain could metabolically degrade TCS up to 8 mg/L, and optimal conditions for TCS degradation were at temperature of 35 °C, pH 7, and an increased inoculum size. During TCS degradation, several intermediates were identified, with the initial degradation occurring mainly through hydroxylation of aromatic ring, followed by dechlorination. Further intermediates such as 2-chlorohydroquinone, 4-chlorocatechol, and 4-chlorophenol were produced via ether bond fission and C-C bond cleavage, which could be further transformed into unchlorinated compounds, ultimately resulting in the complete stoichiometric free chloride release. Bioaugmentation of strain L303 in non-sterile river water demonstrated better degradation than in sterile water. Further exploration of the microbial communities provided insights into the composition and succession of the microbial communities under the TCS stress as well as during the TCS biodegradation process in real water samples, the key microorganisms involved in TCS biodegradation or showing resistance to the TCS toxicity, and the changes in microbial diversity related to exogenous bioaugmentation, TCS input, and TCS elimination. These findings shed light on the metabolic degradation pathway of TCS and highlight the significance of microbial communities in the bioremediation of TCS-contaminated environments.

Unveiling the novel role of ryegrass rhizospheric metabolites in benzo[a]pyrene biodegradation

Rhizoremediation is a promising remediation technology for the removal of soil persistent organic pollutants (POPs), especially benzo[a]pyrene (BaP). However, our understanding of the associations among rhizospheric soil metabolites, functional microorganisms, and POPs degradation in different plant growth stages is limited. We combined stable-isotope probing (SIP), high-throughput sequencing, and metabolomics to analyze changes in rhizospheric soil metabolites, functional microbes, and BaP biodegradation in the early growth stages (tillering, jointing) and later stage (booting) of ryegrass. Microbial community structures differed significantly among growth stages. Metabolisms such as benzenoids and carboxylic acids tended to be enriched in the early growth stage, while lipids and organic heterocyclic compounds dominated in the later stage. From SIP, eight BaP-degrading microbes were identified, and most of which such as Ilumatobacter and Singulisphaera were first linked with BaP biodegradation. Notably, the relationship between the differential metabolites and BaP degradation efficiency further suggested that BaP-degrading microbes might metabolize BaP directly to produce benzenoid metabolites (3-hydroxybenzo[a]pyrene), or utilize benzenoids (phyllodulcin) to stimulate the co-metabolism of BaP in early growth stage; some lipids and organic acids, e.g. 1-aminocyclopropane-1-carboxylic acid, might provide nutrients for the degraders to promote BaP metabolism in later stage. Accordingly, we determined that certain rhizospheric metabolites might regulate the rhizospheric microbial communities at different growth stages, and shift the composition and diversity of BaP-degrading bacteria, thereby enhancing in situ BaP degradation. Our study sheds light on POPs rhizoremediation mechanisms in petroleum-contaminated soils.

Identification of key degraders for controlling toxicity risks of disguised toxic pollutants with division of labor mechanisms in activated sludge microbiomes: Using nonylphenol ethoxylate as an example

Efficient management of disguised toxic pollutants (DTPs), which can undergo microbial degradation and convert into more toxic substances, necessitates the collaboration of diverse microbial populations in wastewater treatment plants. However, the identification of key bacterial degraders capable of controlling the toxicity risks of DTPs through division of labor mechanisms in activated sludge microbiomes has received limited attention. In this study, we investigated the key degraders capable of controlling the risk of estrogenicity associated with nonylphenol ethoxylate (NPEO), a representative DTP, in textile activated sludge microbiomes. The results of our batch experiments revealed that the transformation of NPEO into NP and subsequent NP degradation were the rate-limiting processes for controlling the risk of estrogenicity, resulting in an inverted V-shaped curve of estrogenicity in water samples during the biodegradation of NPEO by textile activated sludge. By utilizing enrichment sludge microbiomes treated with NPEO or NP as the sole carbon and energy source, a total of 15 bacterial degraders, including Sphingbium, Pseudomonas, Dokdonella, Comamonas, and Hyphomicrobium, were identified as capable of participating in these processes, Among them, Sphingobium and Pseudomonas were the two key degraders that could cooperatively interact in the degradation of NPEO with division of labor mechanisms. Co-culturing Sphingobium and Pseudomonas isolates exhibited a synergistic effect in degrading NPEO and reducing estrogenicity. Our study underscores the potential of the identified functional bacteria for controlling estrogenicity associated with NPEO and provides a methodological framework for identifying key cooperators engaged in labor division, contributing to the management of risks associated with DTPs by leveraging intrinsic microbial metabolic interactions.

Phenanthrene removal from a spent sediment washing solution in a continuous-flow stirred-tank reactor

The issue of polycyclic aromatic hydrocarbons (PAHs) is widespread in marine sediments involving ecological systems and human health. Sediment washing (SW) has proven to be the most effective remediation approach for sediments polluted by PAHs, such as phenanthrene (PHE). However, SW still raises waste handling concerns due to a considerable amount of effluents generated downstream. In this context, the biological treatment of a PHE- and ethanol-containing spent SW solution can represent a highly efficient and environmentally-friendly strategy, but its knowledge is still scarce in scientific literature and no studies have so far been conducted in continuous mode. Therefore, a synthetic PHE-polluted SW solution was biologically treated in a 1 L aerated continuous-flow stirred-tank reactor for 129 days by evaluating the effect of different pH values, aeration flowrates and hydraulic retention times as operating parameters over five successive phases. A PHE removal efficiency of up to 75-94% was achieved by an acclimated PHE-degrading consortium mainly composed of Proteobacteria, Bacteroidota and Firmicutes phyla through biodegradation following the adsorption mechanism. PHE biodegradation, mainly occurring via the benzoate route due to the presence of PAH-related-degrading functional genes and a phthalate accumulation up to 46 mg/L, was also accompanied by a reduction of dissolved organic carbon and ammonia nitrogen above 99% in the treated SW solution.

New insight into the mechanisms of autochthonous fungal bioaugmentation of phenanthrene in petroleum contaminated soil by stable isotope probing

Autochthonous fungal bioaugmentation (AFB) is considered a reliable bioremediation approach for polycyclic aromatic hydrocarbon (PAH) contamination, but little is known about its mechanisms in contaminated soils. Here, a microcosm experiment was performed to explore the AFB mechanisms associated with two highly efficient phenanthrene degrading agents of fungi (with laccase-producing Scedosporium aurantiacum GIG-3 and non-laccase-producing Aspergillus fumigatus LJD-29), using stable-isotope-probing (SIP) and high-throughput sequencing. The results showed that each fungus markedly improved phenanthrene removal, and microcosms with both fungi exhibited the best phenanthrene removal performance among all microcosms. Additionally, AFB markedly shifted the composition of the microbial community, particularly the phenanthrene-degrading bacterial taxa. Interestingly, based on SIP results, strains GIG-3 and LJD-29 did not assimilate phenanthrene directly during AFB, but instead played key roles in the preliminary decomposition of phenanthrene though secretion of different extracellular enzymes to oxidize the benzene ring (GIG-3 bioaugmentation with laccase, and LJD-29 bioaugmentation with manganese and lignin peroxidases). In addition, all functional degraders directly involved in phenanthrene assimilation were indigenous bacteria, while native fungi rarely participated in the direct phenanthrene mineralization. Our findings provide a new mechanism of AFB with multiple fungi, and support AFB as a promising strategy for the in situ bioremediation of PAH-contaminated soil.

Response of the soil microbial community to petroleum hydrocarbon stress shows a threshold effect: research on aged realistic contaminated fields

Introduction

Microbes play key roles in maintaining soil ecological functions. Petroleum hydrocarbon contamination is expected to affect microbial ecological characteristics and the ecological services they provide. In this study, the multifunctionalities of contaminated and uncontaminated soils in an aged petroleum hydrocarbon-contaminated field and their correlation with soil microbial characteristics were analyzed to explore the effect of petroleum hydrocarbons on soil microbes.

Methods

Soil physicochemical parameters were determined to calculate soil multifunctionalities. In addition, 16S high-throughput sequencing technology and bioinformation analysis were used to explore microbial characteristics.

Results

The results indicated that high concentrations of petroleum hydrocarbons (565-3,613 mg•kg^-1, high contamination) reduced soil multifunctionality, while low concentrations of petroleum hydrocarbons (13-408 mg•kg^-1, light contamination) might increase soil multifunctionality. In addition, light petroleum hydrocarbon contamination increased the richness and evenness of microbial community (p < 0.01), enhanced the microbial interactions and widened the niche breadth of keystone genus, while high petroleum hydrocarbon contamination reduced the richness of the microbial community (p < 0.05), simplified the microbial co-occurrence network, and increased the niche overlap of keystone genus.

Conclusion

Our study demonstrates that light petroleum hydrocarbon contamination has a certain improvement effect on soil multifunctionalities and microbial characteristics. While high contamination shows an inhibitory effect on soil multifunctionalities and microbial characteristics, which has significance for the protection and management of petroleum hydrocarbon-contaminated soil.

Enhanced removal of phenanthrene and nutrients in wetland sediment with metallic biochar: Performance and mechanisms

Polycyclic aromatic hydrocarbon (PAHs) are persistent organic pollutants and pose high risk in aquatic environment. The utilization of biochar is a strategy for PAHs-contaminated remediation but is challenging due to the adsorption saturation and reoccurrence of PAHs desorbed back into water. In this study, iron (Fe) and manganese (Mn) were provided as electron acceptors for biochar modification to enhance anaerobic biodegradation of phenanthrene (Phe). Results revealed that, the Mn(Ⅳ) and Fe(Ⅲ) modification improved the removal of Phe by 24.2% and 31.4% than that of biochar, respectively. Additionally, nitrate removal was improved by 19.5% with Fe(Ⅲ) amendment. The Mn-and Fe-biochar decreased Phe contents by 8.7% and 17.4% in sediment, 10.3% and 13.8% in biochar than that of biochar. Much higher DOC contents were observed with Mn- and Fe-biochar, which provided bioavailable carbon source for microbes and contributed to microbial degradation of Phe. The greater degree of humification, higher proportions of humic and fulvic acid like components in metallic biochar participated in electron transport and further enhancing the degradation of PAHs. Microbial analysis proved the high abundance of Phe-degrading bacteria (e.g. PAH-RHD_α, Flavobacterium and Vibrio), nitrogen removal microbes (e.g. amoA, nxrA, and nir), Fe and Mn bioreduction or oxidation (e. g. Bacillus, Thermomonas, Deferribacter) with metallic biochar. Based on the results, the Fe and Mn modification, especially Fe-modified biochar provided well performance for PAHs removal in aquatic sediment.

Autochthonous bioaugmentation accelerates phenanthrene degradation in acclimated soil

Bioaugmentation helps to obtain a microbiome capable of remediating polycyclic aromatic hydrocarbons (PAHs). In this study, acclimation of microorganisms to soil supplemented with phenanthrene (PHE) led to enrichment with PAH-degraders, including those in Actinobacteriota and in the genera Streptomyces, Rhodococcus, Nocardioides, Sphingomonas, and Mycobacterium. Aqueous (28 °C, pH 6.5) and soil cultures inoculated with PHE-acclimated soil showed a high PHE (ca. 50 mg L^-1) degradation efficiency. The PHE degradation kinetics in aqueous and soil incubations fitted to the Gompertz equation and the first-order kinetic equation, respectively. Indigenous microorganisms adapted to PHE in their environment, and this increased their capacity to degrade PHE. The effect of co-contaminants and pathway intermediates on PHE degradation showed that the degradation of PHE improved in the presence of diesel while being hindered by lubricant oil, catechol, salicylic and phthalic acid. Our findings provide theoretical and practical support for bioremediationof PAHs in the environment.

Remediation of benzo[a]pyrene contaminated soils by moderate chemical oxidation coupled with microbial degradation

Chemical oxidation is a promising technology for the remediation of organics-contaminated soils. However, residual oxidants and transformation products have adverse effects on microbial activities. This work aimed at moderate chemical oxidation coupled with microbial degradation (MOMD) for the removal of benzo[a]pyrene (BaP) by optimizing the type and dosage of oxidants. Potassium permanganate (KMnO₄), Fe²⁺ + sodium persulfate (Fe²⁺ + PS), Fenton's reagent (Fe²⁺ + H₂O₂), and hydrogen peroxide (H₂O₂) were compared for BaP removal from loam clay and sandy soils. Overall, the removal efficiency of BaP by a moderate dose of oxidant coupled indigenous microorganism was slightly lower than that by a high dose of relevant oxidant. The contributions of microbial degradation to the total removal of BaP varied for different oxidants and soils. The removal efficiency of BaP from loam clay sandy soil by a moderate dose of KMnO₄ (25 mmol/L) was 94.3 ± 1.1 % and 92.5 ± 1.8 %, respectively, which were both relatively higher than those under other conditions. The indirect carbon footprint yielded by the moderate dose of oxidants was 39.2-72.8 % less than that by the complete oxidation. A moderate dose of oxidants also reduced disturbances to soil pH and OC. The microbial communities after MOMD treatment were dominated by Burkholderiaceae, Enterobacteriaceae, Alicyclobacillaceae, and Oxalobacteraceae. These dominant microorganisms promoted the removal of BaP through the expression of polycyclic aromatic hydrocarbon-ring hydroxylated dioxygenase gene. Compared with complete chemical oxidation, MOMD is also a promising technique with the utilization of indigenous microorganism for remediating BaP-contaminated soils.

Enhanced remediation of oil-contaminated intertidal sediment by bacterial consortium of petroleum degraders and biosurfactant producers

Oil pollution in intertidal zones is an important environmental issue that has serious adverse effects on coastal ecosystems. This study investigated the efficacy of a bacterial consortium constructed from petroleum degraders and biosurfactant producers in the bioremediation of oil-polluted sediment. Inoculation of the constructed consortium significantly enhanced the removal of C₈-C₄₀n-alkanes (80.2 ± 2.8% removal efficiency) and aromatic compounds (34.4 ± 10.8% removal efficiency) within 10 weeks. The consortium played dual functions of petroleum degradation and biosurfactant production, greatly improving microbial growth and metabolic activities. Real-time quantitative polymerase chain reaction (PCR) showed that the consortium markedly increased the proportions of indigenous alkane-degrading populations (up to 3.88-times higher than that of the control treatment). Microbial community analysis demonstrated that the exogenous consortium activated the degradation functions of indigenous microflora and promoted synergistic cooperation among microorganisms. Our findings indicated that supplementation of a bacterial consortium of petroleum degraders and biosurfactant producers is a promising bioremediation strategy for oil-polluted sediments.

Enrichment of tetracycline-degrading bacterial consortia: Microbial community succession and degradation characteristics and mechanism

Tetracycline (TC) is an antibiotic that is recently found as an emerging pollutant with low biodegradability. Biodegradation shows great potential for TC dissipation. In this study, two TC-degrading microbial consortia (named SL and SI) were respectively enriched from activated sludge and soil. Bacterial diversity decreased in these finally enriched consortia compared with the original microbiota. Moreover, most ARGs quantified during the acclimation process became less abundant in the finally enriched microbial consortia. Microbial compositions of the two consortia as revealed by 16 S rRNA sequencing were similar to some extent, and the dominant genera Pseudomonas, Sphingobacterium, and Achromobacter were identified as the potential TC degraders. In addition, consortia SL and SI were capable of biodegrading TC (initial 50 mg/L) by 82.92% and 86.83% within 7 days, respectively. They could retain high degradation capabilities under a wide pH range (4-10) and at moderate/high temperatures (25-40 °C). Peptone with concentrations of 4-10 g/L could serve as a desirable primary growth substrate for consortia to remove TC through co-metabolism. A total of 16 possible intermediates including a novel biodegradation product TP245 were detected during TC degradation. Peroxidase genes, tetX-like genes and the enriched genes related to aromatic compound degradation as revealed by metagenomic sequencing were likely responsible for TC biodegradation.

Different phenanthrene degraders between free-cell mediated and biochar-immobilization assisted soil bioaugmentation as identified by RNA-based stable isotope probing (RNA-SIP)

Bioaugmentation (BA) is an effective approach to remove polycyclic aromatic hydrocarbons (PAHs) from contaminated soils, and biochar is frequently used to enhance PAH degradation performance. In this study, phenanthrene (PHE) degradation behavior and active degraders in a petroleum-contaminated soil were investigated and compared between free-cell mediated and biochar-immobilization assisted bioaugmentation. Biochar-immobilization assisted bioaugmentation (BA-IPB) introduced PHE degraders immobilized on biochar and effectively promoted PHE degradation, achieving higher PHE removal efficiencies within 24 h (~58 %) than free-cell mediated bioaugmentation (BA-FPB, ~39 %). Soil microbial community structure significantly changed in both BA-FPB and BA-IPB treatments. Through RNA-stable isotope probing (SIP), 14 and 11 bacterial lineages responsible for in situ PHE degradation were identified in BA-FPB and BA-IPB treatments, respectively. ASV_17 in BA-FPB treatment was Rhodococcus in the exogenous bacterial mixture; in contrast, none of exogenous bacteria were involved in PHE degradation in BA-IPB treatment. Methylobacterium (ASV_186), Xanthomonas (ASV_41), Kroppenstedtia (ASV_205), Scopulibacillus (ASV_243), Bautia (ASV_356), and Lactobacillus (ASV_376) were identified as PHE degraders for the first time. Our findings expanded the knowledge of the active PHE degraders and underlying mechanisms in bioaugmentation process, and suggested biochar-immobilization assisted bioaugmentation as a promising strategy for the bioremediation of PAH contaminated soils.

Complete pentachlorophenol biodegradation in a dual-working electrode bioelectrochemical system: Performance and functional microorganism identification

Bioelectrochemical system (BES) can effectively promote the reductive dechlorination of chlorophenols (CPs). However, the complete degradation of CPs with sequential dechlorination and mineralization processes has rarely achieved from the BES. Here, a dual-working electrode BES was constructed and applied for the complete degradation of pentachlorophenol (PCP). Combined with DNA-stable isotope probing (DNA-SIP), the biofilms attached on the anodic and cathodic electrode in the BES were analyzed to explore the dechlorinating and mineralizing microorganisms. Results showed that PCP removal efficiency in the dual-working BES (84% for 21 days) was 4.1 and 4.7 times higher than those of conventional BESs with a single anodic or cathodic working electrode, respectively. Based on DNA-SIP and high-throughput sequencing analysis, the cathodic working electrode harbored the potential dechlorinators (Comamonas, Pseudomonas, Methylobacillus, and Dechlorosoma), and the anodic working enriched the potential intermediate mineralizing bacteria (Comamonas, Stenotrophomonas, and Geobacter), indicating that PCP could be completely degraded under the synergetic effect of these functional microorganisms. Besides, the potential autotrophic functional bacteria that might be involved in the PCP dechlorination were also identified by SIP labeled with ¹³C-NaHCO₃. Our results proved that the dual-working BES could accelerate the complete degradation of PCP and enrich separately the functional microbial consortium for the PCP dechlorination and mineralization, which has broad potential for bioelectrochemical techniques in the treatment of wastewater contaminated with CPs or other halogenated organic compounds.

Exploring the PAHs dissipation and indigenous bacteria response in soil amended with two different microbial inoculants

This study investigated the bioremediation of PAHs in soil by two different microbial inoculants prepared with Paracoccus aminovorans HPD-2 and the carrier humic acid (HA) or montmorillonite (Mont). After incubation for 42 d, the greatest removal of PAHs, 42.8 % or 41.6 %, was observed in microcosms with 0.2 % HA inoculant or 2 % Mont inoculant. The PAH removal efficiency in these treatments was significantly greater than that in soil amended only with planktonic HPD-2. Bacterial community analysis showed that the survival of Paracoccus aminovorans was enhanced in the treatments with Mont inoculant compared with the treatments with HA inoculant or with HPD-2 alone. Moreover, the diversity of PAH-degrading bacterial genera was greater in the treatments containing Mont inoculant than in the treatments containing HA inoculant. These results indicate that the organic material HA and inorganic material Mont promote PAH removal in different ways. Specifically, HA promotes PAHs bioavailability to accelerate the degradation of PAHs in soil, whereas Mont protects PAH-degrading microorganisms to promote pollutant removal. Overall, the findings suggest that HA and Mont are promising materials for microbial immobilization for the bioremediation of PAH-contaminated soil.

Crop rotations increased soil ecosystem multifunctionality by improving keystone taxa and soil properties in potatoes

Continuous cropping of the same crop leads to soil degradation and a decline in crop production, and these impacts could be mitigated through rotation cropping. Although crop rotation enhances soil fertility, microbial community diversity, and potato yield, its effects on the soil ecosystem multifunctionality (EMF) remain unclear. In the present research, we comparatively examined the effects of potato continuous cropping (PP) and rotation cropping [potato-oat rotation (PO) and potato-forage maize rotation (PFM)] on the soil EMF as well as the roles of keystone taxa, microbes abundance, and chemical properties in EMF improvement. It was demonstrated that soil EMF is increased in rotation cropping (PO and PFM) than PP. Soil pH was higher in rotation cropping (PO and PFM) than in PP, while total phosphorus (TP) and available phosphorus (AP) were significantly decreased than that in PP. Rotation cropping (PO and PFM) markedly changed the bacterial and fungal community compositions, and improved the potential plant-beneficial fungi, e.g., Schizothecium and Chaetomium, while reducing the abundances of the potentially phytopathogenic fungi, e.g., Alternaria, Fusarium, Verticillium dahiae, Gibberella, Plectosphaerella, Colletotrichum, Phoma, and Lectera in comparison with PP. Also, co-occurrence patterns for bacteria and fungi were impacted by crop rotation, and keystone taxa, e.g., Nitrospira.1, Lysinibacillus, Microlunatus.1, Sphingomonas.3, Bryobacter.1, Micromonospora, and Schizothecium, were enriched in PO and PFM than PP. The structural equation model (SEM) further demonstrated that cropping systems increased soil ecosystem multifunctionality through regulating SOM and keystone taxa (Schizothecium1), and keystone taxa were mediated by soil pH. This study suggested that rotation cropping might contribute to the improvement of soil ecosystem multifunctionality as well as the development of disease-suppressive soils in comparison with potato continuous cropping.

The influence of anaerobic dechlorination on the aerobic degradation of PCBs in e-waste-contaminated soils in an anaerobic-aerobic two-stage treatment

The combination of microbial reductive dechlorination and aerobic oxidation (RD-AO) process was proposed to be a promising strategy for extensive bioremediation of highly chlorinated polychlorinated biphenyls (PCBs). Nonetheless, experimental evidence on the impact of the RD on subsequent AO in anaerobic-aerobic two-stage treatment remains scarce. The present study applied stable-isotope probing (SIP) to explore the RD-AO mediated degradation of PCBs in an e-waste-contaminated soil. The RD-AO treatment resulted in 37.1 % and 48.2 % degradation of PCB180 and PCB9, respectively, while the PCB9 degradation efficiency decreased compared to the sole AO (81.2 %). The inhibition of PCB aerobic degradation might be caused by the alteration of aerobic bacterial community, which was proved by a higher abundance of anaerobic bacteria and a lower abundance of aerobic bacteria being observed in the aerobic stage of RD-AO. Further evidence was obtained using DNA-SIP that the anaerobic stage altered the PCB degraders' community structures and changed three of the five degraders. There were four lineages (Arenimonas, Steroidobacter, Sulfurifustis, and Thermoanaerobacterales) identified as PCB degraders for the first time. Interestingly, three of them were found in RD-AO microcosm, suggesting that anaerobic-aerobic two-stage treatment can recruit novel bacteria involved in PCBs aerobic degradation. The present study provided novel insight into the synergistic integration of anaerobic and aerobic processes for extensive degradation of highly chlorinated PCBs.

Effects of Polyethylene Microplastics and Phenanthrene on Soil Properties, Enzyme Activities and Bacterial Communities

Microplastics (MPs) or polycyclic aromatic hydrocarbons (PAHs) pollution has received increasing concern due to their ubiquitous distribution and potential risks in soils. However, nothing is known about the influences of PAHs-MPs combined pollution on soil ecosystems. To address the knowledge gap, a 1-year soil microcosm experiment was conducted to systematically investigate the single and combined effect of polyethylene (PE) /phenanthrene (PHE) on soil chemical properties, enzymatic activities and bacterial communities (i.e., diversity, composition and function). Results showed that PE and PHE-PE significantly decreased soil pH. The available phosphorus (AP) and neutral phosphatase activity were not considerably changed by PHE, PE and PHE-PE. Significant enhancement of dehydrogenase activity in a PHE-PE amended system might be due to the degradation of PHE by indigenous bacteria (i.e., Sphingomonas, Sphingobium), and PE could enhance this stimulative effect. PHE and PHE-PE led to a slight increase in soil organic matter (SOM) and fluorescein diacetate hydrolase (FDAse) activity but a decrease in available nitrogen (AN) and urease activity. PE significantly enhanced the functions of nitrogen cycle and metabolism, reducing SOM/AN contents but increasing urease/FDAse activities. There were insignificant impacts on overall community diversity and composition in treated samples, although some bacterial genera were significantly stimulated or attenuated with treatments. In conclusion, the addition of PHE and PE influenced the soil chemical properties, enzymatic activities and bacterial community diversity/composition to some extent. The significantly positive effect of PE on the nitrogen cycle and on metabolic function might lead to the conspicuous alterations in SOM/AN contents and urease/FDAse activities. This study may provide new basic information for understanding the ecological risk of PAHs-MPs combined pollution in soils.

New insight into the mechanism underlying the effect of biochar on phenanthrene degradation in contaminated soil revealed through DNA-SIP

Biochar has been widely used for the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil, but its mechanism of influencing PAH biodegradation remains unclear. Here, DNA-stable isotope probing coupled with high-throughput sequencing was employed to assess its influence on phenanthrene (PHE) degradation, the active PHE-degrading microbial community and PAH-degradation genes (PAH-RHD_α). Our results show that both Low-BC and High-BC (soils amended with 1 % and 4 % w/w biochar, respectively) treatments significantly decreased PHE biodegradation and bioavailable concentrations with a dose-dependent effect compared to Non-BC treatment (soils without biochar). This result could be attributed to the immobilisation of PHE and alteration of the composition and abundance of the PHE-degrading microbial consortium by biochar. Active PHE degraders were identified, and those in the Non-BC, Low-BC and High-BC microcosms differed taxonomically. Sphaerobacter, unclassified Diplorickettsiaceae, Pseudonocardia, and Planctomyces were firstly linked with PHE biodegradation. Most importantly, the abundances of PHE degraders and PAH-RHD_α genes in the ¹³C-enriched DNA fractions of biochar-amended soils were greatly attenuated, and were significantly positively correlated with PHE biodegradation. Our findings provide a novel perspective on PAH biodegradation mechanisms in biochar-treated soils, and expand the understanding of the biodiversity of microbes involved in PAH biodegradation in the natural environment.

Shifts of the new functional marker gene (pahE) of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial population and its relationship with PAHs biodegradation

Identification of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial populations and understanding their responses to PAHs are crucial for the designing of appropriate bioremediation strategies. In this study, the responses of PAHs-degrading bacterial populations to different PAHs were studied in terms of the compositions and abundance variations of their new functional marker gene (pahE) by gene-targeted metagenomic and qPCR analysis. Overall, PAHs species significantly affected the composition and abundance of pahE gene within the PAHs-degrading bacteria in each treatment and different pahE of PAHs-degrading bacteria involved in the different stages of PAHs degradation. Noted that new pahE genotypes were also discovered in all PAHs treatment groups, indicating that some potential new PAHs-degrading bacterial genera were also involved in PAHs degradation. Besides, all three PAH removal rates were significantly positively related with pahE gene abundances (R² = 0.908 ~ 0.922, p < 0.01), demonstrating that pahE could be a good indicator of PAHs degradation activity or potential. This is the first study focusing on the dynamic changes of the pahE gene within PAHs-degrading bacterial community during the degradation of PAHs in mangrove sediment, providing novel insights into the use of pahE gene as the functional marker to indicate PAH degradation.

Coupling of desorption of phenanthrene from marine sediments and biodegradation of the sediment washing solution in a novel biochar immobilized-cell reactor

The recurrent dredging of marine sediments needs the use of ex-situ technologies such as sediment washing (SW) to effectively remove polycyclic aromatic hydrocarbons. Notwithstanding, the large volumes of generated spent SW effluents require adequate treatment by employing highly-efficient, inexpensive and environmentally-friendly solutions. This study proposes the phenanthrene (PHE) desorption from sediments using Tween® 80 (TW80) as extracting agent and the treatment of the resulting spent SW solution in a biochar (BC) immobilized-cell bioreactor. The SW process reached the highest PHE removal of about 91% using a surfactant solution containing 10,800 mg L^-1 of TW80. The generated amount of spent PHE-polluted SW solution can be controlled by keeping a solid to liquid ratio of 1:4. A PHE degradation of up to 96% was subsequently achieved after 43 days of continuous reactor operation, aerobically treating the TW80 solution in the BC immobilized-cell bioreactor with a hydraulic retention time of 3.5 days. Brevundimonas, Chryseobacterium, Dysgonomonas, Nubsella, and both uncultured Weeksellaceae and Xanthobacteraceae genera were mainly involved in PHE biodegradation. A rough economic study showed a total cost of 342.60 € ton^-1 of sediment, including the SW operations, TW80 and BC supply and the biological treatment of the SW solution.

Microbial community composition and function prediction involved in the hydrolytic bioreactor of coking wastewater treatment process

The hydrolytic acidification process has a strong ability to conduct denitrogenation and increase the biological oxygen demand/chemical oxygen demand ratio in O/H/O coking wastewater treatment system. More than 80% of the total nitrogen (TN) was removed in the hydrolytic bioreactor, and the hydrolytic acidification process contributed to the provision of carbon sources for the subsequent nitrification process. The structure and diversity of microbial communities were elaborated using high-throughput MiSeq of the 16S rRNA genes. The results revealed that the operational taxonomic units (OTUs) belonged to phyla Bacteroidetes, Betaproteobacteria, and Alphaproteobacteria were the dominant taxa involved in the denitrogenation and degradation of refractory contaminants in the hydrolytic bioreactor, with relative abundances of 22.94 ± 3.72, 29.77 ± 2.47, and 18.23 ± 0.26%, respectively. The results of a redundancy analysis showed that the OTUs belonged to the genera Thiobacillus, Rhodoplanes, and Hylemonella in the hydrolytic bioreactor strongly positively correlated with the chemical oxygen demand, TN, and the removal of phenolics, respectively. The results of a microbial co-occurrence network analysis showed that the OTUs belonged to the phylum Bacteroidetes and the genus Rhodoplanes had a significant impact on the efficiency of removal of contaminants that contained nitrogen in the hydrolytic bioreactor. The potential function profiling results indicate the complementarity of nitrogen metabolism, methane metabolism, and sulfur metabolism sub-pathways that were considered to play a significant role in the process of denitrification. These results provide new insights into the further optimization of the performance of the hydrolytic bioreactor in coking wastewater treatment.

Field-applied biochar-based MgO and sepiolite composites possess CO2 capture potential and alter organic C mineralization and C-cycling bacterial structure in fertilized soils

Agricultural soils contribute a significant amount of anthropogenic CO₂ emission, a greenhouse gas of global environmental concern. Hence, discovering sustainable materials that can capture CO₂ in cultivated soils is paramount. Since the effect of biochar on C mineralization/retention in fertilized soils is unclear, we produced biochar-based MgO and sepiolite-nanocomposites with CO₂ capture potential. The field-scale impacts of the modified-biochars were evaluated on net C exchange rate (NCER) periodically for 3 months in fertilized plots. The effects of the modified-biochar on organic-C mineralization, the activities, and dynamics of C-cycling-related 16S rRNA which are unknown, were investigated. Results revealed an initial rapid and higher cumulative CO₂ emission from the sole fertilizer treatment (F). Unlike the biochar treatment (BF), the successful incorporation of MgO/Mg(OH)₂ nanoparticles into the matrix and surface of biochar, and the potential formation of MgCO₃ with soil CO₂, mitigated CO₂ emission, especially in the MgO-modified biochar (MgOBF), compared to the sepiolite-biochar treatment (SBF). Compared to F and BF, the higher C retention as MgCO₃ in the modified biochar treatments led to an increase in cellulase activity, stimulation of key C-cycling-related bacteria, and the expression of genes associated with starch, sucrose, amino sugar, nucleotide sugar, ascorbate, aldarate, cellulose, and chitin degradation, thus, increasing organic C mineralization. Among the modified-biochar treatments, higher C mineralization was recorded in SBF, resulting in increased cumulative CO₂ emission, despite its initial capture for up to 42 days. However, MgOBF was effective in capturing soil-derived CO₂, despite the increased C mineralization compared to biochar. The changes in soil moisture and temperature significantly regulated NCER. Also, the modified biochars positively influenced the distribution of C-cycling-related bacteria by improving soil pH and available nutrients. Among the modified biochars, the observed higher mitigation effect of MgOBF on NCER indicated that it could be preferably applied in agricultural soils.

Mechanism of salicylic acid in promoting the rhizosphere benzo[a]pyrene biodegradation as revealed by DNA-stable isotope probing

Benzo[a]pyrene (BaP) is a typical high-molecular-weight PAH with carcinogenicity. Rhizoremediation is commonly applied to remove soil BaP, but its mechanism remains unclear. The role of inducers in root exudates in BaP rhizoremediation is rarely studied. Here, to address this problem, we firstly investigated the effect of the inducer salicylic acid on BaP rhizoremediation, rhizosphere BaP degraders, and PAH degradation-related genes by combining DNA-stable-isotope-probing, high-throughput sequencing, and gene function prediction. BaP removal in the rhizosphere was significantly increased by stimulation with salicylic acid, and the rhizosphere BaP-degrading microbial community structure was significantly changed. Fourteen microbes were responsible for the BaP metabolism, and most degraders, e.g. Aeromicrobium and Myceligenerans, were firstly linked with BaP biodegradation. The enrichment of the PAH-ring hydroxylating dioxygenase (PAH-RHD) gene in the heavy fractions of all ¹³C-treatments further indicated their involvement in the BaP biodegradation, which was also confirmed by the enrichment of dominant PAH degradation-related genes (e.g. PAH dioxygenase and protocatechuate 3,4-dioxygenase genes) based on gene function prediction. Overall, our study demonstrates that salicylic acid can enhance the rhizosphere BaP biodegradation by altering the community structure of rhizosphere BaP-degrading bacteria and the abundance of PAH degradation-related genes, which provides new insights into BaP rhizoremediation mechanisms in petroleum-contaminated sites.

Identifying the Active Phenanthrene Degraders and Characterizing Their Metabolic Activities at the Single-Cell Level by the Combination of Magnetic-Nanoparticle-Mediated Isolation, Stable-Isotope Probing, and Raman-Activated Cell Sorting (MMI-SIP-RACS)

Magnetic-nanoparticle-mediated isolation coupled with stable-isotope probing (MMI-SIP) is a cultivation-independent higher-resolution approach for isolating active degraders in their natural habitats. However, it addresses the community level and cannot directly link the microbial identities, phenotypes, and in situ functions of the active degraders at the single-cell level within complex microbial communities. Here, we used ¹³C-labeled phenanthrene as the target and developed a new method coupling MMI-SIP and Raman-activated cell sorting (RACS), namely, MMI-SIP-RACS, to identify the active phenanthrene-degrading bacterial cells from polycyclic aromatic hydrocarbon (PAH)-contaminated wastewater. MMI-SIP-RACS significantly enriched the active phenanthrene degraders and successfully isolated the representative single cells. Amplicon sequencing analysis by SIP, ¹³C shift of the single cell in Raman spectra, and the 16S rRNA gene from single cell sequencing via RACS confirmed that Novosphingobium was the active phenanthrene degrader. Additionally, MMI-SIP-RACS reconstructed the phenanthrene metabolic pathway and genes of Novosphingobium, including two novel genes encoding phenanthrene dioxygenase and naphthalene dioxygenase. Our findings suggested that MMI-SIP-RACS is a powerful method to efficiently and precisely isolate active PAH degraders from complex microbial communities and directly link their identities to functions at the single-cell level.

Negative correlations between cultivable and active-yet-uncultivable pyrene degraders explain the postponed bioaugmentation

Bioaugmentation is an effective approach to remediate soils contaminated by polycyclic aromatic hydrocarbons (PAHs), but suffers from unsatisfactory performance in engineering practices, which is hypothetically explained by the complicated interactions between indigenous microbes and introduced degraders. This study isolated a cultivable pyrene degrader (Sphingomonas sp. YT1005) and an active pyrene degrading consortium (Gp16, Streptomyces, Pseudonocardia, Panacagrimonas, Methylotenera and Nitrospira) by magnetic-nanoparticle mediated isolation (MMI) from soils. Pyrene biodegradation was postponed in bioaugmentation with Sphingomonas sp. YT1005, whilst increased by 30.17% by the active pyrene degrading consortium. Pyrene dioxygenase encoding genes (nidA, nidA3 and PAH-RHDα-GP) were enriched in MMI isolates and positively correlated with pyrene degradation efficiency. Pyrene degradation by Sphingomonas sp. YT1005 only followed the phthalate pathway, whereas both phthalate and salicylate pathways were observed in the active pyrene degrading consortium. The results indicated that the uncultivable pyrene degraders were suitable for bioaugmentation, rather than cultivable Sphingomonas sp. YT1005. The negative correlations between Sphingomonas sp. YT1005 and the active-yet-uncultivable pyrene degraders were the underlying mechanisms of bioaugmentation postpone in engineering practices.

The effect of rhizosphere and the plant species on the degradation of sulfonamides in model constructed wetlands treating synthetic domestic wastewater

The effects of and main contributors in rhizosphere and plant species on the degradation of sulfonamides (SAs) in constructed wetland (CW) models for the treatment of domestic wastewater are currently unclear. To investigate the degradation and key rhizosphere factors of mixed SAs with sulfadiazine (SDZ), sulfapyridine (SPD), sulfamerazine (SMZ1), sulfamethazine (SMZ2), and sulfamethoxazole (SMX) at millimeter distances from the root surface, a multi-interlayer rhizobox experiment planted with Cyperus alternifolius, Juncus effusus, Cyperus papyrus, and an unvegetated control was conducted. There was a higher O₂ saturation and dissolved organic carbon (DOC) content and a lower SA content in the rhizosphere and near/moderate-rhizosphere (0-3 and 3-8 mm from rhizosphere) than the far/non-rhizosphere (8-40 and 40-90 mm from rhizosphere). Bacterial abundance and community composition was indicative of the microbial degradation of SAs. Both the O₂ and DOC contents promoted total bacterial abundance in different zones from CW rhizoboxes. The relative abundance of the most dominant bacteria was significantly correlated with O₂, DOC, and SAs, except SMX, which also indicates other dissipation processes for SMX in the rhizosphere. Furthermore, more metabolites and aerobic SA-degrading bacteria were observed in the rhizosphere and near/moderate-rhizosphere than in the far/non-rhizosphere zones, suggesting that the effect of O₂ in the rhizosphere is important in the degradation of SAs in CWs.

Application oriented bioaugmentation processes: Mechanism, performance improvement and scale-up

Bioaugmentation is an optimization method with great potential to improve the treatment effect by introducing specific strains into the biological treatment system. In this study, a comprehensive review of the mechanism of bioaugmentation from the aspect of microbial community structure, the optimization methods facilitating application as well as feasible approaches of scale-up application has been provided. The different contribution of indigenous and exogenous strains was critically analyzed, the relationship between microbial community variation and system performance was clarified. Operation regulation and immobilization technologies are effective methods to deal with the possible failure of bioaugmentation. The gradual expansion from lab-scale, pilot scale to full-scale, the transformation and upgrading of wastewater treatment plants through the combination of direct dosing and biofilm, and the application of side-stream reactors are feasible ways to realize the full-scale application. The future challenges and prospects in this field were also proposed.

Identification of pyrene degraders via DNA-SIP in oilfield soil during natural attenuation, bioaugmentation and biostimulation

Pyrene is a model contaminant of high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs), which are compounds that have potential carcinogenic effects and pose a serious threat to human health. Finding effective pyrene-degrading bacteria is crucial for removing PAHs from soil. In this study, DNA-based stable isotope probing (DNA-SIP) technology was used to investigate pyrene degraders in PAH-contaminated oilfield soil during natural attenuation (NA), bioaugmentation (BA) and biostimulation (BS). The results show that BA played an important role in pyrene degradation with the highest pyrene removal rate (~95%) after 12 days incubation, followed by removal rates of ~90% for NA and ~30% for BS. In addition, 6 novel pyrene degraders were identified, while 12 well-known PAH degraders were demonstrated to participate in the biodegradation of pyrene. Additionally, the external homologous strains introduced during BA promoted the degradation of pyrene, but not by directly participating in the metabolism of the target compound. Rhamnolipid supplementation during BS promoted the involvement of more microorganisms in the degradation of pyrene, which was beneficial to identifying more pyrene degraders via DNA-SIP. These findings provide new insight into the effects of external homologous strains and supplementary rhamnolipids on pyrene degradation.

Mitigating NO and N2O emissions from a pilot-scale oxidation ditch using bioaugmentation of immobilized aerobic denitrifying bacteria

Nitrous oxide (N₂O) emission from wastewater treatment plants (WWTPs) requires urgent mitigation because of its significant contribution to the greenhouse effect. In this study, bioaugmentation was applied in a pilot-scale oxidation ditch with the aerobic denitrifying bacteria strain PCN-1 immobilized on polyurethane biocarriers, which demonstrated effective N₂O mitigation. Microbial community analysis suggested that the bioaugmentation facilitated a symbiotic relationship of the bacterial populations between the activated sludge and the biocarriers. The denitrifying bacteria with well-known N₂O reducing capabilities predominated on the biocarriers. Correspondingly, the increases of denitrifying genes and NO and N₂O reductase provided evidence for the enhanced genetic potential for NO and N₂O reduction. Besides, the enriched comammox Nitrospira on the biocarriers is proposed as another significant driver for N₂O mitigation by avoiding nitrite accumulation. In addition, the bioaugmentation enhanced the stability and recovery capability of the system in the ammonia overload and aeration failure shock tests.

Unveiling metabolic characteristics of an uncultured Gammaproteobacterium responsible for in situ PAH biodegradation in petroleum polluted soil

Exploring the metabolic characteristics of indigenous PAH degraders is critical to understanding the PAH bioremediation mechanism in the natural environment. While stable-isotopic probing (SIP) is a viable method to identify functional microorganisms in complex environments, the metabolic characteristics of uncultured degraders are still elusive. Here, we investigated the naphthalene (NAP) biodegradation of petroleum polluted soils by combining SIP, amplicon sequencing and metagenome binning. Based on the SIP and amplicon sequencing results, an uncultured Gammaproteobacterium sp. was identified as the key NAP degrader. Additionally, the assembled genome of this uncultured degrader was successfully obtained from the ¹³ C-DNA metagenomes by matching its 16S rRNA gene with the SIP identified OTU sequence. Meanwhile, a number of NAP degrading genes encoding naphthalene/PAH dioxygenases were identified in this genome, further confirming the direct involvement of this indigenous degrader in the NAP degradation. The degrader contained genes related to the metabolisms of several carbon sources, energy substances and vitamins, illuminating potential reasons for why microorganisms cannot be cultivated and finally realize their cultivation. Our findings provide novel information on the mechanisms of in situ PAH biodegradation and add to our current knowledge on the cultivation of non-culturable microorganisms by combining both SIP and metagenome binning.

Effects of polycyclic aromatic hydrocarbon structure on PAH mineralization and toxicity to soil microorganisms after oxidative bioremediation by laccase

While bioremediation using soil microorganisms is considered an energy-efficient and eco-friendly approach to treat polycyclic aromatic hydrocarbon (PAH)-contaminated soils, a variety of polar PAH metabolites, particularly oxygenated ones, could increase the toxicity of the soil after biodegradation. In this study, a typical bio-oxidative transformation of PAH into quinones was investigated in soil amended with laccase using three PAHs with different structures (anthracene, benzo[a]anthracene, and benzo[a]pyrene) to assess the toxicity after oxidative bioremediation. The results show that during a 2-month incubation period the oxidation process promoted the formation of non-extractable residues (NERs) of PAHs, and different effects on mineralization were observed among the three PAHs. Oxidation enhanced the mineralization of the high-molecular-weight (HMW) PAHs (benzo[a]anthracene and benzo[a]pyrene) but inhibited the mineralization of the low-molecular-weight (LMW) PAH (anthracene). The inhibition of anthracene suggests increased toxicity after oxidative bioremediation, which coincided with a decrease in soil nitrification activity, bacterial diversity and PAH-ring hydroxylating dioxygenase gene copies. The analysis of PAH metabolites in soil extract indicated that oxidation by laccase was competitive with the natural transformation processes of PAHs and revealed that intermediates other than quinone metabolites increased the toxicity of soil during subsequent degradation. The different metabolic profiles of the three PAHs indicated that the toxicity of soil after PAH oxidation by laccase was strongly affected by the PAH structure. Despite the potential increase in toxicity, the results suggest that oxidative bioremediation is still an eco-friendly method for the treatment of HMW PAHs since the intermediates from HMW PAHs are more easily detoxified via NER formation than LMW PAHs.

Bacterial contribution to 17β-estradiol mineralization in lake sediment as revealed by 13C-DNA stable isotope probing

The accumulation of estrogens in aquatic environments has drawn increasing public concern due to their adverse effects on aquatic ecosystems and human health. Bacteria play important roles in eliminating estrogens from the environment, but knowledge of the identity and functions of the microorganisms involved in metabolizing these steroid hormones in the natural microbial communities is lacking. Here, we added ¹³C-17β-estradiol (¹³C-E2) to sediments collected from Zhushan (ZS) Bay, Meiliang (ML) Bay, Gonghu (GH) Bay, and the central area (CA) of the Taihu Lake. The indigenous assimilators of E2 in the sediments were recognized using ¹³C-DNA stable isotope probing (DNA-SIP), and their effects on ¹³C-E2 mineralization were studied under aerobic condition. During the 30-day incubation period, ZS Bay had the highest cumulative percentage of ¹³C-E2 mineralization to ¹³CO₂ (65.5%), while CA presented the lowest (51.4%). Based on DNA-SIP, we saw that Novosphingobium, Ralstonia, Pseudomonas, Sphingomonas, Nitrosomonas, and Alcaligenes were involved in E2-derived ¹³C assimilation for the entire incubation period. Acinetobacter, Flavobacterium, and Mycobacterium only assimilated ¹³C for the first half of the incubation. H16 was identified as an E2 assimilator for the first time in this study. In addition, the temporal changes in assimilator abundances during the incubation period indicated that these genera played dominant roles at different stages in the process of E2 biodegradation. The bacteria engaged in the assimilation of E2 in situ were identified, and the rate of increase in the relative abundance of assimilators was significantly (P < 0.05) and positively correlated with the E2 mineralization in sediments. This information enhances our knowledge of in situ E2 biodegradation and provides a potential resource that could be used to eliminate estrogens in sediments.

The catabolic pathways of in situ rhizosphere PAH degraders and the main factors driving PAH rhizoremediation in oil-contaminated soil

Rhizoremediation is a potential technique for polycyclic aromatic hydrocarbon (PAH) remediation; however, the catabolic pathways of in situ rhizosphere PAH degraders and the main factors driving PAH rhizoremediation remain unclear. To address these issues, stable-isotope-probing coupled with metagenomics and molecular ecological network analyses were first used to investigate the phenanthrene rhizoremediation by three different prairie grasses in this study. All rhizospheres exhibited a significant increase in phenanthrene removal and markedly modified the diversity of phenanthrene degraders by increasing their populations and interactions with other microbes. Of all the active phenanthrene degraders, Marinobacter and Enterobacteriaceae dominated in the bare and switchgrass rhizosphere respectively; Achromobacter was markedly enriched in ryegrass and tall fescue rhizospheres. Metagenomes of ¹³ C-DNA illustrated several complete pathways of phenanthrene degradation for each rhizosphere, which clearly explained their unique rhizoremediation mechanisms. Additionally, propanoate and inositol phosphate of carbohydrates were identified as the dominant factors that drove PAH rhizoremediation by strengthening the ecological networks of soil microbial communities. This was verified by the results of rhizospheric and non-rhizospheric treatments supplemented with these two substances, further confirming their key roles in PAH removal and in situ PAH rhizoremediation. Our study offers novel insights into the mechanisms of in situ rhizoremediation at PAH-contaminated sites.

Asphaltene biotransformation for heavy oil upgradation

Globally, the reserves of heavy crude oil are seven times more abundant than that of light crude, and yet, they are underutilized because of their high viscosity and density, which is largely due to the presence of large amounts of asphaltenes. Biotransformation of heavy oil asphaltenes into smaller metabolites can be used for reducing their viscosity. Several microorganisms capable of asphaltene biodegradation have been reported but only few have been characterized for its biotransformation. In the present study, a 9-membered microbial consortium was isolated from an oil contaminated soil. About 72% and 75% asphaltene biotransformation was achieved by growing cells at shake flask level and in a 1.5 l bioreactor, respectively. A representative structure of asphaltene was constructed based on LC–MS, ¹H-NMR, ¹³C-NMR, FT-IR, ICPMS and elemental analysis (CHNS) of n-heptane purified asphaltene from Maya crude oil. Biotransformation of asphaltene, as analyzed by performing ¹H-NMR, FT-IR and elemental analysis, resulted in 80% decrease in S and N when compared to the control along with incorporation of oxygen in the structure of asphaltene. About 91% decrease in the viscosity of the Maya crude oil was observed after two weeks when oil: aqueous phase ratio was 1:9. The results suggest that the isolated microbial consortium can be used for biological upgradation of heavy crude oil. To our knowledge, this is the first report where a microbial consortium resulted in such high asphaltene biotransformation.

Field study on the soil bacterial associations to combined contamination with heavy metals and organic contaminants

The understanding of soil microbial associations to combined contamination would substantially benefit the restoration of damaged ecosystems, which is currently limited at the field scale. In this study, we investigated the soil bacterial associations to combined contamination with metals (Cd, Cu, Hg, Pb, and Zn), polyaromatic hydrocarbons (PAHs), and polybrominated diphenyl ethers (PBDEs). Samples were collected from field sites under five land-use patterns with electronic waste recycling. Results showed that the contents of Cd (0.22-12.86 mg/kg), Cu (17-14,136 mg/kg), Pb (4.6-77,014 mg/kg), Hg (0.28-22 mg/kg), Zn (26-42,495 mg/kg), PAHs (4.6-1753 μg/kg), and PBDEs (1.9-1079 μg/kg) varied significantly across sites. We observed positive correlations between catalase activity and heavy metals, indicative of a resistance response to the oxidative stress induced by metals. Furthermore, the bacterial community diversity was found to be determined primarily by PBDEs, whereas acenaphthylene, available phosphorus, and 2,2',3,3',4,5,6-heptabrominated diphenyl ether (BDE-183) were the three major drivers affecting community composition. The co-occurrence network constructed for bacterial communities exposed to combined contamination was non-random with scale-free, small-world and modularity features. We further proposed functional roles of the modules including stress resistance, hydrocarbon degradation, and nutrient cycling. Overall, the findings of redundancy analysis, variation partition analysis and the co-occurrence network indicated that soil bacterial community under combined contamination cooperated to survive. Members including Rhodoplanes and Nitrospira were capable of degrading PAHs and PBDEs in various pathways, while others, including Acinetobacter, Citrobacter, and Pseudomonas, reduced the metal toxicity to the community. Our findings provide new insights into the responses of soil bacteria, particularly in terms of inter-specific relationships, under combined contamination at the field scale.

Metagenomic analysis of aromatic ring-cleavage mechanism in nano-Fe3O4@activated coke enhanced bio-system for coal pyrolysis wastewater treatment

In current study, nano-Fe₃O₄@activated coke enhanced bio-system (FEBS) under limited-oxygen condition was applied for efficient treatment of aromatic organics in coal pyrolysis wastewater. Metagenomic analyses revealed functional microbiome linkages and mechanism involved in aromatic ring-cleavage. Based on biodegradation efficiency in different reactors, FEBS supplementation conferred the best organic removal (avg. 92.29%). It also showed a remarkable advantage in biodegradability maintenance (>40%) over control reactors. Metagenomics profiling revealed the degradation processes were driven by Fe₃O₄ redox reactions and microbial biofilm, while the suspended sludge was the principal force for aromatic mineralization. Based on the analysis of functional species and genes, most bacteria cleaved the benzene ring preferably through the aerobic pathways, mediated by catechol 1, 2-dioxygenase, catechol 2, 3-dioxygenase and protocatechuate 3, 4-dioxygenase (66-84%). Ecological network showed that Comamonas testosterone-centered microbiome and Azotobacter linked to the nitrogen (N)-heterocyclic ring-cleavage. Network linkage further demonstrated that Alicycliphilus and Acidovorax were the key tone taxa involved in benzene ring-cleavage. Finally, combined with analysis of degradation products, bacteria degraded N-heterocyclic ring containing organic aromatic compounds (quinoline) mainly through anaerobic processes, whereas cleavage of benzene ring preferred aerobic pathways. The enriched functional species were the primary reason for the enhanced biodegradation in FEBS.

Distinct Functions and Assembly Mechanisms of Soil Abundant and Rare Bacterial Taxa Under Increasing Pyrene Stresses

Elucidating the relative importance of species interactions and assembly mechanisms in regulating bacterial community structure and functions, especially the abundant and rare subcommunities, is crucial for understanding the influence of environmental disturbance in shaping ecological functions. However, little is known about how polycyclic aromatic hydrocarbon (PAH) stress alters the stability and functions of the abundant and rare taxa. Here, we performed soil microcosms with gradient pyrene stresses as a model ecosystem to explore the roles of community assembly in determining structures and functions of the abundant and rare subcommunities. The dose–effect of pyrene significantly altered compositions of abundant and rare subcommunities. With increasing pyrene stresses, diversity increased in abundant subcommunities, while it decreased in the rare. Importantly, the abundant taxa exhibited a much broader niche width and environmental adaptivity than the rare, contributing more to pyrene biodegradation, whereas rare taxa played a key role in improving subcommunity resistance to stress, potentially promoting community persistence and stability. Furthermore, subcommunity co-occurrence network analysis revealed that abundant taxa inclined to occupy the core and central position in adaptation to the pyrene stresses. Stochastic processes played key roles in the abundant subcommunity rather than the rare subcommunity. Overall, these findings extend our understanding of the ecological mechanisms and interactions of abundant and rare taxa in response to pollution stress, laying a leading theoretical basis that abundant taxa are core targets for biostimulation in soil remediation.

Stable-isotope probing coupled with high-throughput sequencing reveals bacterial taxa capable of degrading aniline at three contaminated sites with contrasting pH

The biodegradation of aniline is an important process related to the attenuation of aniline pollution at contaminated sites. Aniline contamination could occur in various pH (i.e., acidic, neutral, and alkaline) environments. However, little is known about preferred pH conditions of diverse aniline degraders at different sites. This study investigated the active aniline degraders present under contrasting pH environments using three aniline-contaminated cultures, namely, acidic sludge (ACID-S, pH 3.1), neutral river sediment (NEUS, pH 6.6), and alkaline paddy soil (ALKP, pH 8.7). Here, DNA-based stable isotope probing coupled with high-throughput sequencing revealed that aniline degradation was associated with Armatimonadetes sp., Tepidisphaerales sp., and Rhizobiaceae sp. in ACID-S; Thauera sp., Zoogloea sp., and Acidovorax sp. in NEUS; Delftia sp., Thauera sp., and Nocardioides sp. in ALKP. All the putative aniline-degrading bacteria identified were present in the "core" microbiome of these three cultures; however, only an appropriate pH may facilitate their ability to metabolize aniline. In addition, the biotic interactions between putative aniline-degrading bacteria and non-direct degraders showed different characteristics in three cultures, suggesting aniline-degrading bacteria employ diverse survival strategies in different pH environments. These findings expand our current knowledge regarding the diversity of aniline degraders and the environments they inhabit, and provide guidance related to the bioremediation of aniline contaminated sites with complex pH environments.

Effects of Different Continuous Cropping Years on Bacterial Community and Diversity of Cucumber Rhizosphere Soil in Solar-Greenhouse

The rhizosphere soils from 1, 3, 5, and 7 years of cucumber continuous cropping in solar-greenhouse were used as the research objects. The region of bacterial 16S rRNA was analyzed by Illumina MiSeq high-throughput sequencing technology. The effect of continuous cropping years on the microbial community structure and diversity in cucumber soil in the greenhouse was investigated. The physical and chemical properties of soil and the activities of urease and catalase were determined. The results showed that cucumber crop succession for different years affected the community composition of the bacteria at the phylum level, and the abundance of Proteobacteria, Chloroflexi, Gemmatimonadetes, Patescibacteria and Firmicutes gradually increased, while Actinobacteria in the soil significantly decreased. Among the top 15 significantly different genera, with the extension of successive years, the relative abundance of most genera in bacteria decreased after a small increase in year 3. The diversity results indicated that soil samples from continuous cropping for 7 years had the lowest community diversity. PICRUSt analysis showed a decreasing trend in soil bacterial function as the cucumber crop succession age increased. In environmental factor clustering analysis, the soil bacterial community was significantly correlated with pH, available nitrogen (AN), soil urease (SUR) and available phosphorus (AP), and the effect on the bacterial community was expressed as SUR > AP > AN > pH.

DNA-SIP identification of phenanthrene-degrading bacteria undergoing bioaugmentation and natural attenuation in petroleum-contaminated soil

DNA-stable isotope probing (SIP) with ¹³C labeled phenanthrene (PHE) as substrate was used to identify specific bacterial degraders during natural attenuation (NA) and bioaugmentation (BA) in petroleum contaminated soil. BA, with the addition of a bacterial suspension mixture named GZ, played a significant role in PHE degradation with a higher PHE removal rate (∼90%) than that of NA (∼80%) during the first 3 days, and remarkably altered microbial communities. Of the five strains introduced in BA, only two genera, particularly, Ochrobactrum, Rhodococcus were extensively responsible for PHE-degradation. Six (Bacillus sp., Acinetobacter sp., Xanthomonas sp., Conexibacter sp., Acinetobacter sp. and Staphylococcus sp.) and seven (Ochrobactrum sp., Rhodococcus sp., Alkanindiges sp., Williamsia sp., Sphingobium sp., Gillisia sp. and Massilia sp.) bacteria responsible for PHE degradation were identified in NA and BA treatments, respectively. This study reports for the first time the association of Xanthomonas sp., Williamsia sp., and Gillisia sp. to PHE degradation.