Phenol hydroxylase and toluene/o-xylene monooxygenase from Pseudomonas stutzeri OX1: interplay between two enzymes

Stable-isotope probing combined with amplicon sequencing and metagenomics identifies key bacterial benzene degraders under microaerobic conditions

The primary aim of the present study was to reveal the major differences between benzene-degrading bacterial communities evolve under aerobic versus microaerobic conditions and to reveal the diversity of those bacteria, which can relatively quickly degrade benzene even under microaerobic conditions. For this, parallel aerobic and microaerobic microcosms were set up by using groundwater sediment of a BTEX-contaminated site and 13C labelled benzene. The evolved total bacterial communities were first investigated by 16S rRNA gene Illumina amplicon sequencing, followed by a density gradient fractionation of DNA and a separate investigation of "heavy" and "light" DNA fractions. Results shed light on the fact that the availability of oxygen strongly determined the structure of the degrading bacterial communities. While members of the genus Pseudomonas were overwhelmingly dominant under clear aerobic conditions, they were almost completely replaced by members of genera Malikia and Azovibrio in the microaerobic microcosms. Investigation of the density resolved DNA fractions further confirmed the key role of these two latter genera in the microaerobic degradation of benzene. Moreover, analysis of a previously acquired metagenome-assembled Azovibrio genome suggested that benzene was degraded through the meta-cleavage pathway by this bacterium, with the help of a subfamily I.2.I-type catechol 2,3-dioxygenase. Overall, results of the present study implicate that under limited oxygen availability, some potentially microaerophilic bacteria play crucial role in the aerobic degradation of aromatic hydrocarbons.

Proteogenomic Characterization of Pseudomonas veronii SM-20 Growing on Phenanthrene as Only Carbon and Energy Source

In this study, we conducted an extensive investigation of the biodegradation capabilities and stress response of the newly isolated strain Pseudomonas veronii SM-20 in order, to assess its potential for bioremediation of sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Initially, phenotype microarray technology demonstrated the strain's proficiency in utilizing various carbon sources and its resistance to certain stressors. Genomic analysis has identified numerous genes involved in aromatic hydrocarbon metabolism. Biodegradation assay analyzed the depletion of phenanthrene (PHE) when it was added as a sole carbon and energy source. We found that P. veronii strain SM-20 degraded approximately 25% of PHE over a 30-day period, starting with an initial concentration of 600 µg/mL, while being utilized for growth. The degradation process involved PHE oxidation to an unstable arene oxide and 9,10-phenanthrenequinone, followed by ring-cleavage. Comparative proteomics provided a comprehensive understanding of how the entire proteome responded to PHE exposure, revealing the strain's adaptation in terms of aromatic metabolism, surface properties, and defense mechanism. In conclusion, our findings shed light on the promising attributes of P. veronii SM-20 and offer valuable insights for the use of P. veronii species in environmental restoration efforts targeting PAH-impacted sites.

A novel soluble di-iron monooxygenase from the soil bacterium Solimonas soli

Soluble di-iron monooxygenase (SDIMO) enzymes enable insertion of oxygen into diverse substrates and play significant roles in biogeochemistry, bioremediation and biocatalysis. An unusual SDIMO was detected in an earlier study in the genome of the soil organism Solimonas soli, but was not characterized. Here, we show that the S. soli SDIMO is part of a new clade, which we define as 'Group 7'; these share a conserved gene organization with alkene monooxygenases but have only low amino acid identity. The S. soli genes (named zmoABCD) could be functionally expressed in Pseudomonas putida KT2440 but not in Escherichia coli TOP10. The recombinants made epoxides from C2 C8 alkenes, preferring small linear alkenes (e.g. propene), but also epoxidating branched, carboxylated and chlorinated substrates. Enzymatic epoxidation of acrylic acid was observed for the first time. ZmoABCD oxidised the organochlorine pollutants vinyl chloride (VC) and cis-1,2-dichloroethene (cDCE), with the release of inorganic chloride from VC but not cDCE. The original host bacterium S. soli could not grow on any alkenes tested but grew well on phenol and n-octane. Further work is needed to link ZmoABCD and the other Group 7 SDIMOs to specific physiological and ecological roles.

Revealing the degradation mechanisms of the hyper-tolerant bacterium Pseudomonas aeruginosa STV1713 under high phenol and 2,4-DCP-induced stress conditions through RNA-seq analysis

The ability of bacteria to efficiently remove phenolic pollutants depends on their genetic makeup and environmental conditions. This study examined a novel strain, Pseudomonas aeruginosa STV1713, for degrading higher concentrations of phenol and 2,4-dichlorophenol. After optimization, a combination of degradation parameters, such as pH (7.0), temperature (32.5 °C), and ammonium nitrate concentration (0.7 g/L), was found to reduce degradation time while promoting cell growth. Under these optimal conditions, the bacterium effectively degraded up to 2000 mg/L of phenol and 1400 mg/L of 2,4-dichlorophenol, while maximum tolerance was observed till 2100 mg/L and 1500 mg/L, respectively. Metabolic profiling identified crucial metabolites in the ortho-degradation pathway during pollutant removal. Additionally, transcriptome analysis revealed that P. aeruginosa STV1713 utilizes different branches of the beta ketoadipate pathway for phenol and 2,4-DCP removal. Moreover, under high pollutant stress, the bacterium survived through differential gene expression in ribosome biogenesis, chemotaxis, membrane transport, and other pathways.

Co-metabolic biodegradation of chlorinated ethene in an oxygen- and ethane-based membrane biofilm reactor

Groundwater contamination by chlorinated ethenes is an urgent concern worldwide. One approach for detoxifying chlorinated ethenes is aerobic co-metabilims using ethane (C2H6) as the primary substrate. This study evaluated long-term continuous biodegradation of three chlorinated alkenes in a membrane biofilm reactor (MBfR) that delivered C2H6 and O2 via gas-transfer membranes. During 133 days of continuous operation, removals of dichloroethane (DCE), trichloroethene (TCE), and tetrachloroethene (PCE) were as high as 94 % and with effluent concentrations below 5 μM. In situ batch tests showed that the co-metabolic kinetics were faster with more chlorination. C2H6-oxidizing Comamonadaceae and "others," such as Methylococcaceae, oxidized C2H6 via monooxyenation reactions. The abundant non-ethane monooxygenases, particularly propane monooxygenase, appears to have been responsible for C2H6 aerobic metabolism and co-metabolism of chlorinated ethenes. This work proves that the C2H6 + O2 MBfR is a platform for ex-situ bioremediation of chlorinated ethenes, and the generalized action of the monooxygenases may make it applicable for other chlorinated organic contaminants.

Novel BTEX-degrading strains from subsurface soil: Isolation, identification and growth evaluation

Monoaromatic hydrocarbons such as benzene, toluene, ethylbenzene, and o, m, and p-xylenes (BTEX) are high-risk pollutants because of their mutagenic and carcinogenic nature. These pollutants are found with elevated levels in groundwater and soil in Canada at several contaminated sites. The intrinsic microbes present in the subsurface have the potential to degrade pollutants by their metabolic pathways and convert them to non-toxic products. However, the low subsurface temperature (5-10 °C) limits their growth and degradation ability. This study examined the feasibility of subsurface heat augmentation using geothermal heating for BTEX bioremediation. Novel potent BTEX-degrading bacterial strains were isolated from soil at 3.0, 42.6, and 73.2 m depths collected from a geothermal borehole during installation and screened using an enrichment technique. The selected strains were identified with Sanger sequencing and phylogenetic tree analysis, revealing that all the strains except Bacillus subtilis are novel with respective to BTEX degradation. The isolates, Microbacterium esteraromaticum and Bacillus infantis showed the highest degradation with 67.98 and 65.2% for benzene, 72.8 and 71.02% for toluene, 77.52 and 76.44% for ethylbenzene, and 74.58 and 74.04% for xylenes respectively. Further, temperature influence at 15 ± 1 °C, 28 ± 1 °C and 40 ± 1 °C was observed, which showed increased growth by two-fold and on average 35-49% more biodegradation at higher temperatures. Results showed that temperature is a positive stimulant for bioremediation, hence geothermal heating could also be a stimulant for in-situ bioremediation.

Bisphenols-A Threat to the Natural Environment

Negative public sentiment built up around bisphenol A (BPA) follows growing awareness of the frequency of this chemical compound in the environment. The increase in air, water, and soil contamination by BPA has also generated the need to replace it with less toxic analogs, such as Bisphenol F (BPF) and Bisphenol S (BPS). However, due to the structural similarity of BPF and BPS to BPA, questions arise about the safety of their usage. The toxicity of BPA, BPF, and BPS towards humans and animals has been fairly well understood. The biodegradability potential of microorganisms towards each of these bisphenols is also widely recognized. However, the scale of their inhibitory pressure on soil microbiomes and soil enzyme activity has not been estimated. These parameters are extremely important in determining soil health, which in turn also influences plant growth and development. Therefore, in this manuscript, knowledge has been expanded and systematized regarding the differences in toxicity between BPA and its two analogs. In the context of the synthetic characterization of the effects of bisphenol permeation into the environment, the toxic impact of BPA, BPF, and BPS on the microbiological and biochemical parameters of soils was traced. The response of cultivated plants to their influence was also analyzed.

An insight into omics analysis and metabolic pathway engineering of lignin-degrading enzymes for enhanced lignin valorization

Lignin, a highly heterogeneous polymer of lignocellulosic biomass, is intricately associated with cellulose and hemicellulose, responsible for its strength and rigidity. Lignin decomposition is carried out through certain enzymes derived from microorganisms to promote the hydrolysis of lignin. Analyzing multi-omics data helps to emphasize the probable value of fungal-produced enzymes to degrade the lignocellulosic material, which provides them an advantage in their ecological niches. This review focuses on lignin biodegrading microorganisms and associated ligninolytic enzymes, including lignin peroxidase, manganese peroxidase, versatile peroxidase, laccase, and dye-decolorizing peroxidase. Further, enzymatic catalysis, lignin biodegradation mechanisms, vital factors responsible for lignin modification and degradation, and the design and selection of practical metabolic pathways are also discussed. Highlights were made on metabolic pathway engineering, different aspects of omics analyses, and its scope and applications to ligninase enzymes. Finally, the advantages and essential steps of successfully applying metabolic engineering and its path forward have been addressed.

Combined Omics Approach Reveals Key Differences between Aerobic and Microaerobic Xylene-Degrading Enrichment Bacterial Communities: Rhodoferax─A Hitherto Unknown Player Emerges from the Microbial Dark Matter

Among monoaromatic hydrocarbons, xylenes, especially the ortho and para isomers, are the least biodegradable compounds in oxygen-limited subsurface environments. Although much knowledge has been gained regarding the anaerobic degradation of xylene isomers in the past 2 decades, the diversity of those bacteria which are able to degrade them under microaerobic conditions is still unknown. To overcome this limitation, aerobic and microaerobic xylene-degrading enrichment cultures were established using groundwater taken from a xylene-contaminated site, and the associated bacterial communities were investigated using a polyphasic approach. Our results show that the xylene-degrading bacterial communities were distinctly different between aerobic and microaerobic enrichment conditions. Although members of the genus Pseudomonas were the most dominant in both types of enrichments, the Rhodoferax and Azovibrio lineages were only abundant under microaerobic conditions, while Sphingobium entirely replaced them under aerobic conditions. Analysis of a metagenome-assembled genome of a Rhodoferax-related bacterium revealed aromatic hydrocarbon-degrading ability by identifying two catechol 2,3-dioxygenases in the genome. Moreover, phylogenetic analysis indicated that both enzymes belonged to a newly defined subfamily of type I.2 extradiol dioxygenases (EDOs). Aerobic and microaerobic xylene-degradation experiments were conducted on strains Sphingobium sp. AS12 and Pseudomonas sp. MAP12, isolated from the aerobic and microaerobic enrichments, respectively. The obtained results, together with the whole-genome sequence data of the strains, confirmed the observation that members of the genus Sphingobium are excellent aromatic hydrocarbon degraders but effective only under clear aerobic conditions. Overall, it was concluded that the observed differences between the bacterial communities of aerobic and microaerobic xylene-degrading enrichments were driven primarily by (i) the method of aromatic ring activation (monooxygenation vs dioxygenation), (ii) the type of EDO enzymes, and (iii) the ability of degraders to respire utilizing nitrate.

Lignin Biodegradation and Its Valorization

Lignin, a rigid polymer composed of phenolic subunits with high molecular weight and complex structure, ranks behind only cellulose in the contribution to the biomass of plants. Therefore, lignin can be used as a new environmentally friendly resource for the industrial production of a variety of polymers, dyes and adhesives. Since laccase was found to be able to degrade lignin, increasing attention had been paid to the valorization of lignin. Research has mainly focused on the identification of lignin-degrading enzymes, which play a key role in lignin biodegradation, and the potential application of lignin degradation products. In this review, we describe the source, catalytic specificity and enzyme reaction mechanism of the four classes of the lignin-degrading enzymes so far discovered. In addition, the major pathways of lignin biodegradation and the applications of the degradative products are also discussed. Lignin-degrading bacteria or enzymes can be used in combination with chemical pretreatment for the production of value-added chemicals from lignin, providing a promising strategy for lignin valorization.

Cupriavidus metallidurans CH34 Possesses Aromatic Catabolic Versatility and Degrades Benzene in the Presence of Mercury and Cadmium

Heavy metal co-contamination in crude oil-polluted environments may inhibit microbial bioremediation of hydrocarbons. The model heavy metal-resistant bacterium Cupriavidus metallidurans CH34 possesses cadmium and mercury resistance, as well as genes related to the catabolism of hazardous BTEX aromatic hydrocarbons. The aims of this study were to analyze the aromatic catabolic potential of C. metallidurans CH34 and to determine the functionality of the predicted benzene catabolic pathway and the influence of cadmium and mercury on benzene degradation. Three chromosome-encoded bacterial multicomponent monooxygenases (BMMs) are involved in benzene catabolic pathways. Growth assessment, intermediates identification, and gene expression analysis indicate the functionality of the benzene catabolic pathway. Strain CH34 degraded benzene via phenol and 2-hydroxymuconic semialdehyde. Transcriptional analyses revealed a transition from the expression of catechol 2,3-dioxygenase (tomB) in the early exponential phase to catechol 1,2-dioxygenase (catA1 and catA2) in the late exponential phase. The minimum inhibitory concentration to Hg (II) and Cd (II) was significantly lower in the presence of benzene, demonstrating the effect of co-contamination on bacterial growth. Notably, this study showed that C. metallidurans CH34 degraded benzene in the presence of Hg (II) or Cd (II).

A multicomponent THF hydroxylase initiates tetrahydrofuran degradation in Cupriavidus metallidurans ZM02

Tetrahydrofuran (THF) has been recognized as a water contaminant because of its human carcinogenicity, extensive use, and widespread distribution. Previously reported multicomponent monooxygenases (MOs) involved in THF degradation were highly conserved, and all of them were from Gram-positive bacteria. In this study, a novel THF-degrading gene cluster (dmpKLMNOP) encoding THF hydroxylase was identified on the chromosome of a newly isolated Gram-negative THF-degrading bacterium, Cupriavidus metallidurans ZM02, and functionally characterized. Transcriptome sequencing and RT-qPCR demonstrated that the expression of dmpKLMNOP was upregulated during the growth of strain ZM02 on THF or phenol. The deletion of oxygenase alpha or beta subunit or the reductase component disrupted the degradation of THF but did not affect the utilization of its hydroxylated product 2-hydroxytetrahydrofuran. Cupriavidus pinatubonensis JMP134 heterologously expressing dmpKLMNOP from strain ZM02 could grow on THF, indicating that the THF hydroxylase Dmp_ZM02KLMNOP is responsible for the initial degradation of THF. Furthermore, the THF and phenol oxidation activities of crude enzyme extracts were detected, and the highest THF and phenol catalytic activities were 1.38±0.24 μmol min^-1 mg^-1 and 1.77±0.37 μmol min^-1 mg^-1, respectively, with the addition of NADPH and Fe²⁺. The characterization of THF hydroxylase associated with THF degradation enriches our understanding of THF-degrading gene diversity and provides a novel potential enzyme for the bioremediation of THF-containing pollutants. IMPORTANCE Multicomponent MOs catalyzing the initial hydroxylation of THF are vital rate-limiting enzymes in the THF degradation pathway. Previous studies of THF degradation gene clusters have focused on Gram-positive bacteria, and the molecular mechanism of THF degradation in Gram-negative bacteria has rarely been reported. In this study, a novel THF hydroxylase encoded by dmpKLMNOP in strain ZM02 was identified to be involved in both THF and phenol degradation. Our findings provide new insights into the THF-degrading gene cluster and enzymes in Gram-negative bacteria.

Classic Pentachlorophenol Hydroxylating Phenylalanine 4-Monooxygenase from Indigenous Bacillus tropicus Strain AOA-CPS1: Cloning, Overexpression, Purification, Characterization and Structural Homology Modelling

The metabolically promiscuous pentachlorophenol (PCP) hydroxylating Phe4MO (represented as CpsB) was detected, amplified (from the genome of Bacillus tropicus strain AOA-CPS1), cloned, overexpressed, purified and characterized here. The 1.755-kb gene cloned in the pET15b vector expressed a ≅ 64 kDa monomeric protein which was purified to homogeneity by single-step affinity chromatography, with a total yield of 82.1%. The optimum temperature and pH of the enzyme were found to be 30 °C and 7.0, respectively. CpsB showed functional stability between pH 6.0-7.5 and temperature 25-30 °C. The enzyme-substrate reaction kinetic studies showed the allosteric nature of the enzyme and followed pre-steady state using NADH as a co-substrate with apparent vmax, Km, kcat and kcat/Km values of 0.465 μM.s-1, 140 μM, 0.099 s-1 and 7.07 × 10-4 μM-1.s-1, respectively, for the substrate PCP. The in-gel trypsin digestion experiments and bioinformatic tools confirmed that the reported enzyme is a Phe4MO with multiple putative conserved domains and metal ion-binding site. Though Phe4MO has been reported to have a diverse catalytic function, here we report, for the first time, that it functions as a PCP dehalogenase or PCP-4-monooxygenase by hydroxylating PCP. Hence, the use of this enzyme may be further explored in the bioremediation of PCP and other related xenobiotics.

Sustainable production and co-immobilization of cold-active enzymes from Pseudomonas sp. for BTEX biodegradation

Toluene/o-Xylene Monooxygenase (ToMO) is equipped with a broad spectrum of aromatic substrate specificity (such as BTEX; benzene, toluene, ethylbenzene, and isomers of xylenes). TOMO has can hydroxylate more than a single position of aromatic rings in two consecutive monooxygenation reactions. Catechol 1,2-dioxygenase (C1,2D) is an iron-containing enzyme able to cleave the ring of catechol (the converted product from ToMO) for complete detoxification of BTEX. In this study, cold-active ToMO and C1,2D were produced using newly isolated psychrophilic Pseudomonas S2TR-14 in the minimal salt medium supplemented with crustacean waste and different concentrations of used motor oil (0.2-2% (v/v)). Crude ToMO and C1,2D were immobilized into micro/nano biochar-chitosan matrices and used for BTEX biodegradation. The results showed that the highest enzyme production (12 U/mg for ToMO and 22 U/mg for C1,2D) was achieved at the presence of 0.5% v/v used motor oil compared to the control group without motor oil (0.07 and 0.06 U/mg). High immobilization yield was achieved due to covalent bonding of ToMO (92.26% for micro matrix and 77.20% for nano matrix) and C1,2D (87.57% for micro matrix and 74.79% for nano matrix) with matrices. FTIR spectra confirmed the immobilization of enzymes on the surface of microbiochar and nanobiochar-chitosan matrices as proper support. The immobilization increased the storage stability of the enzymes with more than 50% residual activity after 30 days at 4 ± 1 °C, while the free form of enzymes had less than 10% of its activity. Immobilized enzymes degraded more than 80% of BTEX (~200 mg/L in groundwater and ~10,000 mg/kg in soil) at 10 ± 1 °C in groundwater and soil. Therefore, integrated use of microbiochar and nanobiochar with chitosan for co-immobilization of ToMO and C1,2D can be a potential way to remove petroleum hydrocarbons with higher efficiency from contaminated groundwater and soil.

Construction of a novel microbial consortium valued for the effective degradation and detoxification of creosote-treated sawdust along with enhanced methane production

Lignocellulosic biomass represents an unlimited and ubiquitous energy source, which can effectively address current global challenges, including climate change, greenhouse gas emissions, and increased energy demand. However, lignocellulose recalcitrance hinders microbial degradation, especially in case of contaminated materials such as creosote (CRO)-treated wood, which necessitates appropriate processing in order to eliminate pollution. This study might be the first to explore a novel bacterial consortium SST-4, for decomposing birchwood sawdust, capable of concurrently degrading lignocellulose and CRO compounds. Afterwards, SST-4 which stands for molecularly identified bacterial strains Acinetobacter calcoaceticus BSW-11, Shewanella putrefaciens BSW-18, Bacillus cereus BSW-23, and Novosphingobium taihuense BSW-25 was evaluated in terms of biological sawdust pre-treatment, resulting in effective lignocellulose degradation and 100% removal of phenol and naphthalene. Subsequently, the maximum biogas production observed was 18.7 L/kg VS, while cumulative methane production was 162.8 L/kg VS, compared to 88.5 without microbial pre-treatment. The cumulative energy production from AD-I and AD-II through biomethanation was calculated as 3177.1 and 5843.6 KJ/kg, respectively. The pretreatment process exhibited a significant increase in the energy yield by 83.9%. Lastly, effective CRO detoxification was achieved with EC₅₀ values exceeding 90%, showing the potential for an integrated process of effective contaminated wood management and bioenergy production.

Isolation and characterization of a halophilic Modicisalibacter sp. strain Wilcox from produced water

We report the isolation a halophilic bacterium that degrades both aromatic and aliphatic hydrocarbons as the sole sources of carbon at high salinity from produced water. Phylogenetic analysis of 16S rRNA-gene sequences shows the isolate is a close relative of Modicisalibacter tunisiensis isolated from an oil-field water in Tunisia. We designate our isolate as Modicisalibacter sp. strain Wilcox. Genome analysis of strain Wilcox revealed the presence of a repertoire of genes involved in the metabolism of aliphatic and aromatic hydrocarbons. Laboratory culture studies corroborated the predicted hydrocarbon degradation potential. The strain degraded benzene, toluene, ethylbenzene, and xylenes at salinities ranging from 0.016 to 4.0 M NaCl, with optimal degradation at 1 M NaCl. Also, the strain degraded phenol, benzoate, biphenyl and phenylacetate as the sole sources of carbon at 2.5 M NaCl. Among aliphatic compounds, the strain degraded n-decane and n-hexadecane as the sole sources of carbon at 2.5 M NaCl. Genome analysis also predicted the presence of many heavy metal resistance genes including genes for metal efflux pumps, transport proteins, and enzymatic detoxification. Overall, due to its ability to degrade many hydrocarbons and withstand high salt and heavy metals, strain Wilcox may prove useful for remediation of produced waters.

Biochemistry of aerobic biological methane oxidation

Methanotrophic bacteria represent a potential route to methane utilization and mitigation of methane emissions. In the first step of their metabolic pathway, aerobic methanotrophs use methane monooxygenases (MMOs) to activate methane, oxidizing it to methanol. There are two types of MMOs: a particulate, membrane-bound enzyme (pMMO) and a soluble, cytoplasmic enzyme (sMMO). The two MMOs are completely unrelated, with different architectures, metal cofactors, and mechanisms. The more prevalent of the two, pMMO, is copper-dependent, but the identity of its copper active site remains unclear. By contrast, sMMO uses a diiron active site, the catalytic cycle of which is well understood. Here we review the current state of knowledge for both MMOs, with an emphasis on recent developments and emerging hypotheses. In addition, we discuss obstacles to developing expression systems, which are needed to address outstanding questions and to facilitate future protein engineering efforts.

Psychrozymes as novel tools to biodegrade p-xylene and potential use for contaminated groundwater in the cold climate

Sites contaminated by petroleum hydrocarbons in cold-climate regions have recently received significant attention due to their sensitive ecosystem and human health impacts. Two cold-adapted pseudomonas strains were isolated from contaminated groundwater and soil. As xylene monooxygenase from Pseudomonas synxantha S2TR-26 and catechol 2,3-dioxygenase from Pseudomonas mandelii S2TR-08, have a matching end product, they acted in symphony to degrade p-xylene. Their unique thermodynamic and kinetic behavior permits them to achieve rapid degradation of p-xylene at low temperatures (<15 °C). The results showed that the sequential action led to the conversion of 200 mg/l of p-xylene within 72 h and complete degradation after 120 h. The cocktail of these enzymes with a ratio of 1:1.5 (xylene monooxygenase: catechol 2, 3-dioxygenase) confirmed the complete degradation of p-xylene within 48 h at 15 °C. This approach will allow efficient biodegradation of p-xylene to minimize the bioremediation duration in cold-climate regions.

Decoding lignin valorization pathways in the extremophilicBacillus ligniniphilusL1 for vanillin biosynthesis

An efficient bioconversion procedure for the accumulation of vanillin from lignin by pathway engineering and milking fermentation has been developed.

In Vitro Reconstitution Reveals a Central Role for the N-Oxygenase PvfB in (Dihydro)pyrazine-N-oxide and Valdiazen Biosynthesis

The Pseudomonas virulence factor (pvf) operon is essential for the biosynthesis of two very different natural product scaffolds: the (dihydro)pyrazine-N-oxides and the diazeniumdiolate, valdiazen. PvfB is a member of the non-heme diiron N-oxygenase enzyme family that commonly convert anilines to their nitroaromatic counterparts. In contrast, we show that PvfB catalyzes N-oxygenation of the α-amine of valine, first to the hydroxylamine and then the nitroso, while linked to the carrier protein of PvfC. PvfB modification of PvfC-tethered valine was observed directly by protein NMR spectroscopy, establishing the intermediacy of the hydroxylamine. This work reveals a central role for PvfB in the biosynthesis of (dihydro)pyrazine-N-oxides and valdiazen.

Effect of oxygen limitation on the enrichment of bacteria degrading either benzene or toluene and the identification of Malikia spinosa (Comamonadaceae) as prominent aerobic benzene-, toluene-, and ethylbenzene-degrading bacterium: enrichment, isolation and whole-genome analysis

The primary aims of this present study were to evaluate the effect of oxygen limitation on the bacterial community structure of enrichment cultures degrading either benzene or toluene and to clarify the role of Malikia-related bacteria in the aerobic degradation of BTEX compounds. Accordingly, parallel aerobic and microaerobic enrichment cultures were set up and the bacterial communities were investigated through cultivation and 16S rDNA Illumina amplicon sequencing. In the aerobic benzene-degrading enrichment cultures, the overwhelming dominance of Malikia spinosa was observed and it was abundant in the aerobic toluene-degrading enrichment cultures as well. Successful isolation of a Malikia spinosa strain shed light on the fact that this bacterium harbours a catechol 2,3-dioxygenase (C23O) gene encoding a subfamily I.2.C-type extradiol dioxygenase and it is able to degrade benzene, toluene and ethylbenzene under clear aerobic conditions. While quick degradation of the aromatic substrates was observable in the case of the aerobic enrichments, no significant benzene degradation, and the slow degradation of toluene was observed in the microaerobic enrichments. Despite harbouring a subfamily I.2.C-type C23O gene, Malikia spinosa was not found in the microaerobic enrichments; instead, members of the Pseudomonas veronii/extremaustralis lineage dominated these communities. Whole-genome analysis of M. spinosa strain AB6 revealed that the C23O gene was part of a phenol-degrading gene cluster, which was acquired by the strain through a horizontal gene transfer event. Results of the present study revealed that bacteria, which encode subfamily I.2.C-type extradiol dioxygenase enzyme, will not be automatically able to degrade monoaromatic hydrocarbons under microaerobic conditions.

Microbial Metabolic Potential of Phenol Degradation in Wastewater Treatment Plant of Crude Oil Refinery: Analysis of Metagenomes and Characterization of Isolates

The drilling, processing and transportation of oil are the main sources of pollution in water and soil. The current work analyzes the microbial diversity and aromatic compounds degradation potential in the metagenomes of communities in the wastewater treatment plant (WWTP) of a crude oil refinery. By focusing on the degradation of phenol, we observed the involvement of diverse indigenous microbial communities at different steps of the WWTP. The anaerobic bacterial and archaeal genera were replaced by aerobic and facultative anaerobic bacteria through the biological treatment processes. The phyla Proteobacteria, Bacteroidetes and Planctomycetes were dominating at different stages of the treatment. Most of the established protein sequences of the phenol degradation key enzymes belonged to bacteria from the class Alphaproteobacteria. From 35 isolated strains, 14 were able to grow on aromatic compounds, whereas several phenolic compound-degrading strains also degraded aliphatic hydrocarbons. Two strains, Acinetobacter venetianus ICP1 and Pseudomonas oleovorans ICTN13, were able to degrade various aromatic and aliphatic pollutants and were further characterized by whole genome sequencing and cultivation experiments in the presence of phenol to ascertain their metabolic capacity in phenol degradation. When grown alone, the intermediates of catechol degradation, the meta or ortho pathways, accumulated into the growth environment of these strains. In the mixed cultures of the strains ICP1 and ICTN13, phenol was degraded via cooperation, in which the strain ICP1 was responsible for the adherence of cells and ICTN13 diminished the accumulation of toxic intermediates.

Pathway and kinetics of malachite green biodegradation by Pseudomonas veronii

Malachite green is a common environmental pollutant that poses a great threat to non-target organisms, including humans. This study reports the characterization of a bacterial strain, Pseudomonas veronii JW3-6, which was isolated from a malachite green enrichment culture. This strain degraded malachite green efficiently in a wide range of temperature and pH levels. Under optimal degradation conditions (32.4 °C, pH 7.1, and inoculum amount of 2.5 × 10⁷ cfu/mL), P. veronii JW3-6 could degrade 93.5% of 50 mg/L malachite green within seven days. Five intermediate products from the degradation of malachite green were identified: leucomalachite green, 4-(dimethylamino) benzophenone, 4-dimethylaminophenol, benzaldehyde, and hydroquinone. We propose a possible degradation pathway based on these findings. The present study is the first to report the degradation of malachite green by P. veronii and the identification of hydroquinone as a metabolite in the degradation pathway.

Phenol hydroxylase from Pseudomonas sp. KZNSA: Purification, characterization and prediction of three-dimensional structure

A 61.3 kDa Phenol hydroxylase (PheA) was purified and characterized from Pseudomonas sp. KZNSA (PKZNSA). Cell free extract of the isolate grown in mineral salt medium supplemented with 600 ppm phenol showed 21.58 U/mL of PheA activity with a specific activity of 7.67 U/mg of protein. The enzyme was purified to 1.6-fold with a total yield of 33.6%. The purified PheA was optimally active at pH 8 and temperature 30 °C, with ≈95% stability at pH 7.5 and temperature 30 °C after 2 h. The Lineweaver-Burk plot showed the v_max and K_m values of 4.04 µM/min and 4.03 µM, respectively, for the substrate phenol. The ES-MS data generated from the tryptic digested fragments of pure protein and PCR amplification of a ≈600 bp gene from genomic DNA of PKZNSA lead to the determination of complete amino acid and nucleotide sequence of PheA. Bioinformatics tools and homology modelling studies indicated that PheA from PKZNSA is likely a probable protein kinase UbiB (2-octaprenylphenol hydroxylase) involving Lys and Asp at positions 153 and 288 for binding and active site, respectively. Characterization and optimization of PheA activity may be useful for a better understanding of 2,4-dichlorophenol degradation by this organism and for potential industrial application of the enzyme.

Fe3+ enhanced degradation of oxytetracycline in water by pseudomonas

The application and fate of antibiotics are closely related to human health and the ecological balance, which has gradually aroused the widespread global concerns. Long-term antibiotic residues can easily induce antibiotic resistance and antibiotic resistance genes (ARGs) in the environment. Although many studies have investigated the metabolic pathways of biosynthesis or degradation of oxytetracycline (OTC) and its influencing factors under laboratory or controlled conditions, the understanding of OTC degradation pathways and influencing factors in the environment is still poor. In the present study, the role of Pseudomonas (T4) in OTC biodegradation were investigated with different carbon sources, metal ions, substrate concentrations, temperatures, and pH values, as well as the temporal changes in the relative abundance of OTC ARGs. It was found that OTC could be degraded by T4 as a sole carbon source. Comparison with Cu²⁺, the addition of Fe³⁺ could significantly promote the growth of T4, and then increased the OTC degradation percentage to 65.3%. The initial concentration of OTC, temperature, and pH had significant impacts on OTC degradation. At the initial OTC concentration of 50 mg L^-1, the percentage degradation of OTC by T4 could reach 81.0% at the presence of Fe³⁺, and at 40 °C and pH = 7. Common tetracycline ARGs were not found during the OTC degradation by T4 in the present study. The eight main putative OTC degradation byproducts were identified by ultra-high definition accurate-mass quadrupole time-of-flight tandem mass spectrometry (QTOF/MS). Six different reaction types and seven possible degradation pathways were proposed, including enol-ketone conversion, hydroxylation, dehydration, deamination, demethylation and decarbonylation. Under optimal conditions, the OTC degradation percentages by T4 could reach to 88.2%, 91.6% and 92.0% in pond water, fish wastewater and industrial wastewater, respectively. These results demonstrate the high effectiveness of T4 at the presence of Fe³⁺ for the enhanced biodegradation of OTC in water environment, without resulting in the occurrence of ARGs. This has important implications for the removal of OTC from aquatic environments by the technology proposed from this study.

Changes in bacterial diversity and catabolic gene abundance during the removal of dimethylphenol isomers in laboratory-scale constructed wetlands

Constructed wetlands (CWs) are well-established wastewater treatment technologies and applied for bioremediation of contaminated water. Despite the optimal performance of CWs, the understanding of the bacterial processes in the rhizosphere, where mainly microbial degradation processes take place, is still limited. In the present study, laboratory-scale CWs planted with Juncus effusus and running under controlled conditions were studied in order to evaluate removal efficiency of dimethylphenols (DMPs), also in comparison to an unplanted bed. Next to removal rates, the bacterial community structure, diversity, and distribution, their correlation with physiochemical parameters, and abundance of the phenol hydroxylase gene were determined. As a result, better removal performance of DMP isomers (3,4-, 3,5-, and 2,6-DMP added as singles compounds or in mixtures) and ammonium loads, together with a higher diversity index, bacterial number, and phenol hydroxylase gene abundance in Juncus effusus CW in comparison with the non-planted CW, indicates a clear rhizosphere effect in the experimental CWs. An enhancement in the DMP removal and the recovery of the phenol hydroxylase gene were found during the fed with the DMP mixture. In addition, the shift of bacterial community in CWs was found to be DMP isomer dependent. Positive correlations were found between the bacteria harboring the phenol hydroxylase gene and communities present with 3,4-DMP and 3,5-DMP isomers, but not with the community developed with 2,6-DMP. These results indicate that CWs are highly dynamic ecosystems with rapid changes in bacterial communities harboring functional catabolic genes.

Delftia sp. LCW, a strain isolated from a constructed wetland shows novel properties for dimethylphenol isomers degradation

BACKGROUND

Dimethylphenols (DMP) are toxic compounds with high environmental mobility in water and one of the main constituents of effluents from petro- and carbochemical industry. Over the last few decades, the use of constructed wetlands (CW) has been extended from domestic to industrial wastewater treatments, including petro-carbochemical effluents. In these systems, the main role during the transformation and mineralization of organic pollutants is played by microorganisms. Therefore, understanding the bacterial degradation processes of isolated strains from CWs is an important approach to further improvements of biodegradation processes in these treatment systems.

RESULTS

In this study, bacterial isolation from a pilot scale constructed wetland fed with phenols led to the identification of Delftia sp. LCW as a DMP degrading strain. The strain was able to use the o-xylenols 3,4-DMP and 2,3-DMP as sole carbon and energy sources. In addition, 3,4-DMP provided as a co-substrate had an effect on the transformation of other four DMP isomers. Based on the detection of the genes, proteins, and the inferred phylogenetic relationships of the detected genes with other reported functional proteins, we found that the phenol hydroxylase of Delftia sp. LCW is induced by 3,4-DMP and it is responsible for the first oxidation of the aromatic ring of 3,4-, 2,3-, 2,4-, 2,5- and 3,5-DMP. The enzyme may also catalyze both monooxygenation reactions during the degradation of benzene. Proteome data led to the identification of catechol meta cleavage pathway enzymes during the growth on ortho DMP, and validated that cleavage of the aromatic rings of 2,5- and 3,5-DMPs does not result in mineralization. In addition, the tolerance of the strain to high concentrations of DMP, especially to 3,4-DMP was higher than that of other reported microorganisms from activated sludge treating phenols.

CONCLUSIONS

LCW strain was able to degraded complex aromatics compounds. DMPs and benzene are reported for the first time to be degraded by a member of Delftia genus. In addition, LCW degraded DMPs with a first oxidation of the aromatic rings by a phenol hydroxylase, followed by a further meta cleavage pathway. The higher resistance to DMP toxicity, the ability to degrade and transform DMP isomers and the origin as a rhizosphere bacterium from wastewater systems, make LCW a suitable candidate to be used in bioremediation of complex DMP mixtures in CWs systems.

Exploring the Promiscuity of Phenol Hydroxylase from Pseudomonas stutzeri OX1 for the Biosynthesis of Phenolic Compounds

Enzyme promiscuity plays an important role in developing biosynthetic pathways for novel target products. Phenol hydroxylase (PH) from Pseudomonas stutzeri OX1 is capable of ortho-hydroxylation of phenol and cresol isomers into counterpart catechols. A small ferredoxin-like protein PHQ was clustered together with the ph gene cluster in the genome of P. stutzeri OX1, and its function was not known. In this study, we found that the existence of PHQ has a promotion effect on the catalytic efficiency of PH. Then, we tested the substrate range of PH using nine different non-natural substrates. We found that PH was a promiscuous hydroxylase that could catalyze ortho-hydroxylation of several non-natural substrates, including catechol, 4-hydroxybenzoic acid and resorcinol. On this basis, linking the catechol biosynthetic pathway with the hydroxylation reaction catalyzed by PH enabled construction of a novel biosynthetic pathway for the synthesis of pyrogallol. This work not only characterized a well-performed PH, but also provided a promising hydroxylation platform for the production of high-value phenolic compounds.

Muconic Acid Production via Alternative Pathways and a Synthetic "Metabolic Funnel"

Muconic acid is a promising platform biochemical and precursor to adipic acid, which can be used to synthesize various plastics and polymers. In this study, the systematic construction and comparative evaluation of a modular network of non-natural pathways for muconic acid biosynthesis was investigated in Escherichia coli, including via three distinct and novel pathways proceeding via phenol as a common intermediate. However, poor recombinant activity and high promiscuity of phenol hydroxylase ultimately limited "phenol-dependent" muconic acid production. A fourth pathway proceeding via p-hydroxybenzoate, protocatechuate, and catechol was accordingly developed, though with muconic acid titers by this route reaching just 819 mg/L, its performance lagged behind that of the established, "3-dehydroshikimiate-derived" route. Finally, these two most promising pathways were coexpressed in parallel to create a synthetic "metabolic funnel" that, by enabling maximal net precursor assimilation and flux while preserving native chorismate biosynthesis, nearly doubled muconic acid production to up to >3.1 g/L at a glucose yield of 158 mg/g while introducing only a single auxotrophy. This generalizable, "funneling" strategy is expected to have broad applications in metabolic engineering for further enhancing production of muconic acid, as well as other important bioproducts of interest.

Diversity shift in bacterial phenol hydroxylases driven by alkyl-phenols in oil refinery wastewaters

Phenol hydroxylases (PHs) play a primary role in the bacterial degradation of phenol and alkylphenols. They are divided into two main classes, single-component and multi-component PHs, having distinctive catalytic subunits designated as PheA1 and LmPH, respectively. The diversity of these enzymes is still largely unexplored. Here, both LmPH and pheA1 gene sequences were examined in activated sludge from oil refinery wastewaters. Phenol, p-cresol, or 3,4-dimethylphenol (3,4-DMP) supplied as extra carbon sources were rapidly mineralized by the microbial community. Analysis of LmPH genes revealed a wide range of sequences, most of which exhibited moderate similarity with homologs found in Proteobacteria. Moreover, the LmPH diversity profiles showed a dramatic shift upon sludge treatment with p-cresol or 3,4-DMP amendment. This resulted in an enrichment in sequences similar to LmPHs from Betaproteobacteria and Gammaproteobacteria. RT-PCR analysis of RNA extracted from wastewater sludge highlighted LmPH genes best expressed in situ. A PCR approach was implemented to analyze the pheA1 gene diversity in the same microbial community. Retrieved sequences fell into four clusters and appeared to be distantly related to pheA1 genes from Actinobacteria. Altogether, our results provide evidence that phenol degraders carrying LmPH are more diverse than PheA1 carrying bacteria and suggest that PHs with best adapted substrate specificity are recruited in response to (methyl)phenol availability.

Proteomic Assessment of the Expression of Genes Related to Toluene Catabolism and Porin Synthesis in Pseudomonas stutzeri ST-9

The organization and expression of Pseudomonas stutzeri ST-9 genes related to toluene catabolism and porin synthesis was investigated. Toluene-degrading genes were found to be localized in the chromosome close to a phage-type integrase. A regulatory gene and 21 genes related to an aromatics degradation pathway are organized as a putative operon. These proteins are upregulated in the presence of toluene. Fourteen outer membrane proteins were identified as porins in the ST-9 genome. The identified porins showed that the main detected porins are related to the OmpA and OprD superfamilies. The percentage of porins in the outer membrane protein fraction, as determined by mass spectrometry, was 73% and 54% when the cells were cultured with toluene and with glucose, respectively. Upregulation of OmpA and downregulation of OprD occurred in the presence of toluene. A porin fraction (90% OprD) from both cultures was isolated and examined as a toluene uptake system using the liposome-swelling assay. Liposomes were prepared with the porin fraction from a culture that was grown on toluene (T-proteoliposome) or glucose (G-proteoliposome). There was no significant difference in the permeability rate of the different solutes through the T-proteoliposome and the G-proteoliposome.

Pathways for Arene Oxidation in Non-Heme Diiron Enzymes: Lessons from Computational Studies on Benzoyl Coenzyme A Epoxidase

Oxygenation of aromatic rings using O₂ is catalyzed by several non-heme carboxylate-bridged diiron enzymes. In order to provide a general mechanistic description for these reactions, computational studies were carried out at the ONIOM(B3LYP/BP86/Amber) level on the non-heme diiron enzyme benzoyl coenzyme A epoxidase, BoxB. The calculations revealed four possible pathways for attacking the aromatic ring: (a) electrophilic (2e^-) attack by a bis(μ-oxo)-diiron(IV) species (Q pathway); (b) electrophilic (2e^-) attack via the σ* orbital of a μ-η²:η²-peroxo-diiron(III) intermediate (Pσ* pathway); (c) radical (1e^-) attack via the π*-orbital of a superoxo-diiron(II,III) species (Pπ* pathway); (d) radical (1e^-) attack of a partially quenched bis(μ-oxo)-diiron(IV) intermediate (Q' pathway). The results allowed earlier work of de Visser on olefin epoxidation by diiron complexes and QM-cluster studies of Liao and Siegbahn on BoxB to be put into a broader perspective. Parallels with epoxidation using organic peracids were also examined. Specifically for the BoxB enzyme, the Q pathway was found to be the most preferred, but the corresponding bis(μ-oxo)-diiron(IV) species is significantly destabilized and not expected to be directly observable. Epoxidation via the Pσ* pathway represents an energetically somewhat higher lying alternative; possible strategies for experimental discrimination are discussed. The selectivity toward epoxidation is shown to stem from a combination of inherent electronic properties of the thioacyl substituent and enzymatic constraints. Possible implications of the results for toluene monooxygenases are considered as well.

Methane-Oxidizing Enzymes: An Upstream Problem in Biological Gas-to-Liquids Conversion

Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditional industrial hosts. With turnover numbers of 0.16-13 s(-1), these enzymes pose a considerable upstream problem in the biological production of fuels or chemicals from methane. Methane oxidation enzymes will need to be engineered to be faster to enable high volumetric productivities; however, efforts to do so and to engineer simpler enzymes have been minimally successful. Moreover, known methane-oxidizing enzymes have different expression levels, carbon and energy efficiencies, require auxiliary systems for biosynthesis and function, and vary considerably in terms of complexity and reductant requirements. The pros and cons of using each methane-oxidizing enzyme for Bio-GTL are considered in detail. The future for these enzymes is bright, but a renewed focus on studying them will be critical to the successful development of biological processes that utilize methane as a feedstock.

Functional redundancy in phenol and toluene degradation in Pseudomonas stutzeri strains isolated from the Baltic Sea

In the present study we describe functional redundancy of bacterial multicomponent monooxygenases (toluene monooxygenase (TMO) and toluene/xylene monooxygenase (XylAM) of TOL pathway) and cooperative genetic regulation at the expression of the respective catabolic operons by touR and xylR encoded regulatory circuits in five phenol- and toluene-degrading Pseudomonas stutzeri strains. In these strains both toluene degradation pathways (TMO and Xyl) are active and induced by toluene and phenol. The whole genome sequence of the representative strain 2A20 revealed the presence of complete TMO- and Xyl-upper pathway operons together with two sets of lower catechol meta pathway operons, as well as phenol-degrading operon in a single 292,430bp contig. The much lower GC content and analysis of the predicted ORFs refer to the plasmid origin of the approximately 130kb region of this contig, containing the xyl, phe and tou genes. The deduced amino acid sequences of the TMO, XylA and the large subunit of phenol monooxygenase (LmPH) show 98-100% identity with the respective gene products of the strain Pseudomonas sp. OX1. In both strains 2A20 and OX1 the meta-cleavage pathways for catechol degradation are coded by two redundant operons (phe and xyl). We show that in the strain 2A20 TouR and XylR are activated by different effector molecules, phenol and toluene, respectively, and they both control transcription of the xyl upper, tou (TMO) and phe catabolic operons. Although the growth parameters of redundant strains did not show advantage at toluene biodegradation, the functional redundancy could provide better flexibility to the bacteria in environmental conditions.

Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched.

Metabolic Pathways for Degradation of Aromatic Hydrocarbons by Bacteria

The aim of this review was to build an updated collection of information focused on the mechanisms and elements involved in metabolic pathways of aromatic hydrocarbons by bacteria. Enzymes as an expression of the genetic load and the type of electron acceptor available, as an environmental factor, were highlighted. In general, the review showed that both aerobic routes and anaerobic routes for the degradation of aromatic hydrocarbons are divided into two pathways. The first, named the upper pathways, entails the route from the original compound to central intermediate compounds still containing the aromatic ring but with the benzene nucleus chemically destabilized. The second, named the lower pathway, begins with ring de-aromatization and subsequent cleavage, resulting in metabolites that can be used by bacteria in the production of biomass. Under anaerobic conditions the five mechanisms of activation of the benzene ring described show the diversity of chemical reactions that can take place. Obtaining carbon and energy from an aromatic hydrocarbon molecule is a process that exhibits the high complexity level of the metabolic apparatus of anaerobic microorganisms. The ability of these bacteria to express enzymes that catalyze reactions, known only in non-biological conditions, using final electron acceptors with a low redox potential, is a most interesting topic. The discovery of phylogenetic and functional characteristics of cultivable and noncultivable hydrocarbon degrading bacteria has been made possible by improvements in molecular research techniques such as SIP (stable isotope probing) tracing the incorporation of (13)C, (15)N and (18)O into nucleic acids and proteins. Since many metabolic pathways in which enzyme and metabolite participants are still unknown, much new research is required. Therefore, it will surely allow enhancing the known and future applications in practice.

Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway

In the present study, microbial toluene degradation in controlled constructed wetland model systems, planted fixed-bed reactors (PFRs), was queried with DNA-based methods in combination with stable isotope fractionation analysis and characterization of toluene-degrading microbial isolates. Two PFR replicates were operated with toluene as the sole external carbon and electron source for 2 years. The bulk redox conditions in these systems were hypoxic to anoxic. The autochthonous bacterial communities, as analyzed by Illumina sequencing of 16S rRNA gene amplicons, were mainly comprised of the families Xanthomonadaceae, Comamonadaceae, and Burkholderiaceae, plus Rhodospirillaceae in one of the PFR replicates. DNA microarray analyses of the catabolic potentials for aromatic compound degradation suggested the presence of the ring monooxygenation pathway in both systems, as well as the anaerobic toluene pathway in the PFR replicate with a high abundance of Rhodospirillaceae. The presence of catabolic genes encoding the ring monooxygenation pathway was verified by quantitative PCR analysis, utilizing the obtained toluene-degrading isolates as references. Stable isotope fractionation analysis showed low-level of carbon fractionation and only minimal hydrogen fractionation in both PFRs, which matches the fractionation signatures of monooxygenation and dioxygenation. In combination with the results of the DNA-based analyses, this suggests that toluene degradation occurs predominantly via ring monooxygenation in the PFRs.

The Toluene o-Xylene Monooxygenase Enzymatic Activity for the Biosynthesis of Aromatic Antioxidants

Monocyclic phenols and catechols are important antioxidant compounds for the food and pharmaceutic industries; their production through biotransformation of low-added value starting compounds is of major biotechnological interest. The toluene o-xylene monooxygenase (ToMO) from Pseudomonas sp. OX1 is a bacterial multicomponent monooxygenase (BMM) that is able to hydroxylate a wide array of aromatic compounds and has already proven to be a versatile biochemical tool to produce mono- and dihydroxylated derivatives of aromatic compounds. The molecular determinants of its regioselectivity and substrate specificity have been thoroughly investigated, and a computational strategy has been developed which allows designing mutants able to hydroxylate non-natural substrates of this enzyme to obtain high-added value compounds of commercial interest. In this work, we have investigated the use of recombinant ToMO, expressed in cells of Escherichia coli strain JM109, for the biotransformation of non-natural substrates of this enzyme such as 2-phenoxyethanol, phthalan and 2-indanol to produce six hydroxylated derivatives. The hydroxylated products obtained were identified, isolated and their antioxidant potential was assessed both in vitro, using the DPPH assay, and on the rat cardiomyoblast cell line H9c2. Incubation of H9c2 cells with the hydroxylated compounds obtained from ToMO-catalyzed biotransformation induced a differential protective effect towards a mild oxidative stress induced by the presence of sodium arsenite. The results obtained confirm once again the versatility of the ToMO system for oxyfunctionalization reactions of biotechnological importance. Moreover, the hydroxylated derivatives obtained possess an interesting antioxidant potential that encourages the use of the enzyme for further functionalization reactions and their possible use as scaffolds to design novel bioactive molecules.

Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern

Background

Novosphingobium sp. strain PP1Y is a marine α-proteobacterium adapted to grow at the water/fuel oil interface. It exploits the aromatic fraction of fuel oils as a carbon and energy source. PP1Y is able to grow on a wide range of mono-, poly- and heterocyclic aromatic hydrocarbons. Here, we report the complete functional annotation of the whole Novosphingobium genome.

Results

PP1Y genome analysis and its comparison with other Sphingomonadal genomes has yielded novel insights into the molecular basis of PP1Y’s phenotypic traits, such as its peculiar ability to encapsulate and degrade the aromatic fraction of fuel oils. In particular, we have identified and dissected several highly specialized metabolic pathways involved in: (i) aromatic hydrocarbon degradation; (ii) resistance to toxic compounds; and (iii) the quorum sensing mechanism.

Conclusions

In summary, the unraveling of the entire PP1Y genome sequence has provided important insight into PP1Y metabolism and, most importantly, has opened new perspectives about the possibility of its manipulation for bioremediation purposes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-384) contains supplementary material, which is available to authorized users.

Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601(T.)

The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601^T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601^T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601^T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601^T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601^T. Genes involved in cyclohexanol degradation were only found in strain K601^T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.

Regulation of aromatics biodegradation by rhl quorum sensing system through induction of catechol meta-cleavage pathway

The mechanism for quorum sensing (QS) regulation on aromatics degradation was investigated. Deletion of rhl QS system resulted in a significant decrease in aromatics biodegradation as well as the activity of catechol 2,3-dioxygenase (C23O, key enzyme for catechol meta-cleavage pathway) in Pseudomonas aeruginosa CGMCC1.860. Interestingly, this repression could be relieved by N-butyryl homoserine lactone (the signaling molecule of rhl QS system) addition. In accordance, the transcription level of nahH (the gene encoding C23O) and nahR (transcriptional activator) also responded to rhl perturbation in a similar way. The results indicated that rhl QS system positively controlled the catechol meta-cleavage pathway, and hence improved aromatics biodegradation. It suggested manipulation of QS system could be a promising strategy to tune the catechol cleavage pathway and to control aromatics biodegradation.

Triptycene-based Bis(benzimidazole) Carboxylate-Bridged Biomimetic Diiron(II) Complexes

A triptycene-based bis(benzimidazole) ester ligand, L3, was designed to enhance the electron donating ability of the heterocyclic nitrogen atoms relative to those of the first generation bis(benzoxazole) analogs, L1 and L2. A convergent synthesis of L3 was designed and executed. Three-component titration experiments using UV-visible spectroscopy revealed that the desired diiron(II) complex could be obtained with a 1:2:1 ratio of L3:Fe(OTf)2(MeCN)2:external carboxylate reactants. X-ray crystallographic studies of two diiron complexes derived in this manner from L3 revealed their formulas to be [Fe2L3(μ-OH)(μ-O2CR)(OTf)2], where R = 2,6-bis(p-tolyl)benzoate (7) or triphenylacetate (8). The structures are similar to that of a diiron complex derived from L1, [Fe2L1(μ-OH)(μ-O2CArTol)(OTf)2] (9) with a notable difference being that, in 7 and 8, the geometry at iron more closely resembles square-pyramidal than trigonal-bipyramidal. Mössbauer spectroscopic analyses of 7 and 8 indicate the presence of high-spin diiron(II) cores. These results demonstrate the importance of substituting benzimidazole for benzoxazole for assembling biomimetic diiron complexes with syn disposition of two N-donor ligands, as found in O2-activating carboxylate-bridged diiron centers in biology.

Deepening TOL and TOU catabolic pathways of Pseudomonas sp. OX1: cloning, sequencing and characterization of the lower pathways

Pseudomonas sp. OX1 is able to metabolize toluene and o-xylene through the TOU catabolic pathway, whereas its mutant M1 strain was found to be able to use m- and p-xylene as carbon and energy source, using the TOL catabolic pathway. Here we report the complete nucleotide sequence of the phe lower operon of the TOU catabolic pathway, and the sequence of the last four genes of the xyl-like lower operon of the TOL catabolic pathway. DNA sequence analysis shows the gene order within the operons to be pheCDEFGHI (phe operon) and xyl-likeQKIH (xyl-like operon), identical to the order found for the isofunctional genes of meta operons in the toluene/xylene pathway of TOL plasmid pWW0 from Pseudomonas putida mt-2 and the phenol/methylphenol pathway of pVIl50 from Pseudomonas sp. CF600. The nucleotide and the deduced amino acid sequences are homologous to the equivalent gene and enzyme sequences from other Pseudomonas meta pathways. Recombinant 2-hydroxymuconic semialdehyde dehydrogenase (HMSD) and 2-hydroxymuconic semialdehyde hydrolase (HMSH), coded by pheCD genes, respectively, and ADA and HOA enzymes from both phe and xyl operons were expressed in E. coli and steady-state kinetic analysis was carried out. The analysis of the kinetic parameters of HMSD and HMSH showed that the enzymes from Pseudomonas sp. OX1 are more specialized to channel metabolites into the two branches of the lower pathway than homologous enzymes from other pseudomonads. The kinetics parameters of recombinant ADA from phe and xyl-like operon were found to be similar to those of homologous enzymes from other Pseudomonas strains. In addition, the enzyme from xyl-like operon showed a substrate affinity three times higher than the enzyme from phe operon.

Proteogenomic elucidation of the initial steps in the benzene degradation pathway of a novel halophile, Arhodomonas sp. strain Rozel, isolated from a hypersaline environment

Lately, there has been a special interest in understanding the role of halophilic and halotolerant organisms for their ability to degrade hydrocarbons. The focus of this study was to investigate the genes and enzymes involved in the initial steps of the benzene degradation pathway in halophiles. The extremely halophilic bacteria Arhodomonas sp. strain Seminole and Arhodomonas sp. strain Rozel, which degrade benzene and toluene as the sole carbon source at high salinity (0.5 to 4 M NaCl), were isolated from enrichments developed from contaminated hypersaline environments. To obtain insights into the physiology of this novel group of organisms, a draft genome sequence of the Seminole strain was obtained. A cluster of 13 genes predicted to be functional in the hydrocarbon degradation pathway was identified from the sequence. Two-dimensional (2D) gel electrophoresis and liquid chromatography-mass spectrometry were used to corroborate the role of the predicted open reading frames (ORFs). ORFs 1080 and 1082 were identified as components of a multicomponent phenol hydroxylase complex, and ORF 1086 was identified as catechol 2,3-dioxygenase (2,3-CAT). Based on this analysis, it was hypothesized that benzene is converted to phenol and then to catechol by phenol hydroxylase components. The resulting catechol undergoes ring cleavage via the meta pathway by 2,3-CAT to form 2-hydroxymuconic semialdehyde, which enters the tricarboxylic acid cycle. To substantiate these findings, the Rozel strain was grown on deuterated benzene, and gas chromatography-mass spectrometry detected deuterated phenol as the initial intermediate of benzene degradation. These studies establish the initial steps of the benzene degradation pathway in halophiles.