A comprehensive feasibility study of effectiveness and environmental impact of PAH bioremediation using an indigenous microbial degrader consortium and a novel strain Stenotrophomonas maltophilia CPHE1 isolated from an industrial polluted soil

Enhanced phenanthrene biodegradation in river sediments by harnessing calcium peroxide nanoparticles and minerals in Sphingomonas sp. DSM 7526 cultivation

Coupling chemical oxidation and biodegradation to remediate polycyclic aromatic hydrocarbon (PAH)-contaminated sediment has recently gained significant attention. In this study, calcium peroxide nanoparticles (nCaO2) were utilized as an innovative oxygen-releasing compound for in-situ chemical oxidation. The study investigates the bioremediation of phenanthrene (PHE)-contaminated sediment inoculated with Sphingomonas sp. DSM 7526 bacteria and treated with either aeration or nCaO2. Using three different culture media, the biodegradation efficiencies of PHE-contaminated anoxic sediment, aerobic sediment, and sediment treated with 0.2% w/w nCaO2 ranged from 57.45% to 63.52%, 69.87% to 71.00%, and 92.80% to 94.67%, respectively. These values were significantly higher compared to those observed in non-inoculated sediments. Additionally, the type of culture medium had a prominent effect on the amount of PHE removal. The presence of minerals in the culture medium increased the percentage of PHE removal compared to distilled water by about 2-10%. On the other hand, although the application of CaO2 nanoparticles negatively impacted the abundance of sediment bacteria, resulting in a 30-42% decrease in colony-forming units after 30 days of treatment, the highest PHE removal was obtained when coupling biodegradation and chemical oxidation. These findings demonstrate the successful application of bioaugmentation and chemical oxidation processes for treating PAH-contaminated sediment.

Removal of Ibuprofen in Water by Bioaugmentation with Labrys neptuniae CSW11 Isolated from Sewage Sludge-Assessment of Biodegradation Pathway Based on Metabolite Formation and Genomic Analysis

Ibuprofen (IBP) is one of the most consumed drugs in the world. It is only partially removed in wastewater treatment plants (WWTPs), being present in effluent wastewater and sewage sludge, causing the widespread introduction of IBP as an emergent xenobiotic in different environmental compartments. This study describes the use of Labrys neptuniae CSW11, recently described as an IBP degrader, through bioaugmentation processes for the removal of IBP from water under different conditions (additional carbon sources, various concentrations of glucose and IBP). L. neptuniae CSW11 showed very good results in a wide range of IBP concentrations, with 100% removal in only 4 days for 1 and 5 mg L-1 IBP and 7 days for 10 mg L-1, and up to 48.4% removal in 28 days for IBP 100 mg L-1 when using glucose 3 g L-1 as an additional carbon source. Three IBP metabolites were identified during the biotransformation process: 1-hydroxyibuprofen (1-OH-IBP), 2-hydroxyibuprofen (2-OH-IBP), and carboxyibuprofen (CBX-IBP), whose concentrations declined drastically in the presence of glucose. IBP metabolites maintained a certain degree of toxicity in solution, even when IBP was completely removed. The results indicate that L. neptuniae CSW11 can be quite effective in degrading IBP in water, but the bioaugmentation method should be improved using CSW11 in consortia with other bacterial strains able to degrade the toxic metabolites produced. A genome-based analysis of L. neptuniae CSW11 revealed different enzymes that could be involved in IBP biodegradation, and a potential metabolic pathway was proposed based on the metabolites observed and genome analysis.

Enhancement of repeated inoculation strategy with a domesticated bacterial consortium on the biodegradation of high-level crude oil in soil

Repeated inoculation of hydrocarbon degrading microbes should be powerful to improve the survival of inoculant, which is vital to achieve efficient remediation of petroleum contaminated soil. This paper aims to study the repeated inoculation (with different inoculum size and time interval) enhanced bioremediation of high-level petroleum contaminated soil with a domesticated bacterial consortium. The copy number of bacterium and alkB gene, soil enzyme activities and microbial community structure during the remediation were systematically analyzed to preliminarily reveal the mechanism of repeated inoculation affecting remediation for the first time. The results revealed that repeated inoculation remarkably improved the total petroleum hydrocarbon (TPH) removal in soil (86.5 % in HC120) compared with a single inoculation (68.9 % in HA120). The TPH removal of repeated inoculation with high inoculum size (HC) on the 60th day was close to that of once inoculation (HA) on the 120th day, suggesting that repeated inoculation led to faster degradation. Interestingly, the effect of inoculation with low dose and more times (LC120, 78.5 %) was equal to that with high dose and less times (HB120, 78.0 %), even much better than that with high dose and once inoculation (HA120). Treatment HC had a significant impact on the soil bacterial diversity and community structure, and the dominant species in the inoculants, such as Stenotrophomonas and Pseudomonas, which was low abundance in the blank group (CK), still maintained high abundance during the remediation process. The soil catalase activities and the number of alkB gene were the highest in HC. Correlation analysis implied that repeated inoculation of hydrocarbon degrading bacteria did improve the survival of inoculant, soil enzyme activities and maintain the number of degrading bacteria, thus promoting the TPH removal. These findings will facilitate the practical application of bioremediation technology to contaminated environment, which has important environmental and economic benefits.

Bacterial bioaugmentation for paracetamol removal from water and sewage sludge. Genomic approaches to elucidate biodegradation pathway

Wastewater treatment plants (WWTPs) are recognized as significant contributors of paracetamol (APAP) into the environment due to their limited ability to degrade it. This study used a bioaugmentation strategy with Pseudomonas extremaustralis CSW01 and Stutzerimonas stutzeri CSW02 to achieve APAP biodegradation in solution in wide ranges of temperature (10-40 °C) and pH (5-9), reaching DT50 values < 1.5 h to degrade 500 mg L-1 APAP. Bacterial strains also mineralized APAP in solution (<30 %), but when forming consortia with Mycolicibacterium aubagnense HPB1.1, mineralization significantly increased (up to 74 % and 58 % for CSW01 +HPB1.1 and CSW02 +HPB1.1, respectively), decreasing DT50 values to only 1 and 9 days. Despite the complete degradation of APAP and its high mineralization, residual toxicity throughout the process was observed. Three APAP metabolites were identified (4-aminophenol, hydroquinone and trans-2-hexenoic acid) that quickly disappeared, but residual toxicity remained, indicating the presence of other non-detected intermediates. CSW01 and CSW02 degraded also 100 % APAP (50 mg kg-1) adsorbed on sewage sludge, with DT50 values of only 0.7 and 0.3 days, respectively, but < 15 % APAP was mineralized. A genome-based analysis of CSW01 and CSW02 revealed that amidases, deaminases, hydroxylases, and dioxygenases enzymes were involved in APAP biodegradation, and a possible metabolic pathway was proposed.

Carbon-based adsorbents for the mitigation of polycyclic aromatic hydrocarbon: a review of recent research

Accumulation of polycyclic aromatic hydrocarbons (PAH) poses significant dangers to the environment and human health. The advancement of technology for cleaning up PAH-contaminated environments is receiving more attention. Adsorption is the preferred and most favorable approach for cleaning up sediments polluted with PAH. Due to their affordability and environmental friendliness, carbonaceous adsorbents (CAs) have been regarded as promising for adsorbing PAH. However, adsorbent qualities, environmental features, and factors may all significantly impact how well CAs remove PAH. According to growing data, CAs, most of which come from laboratory tests, may be utilized to decontaminate PAH in aquatic setups. However, their full potential has not yet been established, especially concerning field applications. This review aims to concisely summarize recent developments in CA, PAH stabilization processes, and essential field application-controlling variables. This review analysis emphasizes activated carbon, biochar, Graphene, carbon nanotubes, and carbon-nanomaterials composite since these CAs are most often utilized as adsorbents for PAH in aquatic systems.

Establishment of evaluation system for biological remediation on organic pollution in groundwater using slow-release agents

In situ bioremediation through slow-release agents can continuously degrade organic pollutants for a long time and have high application potential in solving problems such as tailing and rebound. However, the existing evaluation system is difficult to reflect the performance of bioremediation through slow-release agents, which is not conducive to the promotion of technology. It is urgent to establish a targeted evaluation system. Therefore, based on the multi-criteria decision-making method (MCDA), a comprehensive evaluation model was established. The evaluation index system was constructed for bioremediation through slow-release agents consisting of 16 indicators including pollutant degradation rate, agent preparation cost, engineering operation and maintenance cost, secondary pollution, long-term degradation stability, slow release time, slow release stability, increase in functional microbial flora, increase in total DNA content, agent particle size, solid agent morphology, liquid agent viscosity, dispersibility in aqueous phase, zeta potential, operability of agent preparation, and engineering operation management difficulty. Then, the weight of the indicators was determined by using the best-worst method (BWM), and evaluation criteria was established based on relevant norms and literature. Both and the indicators aggregation simple additive weighting (SAW) method constitute a quantitative evaluation model. The above content together constitutes a new evaluation system for biological remediation on organic pollution in groundwater using slow-release agents, which was defined as AOBS evaluation system. In order to verify the rationality and scientificity of the evaluation system, a typical bioremediation slow-release agent was evaluated using the established AOBS evaluation system. The results showed that the evaluation system could reasonably and comprehensively evaluate bioremediation through slow-release agents and provide suggestions for agent improvement.

Advantages of residual phenol in coal chemical wastewater as a co-metabolic substrate for naphthalene degradation by microbial electrolysis cell

The use of co-metabolic substrates is effective for polycyclic aromatic hydrocarbons (PAHs) removal, but the potential of the high phenol concentrations in coal chemical wastewater (CCW) as a co-metabolic substrate in microbial electrolysis cell (MEC) has been neglected. In this study, the efficacy of varying phenol concentrations in comparison to simple substrates for degrading naphthalene in MEC under comparable COD has been explored. Results showed that phenol as a co-metabolic substrate outperformed sodium acetate and glucose in facilitating naphthalene degradation efficiency at 50 mg-COD/L. The naphthalene removal efficiency from RP, RA, and RG was found to be 84.11 ± 0.44 %, 73.80 ± 0.27 % and 72.43 ± 0.34 %, respectively. Similarly, phenol not only enhanced microbial biomass more effectively, but also exhibited optimal COD metabolism capacity. The addition of phenol resulted in a stepwise reduction in the molecular weight of naphthalene, whereas sodium acetate and glucose led to more diverse degradation pathways. Some bacteria with the potential ability to degrade PAHs were detected in phenol-added MEC, including Alicycliphilus, Azospira, Stenotrophomonas, Pseudomonas, and Sedimentibacter. Besides, phenol enhanced the expression of ncrA and nmsA genes, leading to more efficient degradation of naphthalene, with ncrA responsible for mediating the reduction of the benzene ring in naphthalene and nmsA closely associated with the decarboxylation of naphthalene. This study provides guidance for the effective co-degradation of PAHs in CCW with MEC, demonstrating the effectiveness of using phenol as a co-substrate relative to simple substrates in the removal of naphthalene.

Microbial Consortium HJ-SH with Very High Degradation Efficiency of Phenanthrene

Phenanthrene (PHE) is one of the model compounds of polycyclic aromatic hydrocarbons (PAHs). In this study, a natural PHE-degrading microbial consortium, named HJ-SH, with very high degradation efficiency was isolated from soil exposed to long-term PHE contamination. The results of GC analysis showed that the consortium HJ-SH degraded 98% of 100 mg/L PHE in 3 days and 93% of 1000 mg/L PHE in 5 days, an efficiency higher than that of any other natural consortia, and even most of the engineered strains and consortia reported so far. Seven dominating strains were isolated from the microbial consortium HJ-SH, named SH-1 to SH-7, which were identified according to morphological observation and 16S rDNA sequencing as Pseudomonas sp., Stenotrophomonas sp., Delftia sp., Pseudomonas sp., Brevundimonas sp., Curtobacterium sp., and Microbacterium sp., respectively. Among all the seven single strains, SH-4 showed the strongest PHE degradation ability, and had the biggest degradation contribution. However, it is very interesting that the microbial consortium can hold its high degradation ability only with the co-existence of all these seven single strains. Moreover, HJ-SH exhibited a very high tolerance for PHE, up to 4.5 g/L, and it can degrade some other typical organic pollutants such as biphenyl, anthracene, and n-hexadecane with the degradation ratios of 93%, 92% and 70%, respectively, under 100 mg/L initial concentration in 5 days. Then, we constructed an artificial consortium HJ-7 consisting of the seven single strains, SH-1 to SH-7. After comparing the degradation ratios, cell growth, and relative degradation rates, it was concluded that the artificial consortium HJ-7 with easier reproducibility, better application stability, and larger room for modification can largely replace the natural consortium HJ-SH. In conclusion, this research provided novel tools and new insights for the bioremediation of PHE and other typical organic pollutants using microbial consortia.

Effects of bioaugmentation by isolated Achromobacter xylosoxidans BP1 on PAHs degradation and microbial community in contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are a group of organic pollutants ubiquitous and persistent in soil. In order to provide a viable solution for bioremediation of PAHs-contaminated soil, a strain of Achromobacter xylosoxidans BP1 with superior PAHs degradation ability was isolated from contaminated soil at a coal chemical site in northern China. The degradation of phenanthrene (PHE) and benzo[a]pyrene (BaP) by strain BP1 was investigated in three different liquid phase cultures, and the removal rates of PHE and BaP by strain BP1 were 98.47% and 29.86% after 7 days under the conditions of PHE and BaP as the only carbon source, respectively. In the medium with the coexistence of PHE and BaP, the removal rates of BP1 were 89.44% and 9.42% after 7 days, respectively. Then, strain BP1 was investigated for its feasibility in remediating PAH-contaminated soil. Among the four PAHs-contaminated soils treated differently, the treatment inoculated with BP1 exhibited higher removal rates of PHE and BaP (p < 0.05), especially the CS-BP1 treatment (inoculation of BP1 into unsterilized PAHs-contaminated soil) showed 67.72%, 13.48% removal of PHE and BaP, respectively, over 49 days of incubation. Bioaugmentation also significantly increased the activity of dehydrogenase and catalase in the soil (p＜0.05). Furthermore, the effect of bioaugmentation on the removal of PAHs was investigated by measuring the activity of dehydrogenase (DH) and catalase (CAT) during incubation. Among them, the DH and CAT activities of CS-BP1 and SCS-BP1 (inoculation of BP1 into sterilized PAHs-contaminated soil) treatments inoculated with strain BP1 were significantly higher than those of treatments without BP1 addition during incubation (p < 0.01). The structure of the microbial community varied among treatments, but the Proteobacteria phylum showed the highest relative abundance in all treatments of the bioremediation process, and most of the bacteria with higher relative abundance at the genus level also belonged to the Proteobacteria phylum. Prediction of microbial functions in soil by FAPROTAX analysis showed that bioaugmentation enhanced microbial functions associated with the degradation of PAHs. These results demonstrate the effectiveness of Achromobacter xylosoxidans BP1 as a PAH-contaminated soil degrader for the risk control of PAHs contamination.

Genome analysis for the identification of genes involved in phenanthrene biodegradation pathway in Stenotrophomonas indicatrix CPHE1. Phenanthrene mineralization in soils assisted by integrated approaches

Phenanthrene (PHE) is a highly toxic compound, widely present in soils. For this reason, it is essential to remove PHE from the environment. Stenotrophomonas indicatrix CPHE1 was isolated from an industrial soil contaminated by polycyclic aromatic hydrocarbons (PAHs) and was sequenced to identify the PHE degrading genes. Dioxygenase, monooxygenase, and dehydrogenase gene products annotated in S. indicatrix CPHE1 genome were clustered into different trees with reference proteins. Moreover, S. indicatrix CPHE1 whole-genome sequences were compared to genes of PAHs-degrading bacteria retrieved from databases and literature. On these basis, reverse transcriptase-polymerase chain reaction (RT-PCR) analysis pointed out that cysteine dioxygenase (cysDO), biphenyl-2,3-diol 1,2-dioxygenase (bphC), and aldolase hydratase (phdG) were expressed only in the presence of PHE. Therefore, different techniques have been designed to improve the PHE mineralization process in five PHE artificially contaminated soils (50 mg kg^-1), including biostimulation, adding a nutrient solution (NS), bioaugmentation, inoculating S. indicatrix CPHE1 which was selected for its PHE-degrading genes, and the use of 2-hydroxypropyl-β-cyclodextrin (HPBCD) as a bioavailability enhancer. High percentages of PHE mineralization were achieved for the studied soils. Depending on the soil, different treatments resulted to be successful; in the case of a clay loam soil, the best strategy was the inoculation of S. indicatrix CPHE1 and NS (59.9% mineralized after 120 days). In sandy soils (CR and R soils) the highest percentage of mineralization was achieved in presence of HPBCD and NS (87.3% and 61.3%, respectively). However, the combination of CPHE1 strain, HPBCD, and NS showed to be the most efficient strategy for sandy and sandy loam soils (LL and ALC soils showed 35% and 74.6%, respectively). The results indicated a high degree of correlation between gene expression and the rates of mineralization.

Versatility of Stenotrophomonas maltophilia: Ecological roles of RND efflux pumps

S. maltophilia is a widely distributed bacterium found in natural, anthropized and clinical environments. The genome of this opportunistic pathogen of environmental origin includes a large number of genes encoding RND efflux pumps independently of the clinical or environmental origin of the strains. These pumps have been historically associated with the uptake of antibiotics and clinically relevant molecules because they confer resistance to many antibiotics. However, considering the environmental origin of S. maltophilia, the ecological role of these pumps needs to be clarified. RND efflux systems are highly conserved within bacteria and encountered both in pathogenic and non-pathogenic species. Moreover, their evolutionary origin, conservation and multiple copies in bacterial genomes suggest a primordial role in cellular functions and environmental adaptation. This review is aimed at elucidating the ecological role of S. maltophilia RND efflux pumps in the environmental context and providing an exhaustive description of the environmental niches of S. maltophilia. By looking at the substrates and functions of the pumps, we propose different involvements and roles according to the adaptation of the bacterium to various niches. We highlight that i°) regulatory mechanisms and inducer molecules help to understand the conditions leading to their expression, and ii°) association and functional redundancy of RND pumps and other efflux systems demonstrate their complex role within S. maltophilia cells. These observations emphasize that RND efflux pumps play a role in the versatility of S. maltophilia.

Genome sequence of Stenotrophomonas indicatrix CPHE1, a powerful phenanthrene-degrading bacterium

Environmental pollution caused by polycyclic aromatic hydrocarbons (PAHs) involves a high-risk and have received considerable attention due to their carcinogenic, teratogenic, and mutagenic properties. Phenanthrene (PHE) is a low molecular weight PAH, which has three benzene rings. It is one of the most common PAH found in contaminated environments mainly due to its low volatilization ability and hydrophobic character. A PHE degrading bacterium was isolated from an industrial contaminated soil using enrichment culture techniques. Based on macroscopic, microscopic examination and phylogenetic analysis, this bacterium was classified as Stenotrophomonas indicatrix and named strain CPHE1. Several authors have reported about bacteria stains, which can degrade PHE, but this is the first time where the ability of S. indicatrix to biodegrade and mineralize PHE has been demonstrated.

Biochar application strategies for polycyclic aromatic hydrocarbons removal from soils

Polycyclic aromatic hydrocarbons (PAHs) are known as a hazardous group of pollutants in the soil which causes many challenges to the environment. In this study, the potential of biochar (BC), as a carbonaceous material, is evaluated for the immobilization of PAHs in soils. For this purpose, various bonding mechanisms of BC and PAHs, and the strength of bonds are firstly described. Also, the effect of impressive criteria including BC physicochemical properties (such as surface area, porosity, particle size, polarity, aromaticity, functional group, etc., which are mostly the function of pyrolysis temperature), number of rings in PAHs, incubation time, and soil properties, on the extent and rate of PAHs immobilization by BC are explained. Then, the utilization of BC in collaboration with biological tools which simplifies further dissipation of PAHs in the soil is described considering detailed interactions among BC, microbes, and plants in the soil matrix. The co-effect of BC and biological remediation has been authenticated by previous studies. Moreover, recent technologies and challenges related to the application of BC in soil remediation are explained. The implementation of a combined BC-biological remediation method would provide excellent prospects for PAHs-contaminated soils.

Dissipation of a mix of priority PAHs in soils by using availability enhancers. Effect of aging and pollutant interactions

A remediation strategy using three non-toxic availability enhancers (two cyclodextrins and a rhamnolipid biosurfactant) was applied to various soils artificially contaminated with a mix of Polycyclic Aromatic Hydrocarbons (PAHs) considered priority pollutants at two levels of contamination: only with 7 low molecular weight PAHs (LMW PAHs, 5 with 3-ring and 2 with 4-ring - fluoranthene and pyrene) or with 14 PAHs (from 3 to 6 rings). Natural attenuation of PAHs in all soils showed degradation capacity for the LMW PAHs, with a final content of LMW PAHs <5% of their initial concentration. Conversely, the rest of PAHs (high molecular weight PAHs, HMW) remained in the soils (61% - 83.5%), indicating abiotic dissipation of HMW PAHs due to formation of non-extractable residues in soils. The influence of the presence of HMW PAHs on the degradation of the 7 LMW PAHs was also tested, showing a general decrease in the time to obtain 50% dissipation (DT₅₀), statistically significant for acenaphthene, acenaphthylene and fluorene. Availability enhancers showed different effects on PAHs dissipation. 2-hydroxypropyl-β-cyclodextrin (HP) decreased DT₅₀ of some of the lighter PAHs, whereas the rhamnolipid (RL) caused a slight DT₅₀ increase due to its initial toxicity on native soil microorganisms, but showing later high degradation rate for LMW PAHs. On the contrary, randomly methylated-β-cyclodextrin (RAMEB) slowed down PAHs degradation due to its high adsorption onto soil surface, blocking the desorption of PAHs from the soils. The high number of experimental factors not studied simultaneously before (soil type, co-contamination, availability enhancers and incubation time) allowed to conduct a statistical analysis which supported the conclusions reached. Principal Component Analysis separated the studied PAHs in 3 groups, in relation with their molecular weight and Kow. The first principal component was related with LMW PAHs, and separate the inefficient RAMEB from the other availability enhancers.

Azole fungicides: (Bio)degradation, transformation products and toxicity elucidation

The increasing consumption of azole antifungal agents leads to their uncontrolled release into the environment. Therefore, it is crucial to remove their residues from natural ecosystems. This study aimed to examine the biological and chemical degradation of four typical azole fungicides: fluconazole (Fc), clotrimazole (Cl), climbazole (Cb), and epoxiconazole (Ep). The biodegradation was investigated using activated sludge and two novel Gram-negative bacterial strains. The chemical degradation experiments aimed to assess the efficiency of fungicides removal through UV treatment, the Fenton reaction, and a combination of these methods. Transformation products of Cb, Ep, and Cl photocatalytic removal were identified by mass spectrometry. In addition, the AlamarBlue® Assay and the MTT Assay allowed careful evaluation of the toxicity of azole derivatives and their transformation products towards newly isolated strains, Stenotrophomonas maltophilia AsPCl2.3 and Pseudomonas monteilii LB2. Among all azole fungicides, Cb was the most susceptible to biological removal while Fc, Ep, and Cl were basically resistant to biodegradation. Cl and Ep showed a significant biosorption on the activated sludge. Under optimized photolysis conditions, the removal efficiency of Cl, Cb, and Ep was significantly higher than that of biodegradation. The Fenton reaction supported by the UV-irradiation offered the best results of fungicides elimination. After 1 min of the experiment, Cl was almost completely removed while Cb and Ep removal rates reached an average of 60%. The proposed main degradation route of azole fungicides during UV-irradiation includes halogen atoms substitution by hydroxyl moieties. The final degradation product was imidazole or triazole. Azole fungicides and their transformation products differently affected the metabolic activity of Gram-negative bacteria. Cl and Cb intermediates showed lower toxicity than parent compounds. The findings help better understand the environmental impact of azole fungicides, their degradation, and toxicity. They also stress the need for reducing their uncontrolled release to the environment.