Bacterial degradation of pyrene in minimal salt medium mediated by catechol dioxygenases: enzyme purification and molecular size determination

Fulvic acid enhancing pyrene biodegradation by immobilized Stenotrophomonas maltophilia: Effect and mechanism

Immobilization technology is a promising way to improve effectiveness and stability of microbial remediation for polycyclic aromatic hydrocarbons (PAHs), in which carrier material is one of key factors restricting removal efficiency. In this study, fulvic acid-wheat straw biochar (FA/WS) composites were applied for immobilization of an efficient PAHs degrading bacterium Stenotrophomonas maltophilia (SPM). FA/WS&SPM showed superior degradation capacity than free bacteria and biochar-immobilized bacteria, with the removal efficiency of pyrene (20 mg L-1) reaching 90.5 % (7 days). Transcriptome analysis revealed that FA in the carrier materials can promote transportation and degradation of pyrene, and cell growth, as well as inhibit cell apoptosis. Enzyme activity and degradation products detection showed that SPM utilized both phthalic acid and salicylic acid metabolic pathways to degrade pyrene. Practicality of FA/WS&SPM for different kinds of PAHs remediation had been verified in contaminated soil, demonstrating a great potential in the field of PAHs polluted sites remediation.

Chemotaxis-mediated degradation of PAHs and heterocyclic PAHs under low-temperature stress by Pseudomonas fluorescens S01: Insights into the mechanisms of biodegradation and cold adaptation

As wellknown persistent contaminants, polycyclic aromatic hydrocarbons (PAHs) and heterocyclic polyaromatic hydrocarbons (Heterocyclic PAHs)'s fates in cryogenic environments are remains uncertain. Herein, strain S01 was identified as Pseudomonas fluorescens, a novel bacterium tolerant to low temperature and capable of degrading PAHs and heterocyclic PAHs. Strain S01 exhibited growth at 5-40 ℃ and degradation rate of mixed PAHs and heterocyclic PAHs reached 52% under low-temperature. Through comprehensive metabolomic, genomic, and transcriptomic analyses, we reconstructed the biodegradation pathway for PAHs and heterocyclic PAHs in S01 while investigating its response to low temperature. Further experiments involving deletion and replacement of methyl-accepting chemotaxis protein (MCP) confirmed its crucial role in enabling strain S01's adaptation to dual stress of low temperature and pollutants. Additionally, our analysis revealed that MCP was upregulated under cold stress which enhanced strain S01's motility capabilities leading to increased biofilm formation. The establishment of biofilm promoted preservation of distinct cellular membrane stability, thereby enhancing energy metabolism. Consequently, this led to heightened efficiency in pollutant degradation and improved cold resistance capabilities. Our findings provide a comprehensive understanding of the environmental fate of both PAHs and heterocyclic PAHs under low-temperature conditions while also shedding light on cold adaptation mechanism employed by strain S01.

Integrated approach of nano assisted biodegradation of anthracene by Pseudomonas aeruginosa and iron oxide nanoparticles

Poly aromatic hydrocarbons (PAHs) are considered as hazardous compounds which causes serious threat to the environment dua to their more carcinogenic and mutagenic impacts. In this study, Pseudomonas aeruginosa PP4 strain and synthesized iron nanoparticles were used to evaluate the biodegradation efficiency (BE %) of residual anthracene. The BE (%) of mixed degradation system (Anthracene + PP4+ FeNPs) was obtained about 67 %. The FTIR spectra result revealed the presence of functional groups (C-H, -CH3, CC, =C-H) in the residual anthracene. The FESEM and TEM techniques were used to determine the surface analysis of the synthesized FeNPs and the average size was observed by TEM around 5-50 nm. The crystalline nature of the synthesized iron nanoparticles was confirmed by the observed different respective peaks of XRD pattern. The various functional constituents (OH, C-H, amide I, CH3) were identified in the synthesized iron nanoparticles by FTIR spectrum. In conclusion, this integrated nano-bioremediation approach could be an promising and effective way for many environmental fields like cleanup of hydrocarbon rich environment.

Diverse hydrocarbon degradation genes, heavy metal resistome, and microbiome of a fluorene-enriched animal-charcoal polluted soil

Environmental compartments polluted with animal charcoal from the skin and hide cottage industries are rich in toxic heavy metals and diverse hydrocarbon classes, some of which are carcinogenic, mutagenic, and genotoxic, and thus require a bio-based eco-benign decommission strategies. A shotgun metagenomic approach was used to decipher the microbiome, hydrocarbon degradation genes, and heavy metal resistome of a microbial consortium (FN8) from an animal-charcoal polluted site enriched with fluorene. Structurally, the FN8 microbial consortium consists of 26 phyla, 53 classes, 119 orders, 245 families, 620 genera, and 1021 species. The dominant phylum, class, order, family, genus, and species in the consortium are Proteobacteria (51.37%), Gammaproteobacteria (39.01%), Bacillales (18.09%), Microbulbiferaceae (11.65%), Microbulbifer (12.21%), and Microbulbifer sp. A4B17 (19.65%), respectively. The microbial consortium degraded 57.56% (28.78 mg/L) and 87.14% (43.57 mg/L) of the initial fluorene concentration in 14 and 21 days. Functional annotation of the protein sequences (ORFs) of the FN8 metagenome using the KEGG GhostKOALA, KofamKOALA, NCBI's conserved domain database, and BacMet revealed the detection of hydrocarbon degradation genes for benzoate, aminobenzoate, polycyclic aromatic hydrocarbons (PAHs), chlorocyclohexane/chlorobenzene, chloroalkane/chloroalkene, toluene, xylene, styrene, naphthalene, nitrotoluene, and several others. The annotation also revealed putative genes for the transport, uptake, efflux, and regulation of heavy metals such as arsenic, cadmium, chromium, mercury, nickel, copper, zinc, and several others. Findings from this study have established that members of the FN8 consortium are well-adapted and imbued with requisite gene sets and could be a potential bioresource for on-site depuration of animal charcoal polluted sites.

Genome features of a novel hydrocarbonoclastic Chryseobacterium oranimense strain and its comparison to bacterial oil-degraders and to other C. oranimense strains

For the first time, we report the whole genome sequence of a hydrocarbonoclastic Chryseobacterium oranimense strain isolated from Trinidad and Tobago (COTT) and its genes involved in the biotransformation of hydrocarbons and xenobiotics through functional annotation. The assembly consisted of 11 contigs with 2,794 predicted protein-coding genes which included a diverse group of gene families involved in aliphatic and polycyclic hydrocarbon degradation. Comparative genomic analyses with 18 crude-oil degrading bacteria in addition to two C. oranimense strains not associated with oil were carried out. The data revealed important differences in terms of annotated genes involved in the hydrocarbon degradation process that may explain the molecular mechanisms of hydrocarbon and xenobiotic biotransformation. Notably, many gene families were expanded to explain COTT's competitive ability to manage habitat-specific stressors. Gene-based evidence of the metabolic potential of COTT supports the application of indigenous microbes for the remediation of polluted terrestrial environments and provides a genomic resource for improving our understanding of how to optimize these characteristics for more effective bioremediation.

Altered active pyrene degraders in biosurfactant-assisted bioaugmentation as revealed by RNA stable isotope probing

Bioaugmentation is an effective approach for removing pyrene from contaminated sites, and its performance is enhanced by a biosurfactant. To reveal the mechanisms of biosurfactant-assisted bioaugmentation, we introduced RNA stable isotope probing (RNA-SIP) in the pyrene-contaminated soils and explored the impacts of rhamnolipid on the pyrene degradation process. After 12-day degradation, residual pyrene was the lowest in the bioaugmentation treatment (7.76 ± 1.57%), followed by biosurfactant-assisted bioaugmentation (9.86 ± 2.58%) and enhanced natural attenuation (23.97 ± 1.05%). Thirteen well-known and two novel pyrene-degrading bacteria were confirmed to participate in the pyrene degradation. Pyrene degradation was accelerated in the biosurfactant-assisted bioaugmentation, manifested by the high diversity of active pyrene degraders. Our findings expand the knowledge on pyrene degrading bacteria and the mechanisms of pyrene degradation in a bioaugmentation process.

Biological machinery for polycyclic aromatic hydrocarbons degradation: A review

Polycyclic aromatic hydrocarbons (PAHs) are hazardous environmental pollutants with widespread and well-recognized health concerns. Amidst more than a hundred known PAHs, 16 are categorized as priority pollutants. Use of widely diverse biological machinery comprising bacteria, fungi, and algae harnessed from contaminated sites has emerged as an ecologically safe and sustainable approach for PAH degradation. The potential of these biological systems has been thoroughly examined to maximize the degradation of specific PAHs by understanding their detailed biochemical pathways, enzymatic system, and gene organization. Recent advancements in microbial genetic engineering and metabolomics using modern analytical tools have facilitated the bioremediation of such xenobiotics. This review explores the role of microbes, their biochemical pathways, genetic regulation of metabolic pathways, and the effect of biosurfactants against the backdrop of PAH substrate structures.

Enhanced biodegradation of hydrophobic organic pollutants by the bacterial consortium: Impact of enzymes and biosurfactants

Hydrocarbons and their derivative compounds are recalcitrant in nature and causing adverse impacts to the environment and are classified as important pollutants. Removal of these pollutants from the atmosphere is a challenging process. Hydrophobic organic pollutants (HOPs) including crude oil, diesel, dotriacontane (C₃₂), and tetracontane (C₄₀) are subjected to the biodegradation study by using a bacterial consortium consist of Bacillus subtilis, Pseudomonas stutzeri, and Acinetobacter baumannii. The impact of pH and temperature on the biodegradation process was monitored. During the HOPs biodegradation, the impact of hydrocarbon-degrading extracellular enzymes such as alcohol dehydrogenase, alkane hydroxylase, and lipase was examined, and found average activity about 47.2, 44.3, and 51.8 μmol/mg^-1, respectively. Additionally, other enzymes such as catechol 1,2 dioxygenase and catechol 2,3 dioxygenase were found as 118 and 112 μmol/mg^-1 Enzyme as an average range in all the HOPs degradation, respectively. Also, the impact of the extracellular polymeric substance and proteins were elucidated during the biodegradation of HOPs with the average range of 116.90, 54.98 mg/L^-1 respectively. The impact of biosurfactants on the degradation of different types of HOPs is elucidated. Very slight changes in the pH were also noticed during the biodegradation study. Biodegradation efficiency was calculated as 90, 84, 76, and 72% for crude oil, diesel, C_32, and C₄₀, respectively. Changes in the major functional groups (CH, C-O-C, CO, =CH₂, CH₂, CH₃) were confirmed by FTIR analysis and intermediated metabolites were identified by GCMS analysis. The surface-active molecules along with the enzymes played a crucial role in the biodegradation process.

Semi-continuous monitoring of HMWPAH in microalgae cultures by PT-SPE/HPLC/FD-UV: Estimation of the degradation constant

A degradation study has been performed with Selenastrum capricornutum incubated with benzo[a]anthracene and benzo[a]pyrene at 50, 100 and 266 ng mL^-1 in liquid cultures. After incubation, these high molecular weight polycyclic aromatic hydrocarbons (HMW PAH) were extracted from both, the medium and biomass in a single step, and then quantified by a sensitive and validated analytical methodology based on pipette-tip SPE and HPLC with fluorescence and UV detection (PT-SPE/HPLC/FD-UV). The methodology presented good linearity r² > 0.99, LOD of 0.9 and 0.7 ng mL^-1 for BaA and BaP, respectively. A fast and semi-continuous appreciation of the degradation behavior was achieved. The pollutants were monitored at different times (0.5-18 h) in the same culture flask, with sampling volume of 1 mL. Biodegradation percentages close to-90% were observed at 18 h. The degradation curves were fitted to the first order reaction (r² > 0.95) and the degradation rate constants were similar in all bioassays (0.1 h^-1) and independent of concentration and compound. The degradation pathways of HMW PAH by microalgae and their enzyme are poorly known but the hypothesis of the degrading enzyme proportionally activated according to the PAH concentration is supported by this result. The early emergence dihydrodiol-type metabolites were detected.

Binding interaction of a ring-hydroxylating dioxygenase with fluoranthene in Pseudomonas aeruginosa DN1

Pseudomonas aeruginosa DN1 can efficiently utilize fluoranthene as its sole carbon source, and the initial reaction in the biodegradation process is catalyzed by a ring-hydroxylating dioxygenase (RHD). To clarify the binding interaction of RHD with fluoranthene in the strain DN1, the genes encoding alpha subunit (RS30940) and beta subunit (RS05115) of RHD were functionally characterized through multi-technique combination such as gene knockout and homology modeling as well as molecular docking analysis. The results showed that the mutants lacking the characteristic alpha subunit and/or beta subunit failed to degrade fluoranthene effectively. Based on the translated protein sequence and Ramachandran plot, 96.5% of the primary amino-acid sequences of the alpha subunit in the modeled structure of the RHD were in the permitted region, 2.3% in the allowed region, but 1.2% in the disallowed area. The catalytic mechanism mediated by key residues was proposed by the simulations of molecular docking, wherein the active site of alpha subunit constituted a triangle structure of the mononuclear iron atom and the two oxygen atoms coupled with the predicted catalytic ternary of His₂₁₇-His₂₂₂-Asp₃₇₂ for the dihydroxylation reaction with fluoranthene. Those amino acid residues adjacent to fluoranthene were nonpolar groups, and the C₇-C₈ positions on the fluoranthene ring were estimated to be the best oxidation sites. The distance of C₇-O and C₈-O was 3.77 Å and 3.04 Å respectively, and both of them were parallel. The results of synchronous fluorescence and site-directed mutagenesis confirmed the roles of the predicted residues during catalysis. This binding interaction could enhance our understanding of the catalytic mechanism of RHDs and provide a solid foundation for further enzymatic modification.

Synergistic degradation of pyrene by Pseudomonas aeruginosa PA06 and Achromobacter sp. AC15 with sodium citrate as the co-metabolic carbon source

Two pyrene-degrading strains, Pseudomonas aeruginosa PA06 and Achromobacter sp. AC15 were co-incubated in equal proportions as a microbiological consortium and could enhance the degradation of pyrene. The enzymatic activities of the catechol 1,2-dioxygenase (C12O) and 2,3-dioxygenase activities (C23O) were produced complementary expression by P. aeruginosa PA06 and Achromobacter sp. AC15, respectively. Meanwhile, results showed that pyrene degradation was sufficiently promoted in the presence of sodium citrate as a co-metabolic carbon source, likely a result of enhanced biomass and biosurfactant production. The optimized dosage and ideal initial pHs were 1.4 g L^-1 and 5.5, respectively. We also analyzed the rate constant of pyrene degradation, cell growth, and enzyme activity. Results show that P. aeruginosa PA06 had a better effect than Achromobacter sp. AC15 in bacterial growth. However, the C23O or C12O activity produced by Achromobacter sp. AC15 continued at a similar or even faster than that of P. aeruginosa PA06. The mixed bacteria had a better effect than any single bacteria, suggesting the strains worked synergistically to enhance the degradation efficiency. In the co-metabolism system of 600 mg/L pyrene and 1.4 g/L sodium citrate, pyrene degradation reached 74.6%, was 1.57 times, 2.06 times, and 3.89 times that of the mix-culture strains, single PA06 and single AC15 without sodium citrate, respectively. Overall, these findings are valuable as a potential tool for the bioremediation of high-molecular-weight PAHs.

Characterization of lipopeptide biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis: The role of biosurfactant in carbazole solubilisation

AIM

Characterization of biosurfactant produced by a carbazole-degrading bacterium Roseomonas cervicalis and proteomic analysis of intracellular proteins of bacterium while growing on glucose and carbazole medium.

METHODS AND RESULTS

The bacterium R. cervicalis was isolated from a soil sample contaminated with crude petroleum oil. PCR amplification ascertained the existence of some hydrocarbon-degrading catabolic genes (alkB and PAH-RHDα, C12O, and C23O) in the bacterial genome. GC-MS and RP-HPLC analyses demonstrated 62% and 60% carbazole degradation, respectively, by R. cervicalis 144 h post-incubation at 37℃ and pH 6.5. Due to the paucity of protein databases, expressions of only 29 and 14 intracellular proteins were explicitly recognized and quantitated by mass spectrometry analysis when R. cervicalis was grown in carbazole and glucose medium, respectively. FTIR, NMR and HR-MS/MS analyses demonstrated the lipopeptide nature of the purified biosurfactant produced by R. cervicalis. The biosurfactant is also presumed to assist in the solubilization of carbazole.

CONCLUSION

The isolated R. cervicalis strain is a potential candidate for the bioremediation of carbazole in petroleum-oil-contaminated sites.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report of the promising R. cervicalis strain proficient in carbazole biodegradation.

Function and Molecular Ecology Significance of Two Catechol-Degrading Gene Clusters in Pseudomonas putida ND6

Many bacteria metabolize aromatic compounds via catechol as a catabolic intermediate, and possess multiple genes or clusters encoding catechol-cleavage enzymes. The presence of multiple isozyme-encoding genes is a widespread phenomenon that seems to give the carrying strains a selective advantage in the natural environment over those with only a single copy. In the naphthalene-degrading strain Pseudomonas putida ND6, catechol can be converted into intermediates of the tricarboxylic acid cycle via either the ortho- or meta-cleavage pathways. In this study, we demonstrated that the catechol ortho-cleavage pathway genes (catB_IC_IA_I and catB_IIC_IIA_II) on the chromosome play an important role. The cat_I and cat_II operons are co-transcribed, whereas catA_I and catA_II are under independent transcriptional regulation. We examined the binding of regulatory proteins to promoters. In the presence of cis-cis-muconate, a well-studied inducer of the cat gene cluster, CatR_I and CatR_II occupy an additional downstream site, designated as the activation binding site. Notably, CatR_I binds to both the cat_I and cat_II promoters with high affinity, while CatR_II binds weakly. This is likely caused by a T to G mutation in the G/T-N₁₁-A motif. Specifically, we found that CatR_I and CatR_II regulate catB_IC_IA_I and catB_IIC_IIA_II in a cooperative manner, which provides new insights into naphthalene degradation.

Biodegradation of selected hydrocarbons by novel bacterial strains isolated from contaminated Arabian Gulf sediment

Three strains of novel bacteria were isolated from oil-contaminated sediment from the Arabian Gulf (Brevibacillus brevis T2C2008, Proteus mirabilis T2A12001, and Rhodococcus quinshengi TA13008). The isolated strains were tested for their degrading efficacy of low and high molecular hydrocarbon (naphthalene and pyrene). The efficacy of the two-hydrocarbon degradation by the isolates bacterial was determined at a temperature of 25 °C and 37 °C and pH of 5.0 and 9.0. In inoculated media at 37 °C, Rhodococcus qinshengi fully metabolized naphthalene and degrade 56% of pyrene. Brevibacillus brevis break down over 80% of naphthalene at room temperatures (25 °C). However, it was found that P. mirabilis and R. qinshengi biodegraded nearly 94% of naphthalene in the incubated media. The capacity for pyrene and naphthalene degradation in varying pH and temperature conditions was shown to be significant in Rhodococcus qinshengi because of its mineralization exceeding 50% across the tested pH and temperature. This implies that the isolated strains are ideal for biodegradation of contaminated sediment with naphthalene and pyrene.

Enhancement of Toxic Efficacy of Alkylated Polycyclic Aromatic Hydrocarbons Transformed by Sphingobium quisquiliarum

Alkylated polycyclic aromatic hydrocarbons (PAHs) are abundant in crude oils and refined petroleum products and are considered as major contributors to the toxicity of spilled oils. In this study, the microbial degradation of model (alkylated) PAHs (i.e., phenanthrene, 3-methylphenanthrene, 3,6-dimethylphenanthrene (36DMPhe), pyrene, and 1-methylpyrene (1MP)) by the bacterium Sphingobium quisquiliarum EPA505, a known degrader of PAHs, was studied. To evaluate the toxic potential of the metabolic products, reaction mixtures containing metabolites of 36DMPhe and 1MP were fractionated by high-performance liquid chromatography, and their effects on the luminescence inhibition of Aliivibrio fischeri were evaluated. Although the luminescence inhibition of 36DMPhe and 1MP at their solubility levels was not observed, inhibition was observed in their metabolite fractions at the solubility limit of their parent molecule. This indicates that initial biotransformation increases the toxicity of alkylated PAHs because of the increased solubility and/or inherent toxicity of metabolites. Qualitative analysis of the metabolite fractions suggested that mono-oxidation of the methyl group is the main metabolic pathway of 36DMPhe and 1MP.

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

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

Characterization of Biofilm Formed by Phenanthrene-Degrading Bacteria on Rice Root Surfaces for Reduction of PAH Contamination in Rice

One effective method in to reduce the uptake of organic contaminants by plants is the development of a root barrier. In this study, the characterization of biofilm structure and function by phenanthrene-degrading Pseudomonas sp. JM2-gfp on rice root surfaces were carried out. Our results showed that root surfaces from three rice species, namely Liaojing401, Koshihikari, and Zhenzhuhong all present hydrophobicity and a high initial adhesion of strain JM2-gfp. Matured robust biofilm formation occurred at 48 h on the root surfaces. The biofilm exhibited cell dense aggregates and biomass embedded in the extracellular polymeric substance (EPS) matrix. EPS composition results showed that the proteins, carbohydrates, lipids and nucleic acids are produced in the biofilm, while the content varied with rice species. Under the initial concentration of phenanthrene 50 mg·L-1, the residual phenanthrene in plant roots from 'Zhengzhuhong', 'Koshihikari' and 'Liaojing401' with biofilm mediated were significantly decreased by 71.9%, 69.3% and 58.7%, respectively, compared to those without biofilm groups after 10 days of exposure. Thus, the biofilm colonized on roots plays an important role of degradation in order to reduce the level of phenanthrene uptake of plants. Thereby, the present work provides significant new insights into lowering the environmental risks of polycyclic aromatic hydrocarbons (PAHs) in crop products from contaminated agriculture soils.

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) in a diesel oil-contaminated mangrove by plant growth-promoting rhizobacteria

In this study, Rhizophora mangle L. mangrove plants and plant growth-promoting bacteria were evaluated for their ability to degrade polycyclic aromatic hydrocarbons in diesel oil-contaminated sediment. The diesel-contaminated soil was sown with plant growth-promoting bacteria in the R. mangle L. rhizosphere and monitored for 120 days in a greenhouse. The plant growth-promoting bacteria Pseudomonas aeruginosa and Bacillus sp. were analyzed for their ability to degrade eight priority polycyclic aromatic hydrocarbons, achieving a removal rate for naphthalene (80%), acenaphthene (> 60%), anthracene (> 50%), benzo(a)anthracene (> 60%), benzo(a)pyrene (> 50%) and dibenzo(a,h)anthracene (> 90%) in the treatments with and without plants. R. mangle L. demonstrated a removal rate above 50% for acenaphthene and fluoranthene. The bacterial strains promoted the development of the plant propagule in 55% of sediment contaminated with diesel. Scanning electron microscopy revealed the formation of biofilms by the strains in the roots of the plants in contact with the diesel. Thus, the interaction between Rhizophora mangle L. and the bacterial strains (Bacillus sp. and P. aeruginosa) demonstrated the potential of the strains to degrade diesel and bioremediate mangroves impacted by diesel oil.

Co-biodegradation of pyrene and other PAHs by the bacterium Acinetobacter johnsonii

Polycyclic aromatic hydrocarbons (PAHs) usually co-exist in environment with interactional effects. Currently, Acinetobacter johnsonii was employed to degrade 400 mg L^-1 of pyrene (PYR) and kinetic modeling indicated substrate inhibition over 76 mg L^-1 by introducing an inhibition constant parameter. In PAHs co-biodegradation, naphthalene (NAP) dominated biodegradation processes through the preferential utilization as growth substrate. The peak biodegradation of PYR increased to 415 mg L^-1 with 65 mg L^-1 of NAP. Furthermore, phenanthrene (PHE), PYR and anthracene (ANT) were degraded in turn and ended in reverse order. When the concentrations reached their respective limiting concentration of 22%, ANT could not be degraded and PHE and PYR biodegradations also respectively terminated at 66 and 45 h later with a removal rate of 40% and 26% due to very low specific activities of salicylate hydroxylase and catechol 2,3-dioxygenase. However, by introducing 125-133 mg L^-1 of NAP, the bacterial potential was effectively enhanced to 29% after cell underwent a re-stimulation stage with the exhaustion of NAP. NAP prominently contributed to cell growth to stimulate secretion of key enzymes, but the advantage would gradually get lost with the decline of its titer. To research the interplay of PAHs is conducive to targeted decontamination.

Bacterial Biodegradation of 4-Monohalogenated Diphenyl Ethers in One-Substrate and Co-Metabolic Systems

The use of diphenyl ether (DE) and its 4-monohalogenated derivatives (4-HDE) as flame retardants, solvents, and substrates in biocide production significantly increases the risk of ecosystem contamination. Their removal is important from the point of view of environmental protection. The aim of this study was to evaluate the degradation processes of DE and 4-HDE by enzymes of the environmental bacterial strains under one-substrate and co-metabolic conditions. The study is focused on the biodegradation of DE and 4-HDE, the enzymatic activity of microbial strains, and the cell surface properties after contact with compounds. The results show that the highest biodegradation (96%) was observed for 4-chlorodiphenyl ether in co-metabolic culture with P. fluorescens B01. Moreover, the activity of 1,2-dioxygenase during degradation of 4-monohalogenated diphenyl ethers was higher than that of 2,3-dioxygenase for each strain tested. The presence of a co-substrate provoked changes in dioxygenase activity, resulting in the increased activity of 1,2-dioxygenase. Moreover, the addition of phenol as a co-substrate allowed for increased biodegradation of the diphenyl ethers and noticeable modification of the cell surface hydrophobicity during the process. All observations within the study performed have led to a deeper understanding of the contaminants’ biodegradation processes catalyzed by environmental bacteria.

Degradation of Chrysene by Enriched Bacterial Consortium

Chrysene is a high molecular weight (HMW), polycyclic aromatic hydrocarbon (PAH) known for its recalcitrance and carcinogenic properties and sparsely soluble (0.003 mg/L) in aqueous medium. Due to these refractory properties, bioavailability of chrysene is very low and therefore is persistence in the environment escaping the metabolism by microorganisms. However, few bacterial and fungal strains are reported to degrade chrysene, but with lower efficiency, requiring additional/extraneous carbon sources (co-substrates) for it’s complete mineralization. In this study, development, enrichment and characterization of bacterial consortium ASDC, consisting of Rhodococcus sp., ASDC1; Bacillus sp. ASDC2; and Burkholderia sp. ASDC3 were reported. Chrysene was utilized as a sole source of carbon and energy by the consortium, having maximum degradation rate of 1.5 mg/L/day and maximum growth rate of 0.125/h, under optimized conditions of pH 7.0, 37°C under aeration of 150 rpm on gyrating shaking. Chrysene degradation was unaffected in presence of other PAHs like pyrene, fluoranthene, naphthalene, phenanthrene, benzene, toluene and xylene, individually as well as in mixture. The results revealed that peptone, ammonium nitrate, sodium succinate have enhanced the chrysene degradation rate during first 24 h of experimentation, which was later on inhibited with increase in incubation time. The chrysene degradation was inhibited by mercury even at lower concentration (1 mM). The results also revealed that SDS has enhanced its degradation by 5.2-fold for initial 24 h of growth, but with increasing in the incubation period, it decreases by 1.2-fold on 7^th day of experimentation. The HPLC studies suggested that chrysene was degraded through phthalic acid pathway by the consortium ASDC and the stoichiometric measurements indicated the complete mineralization of chrysene. The flask scale results were validated at simulated microcosm models, where enriched consortium ASDC exhibited maximum degradation (96%) in polluted, non-sterile soil sediment, indicating that consortial strains along with indigenous metabolism showed synergistic metabolism for degradation of chrysene. Thus, the above study revealed the useful enrichment of bacterial community for synergistic degradation of PAHs (chrysene) which could be further exploited for in situ remediation of PAH contaminated sites.

Untapped bacterial diversity and metabolic potential within Unkeshwar hot springs, India

Hot springs support diverse and interesting groups of microorganisms adapted to extreme conditions and gaining attention in biotechnological applications. However, due to limitations of cultivation methods, a majority of such extremophiles remain uncultivated and unexplored. The advent of multiple cultivation conditions and specialized culture media could possibly aid to access the unexplored microbial portion of hot springs. In the present study, different media and isolation strategies were applied to isolate hitherto unexplored bacterial taxa in the water samples collected from Unkeshwar hot springs, India. Molecular, phylogenetic and predictive functional characterization of the isolated bacterial population was done using 16S rRNA sequencing coupled with Tax4Fun tools. Furthermore, representative isolates were screened for important enzymes (cellulase, xylanase, amylase, and protease) and heavy metal tolerance (chromium, arsenic) properties. A total of 454 bacterial isolates obtained were mapped into 57 unique bacterial genera and 4 different bacterial phyla. Interestingly, 37 genera not previously isolated from Indian hot springs, were isolated for the first time in the present study. However, most of these genera (23 out of 37) were reported only in metagenomics studies from Indian and global hot springs. Furthermore, around 14 genera not previously cultivated and not detected in metagenomics studies of hot springs are documented here. The metabolic potential was ascertained by determining the abundance of specific genes using in silico based Tax4Fun tool, which identified around 315 metabolic pathways for metabolism of carbohydrates, synthesis of secondary metabolites and degradation of xenobiotic compounds. Bioprospection study revealed that 33 and 25 bacterial genera were positive for enzyme production and resistance to the heavy metals, respectively. The present study revealed the advantages of cultivation methods using a comprehensive multiple isolation approach for exploring untapped and unique bacterial diversity, and also utilities for various biotechnological and environmental applications.

Characteristics and proteomic analysis of pyrene degradation by Brevibacillus brevis in liquid medium

Polycyclic aromatic hydrocarbons (PAHs) are widely spread in various ecosystems and are of great concern due to their potential toxicity, mutagenicity and carcinogenicity. Bioremediation has been proposed as an effective approach to remove PAHs. In this study, the physiological responses and proteome of Brevibacillus brevis under exposure to pyrene, a four-ring compound from PAHs family, were investigated. The changes of cell viability of B. brevis were observed during the degradation of pyrene by means of flow cytometry. The results indicated that pyrene stimulated superoxide dismutase (SOD) activity from 93.9 to 100.6 U mg^-1 prot, whereas inhibited catalase (CAT) activity from 29.1 to 20.3 U mg^-1 prot. The main compositions of B. brevis changed during pyrene degradation, with the proportion of unsaturated fatty acids increased by 13.4%. In addition, we performed a proteomic approach (two-dimensional gel electrophoresis and MALDI-TOF/TOF-MS) in order to explore how B. brevis survived upon treatment with pyrene. It was showed that the expression of 13 proteins increased whereas 10 other decreased after pyrene-treatment. The differentially expressed proteins were identified and the results indicated that they were involved in multiple biological processes including energy metabolism, biosynthesis, transmembrane transport and oxidative stress. Overall, these findings offered a new insights into the cellular response strategy developed by B. brevis to overcome the pyrene stress.

Biodegradation of pyrene by pseudomonas sp. JPN2 and its initial degrading mechanism study by combining the catabolic nahAc gene and structure-based analyses

In this study, a pyrene-degrading bacterial strain Pseudomonas sp. JPN2 was isolated from crude oil in Dagang Oilfield, China. The degrading percent of the strain JPN2 to pyrene was increased with the extension of culture time and achieved a maximum of 82.88% after 25 d culture. Meanwhile, four metabolites 4,5-dihydroxy-4,5-dihydropyrene, 4-phenanthrol, 1-hydroxy-2-naphthoic acid and phthalate were detected in the culture solution by GC-MS analysis. In addition, DNA fragments of nahAc gene, encoding α subunit of naphthalene dioxygenase, were amplified by PCR program and sequenced. As a result, it was presumed that the initial cleavage of the aromatic rings on pyrene was occurred at C₄ and C₅ positions and formed the intermediate 4,5-dihydroxy-4,5-dihydropyrene. This issue had been verified by the interaction analysis between pyrene and the active site of naphthalene dioxygenase in the strain JPN2 by molecular docking. Meanwhile, the differences of the amino acid residues in the active sites of template and target enzymes may be a factor leading to the different biological activity between the strain JPN2 and the other bacteria from the genus Pseudomonas. Additionally, the microcalorimetry analysis displayed that the strain JPN2 had high tolerance for pyrene, and the effect could be negligible under the experimental concentration (100 mg L^-1). Consequently, the strain JPN2 was considered as an excellent candidate for the further bioremediation study of pyrene and the other aromatic contaminants.

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

Isolation and characterisation of crude oil sludge degrading bacteria

Background

The use of microorganisms in remediating environmental contaminants such as crude oil sludge has become a promising technique owing to its economy and the fact it is environmentally friendly. Polycyclic aromatic hydrocarbons (PAHs), as the major components of oil sludge, are hydrophobic and recalcitrant. An important way of enhancing the rate of PAH desorption is to compost crude oil sludge by incorporating commercial surfactants, thereby making them available for microbial degradation. In this study, crude oil sludge was composted for 16 weeks during which surfactants were added in the form of a solution.

Results

Molecular characterisation of the 16S rRNA genes indicated that the isolates obtained on a mineral salts medium belonged to different genera, including Stenotrophmonas, Pseudomonas, Bordetella, Brucella, Bacillus, Achromobacter, Ochrobactrum, Advenella, Mycobacterium, Mesorhizobium, Klebsiella, Pusillimonas and Raoultella. The percentage degradation rates of these isolates were estimated by measuring the absorbance of the 2,6-dichlorophenol indophenol medium. Pseudomonas emerged as the top degrader with an estimated percentage degradation rate of 73.7% after 7 days of incubation at 28 °C. In addition, the presence of the catabolic gene, catechol-2,3-dioxygenase was detected in the bacteria isolates as well as in evolutionary classifications based on phylogeny.

Conclusions

The bacteria isolated in this study are potential agents for the bioremediation of crude oil sludge.

Preliminary characterization of biosurfactant produced by a PAH-degrading Paenibacillus sp. under thermophilic conditions

The capacities of a biosurfactant producing and polycyclic aromatic hydrocarbon (PAH) utilizing bacterium, namely, strain 1C, isolated from an Algerian contaminated soil, were investigated. Strain 1C belonged to the Paenibacillus genus and was closely related to the specie Paenibacillus popilliae, with 16S rRNA gene sequence similarity of 98.4 %. It was able to produce biosurfactant using olive oil as substrate. The biosurfactant production was shown by surface tension (32.6 mN/m) after 24 h of incubation at 45 °C and 150 rpm. The biosurfactant(s) retained its properties during exposure to elevated temperatures (70 °C), relatively high salinity (20 % NaCl), and a wide range of pH values (2-10). The infrared spectroscopy (FTIR) revealed that its chemical structure belonged to lipopeptide class. The critical micelle concentration (CMC) of this biosurfactant was about 0.5 g/l with 29.4 mN/m. In addition, the surface active compound(s) produced by strain 1C enhanced PAH solubility and showed a significant antimicrobial activity against pathogens. In addition to its biosurfactant production, strain 1C was shown to be able to utilize PAHs as the sole carbon and energy sources. Strain 1C as hydrocarbonoclastic bacteria and its interesting surface active agent may be used for cleaning the environments polluted with polyaromatic hydrocarbons.

Biosorption and biodegradation of pyrene by Brevibacillus brevis and cellular responses to pyrene treatment

Biodegradation has been proposed as an effective approach to remove pyrene, however, the information regarding cellular responses to pyrene treatment is limited thus far. In this study, the biodegradation and biosorption of pyrene by Brevibacillus brevis, along with cellular responses caused by pollutant were investigated by means of flow cytometry assay and scanning electron microscopy. The experimental results showed that pyrene was initially adsorbed by B. brevis and subsequently transported and intracellularly degraded. During this process, pyrene removal was primarily dependent on biodegradation. Cell invagination and cell surface corrugation occurred due to pyrene exposure. Nevertheless, cell regrowth after 96h treatment was observed, and the proportion of necrotic cell was only 2.8% after pyrene exposure for 120h, confirming that B. brevis could utilize pyrene as a sole carbon source for growth. The removal and biodegradation amount of pyrene (1mg/L) at 168h were 0.75 and 0.69mg/L, respectively, and the biosorption amount by inactivated cells was 0.41mg/L at this time.

Effect of Pb(ii) on phenanthrene degradation by new isolated Bacillus sp. P1

A new strain of bacteria, Bacillus sp. P1, was isolated from compost to degrade PHE in the presence of Pb(ii).

Characterization of Stenotrophomonas acidaminiphila NCW-702 biofilm for implication in the degradation of polycyclic aromatic hydrocarbons

AIMS

Biofilm formation and polycyclic aromatic hydrocarbons (PAHs) degradation by a marine bacterium Stenotrophomonas acidaminihila NCW-702 was investigated.

METHODS AND RESULTS

The biofilm structure was studied by confocal laser scanning microscopy (CLSM). Both planktonic and biofilm cultures were used for PAHs (phenanthrene and pyrene) degradation. In 7 days, Sten. acidaminiphila biofilm culture efficiently degraded 71·1 ± 3·1% and 40·2 ± 2·4% of phenanthrene and pyrene, respectively, whereas 38·7 ± 2·5% of phenanthrene and 29·7 ± 1% of pyrene degradation was observed in planktonic culture. The presence of phenolic intermediates in the culture supernatant during degradation process was evaluated by Folin-Ciocalteu reagent. The average thickness and diffusion distance of Sten. acidaminiphila NCW-702 biofilm was found to be 23·94 ± 2·62 μm and 2·68 ± 0·7 μm, respectively. Bacterial biofilms have numerous metabolic features that aid in the degradation of hydrophobic organic pollutants.

CONCLUSIONS

Biofilm of Sten. acidaminiphila NCW-702 was able to degrade PAHs more efficiently as compared to planktonic cells. The findings support the efficacy of biofilms over planktonic culture in bioremediation applications.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study provides a constructive application of bacterial biofilms for the bioremediation of hydrophobic organic contaminants. The biofilm mode remediation process has the advantage of reusability of bacterial biomass and is also a low cost process as compared to cell immobilization techniques.

Bacteria induced degradation of fluoranthene in minimal salt medium mediated by catabolic enzymes in vitro condition

Fluoranthene is highly toxic and ubiquitous in the environment. A study on degradation of 200 ppm of fluoranthene in MSM by two bacterial strains Pseudomonas aeruginosa PSA5, Rhodococcus sp. NJ2 and their consortium revealed that fluoranthene was degraded 74% by Rhodococcus sp. NJ2, 61% by Pseudomonas sp. PSA5 and 97% by their consortium. Higher degradation in the consortium may be attributed to synergistic action between two bacteria. It was also observed that several degradative enzymes catechol 1,2 dioxygenase, catechol 2,3 dioxygenase, protocatechuate 2,3 dioxygenase, protocatechuate 3,4 dioxygenase, protocatechuate 4,5 dioxygenase, salicylate hydroxylase and 2-carboxybenzaldehyde dehydrogenase were differentially induced at different stages of fluoranthene degradation. Biodegradation kinetics indicated half life period of fluoranthene degradation. Besides, glycolipid, as a biosurfactant, was induced to facilitate the degradation process. Hence, both the bacteria may be used individually or in combination for effective decontamination of oil and sludge contaminated soil.

Isolation and characterization of a newly isolated pyrene-degrading Acinetobacter strain USTB-X

The pryene-degradation bacterium strain USTB-X was newly isolated from the polycyclic aromatic hydrocarbon (PAH)-contaminated soil in Beijing Coking Plant, China. The strain was identified as Acinetobacter with respect to its 16S rDNA and morphological and physiological characteristics. The strain was Gram-negative, non-mobile, non-acid-fast, and non-spore-forming, short rods in young culture and 0.8-1.6 μm in diameter and 1.2-2.5 μm long in the stationary phase of growth. Strain USTB-X could utilize pyrene, naphthalene, fluorene, phenanthrene, benzene, toluene, ethylbenzene, ethanol, methanol, and Tween 80 as sole source of carbon and energy. The strain could produce biosurfactants which enhanced the removal of pyrene and could remove 63 % of pyrene with an initial concentration of 100 mg·L-1 in 16 days without other substrates. Based on the intermediates analyzed by gas chromatography-mass spectrometry, we also deduced the possible metabolic pathway of strain USTBX for pyrene biodegradation. Results indicated that the strain USTB-X had high potential to enhance the removal of PAHs in contaminated sites.