Alkane hydroxylases involved in microbial alkane degradation

Development of a device to trap soil bacteria capable of degrading organic contaminants such as alkanes and polycyclic aromatic hydrocarbons

The microbial biodegradation potential of contaminated sites is critical for efficient bioremediation, particularly through bioaugmentation with microorganisms that degrade organic pollutants. The BactoTrapS tool was developed to select and enrich bacteria tolerant to contaminants and capable of biodegradation directly from soils. It comprises a nylon mesh filled with activated carbon or vermiculite spiked with PAHs (phenanthrene, pyrene, dibenzo-a,h-anthracene) or alkanes (n-hexadecane, cyclohexane), while control traps remained unspiked. After five weeks of soil incubation, spiked traps showed significantly higher mineralisation. Bacterial colonisation was evaluated via CFU counts and 16S rDNA qPCR, revealing increased densities in spiked conditions. Alpha diversity analysis showed reduced diversity in spiked traps, while beta diversity confirmed selective enrichment of genera such as Mycobacterium and Polaromonas under PAHs, and Nocardioides and Nocardia under alkanes. These genera were identified as indicator species for the respective contaminants. qPCR of key biodegradation genes (PAH-RHDα, AlkB, CYP153) revealed elevated gene copy numbers in spiked traps. Most isolates from spiked conditions metabolised phenanthrene and hexadecane as sole carbon sources. BactoTrapS offers a rapid, efficient method to enrich biodegrading bacteria for hydrocarbons and other organic contaminants, promising broad applicability for future remediation efforts.

Exploring biodegradation limits of n-alkanes as polyethylene models using multi-omics approaches

Polyethylene (PE) is widely regarded as non-biodegradable in natural environments, despite reports suggesting partial biotic degradation. Using multi-omics analysis, this study investigated the biodegradation mechanisms of n-alkanes-structural analogs of PE-to determine the threshold carbon number in PE that allows for environmental biodegradation. n-Alkanes with 6-40 carbons (C6-C40) were biodegraded in the soil, whereas C44 and PE were not. 16S rRNA gene amplicon sequence analysis identified distinct microbial communities associated with non-degradable compounds (PEs and C44) and biodegradable alkanes (C6-C40). Notably, the microbial community composition for C40 differed from those associated with biodegradable alkanes below C36. Multi-omics analysis identified the genera Aeromicrobium, Nocardia, Nocardioides, Rhodococcus, Acinetobacter, and Fontimonas as key degraders of n-alkanes at C36 and below, utilizing alkane hydroxylases such as alkane monooxygenase (AlkB), LC-alkane monooxygenase from Acinetobacter (AlmA), and cytochrome P450 (CYP153). Conversely, the biodegradation of C40 was facilitated by taxa, including the order Acidimicrobiales and the genera, Acidovorax, Sphingorhabdus, Prosthecobacter, and Roseimicrobium using AlmA and CYP153-type hydroxylases. This difference in key degraders and alkane hydroxylases may explain the reduced biodegradability of n-alkanes above C40, including PE.

Comparative Genomics, Transcriptome, and Prokaryotic Expression Analysis of alkB1_1 in Acinetobacter vivianii KJ-1: Revealing the Mechanism of Petroleum Hydrocarbon Degradation

The present study aimed to comprehensively dissect the petroleum hydrocarbon degradation mechanism of Acinetobacter vivianii KJ-1. The isolated and identified strain was able to proliferate using diesel as the sole carbonaceous substrate. Via comparative genomics, an in-depth analysis was performed to elucidate the genome similarities and disparities between this strain and related strains, thereby uncovering a core genome as well as genes with uncharacterized functions. Transcriptome analysis, carried out under different substrate conditions (C16, diesel, sodium acetate) manifested distinct gene expression modalities. A multitude of genes associated with alkane metabolism were differentially expressed, among which alkB1_1 and alkB1_2 was conspicuously upregulated. Prokaryotic expression of alkB1_1 was implemented, and the enzyme activity of the recombinant protein peaked at a pH level of approximately 7.0 and within a temperature range of 30 to 40 °C. The recombinant strain was shown to possess the ability to degrade n-hexadecane. Collectively, this research not only augments the understanding of the degradation mechanism of A. vivianii KJ-1 but also provides a fundamental basis for developing bioremediation strategies targeting petroleum hydrocarbon-contaminated environments.

The GntR/VanR transcription regulator AlkR represses AlkB2 monooxygenase expression and regulates n-alkane degradation in Pseudomonas aeruginosa SJTD-1

Transmembrane alkane monooxygenase (AlkB)-type monooxygenases, especially AlkB2 monooxygenases, are crucial for aerobic degradation of the medium-to-long-chain n-alkanes in hydrocarbon-utilizing microorganisms. In this study, we identified a GntR/VanR transcription regulator AlkR of Pseudomonas aeruginosa SJTD-1 involved in the negative regulation of AlkB2 and deciphered its nature of DNA binding and ligand release. The deletion of alkR enhanced the transcription levels of the alkB2 gene and the utilization efficiency of the medium-to-long-chain n-alkanes by strain SJTD-1. The dimer of AlkR recognizes and binds to a conserved palindromic motif in the promoter of the alkB2 gene, and structural symmetry is vital for DNA binding and transcription repression. The long-chain fatty acyl coenzyme A compounds can release AlkR and stimulate transcription of alkB2, reflecting the effect of alkane catabolic metabolites. Structural insights unveiled that the arginine residues and scaffold residues of AlkR are critical for DNA binding. Further bioinformatics analysis of AlkR revealed the widespread VanR-AlkB couples distributed in Pseudomonadaceae with high conservation in the sequences of functional genes and intergenic regions, highlighting a conserved regulatory pattern for n-alkane utilization across this family. These findings demonstrate the regulatory mechanism and structural basis of GntR/VanR transcription regulators in modulating n-alkane biodegradation and provide valuable insights in improving the bioremediation efficiency of hydrocarbon pollution.

Biofilm-mediated bioremediation of xenobiotics and heavy metals: a comprehensive review of microbial ecology, molecular mechanisms, and emerging biotechnological applications

Environmental pollution, driven by rapid industrialization and urbanization, has emerged as a critical global challenge in the twenty-first century. This comprehensive review explores the potential of bacterial biofilms in bioremediation, focusing on their ability to degrade and transform a wide array of pollutants, including heavy metals, persistent organic pollutants (POPs), oil spills, pesticides, and emerging contaminants, such as pharmaceuticals and microplastics. The unique structural and functional characteristics of biofilms, including their extracellular polymeric substance (EPS) matrix, enhanced genetic exchange, and metabolic cooperation, contribute to their superior pollutant degradation capabilities compared to planktonic bacteria. Recent advancements in biofilm-mediated bioremediation include the application of genetically engineered microorganisms, nanoparticle-biofilm interactions, and innovative biofilm reactor designs. The CRISPR-Cas9 system has shown promise in enhancing the degradative capabilities of biofilm-forming bacteria while integrating nanoparticles with bacterial biofilms demonstrates significant improvements in pollutant degradation efficiency. As global pollution rises, biofilm-based bioremediation emerges as a cost-effective and environmentally friendly approach to address diverse contaminants. This review signifies the need for further research to optimize these techniques and harness their full potential in addressing pressing environmental challenges.

Engineering of Transmembrane Alkane Monooxygenases to Improve a Key Reaction Step in the Synthesis of Polymer Precursor Tulipalin A

The α-methylene-γ-butyrolactone tulipalin A, a defense compound found in tulips, can polymerize via addition at the vinyl group or via ring-opening polymerization, making it a highly promising monomer for bio-based polymers. Since the biosynthesis of tulipalin A in plants remains elusive, we propose an alternative pathway for its synthesis starting from the terpenoid intermediate isoprenyl acetate. While fungal unspecific peroxygenases showed a preference for the unwanted epoxidation of the exo-olefin group, bacterial alkane monooxygenases were selective for terminal hydroxylation. By combining protein engineering based on de novo structure prediction of the membrane enzymes with cell engineering, the specific activity was increased 6-fold to 1.83 U gcdw -1. Oxidation of the formed allylic alcohol by a three-enzyme cascade and subsequent lactonization yielded tulipalin A. Our results demonstrate the feasibility of producing the polymer precursor tulipalin A from terpenoid intermediates and provide a solid foundation for future metabolic engineering endeavors.

Long-term microbial functional responses in soil contaminated with biofuel/fossil fuel blends triggered by different bioremediation treatments

The use of biofuel blends with fossil fuels is widespread globally, raising concerns over novel contamination types in environments impacted by these mixtures. This study investigates the microbial functional in soils contaminated by biofuel and fossil fuel blends and subjected to various bioremediation treatments. Using metagenomic analysis, it was compared hydrocarbon degradation functional profiles across areas polluted with ethanol/gasoline and biodiesel/diesel blends. Results indicate that long-term natural attenuation areas exhibited distinct functional profiles compared to actively bioremediated areas. However, same hydrocarbon degradation genes were enriched across all areas, highlighting functional redundancy despite taxonomic variation in hydrocarbon-degrading microbes. Finally, several of the keystone species found were hydrocarbon degraders, such as members of the families Clostridiaceae and Comamonadaceae, representing potential targets for biostimulation in future remediation efforts. This long-term, field-scale study uniquely focuses on the functional profiles of microbial communities, offering new insights into the bioremediation of complex biofuel/fossil fuel contaminants in situ.

Co-occurrence of PFASs, TPHs, and BTEX in subsurface soils: Impacts on native microbial communities and implications for bioremediation

This study investigates the co-occurrence of per- and polyfluoroalkyl substances (PFASs), petroleum hydrocarbons (TPHs) and benzene, toluene, ethylbenzene, and xylene (BTEX) and their effects on the indigenous microbial communities in soils at a contaminated site with a history of petroleum refinery operations. PFASs concentrations were in the range of 5.65-6.73 ng/g, and fluorooctane sulfonate (PFOS) and perfluorobutane sulfonic acid (PFBS) were the dominating compounds. No significant difference was observed in the PFASs concentration profiles between the site and background locations, indicating that PFASs detected in the soil samples were mainly contributed from non-point sources, due to the long-distance transport of PFASs in the region. The concentrations of TPHs and BTEX ranged from 227 to 72,360 mg/kg and 0.06-2109.77 mg/kg, respectively, mainly contributed by the historical refinery activities. The presence of PFASs, TPHs, and BTEX significantly impacted soil microbial community diversity and abundance, altering microbial compositions and enriching bacteria with higher resistance or metabolic capabilities against contamination. Strong correlations were observed between TPHs and its degraders such as Pseudomonas, Azoarcus, and Polaromonas. Significant positive relationship between PFASs and Trichlorobacter implied the potential defluorination capabilities of Trichlorobacter, warranting further investigation. Moreover, the higher energy metabolism including carbon, nitrogen and sulfur metabolisms and higher abundance of metabolic enzymes for alkane, cyclohexane and toluene in the refinery site revealed the potential occurrence of natural biodegradation of contaminants with indigenous microbial community. These findings highlight the complexity of sites contaminated with a mixture of traditional and emerging contaminants, providing valuable insights into the potential for biodegradation of mixed contaminants and underscoring the need for integrated approaches in environmental remediation strategies. This study contributes to understanding the ecological impacts of co-occurring contaminants and emphasizes the importance of considering multiple contaminant types in environmental risk assessments and remediation efforts.

Regulation mechanism of the long-chain n-alkane monooxygenase gene almA in Acinetobacter venetianus RAG-1

As toxic pollutants, n-alkanes are pervasively distributed in most environmental matrices. Although the alkane monooxygenase AlmA plays a critical role in the metabolic pathway of solid long-chain n-alkanes (≥C20) that are extremely difficult to degrade, the mechanism regulating this process remains unclear. Here, we characterized the function of AlmA in Acinetobacter venetianus RAG-1, which was mainly involved in the degradation of long-chain n-alkanes (C26-C38), among which, n-C32 induced the almA promoter activity most. APR1 (AlmA Positive Regulator) that it is an AraC/XylS-type transcription regulator, a potential transcriptional regulator of almA, was screened by DNA-pull down, which was determined by conserved domain analysis. The deletion of apR1 severely reduced the capacity of strain RAG-1 to utilize long-chain n-alkanes (C22-C38), indicating the involvement of APR1 in n-alkanes degradation. The results of the APR1-dependent reporter system, electrophoretic mobility shift assay, and microscale thermophoresis further proved that APR1 was able to directly bind to the almA promoter region, thus activating the almA transcription. Furthermore, APR1 could inhibit self-expression through autoregulation in the absence of long-chain n-alkanes. n-C32 acted as a ligand of APR1, and the amino acid residues Val10, Gln50, Ala99, and Ile106 at the N-terminus of APR1 were necessary for binding n-C32. In addition, the key amino acid residues of APR1 within the C-terminal helix-turn-helix motif that bound to the downstream promoter region were confirmed by multiple sequence alignment and site-directed mutagenesis. The homologs of AlmA and APR1 shared a similar evolutionary course in the Proteobacteria; thus, this mode of regulation might be relatively conserved.

IMPORTANCE

The extreme hydrophobicity of long-chain n-alkanes ({greater than or equal to}C20) presents a significant challenge to their degradation in natural environments. It is, therefore, imperative to elucidate the regulatory mechanisms of the metabolic pathways of long-chain n-alkanes, which will be of great significance for the future application of hydrocarbon-degrading bacteria to treat oil spills. However, the majority of current studies have focused on the regulatory mechanisms of short- and medium-chain n-alkanes, with long-chain n-alkanes receiving comparatively little attention. In this study, we identified APR1, a transcriptional regulator of the alkane monooxygenase AlmA in Acinetobacter venetianus RAG-1, and characterized its function and regulatory mechanism. In the presence of ligand n-C32, APR1 could directly activate the transcription of almA, which was involved in the n-C32 metabolism. The amino acid residue unique to the C-terminal DNA-binding domain of AraC/XylS type n-alkanes transcription regulators was also identified. These findings further improved our understanding of the long-chain n-alkanes degradation mechanism, which is important for the management of petroleum pollution.

Microbial adaptation and genetic modifications for enhanced remediation in low-permeability soils

Low-permeability soils, characterized by fine texture and high clay content, pose significant challenges to traditional soil remediation techniques due to limited hydraulic conductivity, restricted nutrient flow, and reduced oxygen availability. These unique properties enable low-permeability soils to function as natural barriers in environmental protection; however, they also trap contaminants, making traditional remediation efforts challenging. This review synthesizes current knowledge on microbial adaptation and genetic engineering approaches that enhance the effectiveness of bioremediation in such environments. Key microbial adaptations, including anaerobic metabolism, extracellular enzyme production, and stress response mechanisms, allow individual microbes to adapt in low-permeability soils. Additionally, community-level strategies like microhabitat creation, biofilm formation, and functional redundancy further support microbial resilience. Advancements in genetic engineering now enable the modification of microbial traits-such as soil adhesion, nutrient utilization, and stress tolerance-to enhance bioremediation efficacy. Synthetic biology techniques further allow for the design of tailored microbial consortia that work cooperatively to degrade contaminants in complex soil matrices. This review highlights the integration of microbial and genetic engineering strategies, offering a comprehensive overview that informs current practices and guides future research in low-permeability soil remediation.

Combined thermochemical-biotechnological approach for the valorization of polyolefins into polyhydroxyalkanoates: Development of an integrated bioconversion process by microbial consortia

Waste management of persistent polymers such as polyolefins (PO)1 still represents a major challenge, often leading to material loss from the value chain and contributing to plastic pollution. This study investigated an integrated process to valorize PO pyrolysis side stream. PO wax was recovered and used as a feedstock for a microbial bioconversion process. A modified emulsification protocol (using two-surfactants system) allowed the successful dispersion and bioconversion of PO wax without the need of the extra oxidation step. Enrichment of plastic landfill inocula allowed to develop efficient mixed microbial consortia (MMC) able to grow on PO wax. Adaptive laboratory evolution improved 4 times cell growth, leading to 2.6-17.3 times shorter lag phase. The bioconversion process using the adapted MMC was performed in a 2 L-bioreactor with PO wax-emulsified media (10 g L-1) at neutral pH and 20% pO2. 87% of substrate was consumed within 12 h and complete consumption was achieved within 48 h (4 times faster than previously reported). A maximum of 2.95 gCDW L-1of biomass was produced, while the intracellular triglycerides reached a maximum of 105.5 mg L-1 at 30 h. Moreover, the conversion of PO wax into polyhydroxyalkanoates (PHAs) was demonstrated and the production was maximized by statistical optimization. Maximum PHA titer of 384 0.1 mg L-1 was achieved, which represents a 1.5-17 times improvement from previous reports. This integrated thermochemical-biotechnological approach might represent an interesting strategy to valorize and upcycle currently unrecyclable PO-rich mixed plastic waste streams, thus improving the circularity of the plastic sector.

Variations in cuticular hydrocarbons of Calliphora vicina (Diptera: Calliphoridae) empty puparia: Insights for estimating late postmortem intervals

Necrophagous flies, particularly blowflies, serve as vital indicators in forensic entomology and ecological studies, contributing to minimum postmortem interval estimations and environmental monitoring. The study investigates variations in the predominant cuticular hydrocarbons (CHCs) viz. n-C25, n-C27, n-C28, and n-C29 of empty puparia of Calliphora vicina Robineau-Desvoidy, 1830, (Diptera: Calliphoridae) across diverse environmental conditions, including burial, above-ground and indoor settings, over 90 days. Notable trends include a significant decrease in n-C25 concentrations in buried and above-ground conditions over time, while n-C27 concentrations decline in buried and above-ground conditions but remain stable indoors. Burial conditions show significant declines in n-C27 and n-C29 concentrations over time, indicating environmental influences. Conversely, above-ground conditions exhibit uniform declines in all hydrocarbons. Indoor conditions remain relatively stable, with weak correlations between weathering time and CHC concentrations. Additionally, machine learning techniques, specifically Extreme Gradient Boosting (XGBoost), are employed for age estimation of empty puparia, yielding accurate predictions across different outdoor and indoor conditions. These findings highlight the subtle responses of CHC profiles to environmental stimuli, underscoring the importance of considering environmental factors in forensic entomology and ecological research. The study advances the understanding of insect remnant degradation processes and their forensic implications. Furthermore, integrating machine learning with entomological expertise offers standardized methodologies for age determination, enhancing the reliability of entomological evidence in legal contexts and paving the way for future research and development.

Assembly and functional profile of rhizosphere microbial community during the Salix viminalis-AMF remediation of polycyclic aromatic hydrocarbon polluted soils

Arbuscular mycorrhizal fungi (AMF) are positive to the phytoremediation by improving plant biomass and soil properties. However, the role of AM plants to the remediation of polycyclic aromatic hydrocarbons (PAHs) is yet to be widely recognized, and the impact of AM plants to indigenous microbial communities during remediation remains unclear. In this work, a 90-day study was conducted to assess the effect of AMF-Salix viminalis on the removal of PAHs, and explore the impact to the microbial community composition, abundance, and function. Results showed that AMF-Salix viminalis effectively enhanced the removal of benzo[a]pyrene, and enriched more PAH-degrading bacteria, consisting of Actinobacteria, Chloroflexi, Sphingomonas, and Stenotrophobacter, as well as fungi including Basidiomycota, Pseudogymnoascus, and Tomentella. For gene function, AM willow enhanced the enrichment of genes involved in amino acid synthesis, aminoacyl-tRNA biosynthesis, and cysteine and methionine metabolism pathways. F. mosseae inoculation had a greater effect on alpha- and beta-diversity of microbial genes at 90 d. Additionally, AMF inoculation significantly increased the soil microbial biomass carbon and organic matter concentration. All together, the microbial community assembly and function shaped by AM willow promoted the dissipation of PAHs. Our results support the effectiveness of AM remediation and contribute to reveal the enhancing-remediation mechanism to PAHs using multi-omics data.

Dynamics of microbial-induced oil degradation at the microscale

Microbial-induced oil degradation (MIOD) has a wide range of applications, such as microbial enhanced oil recovery and bioremediation of oil pollution. However, our understanding of MIOD is still far from complete. Particularly, how is the dynamics of degradation process at the microscale level with a single-cell resolution remains to be disclosed. In this work, using hexadecane droplets in water as a model system, we have studied the dynamics of hexadecane degradation by different strains, including Pseudomonas aeruginosa PAO1, IMP68, O-2-2, and Dietzia sp. DQ12-45-1b, at the microscale. Based on visualization of MIOD, the dynamics of MIOD can be characterized by a three-stage process, including adhesion, adaptation, and degradation stages. Although different strains showed similar three-stage dynamics of MIOD, the effective degradation rate varied and followed an order of PAO1 > O-2-2 > IMP68 > DQ12-45-1b under aerobic conditions. Different oxygen conditions were also tested, and the dynamics of MIOD was slowed down under anaerobic conditions in comparison to under aerobic conditions. Further investigations at the degradation stage revealed that biofilms formed at the oil-water interface enhanced oil degradation, but a prerequisite for such enhanced degradation is proper stimulation of biofilm cells in the course of biofilm formation. The findings in this work provided a detailed picture on the dynamics of MIOD at the microscale and would be beneficial for better applications of MIOD.IMPORTANCEMicrobial-induced oil degradation is environmental friendly and economic and has become a promising technique in the fields of enhanced oil recovery and remediation of crude oil-polluted environments. For better applications of microbial-induced oil degradation, understanding the degradation dynamics particularly at the microscale is crucial. In this study, we investigated the degradation dynamics of hexadecane oil droplets incubated with different strains, including Pseudomonas aeruginosa PAO1, O-2-2, IMP68, and Dietzia sp. DQ12-45-1b at the microscale by employing microdroplet-based methods and bacterial tracking techniques. The findings in this study provided a detailed picture on the dynamics of microbial-induced oil degradation at the microscale, which will deepen our understandings on the biodegradation mechanisms of alkanes and shed insights for developing more effective biodegradation techniques.

Recent advances in Emulsan production, purification, and application: Exploring bioemulsifiers unique potentials

Bioemulsifiers are compounds produced by microorganisms that reduce the interfacial forces between hydrophobic substances and water. Due to their potential in the pharmaceutical and food industries and their efficiency in oil spill remediation, they have been the subject of study in the scientific community while being safe, biodegradable, and sustainable compared to synthetic options. These biomolecules have high molecular weight and polymeric structures, distinguishing them from traditional biosurfactants. Emulsan, a bioemulsifier exopolysaccharide, is produced by Acinetobacter strains and is highly efficient in forming stable emulsions. Its low toxicity and high potential as an emulsifying agent promote its application in pharmaceutical and food industries as a drug-delivery vehicle and emulsion stabilizer. Due to the high environmental impact of oil spills, bioemulsifiers have great potential for environmental applications, such as bioremediation. This unique feature gives them a distinct mechanism of action in forming emulsions, resulting in minimal environmental impact. A better understanding of these aspects can improve the use of bioemulsifiers and environmental remediation in various industries. This review will discuss the production and characterization of Emulsan, focusing on recent advancements in cultivation conditions, purification techniques, compound identification, and ecotoxicity.

Attached indigenous microalgal-bacterial consortium with greater stress-resistance facilitated recovery of integrated fixed-film system after experiencing short-term stagnation inhibition

Stability of integrated fixed-film indigenous microalgal-bacterial consortium (IF-IMBC) requires further investigation. This study focused on the influence of short-term stagnation (STS), caused by influent variations or equipment maintenance, on IF-IMBC. Results showed that the IF-IMBC system experienced initial inhibition followed by subsequent recovery during STS treatment. Enhanced organics utilization was believed to contribute to system recovery. It is proposed that the attached IMBC possessed greater stress resistance. On the one hand, a higher increase in bacteria potentially participating in organic degradation was observed. Moreover, the dominant eukaryotic species significantly decreased in suspended IMBC while its abundance remained stable in the attached state. On the other hand, increased abundance for most functional enzymes was primarily observed in the attached bacteria. This fundamental research aims to bridge the knowledge gap regarding the response of IMBC to variations in operational conditions.

Multi-omics association study of hexadecane degradation in haloarchaeal strain Halogranum rubrum RO2-11

Haloarchaea with the capacity to degrade alkanes is promising to deal with petroleum pollution in hypersaline environments. However, only a limited number of haloarchaeal species are investigated, and their pathway and mechanism for alkane degradation remain unclear. In this study, Halogranum rubrum RO2-11, a haloarchaeal strain, verified the ability to degrade kerosene and hexadecane in 184 g/L NaCl, with 53% and 52% degradation rates after 9 and 4 days, respectively. Genome sequencing and gene annotation indicated that strain RO2-11 possesses a complete potential alkane-degrading pathway, of which alkane hydroxylases may include CYP450, AlmA, and LadA. Transcriptome and metabolome analyses revealed that the upregulation of related genes in TCA cycle, lysine biosynthesis, and acetylation may help improve hexadecane degradation. Additionally, an alternative degrading pathway of hexadecane based on dual-terminal β-oxidation may occur in strain RO2-11. It is likely to be the first report of alkane degradation by the genus Halogranum, which may be helpful for applications of oil-pollution bioremediation under high-salt conditions.

Degradation and enhanced oil recovery potential of Alcanivorax borkumensis through production of bio-enzyme and bio-surfactant

Microbial enhanced oil recovery (EOR) has become the focus of oilfield research due to its low cost, environmental friendliness and sustainability. The degradation and EOR capacity of A. borkumensis through the production of bio-enzyme and bio-surfactant were first investigated in this study. The total protein concentration, acetylcholinesterase, esterase, lipase, alkane hydroxylase activity, surface tension, and emulsification index (EI) were determined at different culture times. The bio-surfactant was identified as glycolipid compound, and the yield was 2.6 ± 0.2 g/L. The nC12 and nC13 of crude oil were completely degraded, and more than 40.0 % of nC14-nC24 was degraded by by A. borkumensis. The results of the microscopic etching model displacement and core flooding experiments showed that emulsification was the main mechanism of EOR. A. borkumensis enhanced the recovery rate by 20.2 %. This study offers novel insights for the development of environmentally friendly and efficient oil fields.

Soil processes modify the composition of volatile organic compounds (VOCs) from CO2- and CH4-dominated geogenic and landfill gases: A comprehensive study

Degradation mechanisms affecting non-methane volatile organic compounds (VOCs) during gas uprising from different hypogenic sources to the surface were investigated through extensive sampling surveys in areas encompassing a high enthalpy hydrothermal system associated with active volcanism, a CH4-rich sedimentary basin and a municipal waste landfill. For a comprehensive framework, published data from medium-to-high enthalpy hydrothermal systems were also included. The investigated systems were characterised by peculiar VOC suites that reflected the conditions of the genetic environments in which temperature, contents of organic matter, and gas fugacity had a major role. Differences in VOC patterns between source (gas vents and landfill gas) and soil gases indicated VOC transformations in soil. Processes acting in soil preferentially degraded high-molecular weight alkanes with respect to the low-molecular weight ones. Alkenes and cyclics roughly behaved like alkanes. Thiophenes were degraded to a larger extent with respect to alkylated benzenes, which were more reactive than benzene. Furan appeared less degraded than its alkylated homologues. Dimethylsulfoxide was generally favoured with respect to dimethylsulfide. Limonene and camphene were relatively unstable under aerobic conditions, while α-pinene was recalcitrant. O-bearing organic compounds (i.e., aldehydes, esters, ketones, alcohols, organic acids and phenol) acted as intermediate products of the ongoing VOC degradations in soil. No evidence for the degradation of halogenated compounds and benzothiazole was observed. This study pointed out how soil degradation processes reduce hypogenic VOC emissions and the important role played by physicochemical and biological parameters on the effective VOC attenuation capacity of the soil.

Enhancing systematic tolerance in Bermuda grass (Cynodon dactylon L.) through amplified alkB gene expression and bacterial-driven hydrocarbon degradation

This study aimed to access the impact of soil polluted with petroleum (5, 10 g petroleum kg-1 soil) on Bermuda grass (Cynodon dactylon L.) with and without applied bacterial inoculants (Arthrobacter oxydans ITRH49 and Pseudomonas sp. MixRI75). Both soil and seed were given bacterial inoculation. The evaluated morphological parameters of Bermuda grass were fresh and dry weight. The results demonstrated that applied bacterial inoculants enhanced 5.4%, 20%, 28% and 6.4%, 21%, and 29% shoot and root fresh/dry weights in Bermuda grass under controlled environment. The biochemical analysis of shoot and root was affected deleteriously by the 10 g petroleum kg-1 soil pollution. Microbial inoculants enhanced the activities of enzymatic (catalase, peroxidase, glutathione reductase, ascorbate peroxidase, superoxide dismutase) and non-enzymatic (ɑ-tocopherols, proline, reduced glutathione, ascorbic acid) antioxidant to mitigate the toxic effects of ROS (H2O2) under hydrocarbon stressed condition. The maximum hydrocarbon degradation (75%) was recorded by Bermuda grass at 5 g petroleum kg-1 soil contamination. Moreover, bacterial persistence and alkane hydroxylase gene (alkB) abundance and expression were observed more in the root interior than in the rhizosphere and shoot interior of Bermuda grass. Subsequently, the microbe used a biological tool to propose that the application of plant growth-promoting bacteria would be the most favorable choice in petroleum hydrocarbon polluted soil to conquer the abiotic stress in plants and the effective removal of polyaromatic hydrocarbons in polluted soil.

The metabolites of light: Untargeted metabolomic approaches bring new clues to understand light-driven acclimation of intertidal mudflat biofilm

The microphytobenthos (MPB), a microbial community of primary producers, play a key role in coastal ecosystem functioning, particularly in intertidal mudflats. These mudflats experience challenging variations of irradiance, forcing the micro-organisms to develop photoprotective mechanisms to survive and thrive in this dynamic environment. Two major adaptations to light are well described in literature: the excess of light energy dissipation through non-photochemical quenching (NPQ), and the vertical migration in the sediment. These mechanisms trigger considerable scientific interest, but the biological processes and metabolic mechanisms involved in light-driven vertical migration remain largely unknown. To our knowledge, this study investigates for the first time metabolomic responses of a migrational mudflat biofilm exposed for 30 min to a light gradient of photosynthetically active radiation (PAR) from 50 to 1000 μmol photons m-2 s-1. The untargeted metabolomic analysis allowed to identify metabolites involved in two types of responses to light irradiance levels. On the one hand, the production of SFAs and MUFAs, primarily derived from bacteria, indicates a healthy photosynthetic state of MPB under low light (LL; 50 and 100 PAR) and medium light (ML; 250 PAR) conditions. Conversely, when exposed to high light (HL; 500, 750 and 1000 PAR), the MPB experienced light-induced stress, triggering the production of alka(e)nes and fatty alcohols. The physiological and ecological roles of these compounds are poorly described in literature. This study sheds new light on the topic, as it suggests that these compounds may play a crucial and previously unexplored role in light-induced stress acclimation of migrational MPB biofilms. Since alka(e)nes are produced from FAs decarboxylation, these results thus emphasize for the first time the importance of FAs pathways in microphytobenthic biofilms acclimation to light.

Advanced treatment of coking wastewater: Recent advances and prospects

Advanced treatment of refractory industrial wastewater is still a challenge. Coking wastewater is one of coal chemical wastewater, which contains various refractory organic pollutants. To meet the more and more rigorous discharge standard and increase the reuse ratio of coking wastewater, advanced treatment process must be set for treating the biologically treated coking wastewater. To date, several advanced oxidation processes (AOPs), including Fenton, ozone, persulfate-based oxidation, and iron-carbon micro-electrolysis, have been applied for the advanced treatment of coking wastewater. However, the performance of different advanced treatment processes changed greatly, depending on the components of coking wastewater and the unique characteristics of advanced treatment processes. In this review article, the state-of-the-art advanced treatment process of coking wastewater was systematically summarized and analyzed. Firstly, the major organic pollutants in the secondary effluents of coking wastewater was briefly introduced, to better understand the characteristics of the biologically treated coking wastewater. Then, the performance of various advanced treatment processes, including physiochemical methods, biological methods, advanced oxidation methods and combined methods were discussed for the advanced treatment of coking wastewater in detail. Finally, the conclusions and remarks were provided. This review will be helpful for the proper selection of advanced treatment processes and promote the development of advanced treatment processes for coking wastewater.

Tetracycline hydrochloride degradation in polarity inverted microbial fuel cells: Performance, mechanisms and microbiology

Tetracycline antibiotics are widely used in veterinary medicine, human therapy and agriculture, and their presence in natural water raises environmental concerns. In this study, more than 94% of tetracycline hydrochloride (TCH) could be rapidly degraded within 48 h in polarity-inverted microbial fuel cells. The electrochemically active bacteria had the best electrochemical performance at 1 mg/L of TCH with the minimum internal resistance of 77.38 Ω. The electron-rich functional groups of TCH were continuously attacked and finally degradated into small molecules in three possible degradation pathways. Microbial community structure analysis showed that Comamonas and Shinella were enriched at the electrode as polarity-inverted bacteria. Genomic analysis showed that both direct and indirect electron transfer participated in the degradation of TCH in polarity-inverted microbial fuel cell (MFC) and the functional genes related to electrical conductivity in polarity-inverted MFC were more enriched on the electrode surface than non-polarity-inverted MFC. This study can facilitate further investigations about the biodegradation of TCH in polarity-inverted microbial fuel cell.

AlmA involved in the long-chain n-alkane degradation pathway in Acinetobacter baylyi ADP1 is a Baeyer-Villiger monooxygenase

Many Acinetobacter species can grow on n-alkanes of varying lengths (≤C40). AlmA, a unique flavoprotein in these Acinetobacter strains, is the only enzyme proven to be required for the degradation of long-chain (LC) n-alkanes, including C32 and C36 alkanes. Although it is commonly presumed to be a terminal hydroxylase, its role in n-alkane degradation remains elusive. In this study, we conducted physiological, biochemical, and bioinformatics analyses of AlmA to determine its role in n-alkane degradation by Acinetobacter baylyi ADP1. Consistent with previous reports, gene deletion analysis showed that almA was vital for the degradation of LC n-alkanes (C26-C36). Additionally, enzymatic analysis revealed that AlmA catalyzed the conversion of aliphatic 2-ketones (C10-C16) to their corresponding esters, but it did not conduct n-alkane hydroxylation under the same conditions, thus suggesting that AlmA in strain ADP1 possesses Baeyer-Villiger monooxygenase (BVMO) activity. These results were further confirmed by bioinformatics analysis, which revealed that AlmA was closer to functionally identified BVMOs than to hydroxylases. Altogether, the results of our study suggest that LC n-alkane degradation by strain ADP1 possibly follows a novel subterminal oxidation pathway that is distinct from the terminal oxidation pathway followed for short-chain n-alkane degradation. Furthermore, our findings suggest that AlmA catalyzes the third reaction in the LC n-alkane degradation pathway.IMPORTANCEMany microbial studies on n-alkane degradation are focused on the genes involved in short-chain n-alkane (≤C16) degradation; however, reports on the genes involved in long-chain (LC) n-alkane (>C20) degradation are limited. Thus far, only AlmA has been reported to be involved in LC n-alkane degradation by Acinetobacter spp.; however, its role in the n-alkane degradation pathway remains elusive. In this study, we conducted a detailed characterization of AlmA in A. baylyi ADP1 and found that AlmA exhibits Baeyer-Villiger monooxygenase activity, thus indicating the presence of a novel LC n-alkane biodegradation mechanism in strain ADP1.

Bacteria degrading both n-alkanes and aromatic hydrocarbons are prevalent in soils

This study was undertaken to determine the distribution of soil bacteria capable of utilizing both n-alkanes and aromatic hydrocarbons. These microorganisms have not been comprehensively investigated so far. Ten contaminated (4046-43,861 mg of total petroleum hydrocarbons (TPH) kg-1 of dry weight of soil) and five unpolluted (320-2754 mg TPH kg-1 of dry weight of soil) soil samples from temperate, arid, and Alpine soils were subjected to isolation of degraders with extended preferences and shotgun metagenomic sequencing (selected samples). The applied approach allowed to reveal that (a) these bacteria can be isolated from pristine and polluted soils, and (b) the distribution of alkane monooxygenase (alkB) and aromatic ring hydroxylating dioxygenases (ARHDs) encoding genes is not associated with the contamination presence. Some alkB and ARHD genes shared the same taxonomic affiliation; they were most often linked with the Rhodococcus, Pseudomonas, and Mycolicibacterium genera. Moreover, these taxa together with the Paeniglutamicibacter genus constituted the most numerous groups among 132 culturable strains growing in the presence of both n-alkanes and aromatic hydrocarbons. All those results indicate (a) the prevalence of the hydrocarbon degraders with extended preferences and (b) the potential of uncontaminated soil as a source of hydrocarbon degraders applied for bioremediation purposes.

Polyethylene Biodegradation by an Artificial Bacterial Consortium: Rhodococcus as a Competitive Plastisphere Species

Polyethylene (PE), a widely used recalcitrant synthetic polymer, is a major global pollutant. PE has very low biodegradability due to its rigid C-C backbone and high hydrophobicity. Although microorganisms have been suggested to possess PE-degrading enzymes, our understanding of the PE biodegradation process and its overall applicability is still lacking. In the present study, we used an artificial bacterial consortium for PE biodegradation to compensate for the enzyme availability and metabolic capabilities of individual bacterial strains. Consortium members were selected based on available literature and preliminary screening for PE-degrading enzymes, including laccases, lipases, esterases, and alkane hydroxylases. PE pellets were incubated with the consortium for 200 days. A next-generation sequencing ana-lysis of the consortium community of the culture broth and on the PE pellet identified Rhodococcus as the dominant bacteria. Among the Rhodococcus strains in the consortium, Rhodococcus erythropolis was predominant. Scanning electron microscopy (SEM) revealed multilayered biofilms with bacteria embedded on the PE surface. SEM micrographs of PE pellets after biofilm removal showed bacterial pitting and surface deterioration. Multicellular biofilm structures and surface biodeterioration were observed in an incubation of PE pellets with R. erythropolis alone. The present study demonstrated that PE may be biodegraded by an artificially constructed bacterial consortium, in which R. erythropolis has emerged as an important player. The results showing the robust colonization of hydrophobic PE by R. erythropolis and that it naturally possesses and extracellularly expresses several target enzymes suggest its potential as a host for further improved PE biodeterioration by genetic engineering technology using a well-studied host-vector system.

Structure and Function of Alkane Monooxygenase (AlkB)

Every year, perhaps as much as 800 million tons of hydrocarbons enters the environment; alkanes make up a large percentage of it. Most are transformed by organisms that utilize these molecules as sources of energy and carbon. Both aerobic and anaerobic alkane transformation chemistries exist, capitalizing on the presence of alkanes in both oxic and anoxic environments. Over the past 40 years, tremendous progress has been made in understanding the structure and mechanism of enzymes that catalyze the transformation of methane. By contrast, progress involving enzymes that transform liquid alkanes has been slower with the first structures of AlkB, the predominant aerobic alkane hydroxylase in the environment, appearing in 2023. Because of the fundamental importance of C-H bond activation chemistries, interest in understanding how biology activates and transforms alkanes is high.In this Account, we focus on steps we have taken to understand the mechanism and structure of alkane monooxygenase (AlkB), the metalloenzyme that dominates the transformation of liquid alkanes in the environment (not to be confused with another AlkB that is an α-ketogluturate-dependent enzyme involved in DNA repair). First, we briefly describe what is known about the prevalence of AlkB in the environment and its role in the carbon cycle. Then we review the key findings from our recent high-resolution cryoEM structure of AlkB and highlight important similarities and differences in the structures of members of class III diiron enzymes. Functional studies, which we summarize, from a number of single residue variants enable us to say a great deal about how the structure of AlkB facilitates its function. Next, we overview work from our laboratories using mechanistically diagnostic radical clock substrates to characterize the mechanism of AlkB and contextualize the results we have obtained on AlkB with results we have obtained on other alkane-oxidizing enzymes and explain these results in light of the enzyme's structure. Finally, we integrate recent work in our laboratories with information from prior studies of AlkB, and relevant model systems, to create a holistic picture of the enzyme. We end by pointing to critical questions that still need to be answered, questions about the electronic structure of the active site of the enzyme throughout the reaction cycle and about whether and to what extent the enzyme plays functional roles in biology beyond simply initiating the degradation of alkanes.

Genome-Wide Expression Analysis Unravels Fluoroalkane Metabolism in Pseudomonas sp. Strain 273

Pseudomonas sp. strain 273 grows with medium-chain terminally fluorinated alkanes under oxic conditions, releases fluoride, and synthesizes long-chain fluorofatty acids. To shed light on the genes involved in fluoroalkane metabolism, genome, and transcriptome sequencing of strain 273 grown with 1,10-difluorodecane (DFD), decane, and acetate were performed. Strain 273 harbors three genes encoding putative alkane monooxygenases (AlkB), key enzymes for initiating alkane degradation. Transcripts of alkB-2 were significantly more abundant in both decane- and DFD-grown cells compared to acetate-grown cells, suggesting AlkB-2 catalyzes the attack on terminal CH3 and CH2F groups. Coordinately expressed with alkB-2 was an adjacent gene encoding a fused ferredoxin-ferredoxin reductase (Fd-Fdr). Phylogenetic analysis distinguished AlkB that couples with fused Fd-Fdr reductases from AlkB with alternate architectures. A gene cluster containing an (S)-2-haloacid dehalogenase (had) gene was up-regulated in cells grown with DFD, suggesting a possible role in the removal of the ω-fluorine. Genes involved in long-chain fatty acid biosynthesis were not differentially expressed during growth with acetate, decane, or DFD, suggesting the bacterium's biosynthetic machinery does not discriminate against monofluoro-fatty acid intermediates. The analysis sheds first light on genes and catalysts involved in the microbial metabolism of fluoroalkanes.

Unveiling the hidden role of aquatic viruses in hydrocarbon pollution bioremediation

Hydrocarbon pollution poses substantial environmental risks to water and soil. Bioremediation, which utilizes microorganisms to manage pollutants, offers a cost-effective solution. However, the role of viruses, particularly bacteriophages (phages), in bioremediation remains unexplored. This study examines the diversity and activity of hydrocarbon-degradation genes encoded by environmental viruses, focusing on phages, within public databases. We identified 57 high-quality phage-encoded auxiliary metabolic genes (AMGs) related to hydrocarbon degradation, which we refer to as virus-encoded hydrocarbon degradation genes (vHYDEGs). These genes are encoded by taxonomically diverse aquatic phages and highlight the under-characterized global virosphere. Six protein families involved in the initial alkane hydroxylation steps were identified. Phylogenetic analyses revealed the diverse evolutionary trajectories of vHYDEGs across habitats, revealing previously unknown biodegraders linked evolutionarily with vHYDEGs. Our findings suggest phage AMGs may contribute to alkane and aromatic hydrocarbon degradation, participating in the initial, rate-limiting hydroxylation steps, thereby aiding hydrocarbon pollution bioremediation and promoting their propagation. To support future research, we developed vHyDeg, a database containing identified vHYDEGs with comprehensive annotations, facilitating the screening of hydrocarbon degradation AMGs and encouraging their bioremediation applications.

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

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

Characterization of the Mycoremediation of n-Alkanes and Branched-Chain Alkanes by Filamentous Fungi from Oil-Polluted Soil Samples in Kazakhstan

For decades, researchers have focused on containing terrestrial oil pollution. The heterogeneity of soils, with immense microbial diversity, inspires them to transform pollutants and find cost-effective bioremediation methods. In this study, the mycoremediation potentials of five filamentous fungi isolated from polluted soils in Kazakhstan were investigated for their degradability of n-alkanes and branched-chain alkanes as sole carbon and energy sources. Dry weight estimation and gas chromatography-mass spectrometry (GC-MS) monitored the growth and the changes in the metabolic profile during degradation, respectively. Penicillium javanicum SBUG-M1741 and SBUG-M1742 oxidized medium-chain alkanes almost completely through mono- and di-terminal degradation. Pristane degradation by P. javanicum SBUG-M1741 was >95%, while its degradation with Purpureocillium lilacinum SBUG-M1751 was >90%. P. lilacinum SBUG-M1751 also exhibited the visible degradation potential of tetradecane and phytane, whereby in the transformation of phytane, both the mono- and di-terminal degradation pathways as well as α- and ß-oxidation steps could be described. Scedosporium boydii SBUG-M1749 used both mono- and di-terminal degradation pathways for n-alkanes, but with poor growth. Degradation of pristane by Fusarium oxysporum SBUG-M1747 followed the di-terminal oxidation mechanism, resulting in one dicarboxylic acid. These findings highlight the role of filamentous fungi in containing oil pollution and suggest possible degradation pathways.

Cuticular hydrocarbons as weathering biomarkers of empty puparia of the forensically important blowfly Calliphora vicina Robineau-Desvoidy, 1830 (Diptera: Calliphoridae) in soil v/s under room conditions

Forensic entomology uses the age of insects, such as blow flies, to determine a minimum post-mortem interval (PMImin). Recent research has focused on using the analysis of specific cuticular hydrocarbons (CHCs) in adult insects and their empty puparia to estimate their age, as it has been shown that their profile changes are consistent with age. The current work is based on the weathering of five CHCs from empty puparia of Calliphora vicina that were stored in soil (field/outdoor) and non-soil (room/indoor conditions) based pupariation media for a total of six months. The experiment was conducted in a controlled environment chamber at a constant temperature of 25 ± 2 °C under constant darkness. Gas chromatography-mass spectrometry (GC-MS) was used to analyze the cuticular hydrocarbons after they were extracted in n-Hexane. n-Pentacosane, n-Hexacosane, n-Heptacosane, n-Octacosane, and n-Nonacosane were the five CHCs investigated. Results showed that CHCs weathered more quickly in the soil than in the non-soil environment. It was also found that the abundance of Heptacosane increased in the samples during the fifth month when stored in a non-soil medium, while the abundances of all five CHCs were not detected after eight weeks onwards in soil pupation medium.

Functional Analysis of Novel alkB Genes Encoding Long-Chain n-Alkane Hydroxylases in Rhodococcus sp. Strain CH91

Rhodococcus sp. strain CH91 is capable of utilizing long-chain n-alkanes as the sole carbon source. Two new genes (alkB1 and alkB2) encoding AlkB-type alkane hydroxylase were predicted by its whole-genome sequence analysis. The purpose of this study was to elucidate the functional role of alkB1 and alkB2 genes in the n-alkane degradation of strain CH91. RT-qPCR analyses revealed that the two genes were induced by n-alkanes ranging from C16 to C36 and the expression of the alkB2 gene was up-regulated much higher than that of alkB1. The knockout of the alkB1 or alkB2 gene in strain CH91 resulted in the obvious reduction of growth and degradation rates on C16-C36 n-alkanes and the alkB2 knockout mutant exhibited lower growth and degradation rate than the alkB1 knockout mutant. When gene alkB1 or alkB2 was heterologously expressed in Pseudomonas fluorescens KOB2Δ1, the two genes could restore its alkane degradation activity. These results demonstrated that both alkB1 and alkB2 genes were responsible for C16-C36 n-alkanes' degradation of strain CH91, and alkB2 plays a more important role than alkB1. The functional characteristics of the two alkB genes in the degradation of a broad range of n-alkanes make them potential gene candidates for engineering the bacteria used for bioremediation of petroleum hydrocarbon contaminations.

Interpreting the degradation mechanism of triclosan in microbial fuel cell by combining analysis microbiome community and degradation pathway

Microbes play a dominant role for the transformation of organic contaminants in the environment, while a significant gap exists in understanding the degradation mechanism and the function of different species. Herein, the possible bio-degradation of triclosan in microbial fuel cell was explored, with the investigation of degradation kinetics, microbial community, and possible degradation products. 5 mg/L of triclosan could be degraded within 3 days, and an intermediate degradation product (2,4-dichlorophen) could be further degraded in system. 32 kinds of dominant bacteria (relative intensity >0.5%) were identified in the biofilm, and 10 possible degradation products were identified. By analyzing the possible involved bioreactions (including decarboxylation, dehalogenation, dioxygenation, hydrolysis, hydroxylation, and ring-cleavage) of the dominant bacteria and possible degradation pathway of triclosan based on the identified products, biodegradation mechanism and function of the bacteria involved in the degradation of triclosan was clarified simultaneously. This study provides useful information for further interpreting the degradation mechanism of organic pollutants in mixed flora by combining analysis microbiome community and degradation pathway.

Microbial community structure and exploration of bioremediation enzymes: functional metagenomics insight into Arabian Sea sediments

Deep-sea sediments provide important information on oceanic biogeochemical processes mediated by the microbiome and their functional roles which could be unravelled using genomic tools. The present study aimed to delineate microbial taxonomic and functional profiles from Arabian Sea sediment samples through whole metagenome sequencing using Nanopore technology. Arabian Sea is considered as a major microbial reservoir with significant bio-prospecting potential which needs to be explored extensively using recent advances in genomics. Assembly, co-assembly, and binning methods were used to predict Metagenome Assembled Genomes (MAGs) which were further characterized by their completeness and heterogeneity. Nanopore sequencing of Arabian Sea sediment samples generated around 1.73 tera basepairs of data. Proteobacteria (78.32%) was found to be the most dominant phylum followed by Bacteroidetes (9.55%) and Actinobacteria (2.14%) in the sediment metagenome. Further, 35 MAGs from assembled and 38 MAGs of co-assembled reads were generated from long-read sequence dataset with major representations from the genera Marinobacter, Kangiella, and Porticoccus. RemeDB analysis revealed a high representation of pollutant-degrading enzymes involved in hydrocarbon, plastic and dye degradation. Validation of enzymes with long nanopore reads using BlastX resulted in better characterization of complete gene signatures involved in hydrocarbon (6-monooxygenase and 4-hydroxyacetophenone monooxygenase) and dye degradation (Arylsulfatase). Enhancing the cultivability of deep-sea microbes predicted from the uncultured WGS approaches by I-tip method resulted in isolation of facultative extremophiles. This study presents a comprehensive insight into the taxonomic and functional profiles of Arabian Sea sediments, indicating a potential hotspot for bioprospection.

Potential of Indigenous Strains Isolated from the Wastewater Treatment Plant of a Crude Oil Refinery

Contamination of the environment with crude oil or other fuels is an enormous disaster for all organisms. The microbial communities for bioremediation have been an effective tool for eliminating pollution. This study aimed to determine individual cultures’ and a strain mixture’s ability to utilize alkanes (single alkanes and crude oil). The proper study of pure cultures is necessary to design synergistically working consortia. The Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13 strains isolated from a wastewater treatment plant of a crude oil refinery can grow in media containing various aromatic and aliphatic hydrocarbons. The genome of the strain ICP1 contains four genes encoding alkane hydroxylases, whose transcription depended on the length of the alkane in the media. We observed that the hydrophobic cells of the strain ICP1 adhered to hydrophobic substrates, and their biofilm formation increased the bioavailability and biodegradation of the hydrocarbons. Although strain ICTN13 also has one alkane hydroxylase-encoding gene, the growth of the strain in a minimal medium containing alkanes was weak. Importantly, the growth of the mixture of strains in the crude oil-containing medium was enhanced compared with that of the single strains, probably due to the specialization in the degradation of different hydrocarbon classes and co-production of biosurfactants.

Biotransformation of grease waste into fatty acid by Penicillium chrysogenum SNP5 through media engineering and artificial neural network

Degradation of grease waste remains a challenging task. Current work deals with the biotransformation of grease waste into fatty acids under submerged fermentation using Penicillium chrysogenum SNP5 through media formulation and artificial neural network (ANN). Fermentation media was formulated to ameliorate the uptake of hydrocarbon by enhancing alkane hydroxylase (AlkB) activity, extracellular release of fatty acids and inhibiting beta-oxidation of fatty acid by regulating transketolase. Further, the process parameters of fermentation were optimized through Artificial Neural Network (ANN) using three critical variables viz; inoculum size (spores/ml), pH, and incubation time (days) while media engineering was done with the optimal supplementation of various medium components such as glucose, YPD, MnSO₄, tetrahydrobiopterin (THB) and phloretin. The maximum conversion of 66.5% of grease waste into fatty acid was achieved at optimum conditions: inoculums size 3.36 × 10⁷ spores/ml, incubation time 11.5 days, pH 7.2 along with formulated media composed of 1% grease in czapek-dox medium supplemented with 55.5 mM glucose, 0.5% YPD, 16.6 mM hexadecane, 1 mM MnSO₄, 1 mM THB, and 1 mM phloretin. The presence of long-chain fatty acids in purified extracts such as oleic acid and octadecanoic acid as end products has valued the evolved process as another source of alternative fuel.

Influence of Extremely High Pressure and Oxygen on Hydrocarbon-Enriched Microbial Communities in Sediments from the Challenger Deep, Mariana Trench

Recent studies reported that highly abundant alkane content exists in the ~11,000 m sediment of the Mariana Trench, and a few key alkane-degrading bacteria were identified in the Mariana Trench. At present, most of the studies on microbes for degrading hydrocarbons were performed mainly at atmospheric pressure (0.1 MPa) and room temperature; little is known about which microbes could be enriched with the addition of n-alkanes under in-situ environmental pressure and temperature conditions in the hadal zone. In this study, we conducted microbial enrichments of sediment from the Mariana Trench with short-chain (SCAs, C7–C17) or long-chain (LCAs, C18–C36) n-alkanes and incubated them at 0.1 MPa/100 MPa and 4 °C under aerobic or anaerobic conditions for 150 days. Microbial diversity analysis showed that a higher microbial diversity was observed at 100 MPa than at 0.1 MPa, irrespective of whether SCAs or LCAs were added. Non-metric multidimensional scaling (nMDS) and hierarchical cluster analysis revealed that different microbial clusters were formed according to hydrostatic pressure and oxygen. Significantly different microbial communities were formed according to pressure or oxygen (p < 0.05). For example, Gammaproteobacteria (Thalassolituus) were the most abundant anaerobic n-alkanes-enriched microbes at 0.1 MPa, whereas the microbial communities shifted to dominance by Gammaproteobacteria (Idiomarina, Halomonas, and Methylophaga) and Bacteroidetes (Arenibacter) at 100 MPa. Compared to the anaerobic treatments, Actinobacteria (Microbacterium) and Alphaproteobacteria (Sulfitobacter and Phenylobacterium) were the most abundant groups with the addition of hydrocarbon under aerobic conditions at 100 MPa. Our results revealed that unique n-alkane-enriched microorganisms were present in the deepest sediment of the Mariana Trench, which may imply that extremely high hydrostatic pressure (100 MPa) and oxygen dramatically affected the processes of microbial-mediated alkane utilization.

Degradation of biogas in a simulated landfill cover soil at laboratory scale: Compositional changes of main components and volatile organic compounds

A laboratory experiment lasting 28 days was run to simulate a typical landfill system and to investigate the compositional changes affecting the main components (CH₄, CO₂, and H₂) and nonmethane volatile organic compounds from biogas generated by anaerobic digestion of food waste and passing through a soil column. Gas samples were periodically collected from both the digester headspace and the soil column at increasing distances from the biogas source. CH₄ and H₂ were efficiently degraded along the soil column. The isotopic values of δ¹³C measured in CH₄ and CO₂ from the soil column were relatively enriched in ¹³C compared to the biogas. Aromatics and alkanes were the most abundant groups in the biogas samples. Among these compounds, alkylated benzenes and long-chain C₃₊ alkanes were significantly degraded within the soil column, whereas benzene and short-chain alkanes were recalcitrant. Terpene and O-substituted compounds were relatively stable under oxidising conditions. Cyclic, alkene, S-substituted, and halogenated compounds, which exhibited minor amounts in the digester headspace, were virtually absent in the soil column. These results pointed out how many recalcitrant potentially toxic and polluting compounds tend to be relatively enriched along the soil column, claiming action to minimise diffuse landfill gas (LFG) emissions. The proposed experimental approach represents a reliable tool for investigating the attenuation capacities of landfill cover soils for LFG components and developing optimised covers by adopting proper soil treatments and operating conditions to improve their degradation efficiencies.

Bioaugmentation enhance the bioremediation of marine crude oil pollution: Microbial communities and metabolic pathways

Bioaugmentation is an effective strategy used to speed up the bioremediation of marine oil spills. In the present study, a highly efficient petroleum degrading bacterium (Pseudomonas aeruginosa ZS1) was applied to the bioremediation of simulated crude oil pollution in different sampling sites in the South China Sea. The metabolic pathways of ZS1 to degrade crude oil, the temporal dynamics of the microbial community response to crude oil contamination, and the biofortification process were investigated. The results showed that the abundance and diversity of the microbial community decreased sharply after the occurrence of crude oil contamination. The best degradation rate of crude oil, which was achieved in the samples from the sampling site N3 after the addition of ZS1 bacteria, was 50.94% at 50 days. C13 alkanes were totally oxidized by ZS1 in the 50 days. The degradation rate of solid n-alkanes (C18-C20) was about 70%. Based on the whole genome sequencing and the metabolites analysis of ZS1, we found that ZS1 degraded n-alkanes through the terminal oxidation pathway and aromatic compounds through the catechol pathway. This study provides data support for further research on biodegradation pathways of crude oil and contributes to the subsequent development of more reasonable bioremediation strategies.

Transcriptome analysis and cytochrome P450 monooxygenase reveal the molecular mechanism of Bisphenol A degradation by Pseudomonas putida strain YC-AE1

BACKGROUND

Bisphenol A (BPA) is a rapid spreading organic pollutant that widely used in many industries especially as a plasticizer in polycarbonate plastic and epoxy resins. BPA reported as a prominent endocrine disruptor compound that possesses estrogenic activity and fulminant toxicity. Pseudomonas putida YC-AE1 was isolated in our previous study and exerted a strong degradation capacity toward BPA at high concentrations; however, the molecular degradation mechanism is still enigmatic.

RESULTS

We employed RNA sequencing to analyze the differentially expressed genes (DEGs) in the YC-AE1 strain upon BPA induction. Out of 1229 differentially expressed genes, 725 genes were positively regulated, and 504 genes were down-regulated. The pathways of microbial metabolism in diverse environments were significantly enriched among DEGs based on KEGG enrichment analysis. qRT-PCR confirm the involvement of BPA degradation relevant genes in accordance with RNA Seq data. The degradation pathway of BPA in YC-AE1 was proposed with specific enzymes and encoded genes. The role of cytochrome P450 (CYP450) in BPA degradation was further verified. Sever decrease in BPA degradation was recorded by YC-AE1 in the presence of CYP450 inhibitor. Subsequently, CYP450bisdB deficient YC-AE1 strain △ bisdB lost its ability toward BPA transformation comparing with the wild type. Furthermore, Transformation of E. coli with pET-32a-bisdAB empowers it to degrade 66 mg l-1 of BPA after 24 h. Altogether, the results showed the role of CYP450 in biodegradation of BPA by YC-AE1.

CONCLUSION

In this study we propose the molecular basis and the potential role of YC-AE1cytochrome P450 monooxygenase in BPA catabolism.

Impacts of groundwater level fluctuation on soil microbial community, alkane degradation efficiency and alkane-degrading gene diversity in the critical zone: Evidence from an accelerated water table fluctuation simulation

Petroleum hydrocarbons are hazardous to ecosystems and human health, commonly containing n-alkanes and polycyclic aromatic hydrocarbons. Previous researches have studied alkane degraders and degrading genes under aerobic or anaerobic conditions, but seldom discussed them in the intermittent saturation zone which is a connective area between the vadose zone and the groundwater aquifer with periodic alteration of oxygen and moisture. The present study investigated the difference in alkane degradation efficiency, bacterial community, and alkane degrading gene diversity in aerobic, anaerobic, and aerobic-anaerobic fluctuated treatments. All biotic treatments achieved over 90% of n-alkane removal after 120 days of incubation. The removal efficiencies of n-alkanes with a carbon chain length from 16 to 25 were much higher in anaerobic scenarios than those in aerobic scenarios, explained by different dominant microbes between aerobic and anaerobic conditions. The highest removal efficiency was found in fluctuation treatments, indicating an accelerated n-alkane biodegradation under aerobic-anaerobic alternation. In addition, the copy numbers of the 16S rRNA gene and two alkB genes (alkB-P and alkB-R) declined dramatically when switched from aerobic to anaerobic scenarios and oppositely from anaerobic to aerobic conditions. This suggested that water level fluctuation could notably change the presence of aerobic alkane degrading genes. Our results suggested that alkane degradation efficiency, soil microbial community, and alkane-degrading genes were all driven by water level fluctuation in the intermittent saturation zone, helping better understand the effects of seasonal water table fluctuation on the biodegradation of petroleum hydrocarbons in the subsurface environment.

Biotransformation of 8:2 Fluorotelomer Alcohol in Soil from Aqueous Film-Forming Foams (AFFFs)-Impacted Sites under Nitrate-, Sulfate-, and Iron-Reducing Conditions

The environmental fate of per- and polyfluoroalkyl substances (PFAS) in aqueous film-forming foams (AFFFs) remains largely unknown, especially under the conditions representative of natural subsurface systems. In this study, the biotransformation of 8:2 fluorotelomer alcohol (8:2 FTOH), a component of new-generation AFFF formulations and a byproduct in fluorotelomer-based AFFFs, was investigated under nitrate-, iron-, and sulfate-reducing conditions in microcosms prepared with AFFF-impacted soils. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) and high-resolution mass spectrometry (HRMS) were employed to identify biotransformation products. The biotransformation was much slower under sulfate- and iron-reducing conditions with >60 mol % of initial 8:2 FTOH remaining after ∼400 days compared to a half-life ranging from 12.5 to 36.5 days under nitrate-reducing conditions. Transformation products 8:2 fluorotelomer saturated and unsaturated carboxylic acids (8:2 FTCA and 8:2 FTUA) were detected under all redox conditions, while 7:2 secondary fluorotelomer alcohol (7:2 sFTOH) and perfluorooctanoic acid (PFOA) were only observed as transformation products under nitrate-reducing conditions. In addition, 1H-perfluoroheptane (F(CF₂)₆CF₂H) and 3-F-7:3 acid (F(CF₂)₇CFHCH₂COOH) were identified for the first time during 8:2 FTOH biotransformation. Comprehensive biotransformation pathways for 8:2 FTOH are presented, which highlight the importance of accounting for redox condition and the related microbial community in the assessment of PFAS transformations in natural environments.

Activity of alkanmonooxygenase alkB gene in strains of hydrocarbon-oxidizing bacteria isolated from petroleum products

Alkanmonooxygenase enzymes AlkB and Cyp153 are responsible for the aerobic degradation of n-alkanes of petroleum and petroleum products. To prove the usage of n-alkanes from oil and petroleum products by hydrocarbon-oxidizing bacteria isolated from aviation kerosene TS-1 and automobile gasoline AI-95, the detection of the key genes alkB, Alk1, Alk2, Alk3 and Cyp153 encoding alkanmonooxygenases AlkB and Cyp153 (responsible for the oxidation of hydrocarbons with a certain chain length) was carried out. It was found that bacterial strains isolated from TS-1 jet fuel, except Deinococcus sp. Bi7, had at least one of the studied n-alkane degradation genes. The strains Sphingobacterium multivorum Bi2; Alcaligenes faecalis Bi3; Rhodococcus sp. Bi4; Sphingobacterium sp. Bi5; Rhodococcus erythropolis Bi6 contained the alkB gene. In the strains of hydrocarbon-oxidizing bacteria isolated from gasoline AI- 95, this alkanmonooxygenase gene was not detected. Using the real-time PCR method, the activity of the alkB gene in all bacterial strains isolated from petroleum products was analyzed and the number of its copies was determined. By real-time PCR using a primer with a different sequence of nucleotides to detect the alkB gene, its activity was established in all bacterial strains isolated from gasoline AI-95; besides, the strain Paenibacillus agaridevorans Bi11 was assigned to the group with a high level of its activity (1290 copies/ml). According to the assessment of the growth of isolated hydrocarbon-oxidizing bacteria on a solid Evans mineral medium with the addition of the model mixture of hydrocarbons, the strains were divided into three groups. The distributions of strains of hydrocarbon-oxidizing bacteria in the groups based on the activity of the alkB gene and groups formed based on the growth ability and use of the model mixture of hydrocarbons and petroleum products were found to be consistent. The results obtained indicate that we need to use a complex of molecular and physiological methods for a comprehensive analysis of the distribution of the studied genes in bacteria and to assess their activity in the strains of hydrocarbon-oxidizing bacteria capable of biodegradation of petroleum hydrocarbons.

A Novel FadL Homolog, AltL, Mediates Transport of Long-Chain Alkanes and Fatty Acids in Acinetobacter venetianus RAG-1

Due to the barrier effect of lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria, transporters are required for hydrophobic alkane uptake. However, there are few reports on long-chain alkane transporters. In this study, a potential long-chain alkane transporter (AltL) was screened in Acinetobacter venetianus RAG-1 by comparative transcriptome analysis. Growth and degradation experiments showed that altL deletion led to the loss of n-octacosane utilization capacity of RAG-1. To identify the function of AltL, we measured the existence and accumulation of alkanes in cells through the constructed alkane detection system and isotope transport experiment, which proved its long-chain alkane transport function. Growth experiments using different chain-length n-alkanes and fatty acids as substrates showed that AltL was responsible for the transport of (very) long-chain n-alkanes (C₂₀ to C₃₈) and fatty acids (C_18A to C_28A) and was also involved in the uptake of medium-chain n-alkanes (C₁₆ to C₁₈). Subsequently, we analyzed the distribution of AltL in bacteria, and found that AltL homologs are widespread in Gamma-, Beta-, and Deltaproteobacteria. An AltL homolog in Pseudomonas aeruginosa was also identified to participate in long-chain alkane transport by a gene deletion and growth assay. We also found that overexpression of altL in Pseudomonas aeruginosa enhanced the degradation of C₁₆ to C₃₂ n-alkanes. In addition, structure analysis showed that AltL has longer extracellular loops than other FadL family members, which may be involved in the binding of alkanes. These results showed that AltL is a novel transporter and that it is mainly responsible for the transport of long-chain n-alkanes and (very) long-chain fatty acids and has broad application potential. IMPORTANCE Petroleum pollution has caused great harm to the natural environment, and alkanes are the main components of petroleum. Many Gram-negative bacteria can use alkanes as carbon and energy sources, which is an important strategy for oil pollution remediation. Alkane uptake is the first step for its utilization. Hence, the characterization of transport proteins is of great significance for the recovery of oil pollution and other potential applications in industrial engineering bacteria. At present, some short- and medium-chain alkane transporters have been identified, but stronger hydrophobic long-chain alkane transporters have received little attention. In this study, the broad-spectrum transporter AltL, identified in RAG-1, makes up for the lack of research on the transport of long-chain alkanes and (very) long-chain fatty acids. Meanwhile, the structural features of longer extracellular loops might be related to its unique transport function on more hydrophobic and larger substrates, indicating it is a novel type alkane transporter.

A review on biosurfactant producing bacteria for remediation of petroleum contaminated soils

The discharge of potentially toxic petroleum hydrocarbons into the environment has been a matter of concern, as these organic pollutants accumulate in many ecosystems due to their hydrophobicity and low bioavailability. Petroleum hydrocarbons are neurotoxic and carcinogenic organic pollutants, extremely harmful to human and environmental health. Traditional treatment methods for removing hydrocarbons from polluted areas, including various mechanical and chemical strategies, are ineffective and costly. However, many indigenous microorganisms in soil and water can utilise hydrocarbon compounds as sources of carbon and energy and hence, can be employed to degrade hydrocarbon contaminants. Therefore, bioremediation using bacteria that degrade petroleum hydrocarbons is commonly viewed as an environmentally acceptable and effective method. The efficacy of bioremediation can be boosted further by using potential biosurfactant-producing microorganisms, as biosurfactants reduce surface tension, promote emulsification and micelle formation, making hydrocarbons bio-available for microbial breakdown. Further, introducing nanoparticles can improve the solubility of hydrophobic hydrocarbons as well as microbial synthesis of biosurfactants, hence establishing a favourable environment for microbial breakdown of these chemicals. The review provides insights into the role of microbes in the bioremediation of soils contaminated with petroleum hydrocarbons and emphasises the significance of biosurfactants and potential biosurfactant-producing bacteria. The review partly focusses on how nanotechnology is being employed in different critical bioremediation processes.

Soil microbial ecological effect of shale gas oil-based drilling cuttings pyrolysis residue used as soil covering material

The residue derived from oil-based drilling cutting pyrolysis could be used as paving materials. Some petroleum hydrocarbons remain in the residue after pyrolysis and cause severe environmental pollution. In this study, the soil column leaching experiments were carried out under different leaching amounts, and the vertical migration characteristics of petroleum hydrocarbons in soil and the dynamic response mechanism of microorganisms to petroleum hydrocarbons were analyzed. The result showed that the soil pH value and water content with different leaching amounts did not differ significantly, but the vertical migration ability of each petroleum hydrocarbon component was different. In petroleum hydrocarbon contaminated soil, the relative abundance of Proteobacteria maintained a high level (23.6%-60.7%). At the genus level, the relative abundance of Massilia decreased with the leaching amount increased. According to PICRUSt, Monooxygenase [EC: 1.14.13.-] played a significant role in petroleum hydrocarbon degradation. While Long-chain-fatty-acid-CoA ligase [EC: 6.2.1.3] had the highest relative abundance. By studying the influence of shale gas oil-based drilling cuttings pyrolysis residue on soil physical and chemical properties and soil microorganisms, this work provides scientific ecological assessment for the resource application of pyrolysis residue.

M. tuberculosis AlkX Encoded by rv3249c Regulates a Conserved Alkane Hydroxylase System That Is Important for Replication in Macrophages and Biofilm Formation

Mycobacterium tuberculosis is a highly specialized human pathogen. The success of M. tuberculosis is due to its ability to replicate within host macrophages, resist host immune responses, and ultimately enter a persistent state during a latent tuberculosis infection. Understanding how M. tuberculosis adapts to and replicates in the intracellular environment of the host is crucial for the development of novel, targeted therapeutics. We report the characterization of an M. tuberculosis mutant lacking Rv3249c, a TetR transcriptional regulator. We show that Rv3249c directly represses the adjacent alkB-rubA-rubB operon encoding an alkane hydroxylase/rubredoxin system. For consistency with related systems, we have named the rv3249c gene alkX. The alkX mutant survived better than wild-type M. tuberculosis inside macrophages. This could be phenocopied by overexpression of the alkB-rubA-rubB locus. We hypothesized that the improved intracellular survival phenotype is a result of increased fitness of the mutant; however, we found that the alkX mutant had a defect when grown on some host-associated carbon sources in vitro. We also found that the alkX mutant had a defect in biofilm formation, also linked to the overexpression of the alkB-rubAB genes. Combined, these results define the primary role of AlkX as a transcriptional repressor of the alkB-rubAB operon and suggest the operon contributes to intracellular survival of the pathogen. IMPORTANCE Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is the leading cause of death worldwide due to a single infectious agent. It is important to understand how M. tuberculosis adapts to and replicates in the intracellular environment of the host. In this study, we characterized the TetR transcriptional regulator Rv3249c and show that it regulates a highly conserved alkane hydroxylase/rubredoxin system. Our data demonstrate that the AlkBRubAB system contributes to the success of the bacterium in host macrophages.

Characterization of two novel strains of Pseudomonas aeruginosa on biodegradation of crude oil and its enzyme activities

Crude oil contaminant is one of the major problem to environment and its removal process considered as most challenging tool currently across the world. In this degradation study, crude oil hydrocarbons are degraded on various pH optimization conditions (pH 2, 4,6,7,8 and 10) by using two biosurfactant producing bacterial strains Pseudomonas aeruginosa PP3 and Pseudomonas aeruginosa PP4. During crude oil biodegradation, degradative enzymes alkane hydroxylase and alcohol dehydrogenase were examined and found to be higher in PP4 than PP3. Biodegradation efficiency (BE) of crude oil by both PP3 and PP4 were analysed by gas chromatography mass spectroscopy (GCMS). Based on strain PP3, the highest BE was observed in pH 2 and pH 4 were found to be 62% and 69% than pH 6, 7, 8 and 10 (47%, 47%, 49% and 45%). It reveals that PP3 was survived effectively in acidic condition and utilized the crude oil hydrocarbons. In contrast, the highest BE of PP4 was observed in pH 7 (78%) than pH4 (68%) and pH's 2, 6, 8 and 10 (52%, 52%, 43% and 53%) respectively. FTIR spectra results revealed that the presence of different functional group of hydrocarbons (OH, -CH₃, CO, C-H) in crude oil. GCMS results confirmed that both strains PP3 and PP4 were survived in acidic condition and utilized the crude oil hydrocarbons as sole carbon sources. This is the first observation on biodegradation of crude oil by the novel strains of Pseudomonas aeruginosa in acidic condition with higher BE. Overall, the extracellular enzymes and surface active compounds (biosurfactant) produced by bacterial strains were played a key role in crude oil biodegradation process.