Biodegradation of phenanthrene byRhizobium petroleariumSL-1

Unraveling the mechanisms of benzo[a]pyrene degradation by Pigmentiphaga kullae strain KIT-003 using a multi-omics approach

Polycyclic aromatic hydrocarbons (PAHs), notably benzo[a]pyrene (BaP), are environmental contaminants with multiple adverse ecological implications. Numerous studies have suggested the use of BaP biodegradation using various bacterial strains to remove BaP from the environment. This study investigates the BaP biodegradation capability of Pigmentiphaga kullae strain KIT-003, isolated from the Nak-dong River (South Korea) under specific environmental conditions. The optimum conditions of biodegradation were found to be pH 7.0, 35°C, and a salinity of 0 %. GC-MS analysis suggested alternative pathways by which KIT-003 produced catechol from BaP through several intermediate metabolites, including 4-formylchrysene-5-carboxylic acid, 5,6-dihydro-5,6-dihydroxychrysene-5-carboxylic acid (isomer: 3,4-dihydro-3,4-dihydroxychrysene-4-carboxylic acid), naphthalene-1,2-dicarboxylic acid, and 2-hydroxy-1-naphthoic acid. Proteomic profiles indicated upregulation of enzymes associated with aromatic compound degradation, such as nahAc and nahB, and of those integral to the tricarboxylic acid cycle, reflecting the strain's adaptability to and degradation of BaP. Lipidomic analysis of KIT-003 demonstrated that BaP exposure induced an accumulation of glycerolipids such as diacylglycerol and triacylglycerol, indicating their crucial role in bacterial adaptation mechanisms under BaP stress. This study provides significant scientific knowledge regarding the intricate mechanisms involved in BaP degradation by microorganisms.

Biosurfactants-based mixed polycyclic aromatic hydrocarbon degradation: From microbial community structure toward non-targeted metabolomic profile determination

Biosurfactants-based bioremediation is considered an efficient technology to eliminate environmental pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the precise role of rhamnolipids or lipopeptide-biosurfactants in mixed PAH dissipation, shaping microbial community structure, and influencing metabolomic profile remained unclear. In this study, results showed that the maximum PAH degradation was achieved in lipopeptide-assisted treatment (SPS), where the pyrene and phenanthrene were substantially degraded up to 74.28 % and 63.05 % respectively, as compared to rhamnolipids (SPR) and un-aided biosurfactants (SP). Furthermore, the high throughput sequencing analysis revealed a significant change in the PAH-degrading microbial community, with Proteobacteria being the predominant phylum (>98 %) followed by Bacteroidota and Firmicutes in all the treatments. Moreover, Pseudomonas and Pannonibacter were found as highly potent bacterial genera for mixed PAH degradation in SPR, SPS, and SP treatments, nevertheless, the abundance of the genus Pseudomonas was significantly enhanced (>97 %) in SPR treatment groups. On the other hand, the non-targeted metabolomic profile through UHPLC-MS/MS exhibited a remarkable change in the metabolites of amino acids, carbohydrates, and lipid metabolisms by the input of rhamnolipids or lipopeptide-biosurfactants whereas, the maximum intensities of metabolites (more than two-fold) were observed in SPR treatment. The findings of this study suggested that the aforementioned biosurfactants can play an indispensable role in mixed PAH degradation as well as seek to offer new insights into shifts in PAH-degrading microbial communities and their metabolic function, which can guide the development of more efficient and targeted strategies for complete removal of organic pollutants such as PAH from the contaminated environment.

Assessment of Phenanthrene Degradation Potential by Plant-Growth-Promoting Endophytic Strain Pseudomonas chlororaphis 23aP Isolated from Chamaecytisus albus (Hacq.) Rothm

Polycyclic aromatic hydrocarbons (PAHs) are common xenobiotics that are detrimental to the environment and human health. Bacterial endophytes, having the capacity to degrade PAHs, and plant growth promotion (PGP) may facilitate their biodegradation. In this study, phenanthrene (PHE) utilization of a newly isolated PGP endophytic strain of Pseudomonas chlororaphis 23aP and factors affecting the process were evaluated. The data obtained showed that strain 23aP utilized PHE in a wide range of concentrations (6-100 ppm). Ethyl-acetate-extractable metabolites obtained from the PHE-enriched cultures were analyzed by gas chromatography-mass spectrometry (GC-MS) and thin-layer chromatography (HPTLC). The analysis identified phthalic acid, 3-(1-naphthyl)allyl alcohol, 2-hydroxybenzalpyruvic acid, α-naphthol, and 2-phenylbenzaldehyde, and allowed us to propose that the PHE degradation pathway of strain 23aP is initiated at the 1,2-, 3,4-carbon positions, while the 9,10-C pathway starts with non-enzymatic oxidation and is continued by the downstream phthalic pathway. Moreover, the production of the biosurfactants, mono- (Rha-C8-C8, Rha-C10-C8:1, Rha-C12:2-C10, and Rha-C12:1-C12:1) and dirhamnolipids (Rha-Rha-C8-C10), was confirmed using direct injection-electrospray ionization-mass spectrometry (DI-ESI-MS) technique. Changes in the bacterial surface cell properties in the presence of PHE of increased hydrophobicity were assessed with the microbial adhesion to hydrocarbons (MATH) assay. Altogether, this suggests the strain 23aP might be used in bioaugmentation-a biological method supporting the removal of pollutants from contaminated environments.

Efficient biodegradation of acetoacetanilide in hypersaline wastewater with a synthetic halotolerant bacterial consortium

The high concentrations of salt and refractory toxic organics in industrial wastewater seriously restrict biological treatment efficiency and functional stability. However, how to construct a salt-tolerant biocatalytic community and realize the decarbonization coupled with detoxification toward green bio-enhanced treatment, has yet to be well elucidated. Here, acetoacetanilide (AAA), an important intermediate for many dyes and medicine synthesis, was used as the model amide pollutant to elucidate the directional enrichment of halotolerant degradative communities and the corresponding bacterial interaction mechanism. Combining microbial community composition and molecular ecological network analyses as well as the biodegradation efficiencies of AAA and its hydrolysis product aniline (AN) of pure strains, the core degradative bacteria were identified during the hypersaline AAA degradation process. A synthetic bacterial consortium composed of Paenarthrobacter, Rhizobium, Rhodococcus, Delftia and Nitratireductor was constructed based on the top-down strategy to treat AAA wastewater with different water quality characteristics. The synthetic halotolerant consortium showed promising treatment ability toward the simulated AAA wastewater (AAA 100-500 mg/L, 1-5% salinity) and actual AAA mother liquor. Additionally, the comprehensive toxicity of AAA mother liquor significantly reduced after biological treatment. This study provides a green biological approach for the treatment of hypersaline and high concentration of organics wastewater.

Anaerobic phenanthrene biodegradation by a new salt-tolerant/halophilic and nitrate-reducing Virgibacillus halodenitrificans strain PheN4 and metabolic processes exploration

The biodegradation of polycyclic aromatic hydrocarbons (PAHs) under hypersaline environments has received increasing attention, whereas the study of anaerobic PAH biodegradation under hypersaline environments is still lacking. Here, we found a pure culture designated PheN4, which was affiliated with Virgibacillus halodenitrificans and could degrade phenanthrene with nitrate as the terminal electron acceptor and a wide range of salinities (from 0.3% to 20%) under anaerobic environments. The optimal salinity for biodegradation of phenanthrene by PheN4 was 5%, which could degrade 93.5% of 0.62 ± 0.04 mM phenanthrene within 10 days with the initial inoculum of 0.01 gVSS/L. Meanwhile, an increased microbial amount could efficiently promote the phenanthrene biodegradation rate. The metabolic processes of anaerobic phenanthrene biodegradation under hypersaline conditions by PheN4 were proposed based on intermediates and genome analyses. Phenanthrene was initially activated via methylation to form 2-methylphenanthrene. Next, fumarate addition and β-oxidation or direct oxidation of the methyl group, ring reduction and ring cleavage were identified as the midstream and downstream steps. In addition, PheN4 could utilize benzene, naphthalene, and anthracene as carbon sources, but Benz[a]anthracene, pyrene, and Benzo[a]pyrene could not be biodegraded by PheN4. This study could provide some guidance for the bioremediation of PAH pollutants in anaerobic and hypersaline zones.

Polycyclic Aromatic Hydrocarbon Degradation in the Sea-Surface Microlayer at Coastal Antarctica

As much as 400 Tg of carbon from airborne semivolatile aromatic hydrocarbons is deposited to the oceans every year, the largest identified source of anthropogenic organic carbon to the ocean. Microbial degradation is a key sink of these pollutants in surface waters, but has received little attention in polar environments. We have challenged Antarctic microbial communities from the sea-surface microlayer (SML) and the subsurface layer (SSL) with polycyclic aromatic hydrocarbons (PAHs) at environmentally relevant concentrations. PAH degradation rates and the microbial responses at both taxonomical and functional levels were assessed. Evidence for faster removal rates was observed in the SML, with rates 2.6-fold higher than in the SSL. In the SML, the highest removal rates were observed for the more hydrophobic and particle-bound PAHs. After 24 h of PAHs exposure, particle-associated bacteria in the SML showed the highest number of significant changes in their composition. These included significant enrichments of several hydrocarbonoclastic bacteria, especially the fast-growing genera Pseudoalteromonas, which increased their relative abundances by eightfold. Simultaneous metatranscriptomic analysis showed that the free-living fraction of SML was the most active fraction, especially for members of the order Alteromonadales, which includes Pseudoalteromonas. Their key role in PAHs biodegradation in polar environments should be elucidated in further studies. This study highlights the relevant role of bacterial populations inhabiting the sea-surface microlayer, especially the particle-associated habitat, as relevant bioreactors for the removal of aromatic hydrocarbons in the oceans.

Bioremediation of quinclorac injury on tobacco by a rhizosphere bacterium

The presence of herbicides residues in soil represents a serious problem for agriculture. Quinclorac is a common herbicide applied in rice field, but its residue can cause abnormal growth in successive crop of tobacco in Southern China. Remediation by microorganisms is considered to be an environmentally friendly method to remove such pollutants injury. The aims of this study were to obtain quinclorac remediation isolates and to investigate the possible mechanism(s) of remediation. Six bacterial isolates were obtained from rhizosphere of rice-tobacco rotation fields, and were found to be capable of degrading quinclorac on a mineral salt medium (MSM), with degradation efficiency ranging from 2.1 to 23.7%. Among these isolates, J5 had the highest degradation efficiency, and was identified as Klebsiella variicola based on phylogenetic analyses and a metabolic profile generating by Biolog GEN III system. Bioremediation of quinclorac injury was confirmed using pot assays with tobacco, in which J5 reversed the detrimental effect of quinclorac on leaf area, leaf number, and plant height. The J5 isolate also seemed to promote plant growth, in terms of tobacco seedling growth and seed germination, which were 2.2 times and 1.6 times higher compared to untreated control, respectively. The mechanisms of plant growth promoting (PGP) traits were found to involve nitrogen-fixing, indole-3-acetic acid (IAA) production, and phosphate solubilization ability. In addition, proteomic analysis and relative quantitative PCR revealed an elevated level of 4-hydroxyphenylacetate 3-monooxygenase (HPMO) in quinclorac-treated J5, suggesting that this enzyme may play an important role in quinclorac remediation. This study showed that the J5 isolate could be exploited to not only assist in soil remediation due to quinclorac residue issues but also promote tobacco growth.

Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns

Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.

Evaluation of the Effectiveness of the Biopreparation in Combination with the Polymer γ-PGA for the Biodegradation of Petroleum Contaminants in Soil

Biodegradation is a method of effectively removing petroleum hydrocarbons from the natural environment. This research focuses on the biodegradation of aliphatic hydrocarbons, monoaromatic hydrocarbons such as benzene, toluene, ethylbenzene, and all three xylene isomers (BTEX) and polycyclic aromatic hydrocarbons (PAHs) as a result of soil inoculation with a biopreparation A1 based on autochthonous microorganisms and a biopreparation A1 with the addition of γ-PGA. The research used biopreparation A1 made of the following strains: Dietzia sp. IN133, Gordonia sp. IN138 Mycolicibacterium frederiksbergense IN53, Rhodococcus erythropolis IN119, Rhodococcus sp. IN136 and Pseudomonas sp. IN132. The experiments were carried out in laboratory conditions (microbiological tests, respirometric tests, and in semi-technical conditions (ex-situ prism method). The biodegradation efficiency was assessed on the basis of respirometric tests, chromatographic analyses and toxicological tests. As a result of inoculation of AB soil with the biopreparation A1 within 6 months, a reduction of total petroleum hydrocarbons (TPH) (66.03%), BTEX (80.08%) and PAHs (38.86%) was achieved and its toxicity was reduced. Inoculation of AB soil with the biopreparation A1 with the addition of γ-PGA reduced the concentration of TPH, BTEX and PAHs by 79.21%, 90.19%, and 51.18%, respectively, and reduced its toxicity. The conducted research has shown that the addition of γ-PGA affects the efficiency of the biodegradation process of petroleum pollutants, increasing the degree of TPH biodegradation by 13.18%, BTEX by 10.11% and PAHs by 12.32% compared to pure biopreparation A1.

Biodegradation and metabolic pathway of phenanthrene by a newly isolated bacterium Gordonia sp. SCSIO19801

The bacterium Gordonia sp. SCSIO19801, which could effectively utilize phenanthrene as the sole carbon source, was isolated from the seawater of the South China Sea. Its biodegradation characteristics, whole genome sequence, and biodegradation pathway were investigated. The phenanthrene biodegradation process of Gordonia sp. SCSIO19801 was estimated to be a first-order kinetic model with a k value of 0.26/day. Based on the identification of metabolites, utilization of probable intermediates, and genomics analysis of related genes, the degradation of phenanthrene by Gordonia sp. SCSIO19801 was proposed to occur via the salicylate metabolic pathway. This is the first report of a phenanthrene degradation pathway in Gordonia species. In addition, the Gordonia sp. SCSIO19801 could use other aromatic compounds as the sole source of carbon and energy. These characteristics indicate that Gordonia sp. SCSIO19801 can be utilized for developing effective methods for the biodegradation of petroleum hydrocarbons in marine environments.

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

Polycyclic Aromatic Hydrocarbons (PAHs) are major toxic and recalcitrant pollutants in the environment. This study assessed the capacity of an isolated soil microbial consortium (OMC) to biodegrade PAHs. OMC was able to reach 100% biodegradation of naphthalene, acenaphthylene, acenaphthene, fluorene and phenanthrene in solution, and up to 76% and 50% of anthracene and fluoranthene, respectively, from a mix of 16 PAHs. To measure phenanthrene (PHE) mineralization, OMC and eight strains isolated from OMC were used and identified by PCR amplification of the gene 16S ribosomal RNA. A novel Stenotrophomonas maltophilia CPHE1, not previously described as a PAH degrader, was able to mineralize almost 40% PHE and biodegrade 90.5% in solution, in comparison to OMC that reached 100% PHE degradation, but only 18.8% mineralization. Based on metabolites identified during PHE degradation and on the detection of two genes (PAH RHDα and nahAc) in OMC consortium, two possible via were described for its degradation, through salicylic and phthalic acid. PAH RHDα, which codified the first step on PHE biodegradation pathway, was also found in the DNA of S. maltophilia CPHE1. An ecotoxicology study showed that PHE bioremediation after inoculating S. maltophilia CPHE1 for 30 days decreased by half the solution toxicity.

Co-enhanced activated sludge system by static magnetic field and two halotolerant yeasts for azo dye treatment

The effect of static magnetic field (SMF) on azo dye Acid Red B (ARB) decolorization by the co-culture of activated sludge (AS) and two halotolerant yeasts Candida tropicalis A1 and Pichia occidentalis A2 was investigated. Microbial community structure of the co-cultures before and after treatment with SMFs of different intensity was analyzed through high-throughput sequencing and quantitative real-time polymerase chain reaction. The results showed that ARB decolorization efficiency by the defined co-culture was 1.25-fold to 1.51-fold elevated by 24.6-305.0 mT SMF. The best ARB decolorization and chemical oxygen demand (COD) removal performances by the co-culture were both achieved with 95.0 mT SMF. By contrast, biomass multiplication and sedimentation property of AS systems were not significantly influenced by SMF. Higher activities of intracellular key enzymes were determined (with 95.0 mT SMF) as responsible for better decolorization and COD removal performances. Bacteria belonging to Prolixibacter, Corynebacterium, Pelagibacterium, Demequina, and Sphingobacterium which might be responsible for azo dye decolorization and aromatic compounds biodegradation were significantly enriched only in presence of SMF. Fungal genera Candida and Pichia were also significantly enriched by 41.4-305.0 mT SMF, which might be responsible for higher treatment efficiency. PRACTITIONER POINTS: Dye degradation was enhanced by combination of static magnetic field and yeasts. Improvement of enzyme activity was responsible for better treatment performance. Putative azo-degrading-related bacteria and fungi were selectively enriched. High relative abundance of Candida and Pichia ensured high decolorization effects. Potentially effective improvement of bioprocesses for treating hypersaline wastewater.

Bioaugmentation Treatment of a PAH-Polluted Soil in a Slurry Bioreactor

A bioslurry reactor was designed and used to treat loamy clay soil polluted with polycyclic aromatic hydrocarbons (PAHs). To this end, biostimulation alone, or combined with bioaugmentation with two bacterial strains (Rhodocccus erythropolis and Pseudomonas stuzeri) previously isolated from the polluted site, was applied. The PAH concentrations decreased notably after 15 days in all of the treatments. The concentrations of the two- and three-ring compounds fell by >80%, and, remarkably, the four- to six-ring PAHs also showed a marked decrease (>70%). These results thus indicate the capacity of bioslurry treatments to improve, notably, the degradation yields obtained in a previous real-scale remediation carried out using biopiles. In this sense, the remarkable results for recalcitrant PAHs can be attributed to the increase pollutants’ bioavailability achieves in the slurry bioreactors. Regarding bioaugmentation, although treatment with R. erythropolis led to a somewhat greater reduction of lighter PAHs at 15 days, the most time-effective treatment was achieved using P. stutzeri, which led to an 84% depletion of total PAHs in only three days. The effects of microbial degradation of other organic compounds were also monitored by means of combined qualitative and quantitative gas chromatography mass spectrometry (GC–MS) tools, as was the evolution of microbial populations, which was analyzed by culture and molecular fingerprinting experiments. On the basis of our findings, bioslurry technology emerges as a rapid and operative option for the remediation of polluted sites, especially for fine soil fractions with a high load of recalcitrant pollutants.

The impact of phenanthrene on membrane phospholipids and its biodegradation by Sphingopyxis soli

The direct interactions of bacterial membranes and polycyclic aromatic hydrocarbons (PAHs) strongly influence the biological processes, such as metabolic activity and uptake of substrates due to changes in membrane lipids. However, the elucidation of adaptation mechanisms as well as membrane phospholipid alterations in the presence of phenanthrene (PHE) from α-proteobacteria has not been fully explored. This study was conducted to define the degradation efficiency of PHE by Sphingopyxis soli strain KIT-001 in a newly isolated from Jeonju river sediments and to characterize lipid profiles in the presence of PHE in comparison to cells grown on glucose using quantitative lipidomic analysis. This strain was able to respectively utilize 1-hydroxy-2-naphthoic acid and salicylic acid as sole carbon source and approximately 90% of PHE (50 mg/L) was rapidly degraded via naphthalene route within 1 day incubation. In the cells grown on PHE, strain KIT-001 appeared to dynamically change profiles of metabolite and lipid in comparison to cells grown on glucose. The levels of primary metabolites, phosphatidylethanolamines (PE), and phosphatidic acids (PA) were significantly decreased, whereas the levels of phosphatidylcholines (PC) and phosphatidylglycerols (PG) were significantly increased. The adaptation mechanism of Sphingopyxis sp. regarded mainly the accumulation of bilayer forming lipids and anionic lipids to adapt more quickly under restricted nutrition and toxicity condition. Hence, these findings are conceivable that strain KIT-001 has a good adaptive ability and biodegradation for PHE through the alteration of phospholipids, and will be helpful for applications for effective bioremediation of PAHs-contaminated sites.

Degradation of 3-fluoroanilne by Rhizobium sp. JF-3

The interest of fluoroanilines in the environment is due to their extensive applications in industry and their low natural biodegradability. A pure bacterial strain capable of degrading 3-fluoroaniline (3-FA) as the sole source of carbon and energy was isolated from a sequencing batch reactor operating for the treatment of 3-FA. The strain (designated as JF-3) was identified by 16S rRNA gene analysis as a member of the genus Rhizobium. When grown in 3-FA medium at concentrations of 100-700 mg/L, strain JF-3 almost completely removed 3-FA within 72 h. However, the obvious cell growth inhibition was observed in cultures treated with 3-FA concentrations greater than 500 mg/L. The degradation kinetics of 3-FA were consistent with Haldane's model with the maximum degradation rate as 67.66 mg/(g dry cell h). The growth kinetics of strain JF-3 followed Andrew's model with the maximum growth rate as 30.87 h^-1. Also, strain JF-3 was able to degrade 4-fluoroaniline, aniline, and catechol, but hardly grew on 2-fluoroaniline, 2,4-dfluoroaniline, 2,3,4-trifluoroaniline, 3-fluorocatechol, and 4-fluorocatechol. Additionally, it was able to grow over a wide pH range (pH 6-10), and also showed tolerance to salinity with lower than 1.0%. This result, in combination with the enzyme assays and analysis of metabolite intermediates, indicated an unconventional pathway for 3-fluoroaniline metabolism that involved conversion to 3-aminophenol and resorcinol by monooxygenase, and which was subsequently metabolized via the ortho-cleavage pathway. To our knowledge, this is the first report on the utilization of 3-FA as a growth substrate by Rhizobium sp.

Simultaneous determination of dissolved phenanthrene and its metabolites by derivative synchronous fluorescence spectrometry with double scans method in aqueous solution

A simple and sensitive derivative synchronous fluorescence spectrometry with double scans (DS-DSFS) method was developed for simultaneous determination of dissolved Phenanthrene (Phe) and its metabolites 1-hydroxy-2-naphthoic acid (1H2NA) and salicylic acid (SA) in aqueous solution. The value of 69 nm was selected as the optimal Δλ conditions for Phe and 1H2NA, and the Δλ value of 55 nm was selected for SA. The overlapping fluorescence emission spectra of Phe, 1H2NA and SA were resolved by DS-DSFS. The signals detected at wavelength of 296 nm for Phe, 352 nm for 1H2NA and 307 nm for SA vary linearly when the concentrations in the range of 4.0-1.0 × 10³ μg L^-1, 4.0-1.2 × 10³ μg L^-1 and 4.0-8.0 × 10² μg L^-1, respectively. The detection limits were 0.08, 0.07 and 0.88 μg L^-1 for Phe, 1H2NA and SA, with the relatively standard deviations less than 5.0%. The established method was successfully applied in the determination of Phe and the metabolites during the biodegradation of dissolved Phe in the lab. It was evidenced that the method has potential for the in situ investigation of PAH biodegradation.