meta-Cleavage of hydroxynaphthoic acids in the degradation of phenanthrene by Sphingobium sp. strain PNB

Enhancing sugarcane's drought resilience: the influence of Streptomycetales and Rhizobiales

Drought stress is a critical environmental factor affecting sugarcane yield, and the adaptability of the sugarcane rhizosphere bacterial community is essential for drought tolerance. This review examines the adaptive responses of sugarcane rhizosphere bacterial communities to water stress and explores their significant role in enhancing sugarcane drought tolerance. Under drought conditions, the sugarcane rhizosphere bacterial community undergoes structural and functional shifts, particularly the enrichment of beneficial bacteria, including Streptomycetales and Rhizobiales. These bacteria enhance sugarcane resilience to drought through various means, including nutrient acquisition and phytohormone synthesis. Furthermore, changes in the rhizosphere bacterial community were closely associated with the composition and levels of soil metabolites, which significantly influenced the physiological and biochemical processes of sugarcane during drought stress. This study deepens our understanding of rhizosphere bacterial communities and their interactions with sugarcane, laying a scientific foundation for developing drought-resistant sugarcane varieties, optimizing agricultural practices, and opening new avenues for agricultural applications.

Efficient treatment of secondary treated refinery wastewater using sand biofiltration: Removal of hazardous organic pollutants

This study explored the potential of sand biofiltration for tertiary treatment of real refinery wastewater. The biofilter (2 cm (I.D.) x 15 cm (L)) operated on secondary treated refinery wastewater at flow rate of 1 mL/min had empty bed contact time (EBCT) of 47.12 min for one circulation. Maximum reduction in COD after 4, 8 and 12 times recirculation was 25 %, 52 % and 56 %; while the TOC reduction was 33 %, 43 % and 51 %, respectively, after biofilm development over 30 days. Quantification using two dimensional gas chromatography - time of flight mass spectrometry (GCxGC-TOF MS) revealed that several of the identified target compounds could not be detected in the wastewater after 12 recirculations. After 8 times recirculation, most of the compounds showed very high removal efficiency. For biofiltration over the flow rate range 2-10 mL/min, the reduction in COD and NH4+-N ranged from 62-73 % and 78-86 %, respectively, after 8 times recirculation. The nitrite concentration first increased and subsequently decreased, while the nitrate concentration continuously increased with increase in the number of recirculations. Solid phase micro-extraction (SPME) analysis of the aqueous phase using GCxGC-TOF MS and a semi-quantitative approach indicated that the removal of predominant classes of compounds was greater than 95 % after 8 times recirculation, with maximum reduction occurring in the first pass through the biofilter. Assimilable organic carbon (AOC) reduction was 98 % after 8 times recirculation. Metagenomic analysis revealed that Proteobacteria was the most dominant phylum in the biofilter. Many known polynuclear aromatic hydrocarbon (PAH) degraders, such as Sphingomonadales, Burkholderiales, Rhodobacterales and Rhodospirillales, were found in the biofilter leading to high removal efficiency of hazardous organic pollutants.

Revealing the biological significance of multiple metabolic pathways of chloramphenicol by Sphingobium sp. WTD-1

Chloramphenicol (CAP) is an antibiotic that commonly pollutes the environment, and microorganisms primarily drive its degradation and transformation. Although several pathways for CAP degradation have been documented in different bacteria, multiple metabolic pathways in the same strain and their potential biological significance have not been revealed. In this study, Sphingobium WTD-1, which was isolated from activated sludge, can completely degrade 100 mg/L CAP within 60 h as the sole energy source. UPLC-HRMS and HPLC analyses showed that three different pathways, including acetylation, hydroxyl oxidation, and oxidation (C1-C2 bond cleavage), are responsible for the metabolism of CAP. Importantly, acetylation and C3 hydroxyl oxidation reduced the cytotoxicity of the substrate to strain WTD-1, and the C1-C2 bond fracture of CAP generated the metabolite p-nitrobenzoic acid (PNBA) to provide energy for its growth. This indicated that the synergistic action of three metabolic pathways caused WTD-1 to be adaptable and able to degrade high concentrations of CAP in the environment. This study deepens our understanding of the microbial degradation pathway of CAP and highlights the biological significance of the synergistic metabolism of antibiotic pollutants by multiple pathways in the same strain.

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.

Improving the uptake of PAHs by the ornamental plant Sedum spectabile using nano-SiO2 and nano-CeO2

Polycyclic aromatic hydrocarbons (PAHs) pollution is a global ecological soil problem. Screening and establishing an efficient phytoremediation system would be beneficial for alleviating this problem. The ornamental plant Sedum spectabile was selected as the remediation plant to study the removal efficiencies of PAHs after adding different concentrations of nano-SiO₂, nano-CeO₂, and traditional Na-montmorillonite (Na-MMT). The results demonstrated that shoot biomass was increased and photosynthesis was enhanced by the nanomaterial amendments. The uptake of 16 PAHs by S. spectabile was remarkably increased. Moreover, the two highest shoot concentrations were 7.61 (Phe) and 12.03 (Flo) times that of the control, and the two highest translocation factors were 31 (BbF) and 28 (BaP) times that of the control. Furthermore, 16S rRNA gene sequencing showed that the addition of nano-SiO₂ increased the abundance of Acidobacteria, and the genera related to PAH degradation was higher under nanomaterial treatments. The very high Si concentration in the shoots of S. spectabile had a significant linear correlation with the concentration of PAHs. In conclusion, the S. spectabile remediation system assisted by two nanomaterials was effective for the removal of PAHs from soil, and the transfer of PAHs to easily harvested aboveground plant parts was especially worthy of attention.

Insights Into Mechanism of the Naphthalene-Enhanced Biodegradation of Phenanthrene by Pseudomonas sp. SL-6 Based on Omics Analysis

The existence of polycyclic aromatic hydrocarbons (PAHs) in contaminated environment is multifarious. At present, studies of metabolic regulation focus on the degradation process of single PAH. The global metabolic regulatory mechanisms of microorganisms facing coexisting PAHs are poorly understood, which is the major bottleneck for efficient bioremediation of PAHs pollution. Naphthalene (NAP) significantly enhanced the biodegradation of phenanthrene (PHE) by Pseudomonas sp. SL-6. To explore the underlying mechanism, isobaric tags for relative and absolute quantification (iTRAQ) labeled quantitative proteomics was used to characterize the differentially expressed proteins of SL-6 cultured with PHE or NAP + PHE as carbon source. Through joint analysis of proteome and genome, unique proteins were identified and quantified. The up-regulated proteins mainly concentrated in PAH catabolism, Transporters and Electron transfer carriers. In the process, the regulator NahR, activated by salicylate (intermediate of NAP-biodegradation), up-regulates degradation enzymes (NahABCDE and SalABCDEFGH), which enhances the biodegradation of PHE and accumulation of toxic intermediate–1-hydroxy-2-naphthoic acid (1H2Na); 1H2Na stimulates the expression of ABC transporter, which maintains intracellular physiological activity by excreting 1H2Na; the up-regulation of cytochrome C promotes the above process running smoothly. Salicylate works as a trigger that stimulates cell to respond globally. The conjecture was verified at transcriptional and metabolic levels. These new insights contribute to improving the overall understanding of PAHs-biodegradation processes under complex natural conditions, and promoting the application of microbial remediation technology for PAHs pollution.

Draft Whole-Genome Sequence of Sphingobium sp. Strain PNB, a Versatile Polycyclic Aromatic Hydrocarbon-Degrading Bacterium

Sphingobium sp. strain PNB can completely degrade phenanthrene, naphthalene, and biphenyl as the sole carbon and energy source. The strain is also capable of cometabolizing benzo[a]pyrene, pyrene, acenaphthene, fluoranthene, etc. Here, we report the 5.69-Mb assembly and annotation of the genome sequence of strain PNB, obtained using Illumina sequencing.

Application of integrated extremophilic (halo-alkalo-thermophilic) bacterial consortium in the degradation of petroleum hydrocarbons and treatment of petroleum refinery wastewater under extreme condition

Degradation of petroleum hydrocarbon under extreme conditions such as high salinity, temperature and pH was difficult due to unavailability of potential bacterial strains. The present study details the efficiency of extremophilic bacterial consortium in biodegradation of different petroleum hydrocarbons and treatment of petroleum refinery wastewater under extreme condition. Extreme condition for the degradation of petroleum hydrocarbons was optimized at 8% salinity, pH-10 and temperature-60 °C. The consortium recorded complete degradation of low molecular weight (LMW) petroleum hydrocarbons (200 ppm) such as anthracene, phenanthrene, fluorene and naphthalene in 8 days under optimized extreme condition. High molecular weight (HMW) hydrocarbons such as pyrene (100 ppm), benzo(e)pyrene (20 ppm), benzo(k)fluoranthene (20 ppm) and benzo(a)pyrene (20 ppm), revealed 93%, 60%, 55% and 51% degradation by the extremophilic consortium under optimized extreme condition. The extremophilic consortium mineralized fluorene (61%) at high saline condition up to 24%. Addition of yeast extract potently accelerated the biodegradation under extreme condition. Treatment of petroleum refinery wastewater in continuous stirred tank reactor recorded 92% COD removal with complete removal of LMW hydrocarbons in 16 days and 91% of HMW hydrocarbons in 32 days under extreme condition. The hydrocarbons degrading extremophilic consortium possessed Ochrobactrum, Bacillus, Marinobacter, Pseudomonas, Martelella, Stenotrophomonas and Rhodococcus.

PahT regulates carbon fluxes in Novosphingobium sp. HR1a and influences its survival in soil and rhizospheres

Novosphingobium sp. HR1a is a good biodegrader of PAHs and aromatic compounds, and also a good colonizer of rhizospheric environments. It was previously demonstrated that this microbe is able to co-metabolize nutrients existing in root exudates together with the PAHs. We have revealed here that PahT, a regulator of the IclR-family, regulates the central carbon fluxes favouring the degradation of PAHs and mono-aromatic compounds, the ethanol and acetate metabolism and the uptake, phosphorylation and further degradation of mono- and oligo-saccharides through a phosphoenolpyruvate transferase system (PTS). As final products of these fluxes, pyruvate and acetyl-CoA are obtained. The pahT gene is located within a genomic region containing two putative transposons that carry all the genes for PAH catabolism; PahT also regulates these genes. Furthermore, encoded in this genomic region, there are genes that are involved in the recycling of phosphoenolpyruvate, from the obtained pyruvate, which is the motor molecule involved in the saccharide uptake by the PTS system. The co-metabolism of PAHs with different carbon sources, together with the activation of the thiosulfate utilization and an alternative cytochrome oxidase system, also regulated by PahT, represents an advantage for Novosphingobium sp. HR1a to survive in rhizospheric environments.

Low-current electro-oxidation enhanced the biodegradation of the recalcitrant naphthenic acids in oil sands process water

Combining electro-oxidation (EO) with biodegradation for real oil sands process water (OSPW) treatment was evaluated in terms of naphthenic acid (NA) biodegradation enhancement. Ion mobility spectrometry (IMS) qualitative analysis showed that EO by graphite was able to degrade the different NA clusters in OSPW including: classical, oxidized and heteroatomic NAs. Applying EO even at current density as low as 0.2 mA/cm² was still able to reduce classical NAs and acid extractable fraction (AEF) by 19% and 7%, respectively. EO pretreatment preferentially broke long carbon chains and highly cyclic carboxylic fractions of NAs in OSPW to improve the biodegradation of NAs. Aerobic biodegradation for 40 days reduced NAs by up to 30.9% when the samples were pre-treated with EO. Applying EO at current densities below 2 mA/cm² maintained current efficiency as high as 48% and resulted in improvement in the biodegradation rate of remaining NAs by up to 2.7 folds. It was further revealed that applying EO before biodegradation could reduce the biodegradation half-life of classical NAs by up to 4.4 folds. 16S amplicon sequencing analysis showed that the samples subjected to biodegradation had increased abundances of Sphingomonadales and Rhodocyclales with increasing applied current density for EO pre-treatments.

Network Analysis for Prioritizing Biodegradation Metabolites of Polycyclic Aromatic Hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are a diverse group of environmental contaminants released during the combustion of organic materials and the production and utilization of fossil fuels. Once released, PAHs deposit in soil and water bodies where they are subjected to environmental transport and transformations. As they degrade, intermediate transformation products may play an important role in their environmental impact. However, studying the effects of these degradation products has proven challenging because of the complexity, transience, and low concentration of many intermediates. Herein, a novel integration of a pathway prediction system and network theory was developed and applied to a set of four PAHs to demonstrate a possible solution to this challenge. Network analysis techniques were employed to refine the thousands of potential outputs and elucidate compounds of interest. Using these tools, we determined correlations between PAH degradation network data and intermediate metabolite structures, gaining information about the chemical characteristics of compounds based on their placement within the degradation network. Upon applying our developed filtering algorithm, we are able to predict up to 48% of the most common transformation products identified in a comprehensive empirical literature review. Additionally, our integrated approach uncovers potential metabolites which connect those found by past empirical studies but are currently undetected, thereby filling in the gaps of information in PAH degradation pathways.

Degradation and detoxification of phenanthrene by actinobacterium Zhihengliuella sp. ISTPL4

Polycyclic aromatic hydrocarbons (PAHs) are universal environmental contaminants of great concern with regard to their potential exposure and deleterious effect on human health. The current study is the first report of phenanthrene degradation by a psychrotolerant (15 °C), halophilic (5% NaCl), and alkalophilic (pH 8) bacterial strain Zhihengliuella sp. ISTPL4, isolated from the sediment sample of the Pangong Lake, Ladakh, Jammu and Kashmir, India. Degradation studies revealed that the optimum specific growth rate was observed at 250 ppm of phenanthrene with 81% and 87% removal of phenanthrene in 72 h and 168 h, respectively. During the degradation of phenanthrene; 9,10-dihydrophenanthrene; 1-phenanthrenecarboxylic acid; and phthalic acid were detected as intermediates. Whole-genome sequencing of strain ISTPL4 has predicted phenanthrene; 9,10-monooxygense; and epoxide hydrolase B that are involved in the phenanthrene metabolism. Phenanthrene cytotoxicity was evaluated with human hepatic carcinoma cell line (HepG2) and it was observed that the cytotoxicity decreased with increased duration of bacterial incubation and maximum cell viability was observed at 168 h (89.92%). Our results suggest, Zhihengliuella sp. ISTPL4 may promise a great potential for environmental remediation applications.

Direct micro-electric stimulation alters phenanthrene-degrading metabolic activities of Pseudomonas sp. strain DGYH-12 in modified bioelectrochemical system

Bioelectrochemical systems (BESs) have great potential for treating wastewater containing polycyclic aromatic hydrocarbons (PAHs); however, detailed data on cell physiological activities in PAH biodegradation pathways stimulated by BESs are still lacking. In this paper, a novel BES device was assembled to promote the growth of Pseudomonas sp. DGYH-12 in phenanthrene (PHE) degradation. The results showed that in the micro-electric field (0.2 V), cell growth rate and PHE degradation efficiency were 22% and 27.2% higher than biological control without electric stimulation (BC), respectively. The extracellular polymeric substance (EPS) concentration in BES (39.38 mg L^-1) was higher than control (33.36 mg L^-1); moreover, the membrane permeability and ATPase activities were also enhanced and there existing phthalic acid and salicylic acid metabolic pathways in the strain. The degradation genes nahAc, pcaH, and xylE expression levels were upregulated by micro-electric stimulation. This is the first study to analyze the physiological and metabolic effect of micro-electric stimulation on a PHE-degrading strain in detail and systematically.

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.

Environmental characteristics of a tundra river system in Svalbard. Part 2: Chemical stress factors

Bacterial communities in the Arctic environment are subject to multiple stress factors, including contaminants, although typically their concentrations are small. The Arctic contamination research has focused on persistent organic pollutants (POPs) because they are bioaccumulative, resistant to degradation and toxic for all organisms. Pollutants have entered the Arctic predominantly by atmospheric and oceanic long-range transport, and this was facilitated by their volatile or semi-volatile properties, while their chemical stability extended their lifetimes following emission. Chemicals present in the Arctic at detectable and quantifiable concentrations testify to their global impact. Chemical contamination may induce serious disorders in the integrity of polar ecosystems influencing the growth of bacterial communities. In this study, the abundance and the types of bacteria in the Arctic freshwater were examined and the microbial characteristics were compared to the amount of potentially harmful chemical compounds in particular elements of the Arctic catchment. The highest concentrations of all determined PAHs were observed in two samples in the vicinity of the estuary both in June and September 2016 and were 1964 ng L^-1 (R12) and 3901 ng L^-1 (R13) in June, and 2179 ng L^-1 (R12) and 1349 ng L^-1 (R13) in September. Remarkable concentrations of the sum of phenols and formaldehyde were detected also at the outflow of the Revelva river into the sea (R12) and were 0.24 mg L^-1 in June and 0.35 mg L^-1 in September 2016. The elevated concentrations of chemical compounds near the estuary suggest a potential impact of the water from the lower tributaries (including the glacier-fed stream measured at R13) or the sea currents and the sea aerosol as pollutant sources. The POPs' degradation at low temperature is not well understood but bacteria capable to degrading such compounds were noted in each sampling point.

Transcriptional response of Mycobacterium sp. strain A1-PYR to multiple polycyclic aromatic hydrocarbon contaminations

Cometabolism mechanisms of organic pollutants in environmental microbes have not been fully understood. In this study, a global analysis of Mycobacterium sp. strain A1-PYR transcriptomes on different PAH substrates (single or binary of pyrene (PYR) and phenanthrene (PHE)) was conducted. Comparative results demonstrated that expression levels of 23 PAH degradation enzymes were significantly higher in the binary substrate than in the PYR-only one. These enzymes constituted an integrated enzymatic system to actualize all transformation steps of PYR, and most of their encoded genes formed a novel gene cascade in the genome of strain A1-PYR. The roles of different genotypes of enzymes in PYR cometabolism were also discriminated even though all of their gene sequences were presented in the genome of this strain. NidAB and PdoA2B2 instead of NidA3B3 served the initial oxidization of PAHs, and PcaL replaced PcaCD to catalyze the formation of 3-oxoadipate. Novel genes associated with PYR cometabolism was also predicted by the relationships between their transcription profiles and PYR removal. The results showed that ABC-type transporters probably played important roles in the transport of PAHs and their metabolites through cell membrane, and [4Fe-4S] ferredoxin might be essential for dioxygenases (NidAB and PdoA2B2) to achieve oxidative activities. This study provided molecular insight in that microbial degrader subtly cometabolized recalcitrant PAHs with relatively more degradable ones.

Degradation of petroleum hydrocarbons and treatment of refinery wastewater under saline condition by a halophilic bacterial consortium enriched from marine environment (Red Sea), Jeddah, Saudi Arabia

A halophilic bacterial consortium was enriched from Red Sea saline water and sediment samples collected from Abhor, Jeddah, Saudi Arabia. The consortium potentially degraded different low (above 90% for phenanthrene and fluorene) and high (69 ± 1.4 and 56 ± 1.8% at 50 and 100 mg/L of pyrene) molecular weight polycyclic aromatic hydrocarbons (PAHs) at different concentrations under saline condition (40 g/L NaCl concentration). The cell hydrophobicity (91° ± 1°) and biosurfactant production (30 mN/m) confirmed potential bacterial cell interaction with PAHs to facilitate biodegradation process. Co-metabolic study with phenanthrene as co-substrate during pyrene degradation recorded 90% degradation in 12 days. The consortium in continuous stirred tank reactor with petroleum refinery wastewater showed complete and 90% degradation of low and high molecular weight PAHs, respectively. The reactor study also revealed 94 ± 1.8% chemical oxygen demand removal by the halophilic consortium under saline condition (40 g/L NaCl concentration). The halophilic bacterial strains present in the consortium were identified as Ochrobactrum halosaudis strain CEES1 (KX377976), Stenotrophomonas maltophilia strain CEES2 (KX377977), Achromobacter xylosoxidans strain CEES3 (KX377978) and Mesorhizobium halosaudis strain CEES4 (KX377979). Thus, the promising halophilic consortium was highly recommended to be employed in petroleum saline wastewater treatment process.

Insights into the biodegradation of weathered hydrocarbons in contaminated soils by bioaugmentation and nutrient stimulation

The potential for biotransformation of weathered hydrocarbon residues in soils collected from two commercial oil refinery sites (Soil A and B) was studied in microcosm experiments. Soil A has previously been subjected to on-site bioremediation and it was believed that no further degradation was possible while soil B has not been subjected to any treatment. A number of amendment strategies including bioaugmentation with hydrocarbon degrader, biostimulation with nutrients and soil grinding, were applied to the microcosms as putative biodegradation improvement strategies. The hydrocarbon concentrations in each amendment group were monitored throughout 112 days incubation. Microcosms treated with biostimulation (BS) and biostimulation/bioaugmentation (BS + BA) showed the most significant reductions in the aliphatic and aromatic hydrocarbon fractions. However, soil grinding was shown to reduce the effectiveness of a nutrient treatment on the extent of biotransformation by up to 25% and 20% for the aliphatic and aromatic hydrocarbon fractions, respectively. This is likely due to the disruption to the indigenous microbial community in the soil caused by grinding. Further, ecotoxicological responses (mustard seed germination and Microtox assays) showed that a reduction of total petroleum hydrocarbon (TPH) concentration in soil was not directly correlable to reduction in toxicity; thus monitoring TPH alone is not sufficient for assessing the environmental risk of a contaminated site after remediation.

Characterization of the metabolic pathway and catabolic gene expression in biphenyl degrading marine bacterium Pseudomonas aeruginosa JP-11

Metabolic pathway of biphenyl assimilation and the catabolic gene expression in a marine bacterium Pseudomonas aeruginosa JP-11, isolated from the coastal sediments of Odisha, India have been studied. This strain utilized 98.86% ± 2.29% of biphenyl within 72 h when supplied as the sole source of carbon, however, preferential utilization of glucose was observed over catechol and biphenyl when grown in a complex medium. Combination of chromatographic and spectrophotometric techniques confirmed the catechol pathway and identified 2-Hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate as the intermediate metabolic product. Assimilation of biphenyl was initiated by its dioxygenation, forming cis-2, 3-dihydro-2, 3-dihydroxybiphenyl subsequently transformed to 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoate. In the lower pathway, cis-1, 6-dihydroxy-2, 4-cyclohexadiene-1-carboxylic acid was detected which formed catechol before entering into the Krebs cycle. Detection of key enzyme catechol-1, 2-dioxygenase in the cell-free extract of P. aeruginosa JP-11 supported the proposed degradation pathway. The primary enzyme for biphenyl assimilation, biphenyl dioxygenase encoded by bphA gene was found in the genome of the isolate. On increasing biphenyl stress (50, 100, 150 and 200 mg L(-1)), bphA gene showed a significant (P < 0.01) up-regulation upto 43.5 folds. Production of biosurfactant was confirmed and the rhamnolipid synthesizing gene rhlAB was amplified. This gene also showed a significant (P < 0.01) up-regulation upto 258 folds on increasing biphenyl stress.

Biodegradation of polycyclic aromatic hydrocarbons by Novosphingobium pentaromativorans US6-1

Novosphingobium pentaromativorans US6-1, a marine bacterium isolated from muddy sediments of Ulsan Bay, Republic of Korea, was previously shown to be capable of degrading multiple polycyclic aromatic hydrocarbons (PAHs). In order to gain insight into the characteristics of PAHs degradation, a proteome analysis of N. pentaromativorans US6-1 exposed to phenanthrene, pyrene, and benzo[a]pyrene was conducted. Several enzymes associated with PAHs degradation were identified, including 4-hydroxybenzoate 3-monooxygenase, salicylaldehyde dehydrogenase, and PAH ring-hydroxylating dioxygenase alpha subunit. Reverse transcription and real-time quantitative PCR was used to compare RHDα and 4-hydroxybenzoate 3-monooxygenase gene expression, and showed that the genes involved in the production of these two enzymes were upregulated to varying degrees after exposing the bacterium to PAHs. These results suggested that N. pentaromativorans US6-1 degraded PAHs via the metabolic route initiated by ring-hydroxylating dioxygenase, and further degradation occurred via the o-phthalate pathway or salicylate pathway. Both pathways subsequently entered the tricarboxylic acid (TCA) cycle, and were mineralized to CO2.

Metabolism of 2-hydroxy-1-naphthoic acid and naphthalene via gentisic acid by distinctly different sets of enzymes in Burkholderia sp. strain BC1

Burkholderia sp. strain BC1, a soil bacterium, isolated from a naphthalene balls manufacturing waste disposal site, is capable of utilizing 2-hydroxy-1-naphthoic acid (2H1NA) and naphthalene individually as the sole source of carbon and energy. To deduce the pathway for degradation of 2H1NA, metabolites isolated from resting cell culture were identified by a combination of chromatographic and spectrometric analyses. Characterization of metabolic intermediates, oxygen uptake studies and enzyme activities revealed that strain BC1 degrades 2H1NA via 2-naphthol, 1,2,6-trihydroxy-1,2-dihydronaphthalene and gentisic acid. In addition, naphthalene was found to be degraded via 1,2-dihydroxy-1,2-dihydronaphthalene, salicylic acid and gentisic acid, with the putative involvement of the classical nag pathway. Unlike most other Gram-negative bacteria, metabolism of salicylic acid in strain BC1 involves a dual pathway, via gentisic acid and catechol, with the latter being metabolized by catechol 1,2-dioxygenase. Involvement of a non-oxidative decarboxylase in the enzymic transformation of 2H1NA to 2-naphthol indicates an alternative catabolic pathway for the bacterial degradation of hydroxynaphthoic acid. Furthermore, the biochemical observations on the metabolism of structurally similar compounds, naphthalene and 2-naphthol, by similar but different sets of enzymes in strain BC1 were validated by real-time PCR analyses.

Functional characterization of diverse ring-hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in Sphingobium sp. PNB

Sphingobium sp. PNB, like other sphingomonads, has multiple ring-hydroxylating oxygenase (RHO) genes. Three different fosmid clones have been sequenced to identify the putative genes responsible for the degradation of various aromatics in this bacterial strain. Comparison of the map of the catabolic genes with that of different sphingomonads revealed a similar arrangement of gene clusters that harbors seven sets of RHO terminal components and a sole set of electron transport (ET) proteins. The presence of distinctly conserved amino acid residues in ferredoxin and in silico molecular docking analyses of ferredoxin with the well characterized terminal oxygenase components indicated the structural uniqueness of the ET component in sphingomonads. The predicted substrate specificities, derived from the phylogenetic relationship of each of the RHOs, were examined based on transformation of putative substrates and their structural homologs by the recombinant strains expressing each of the oxygenases and the sole set of available ET proteins. The RHO AhdA1bA2b was functionally characterized for the first time and was found to be capable of transforming ethylbenzene, propylbenzene, cumene, p-cymene and biphenyl, in addition to a number of polycyclic aromatic hydrocarbons. Overexpression of aromatic catabolic genes in strain PNB, revealed by real-time PCR analyses, is a way forward to understand the complex regulation of degradative genes in sphingomonads.

Multiple degradation pathways of phenanthrene by Stenotrophomonas maltophilia C6

Stenotrophomonas maltophilia strain C6, capable of utilizing phenanthrene as a sole source of carbon and energy, was isolated from creosote-contaminated sites at Hilo, Hawaii. Twenty-two metabolites of phenanthrene, covering from dihydrodiol to protocatechuic acid, were isolated and characterized. Phenanthrene was degraded via an initial dioxygenation on 1,2-, 3,4-, and 9,10-C, where the 3,4-dioxygenation and subsequent metabolisms were most dominant. The metabolic pathways were further branched by ortho- and meta-cleavage of phenanthrenediols to produce 1-hydroxy-2-naphthoic acid, 2-hydroxy-1-naphthoic acid, and naphthalene-1,2-dicarboxylic acid. These intermediates were then transformed to naphthalene-1,2-diol. 1-Hydroxy-2-naphthoic acid was also degraded via a direct ring cleavage. Naphthalene-1,2-diol underwent primarily ortho-cleavage to produce trans-2-carboxycinnamic acid and then to form phthalic acid, 4,5-dihydroxyphthalic acid and protocatechuic acid. Accumulation of salicylic acid in prolonged incubation indicated that a limited extent of meta-cleavage of naphthalene-1, 2-diol also occurred. This is the first study of detailed phenanthrene metabolic pathways by Stenotrophomonas maltophilia.