Biodegradation, biotransformation, and biocatalysis (b3)

Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin

Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.

Optimization and Comparison of Microwave-Assisted Extraction, Supercritical Fluid Extraction, and Eucalyptus Oil-Assisted Extraction of Polycyclic Aromatic Hydrocarbons from Soil and Sediment

Polycyclic aromatic hydrocarbons (PAHs) are persistent organic compounds of major concern that mainly accumulate in soils and sediments, and their extraction from environmental matrices remains a crucial step when determining the extent of contamination in soils and sediments. The objective of the present study was to compare the extraction of PAHs (phenanthrene, pyrene, chrysene, and benzo[a]pyrene) from spiked soil and sediment using supercritical fluid extraction (SFE) with ethanol as the modifier, microwave-assisted extraction (MAE), and eucalyptus oil-assisted extraction (EuAE). Recoveries of PAHs were comparable between the three methods, and >80% of applied pyrene, chrysene and benzo[a]pyrene were recovered. The most efficient method of extracting PAHs from naturally incurred soils with different levels of contamination was SFE. A longer extraction time was required for the EuAE method compared with SFE and MAE under optimized conditions. However, EuAE required lower extraction temperatures (15-20 °C) compared with SFE (80 °C) and MAE (110-120 °C), and consumed less solvent than SFE and MAE. Compared with hexane/acetone used in MAE, the use of ethanol in SFE and eucalyptus oil in EuAE can be considered as more sustainable approaches to efficiently extract PAHs from spiked/naturally contaminated soils and sediments. And, although less efficient for matrices containing higher carbon content, EuAE offered a cheap, low-tech approach to extracting PAHs. Environ Toxicol Chem 2023;42:982-994. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances

Poly- and perfluorinated chemicals, including perfluorinated alkyl substances (PFAS), are pervasive in today's society, with a negative impact on human and ecosystem health continually emerging. These chemicals are now subject to strict government regulations, leading to costly environmental remediation efforts. Commercial polyfluorinated compounds have been called 'forever chemicals' due to their strong resistance to biological and chemical degradation. Environmental cleanup by bioremediation is not considered practical currently. Implementation of bioremediation will require uncovering and understanding the rare microbial successes in degrading these compounds. This review discusses the underlying reasons why microbial degradation of heavily fluorinated compounds is rare. Fluorinated and chlorinated compounds are very different with respect to chemistry and microbial physiology. Moreover, the end product of biodegradation, fluoride, is much more toxic than chloride. It is imperative to understand these limitations, and elucidate physiological mechanisms of defluorination, in order to better discover, study, and engineer bacteria that can efficiently degrade polyfluorinated compounds.

Biotransformation of Daidzein, Genistein, and Naringenin by Streptomyces Species Isolated from High-Altitude Soil of Nepal

Flavonoids have achieved widespread importance in pharmaceutical, food, and cosmetics industries. Furthermore, modification of these naturally occurring flavonoids to structurally diverse compounds through whole cell biotransformation with enhanced biological activities has numerous biotechnological applications. The present study investigated the biotransformation potential of Streptomyces species isolated from a high-altitude-soil sample towards selected flavonoid molecules. The biotransformed metabolites were confirmed by comparing the HPLC chromatogram with authentic compounds and LC-MS/MS analysis. Of these isolates, Streptomyces species G-18 (Accession number: MW663767.1) catalyzed isoflavone molecules daidzein and genistein to produce hydroxylated products at 24 h of reaction condition in a whole cell system. The hydroxylation of daidzein (4′,7-dihydroxyisoflavone) was confirmed at 3′-position of the B ring to produce 3′,4′,7-trihydroxyisoflavone. In addition, Streptomyces species G-14 (Accession number: MW663770.1) and Streptomyces species S4L (Accession number: MW663769.1) also revealed the transformation of daidzein (4′,7-dihydroxyisoflavone) to hydroxy daidzein at a distinct position than that of G-18 isolates, whereas thee Streptomyces species S4L reaction mixture with naringenin as a substrate also revealed the hydroxylated product. Our results demonstrated that microorganisms isolated from different ecological niches have broad application.

Regulated preparation of Crocin-1 or Crocin-2' Triggered by the Cosolvent DMSO Using Bs-GT/At-SuSy One-Pot Reaction

Crocins are the primary coloring ingredients of saffron. The low-glycosylated members of this compound family, such as crocin-1 (crocetin mono-glucosyl ester) and crocin-2' (crocetin di-glucosyl ester), are rarely distributed in nature and attracting interest for their therapeutic uses. In the present study, a one-pot reaction system was used for efficient preparation of crocin-1 and crocin-2' with in situ regeneration of UDP-Glc by coupling Bs-GT with At-SuSy, a sucrose synthase from Arabidopsis thaliana. Noticeably, DMSO was used as a cosolvent and resulted in improvement of the solubility of the substrate crocetin and regulation of the selectivity of glycosylation. With periodic addition of crocetin, the biosynthesis of crocin-2' was performed with a high yield of 3.25 g/L in 2% DMSO aqueous solution, whereas crocin-1 (2.12 g/L) was selectively obtained in a 10% DMSO aqueous solution. The present study provided a simple approach for the biosynthesis of crocin-1 and crocin-2'.

Applications of Marine-Derived Microorganisms and Their Enzymes in Biocatalysis and Biotransformation, the Underexplored Potentials

Biodiversity has been explored in the search for novel enzymes, including forests, savannas, tundras, deserts, and finally the sea. Marine microorganisms and their enzymes are capable of being active in high-salt concentration, large range of temperature, and high incidence of light and pressure, constituting an important source of unique biocatalysts. This review presents studies employing whole-cell processes of marine bacteria and fungi, aiming for new catalysts for different reactions in organic synthesis, such as reduction, oxidation, hydroxylation, hydrolysis, elimination, and conjugation. Genomics and protein engineering studies were also approached, and reactions employing isolated enzymes from different classes (oxidoreductases, hydrolases, lyases, and ligases) were described and summarized. Future biotechnological studies and process development should focus on molecular biology for the obtention of enzymes with interesting, fascinating and enhanced properties, starting from the exploration of microorganisms from the marine environment. This review approaches the literature about the use of marine-derived bacteria, fungi, and their enzymes for biocatalytic reactions of organic compounds, promoting a discussion about the possibilities of these microorganisms in the synthesis of different substances.

One enzyme, many reactions: structural basis for the various reactions catalyzed by naphthalene 1,2-dioxygenase

Rieske nonheme iron oxygenases (ROs) are a well studied class of enzymes. Naphthalene 1,2-dioxygenase (NDO) is used as a model to study ROs. Previous work has shown how side-on binding of oxygen to the mononuclear iron provides this enzyme with the ability to catalyze stereospecific and regiospecific cis-dihydroxylation reactions. It has been well documented that ROs catalyze a variety of other reactions, including mono-oxygenation, desaturation, O- and N-dealkylation, sulfoxidation etc. NDO itself catalyzes a variety of these reactions. Structures of NDO in complex with a number of different substrates show that the orientation of the substrate in the active site controls not only the regiospecificity and stereospecificity, but also the type of reaction catalyzed. It is proposed that the mononuclear iron-activated dioxygen attacks the atoms of the substrate that are most proximal to it. The promiscuity of delivering two products (apparently by two different reactions) from the same substrate can be explained by the possible binding of the substrate in slightly different orientations aided by the observed flexibility of residues in the binding pocket.

The gut microbiota of insecticide-resistant insects houses insecticide-degrading bacteria: A potential source for biotechnological exploitation

The exploration of new niches for microorganisms capable of degrading recalcitrant molecules is still required. We hypothesized the gut microbiota associated with insect-resistant lines carry pesticide degrading bacteria, and predicted they carry bacteria selected to degrade pesticides they were resistant to. We isolated and accessed the pesticide-degrading capacity of gut bacteria from the gut of fifth instars of Spodoptera frugiperda strains resistant to lambda-cyhalothrin, deltamethrin, chlorpyrifos ethyl, spinosad and lufenuron, using insecticide-selective media. Sixteen isolates belonging to 10 phylotypes were obtained, from which four were also associated with the susceptible strain. However, growth of gut bacteria associated with larvae from the susceptible strain was not obtained in any of the insecticide-based selective media tested. Growth of isolates was affected by the concentration of insecticides in the media, and all grew well up to 40 μg/ml. The insecticide-degrading capacity of selected isolates was assessed by GC or LC-MS/MS analyses. In conclusion, resistant strains of S. frugiperda are an excellent reservoir of insecticide-degrading bacteria with bioremediation potential. Moreover, gut-associated bacteria are subjected to the selection pressure imposed by insecticides on their hosts and may influence the metabolization of pesticides in insects.

Isolation and characterization of different bacterial strains for bioremediation of n-alkanes and polycyclic aromatic hydrocarbons

Crude oil is a common environmental pollutant composed of a large number of both aromatic and aliphatic hydrocarbons. Biodegradation is carried out by microbial communities that are important in determining the fate of pollutants in the environment. The intrinsic biodegradability of the hydrocarbons and the distribution in the environment of competent degrading microorganisms are crucial information for the implementation of bioremediation processes. In the present study, the biodegradation capacities of various bacteria toward aliphatic and aromatic hydrocarbons were determined. The purpose of the study was to isolate and characterize hydrocarbon-degrading bacteria from contaminated soil of a refinery in Arzew, Algeria. A collection of 150 bacterial strains was obtained; the bacterial isolates were identified by 16S rRNA gene sequencing and their ability to degrade hydrocarbon compounds characterized. The isolated strains were mainly affiliated to the Gamma-Proteobacteria class. Among them, Pseudomonas spp. had the ability to metabolize high molecular weight hydrocarbon compounds such as pristane (C19) at 35.11 % by strain LGM22 and benzo[a] pyrene (C20) at 33.93 % by strain LGM11. Some strains were able to grow on all the hydrocarbons tested including octadecane, squalene, phenanthrene, and pyrene. Some strains were specialized degrading only few substrates. In contrast, the strain LGM2 designated as Pseudomonas sp. was found able to degrade both linear and branched alkanes as well as low and high poly-aromatic hydrocarbons (PAHs). The alkB gene involved in alkane degradation was detected in LGM2 and other Pseudomonas-related isolates. The capabilities of the isolated bacterial strains to degrade alkanes and PAHs should be of great practical significance in bioremediation of oil-contaminated environments.

Degradation of 4-chloro-3-nitrophenol via a novel intermediate, 4-chlororesorcinol by Pseudomonas sp. JHN

A 4-chloro-3-nitrophenol (4C3NP)-mineralizing bacterium, Pseudomonas sp. JHN was isolated from a waste water sample collected from a chemically-contaminated area, India by an enrichment method. Pseudomonas sp. JHN utilized 4C3NP as a sole carbon and energy source and degraded it with the release of stoichiometric amounts of chloride and nitrite ions. Gas chromatography and gas chromatography-mass spectrometry detected 4-chlororesorcinol as a major metabolite of the 4C3NP degradation pathway. Inhibition studies using 2,2′-dipyridyl showed that 4-chlororesorcinol is a terminal aromatic compound in the degradation pathway of 4C3NP. The activity for 4C3NP-monooxygenase was detected in the crude extracts of the 4C3NP-induced JHN cells that confirmed the formation of 4-chlororesorcinol from 4C3NP. The capillary assay showed that Pseudomonas sp. JHN exhibited chemotaxis toward 4C3NP. The bioremediation capability of Pseudomonas sp. JHN was monitored to carry out the microcosm experiments using sterile and non-sterile soils spiked with 4C3NP. Strain JHN degraded 4C3NP in sterile and non-sterile soil with same degradation rates. This is the first report of (i) bacterial degradation and bioremediation of 4C3NP, (ii) formation of 4-chlororesorcinol in the degradation pathway of 4C3NP, (iii) bacterial chemotaxis toward 4C3NP.

Enzyme based cleavage strategy of Bacillus lentus BI377 in response to metabolism of azoic recalcitrant

Bacillus lentus BI377 (B. lentus BI377) an alkaliphilic strain has accomplished the discriminate color removal strategy for Reactive Red sulfonated azoic recalcitrant irrespective of their molecular structure. During the decolorization experiment, it was observed that the diazo dye first followed chromophoric cleavage by azoreductase via typical azoreduction whereas, in case of monoazo dye, cleavage took place by peroxidase via successive electron transfers to oxide surface resulting in the asymmetric cleavage of the azo bond. Dismutation of oxidative stress by reactive metabolites has confirmed by superoxide dismutase activity. Carbon monoxide (CO) binding spectra, the content of cytochrome P450 and spectroscopy analysis by GCMS, FTIR and (1)H NMR of intermediate metabolites indicated the differentiate pattern of diazo and monoazo dye decolorization fuse to central metabolic pathway. Declined percentage of TOC and the cytotoxicity (MTT) study confirmed that environmentally benign intermediates may lead to mineralization.

Use of bacteria for rapid, pH-neutral, hydrolysis of the model hydrophobic carboxylic acid ester p-nitrophenyl picolinate

Caulobacter crescentus, Escherichia coli and Bacillus subtilis cultures promote the hydrolysis of the model ester p-nitrophenyl picolinate (PNPP) at neutral pH with high efficiency. Hydrolysis is related to cell concentration, while the interaction of PNPP with both bacterial cells and their extracellular molecules is required for a maximum rate of PNPP hydrolysis in C. crescentus cultures. Furthermore, C. crescentus cultures hydrolyze PNPP at concentrations useful in synthetic chemistry.

Use of intestinal Pseudomonas aeruginosa in fish to detect the environmental pollutant benzo[a]pyrene

This study examined the potential of Pseudomonas aeruginosa abundance in the intestines of fish as an indicator of exposure to benzo[a]pyrene (BaP). P. aeruginosa populations were enumerated in juvenile African catfish (Clarias gariepinus) injected intramuscularly three days previous with 0, 10, 30, 40, 50 or 70mg/kg of BaP. Hepatic EROD and GST activities and biliary fluorescent aromatic compounds (FACs) 1-OH BaP, 3-OH BaP, 7,8-D BaP and BaP were quantified to investigate agreements between the new indicator and established fish biomarkers. The shape of bacterial population (logarithm of colony-forming unit) dose-response curve generally matched those of biliary FACs concentrations. Conversely, the EROD and GST dose-response curves were generally the mirror images of the bacterial population curve. Changes in intestinal P. aeruginosa population appear to be an indirect effect of BaP exposure because exposure to 0-100μg/ml BaP had no effect on P. aeruginosa populations grown on agar plates containing BaP. Using intestinal P. aeruginosa population of fish as a universal indicator of BaP pollution in aquatic environments is discussed.Conversely, the EROD and GST dose-response curves were generally the mirror images of the bacterial population curve.

The role of nutrients in the biodegradation of 2,4,6-trinitrotoluene in liquid and soil

The widely used explosive 2,4,6-trinitrotoluene (TNT) has residues that are potentially explosive, toxic, and mutagenic. TNT and other explosives can be degraded by microorganisms; however, biostimulation is needed for process efficiency. To investigate the effectiveness of using biostimulation to degrade TNT, we added varying concentrations of a nutrient amendment consisting of inorganic salts, plant extracts, and molasses to soil and liquid media. For the inoculum we used a consortium of bacteria AM 06 that had exhibited the ability to degrade TNT and which had been previously isolated from explosives-contaminated soils. Phylogenetically, the clones clustered into seven different genera: Klebsiella, Raoultella, Serratia, Stenotrophomonas, Pseudoxanthomonas, Achromobacter and Pseudomonas. The addition of AM 06 consortium to a liquid environment along with 100% nutrient amendment decreased the amount of TNT (and its degradation products) by up to 90% after 14 days incubation. At the total amount of TNT was less than 100 mg/l, the concentration of TNT did not influence the amount of sugar consumed by the bacteria consortium. In soil media, the TNT degradation process was dependent on the concentration of nutrient amendment added. At higher initial concentrations of TNT (500 mg/kg), bioaugmentation (i.e., addition of bacteria inoculum) had a demonstrated effect, especially when nutrient concentrations of 50% and 100% were added to the soil. Findings of this study could further the understanding of the TNT biodegradation processes in water and soil and provide for optimization of the technological conditions for bioremediation.

Tuning the specificity of the recombinant multicomponent toluene o-xylene monooxygenase from Pseudomonas sp. strain OX1 for the biosynthesis of tyrosol from 2-phenylethanol

Biocatalysis is today a standard technology for the industrial production of several chemicals, and the number of biotransformation processes running on a commercial scale is constantly increasing. Among biocatalysts, bacterial multicomponent monooxygenases (BMMs), a diverse group of nonheme diiron enzymes that activate dioxygen, are of primary interest due to their ability to catalyze a variety of complex oxidations, including reactions of mono- and dihydroxylation of phenolic compounds. In recent years, both directed evolution and rational design have been successfully used to identify the molecular determinants responsible for BMM regioselectivity and to improve their activity toward natural and nonnatural substrates. Toluene o-xylene monooxygenase (ToMO) is a BMM isolated from Pseudomonas sp. strain OX1 which hydroxylates a wide spectrum of aromatic compounds. In this work we investigate the use of recombinant ToMO for the biosynthesis in recombinant cells of Escherichia coli strain JM109 of 4-hydroxyphenylethanol (tyrosol), an antioxidant present in olive oil, from 2-phenylethanol, a cheap and commercially available substrate. We initially found that wild-type ToMO is unable to convert 2-phenylethanol to tyrosol. This was explained by using a computational model which analyzed the interactions between ToMO active-site residues and the substrate. We found that residue F176 is the major steric hindrance for the correct positioning of the reaction intermediate leading to tyrosol production into the active site of the enzyme. Several mutants were designed and prepared, and we found that the combination of different mutations at position F176 with mutation E103G allows ToMO to convert up to 50% of 2-phenylethanol into tyrosol in 2 h.

Biodegradation kinetics of 4-fluorocinnamic acid by a consortium of Arthrobacter and Ralstonia strains

Arthrobacter sp. strain G1 is able to grow on 4-fluorocinnamic acid (4-FCA) as sole carbon source. The organism converts 4-FCA into 4-fluorobenzoic acid (4-FBA) and utilizes the two-carbon side-chain for growth with some formation of 4-fluoroacetophenone as a dead-end side product. We also have isolated Ralstonia sp. strain H1, an organism that degrades 4-FBA. A consortium of strains G1 and H1 degraded 4-FCA with Monod kinetics during growth in batch and continuous cultures. Specific growth rates of strain G1 and specific degradation rates of 4-FCA were observed to follow substrate inhibition kinetics, which could be modeled using the kinetic models of Haldane–Andrew and Luong–Levenspiel. The mixed culture showed complete mineralization of 4-FCA with quantitative release of fluoride, both in batch and continuous cultures. Steady-state chemostat cultures that were exposed to shock loadings of substrate responded with rapid degradation and returned to steady-state in 10–15 h, indicating that the mixed culture provided a robust system for continuous 4-FCA degradation.

A process optimization for bio-catalytic production of substituted catechols (3-nitrocatechol and 3-methylcatechol

BACKGROUND

Substituted catechols are important precursors for large-scale synthesis of pharmaceuticals and other industrial products. Most of the reported chemical synthesis methods are expensive and insufficient at industrial level. However, biological processes for production of substituted catechols could be highly selective and suitable for industrial purposes.

RESULTS

We have optimized a process for bio-catalytic production of 3-substituted catechols viz. 3-nitrocatechol (3-NC) and 3-methylcatechol (3-MC) at pilot scale. Amongst the screened strains, two strains viz. Pseudomonas putida strain (F1) and recombinant Escherichia coli expression clone (pDTG602) harboring first two genes of toluene degradation pathway were found to accumulate 3-NC and 3-MC respectively. Various parameters such as amount of nutrients, pH, temperature, substrate concentration, aeration, inoculums size, culture volume, toxicity of substrate and product, down stream extraction, single step and two-step biotransformation were optimized at laboratory scale to obtain high yields of 3-substituted catechols. Subsequently, pilot scale studies were performed in 2.5 liter bioreactor. The rate of product accumulation at pilot scale significantly increased up to approximately 90-95% with time and high yields of 3-NC (10 mM) and 3-MC (12 mM) were obtained.

CONCLUSION

The biocatalytic production of 3-substituted catechols viz. 3-NC and 3-MC depend on some crucial parameters to obtain maximum yields of the product at pilot scale. The process optimized for production of 3-substituted catechols by using the organisms P. putida (F1) and recombinant E. coli expression clone (pDTG602) may be useful for industrial application.

High-throughput metabolic engineering: advances in small-molecule screening and selection

Metabolic engineering for the overproduction of high-value small molecules is dependent upon techniques in directed evolution to improve production titers. The majority of small molecules targeted for overproduction are inconspicuous and cannot be readily obtained by screening. We provide a review on the development of high-throughput colorimetric, fluorescent, and growth-coupled screening techniques, enabling inconspicuous small-molecule detection. We first outline constraints on throughput imposed during the standard directed evolution workflow (library construction, transformation, and screening) and establish a screening and selection ladder on the basis of small-molecule assay throughput and sensitivity. An in-depth analysis of demonstrated screening and selection approaches for small-molecule detection is provided. Particular focus is placed on in vivo biosensor-based detection methods that reduce or eliminate in vitro assay manipulations and increase throughput. We conclude by providing our prospectus for the future, focusing on transcription factor-based detection systems as a natural microbial mode of small-molecule detection.

The use of oxygen uptake rate to monitor discovery of microbial and enzymatic biocatalysts

Arising from the requirement for discovery of novel biocatalysts with unusual properties, a process was developed which uniquely combines aspects of continuous culture with the measurement of oxygen uptake. This adaptation of the chemostat can be used to facilitate the isolation of a number of microorganisms with desirable properties, particularly those with useful metabolic capabilities and/or enzymes. The technique was also used to provide feedback on the metabolic status of a microbial population and increase the feed flow rate (i.e., dilution rate) thereby enabling the isolation of microorganisms with enhanced 1,3-propanediol dehydrogenase activity. The use of oxygen uptake as an indicator of cellular activity enables indirect measurement of substrate utilization and provides a real-time online assessment of the status of microbial enrichment or evolutionary processes and provides an opportunity, through the use of feedback systems, to control these processes. To demonstrate the utility of the technique, oxygen uptake rate (OUR) was compared with a range of conventional analytical techniques that are typically used to monitor enrichment/evolutionary processes and showed good correlation. Further validation was demonstrated by monitoring a characterizable microbial population shift using OUR. The population change was confirmed using off-line analytical techniques that are traditionally used to determine microbial activity. OUR was then used to monitor the enrichment of microorganisms capable of using a solvent (1-methyl-2-pyrrolidinone) as the sole source of carbon for energy and biomass formation from a heterogeneous microbial population. After purification the microorganisms taken from the enrichment process were able to completely utilize 1 g L(-1) 1-methyl-2-pyrrolidinone within 24 h demonstrating that the technique had correctly indicated the enriched population was capable of growth on 1-methyl-2-pyrrolidinone. The technique improves on conventional microbial enrichment that utilizes continuous culture by providing a real-time assessment of the enrichment process and the opportunity to use the OUR output for automated control and variation of one or more growth parameters.

Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly 'Pseudomonas butanovora'

Soluble butane monooxygenase (sBMO), a three-component di-iron monooxygenase complex expressed by the C(2)-C(9) alkane-utilizing bacterium Thauera butanivorans, was kinetically characterized by measuring substrate specificities for C(1)-C(5) alkanes and product inhibition profiles. sBMO has high sequence homology with soluble methane monooxygenase (sMMO) and shares a similar substrate range, including gaseous and liquid alkanes, aromatics, alkenes and halogenated xenobiotics. Results indicated that butane was the preferred substrate (defined by k(cat) : K(m) ratios). Relative rates of oxidation for C(1)-C(5) alkanes differed minimally, implying that substrate specificity is heavily influenced by differences in substrate K(m) values. The low micromolar K(m) for linear C(2)-C(5) alkanes and the millimolar K(m) for methane demonstrate that sBMO is two to three orders of magnitude more specific for physiologically relevant substrates of T. butanivorans. Methanol, the product of methane oxidation and also a substrate itself, was found to have similar K(m) and k(cat) values to those of methane. This inability to kinetically discriminate between the C(1) alkane and C(1) alcohol is observed as a steady-state concentration of methanol during the two-step oxidation of methane to formaldehyde by sBMO. Unlike methanol, alcohols with chain length C(2)-C(5) do not compete effectively with their respective alkane substrates. Results from product inhibition experiments suggest that the geometry of the active site is optimized for linear molecules four to five carbons in length and is influenced by the regulatory protein component B (butane monooxygenase regulatory component; BMOB). The data suggest that alkane oxidation by sBMO is highly specialized for the turnover of C(3)-C(5) alkanes and the release of their respective alcohol products. Additionally, sBMO is particularly efficient at preventing methane oxidation during growth on linear alkanes > or =C(2,) despite its high sequence homology with sMMO. These results represent, to the best of our knowledge, the first kinetic in vitro characterization of the closest known homologue of sMMO.

Differential degradation of crude oil (Bonny Light) by four Pseudomonas strains

Four hydrocarbon degraders isolated from enriched oil- and asphalt-contaminated soils in Lagos, Nigeria, were tested for their petroleum degradation potentials. All the isolates were identified as species of Pseudomonas. Pseudomonas putida P11 demonstrated a strong ability to degrade kerosene, gasoline, diesel, engine oil and crude oil while P. aeruginosa BB3 exhibited fair degradative ability on crude oil, gasoline, engine oil, anthracene and pyrene but weak on kerosene, diesel and dibenzothiophene. Pseudomonas putida WL2 and P. aeruginosa MVL1 grew on crude oil and all its cuts tested with the latter possessing similar polycyclic aromatic potentials as P11. All the strains grew logarithmically with 1-2 orders of magnitude and with generation time ranging significantly between 3.07 and 8.55 d at 0.05 level of confidence. Strains WL2 and MVL1 utilized the oil substrate best with more than 70% in 6 d experimental period, whereas the same feat was achieved by P11 in 12 d period. BB3 on the other hand degraded only 46% within 6 d. Interestingly, data obtained from gas chromatographic analysis of oil recovered from the culture fluids of MVL1 confirmed near-disappearance of major peaks (including aliphatics and aromatics) in the hydrocarbon mixture.

Use of Genetically Engineered Microorganisms (GEMs) for the Bioremediation of Contaminants

This paper presents a critical review of the literature on the application of genetically engineered microorganisms (GEMs) in bioremediation. The important aspects of using GEMs in bioremediation, such as development of novel strains with desirable properties through pathway construction and the modification of enzyme specificity and affinity, are discussed in detail. Particular attention is given to the genetic engineering of bacteria using bacterial hemoglobin (VHb) for the treatment of aromatic organic compounds under hypoxic conditions. The application of VHb technology may advance treatment of contaminated sites, where oxygen availability limits the growth of aerobic bioremediating bacteria, as well as the functioning of oxygenases required for mineralization of many organic pollutants. Despite the many advantages of GEMs, there are still concerns that their introduction into polluted sites to enhance bioremediation may have adverse environmental effects, such as gene transfer. The extent of horizontal gene transfer from GEMs in the environment, compared to that of native organisms including benefits regarding bacterial bioremediation that may occur as a result of such transfer, is discussed. Recent advances in tracking methods and containment strategies for GEMs, including several biological systems that have been developed to detect the fate of GEMs in the environment, are also summarized in this review. Critical research questions pertaining to the development and implementation of GEMs for enhanced bioremediation have been identified and posed for possible future research.

Diversity of IncP-9 plasmids of Pseudomonas

IncP-9 plasmids are important vehicles for degradation and resistance genes that contribute to the adaptability of Pseudomonas species in a variety of natural habitats. The three completely sequenced IncP-9 plasmids, pWW0, pDTG1 and NAH7, show extensive homology in replication, partitioning and transfer loci (an approximately 25 kb region) and to a lesser extent in the remaining backbone segments. We used PCR, DNA sequencing, hybridization and phylogenetic analyses to investigate the genetic diversity of 30 IncP-9 plasmids as well as the possibility of recombination between plasmids belonging to this family. Phylogenetic analysis of rep and oriV sequences revealed nine plasmid subgroups with 7-35 % divergence between them. Only one phenotypic character was normally associated with each subgroup, except for the IncP-9beta cluster, which included naphthalene- and toluene-degradation plasmids. The PCR and hybridization analysis using pWW0- and pDTG1-specific primers and probes targeting selected backbone loci showed that members of different IncP-9 subgroups have considerable similarity in their overall organization, supporting the existence of a conserved ancestral IncP-9 sequence. The results suggested that some IncP-9 plasmids are the product of recombination between plasmids of different IncP-9 subgroups but demonstrated clearly that insertion of degradative transposons has occurred on multiple occasions, indicating that association of this phenotype with these plasmids is not simply the result of divergent evolution from a single successful ancestral degradative plasmid.

Monoaromatics removal from polluted water through bioreactors-a review

Water contaminated by oil products is becoming a major problem in water supplies as these organic compounds cause hazards for human health. Different types of aerobic and anaerobic bioreactors have been widely used for water cleanup from organic pollutants such as petroleum hydrocarbons. Many studies report that aerobic biofilm processes are a very efficient method for monoaromatic hydrocarbons removal from contaminated water as they are able to reduce up to 99% of the pollutants from water, but generally these works do not discuss possible pollutant loss through gas stripping. On the other hand, some research is related to the ability of anaerobic bioreactors for monoaromatics treatment and results have shown that anaerobic immobilized reactors are able to remove monoaromatic compounds from water with maximal efficiencies between 95-99%. But here again, no data are found about the amount of volatile organic compounds that can be found in the biogas. Also, the data generated when a solid biomass support (activated carbon, polyurethane, etc.) is present in the medium do not take care about possible solute sorption phenomena. This paper reviews various properties of monoaromatic compounds including benzene, toluene, ethylbenzene and mixture of xylenes. The sources of pollutants, various analytical methods suitable for identification and quantitative measurement of monoaromatics, and knowledge gained on the true removal rates by aerobic and anaerobic bioreactors are reviewed and discussed in this study.

Conversion of polycyclic aromatic hydrocarbons by Sphingomonas sp. VKM B-2434

A versatile bacterial strain able to convert polycyclic aromatic hydrocarbons (PAHs) was isolated, and a conversion by the isolate of both individual substances and PAH mixtures was investigated. The strain belonged to the Sphingomonas genus as determined on the basis of 16S rRNA analysis and was designated as VKM B-2434. The strain used naphthalene, acenaphthene, phenanthrene, anthracene and fluoranthene as a sole source of carbon and energy, and cometabolically oxidized fluorene, pyrene, benz[a]anthracene, chrysene and benzo[a]pyrene. Acenaphthene and fluoranthene were degraded by the strain via naphthalene-1,8-dicarboxylic acid and 3-hydroxyphthalic acid. Conversion of most other PAHs was confined to the cleavage of only one aromatic ring. The major oxidation products of naphthalene, phenanthrene, anthracene, chrysene, and benzo[a]pyrene were identified as salicylic acid, 1-hydroxy-2-naphthoic acid, 3-hydroxy-2-naphthoic acid, o-hydroxyphenanthroic acid and o-hydroxypyrenoic acid, respectively. Fluorene and pyrene were oxidized mainly to hydroxyfluorenone and dihydroxydihydropyrene, respectively. Oxidation of phenanthrene and anthracene to the corresponding hydroxynaphthoic acids occurred quantitatively. The strain converted phenanthrene, anthracene, fluoranthene and carbazole of coal-tar-pitch extract.

Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase

Rieske oxygenase (RO) systems are two- and three-component enzyme systems that catalyze the formation of cis-dihydrodiols from aromatic substrates. Degradation of pollutants in contaminated soil and generation of chiral synthons have been the major foci of RO research. Substrate specificity and product regio- and stereoselectivity have been shown to vary between individual ROs. While directed evolution methods for altering RO function have been successful in the past, rational engineering of these enzymes still poses a challenge due to the lack of structural understanding. Here we examine the structural changes induced by mutation of Phe-352 in naphthalene 1,2-dioxygenase from Pseudomonas sp. strain NCIB 9816-4 (NDO-O(9816-4)). Structures of the Phe-352-Val mutant in native form and in complex with phenanthrene and anthracene, along with those of wild-type NDO-O(9816-4) in complex with phenanthrene, anthracene, and 3-nitrotoluene, are presented. Phenanthrene was shown to bind in a different orientation in the Phe-352-Val mutant active site from that in the wild type, while anthracene was found to bind in similar positions in both enzymes. Two orientations of 3-nitrotoluene were observed, i.e., a productive and a nonproductive orientation. These orientations help explain why NDO-O(9816-4) forms different products from 3-nitrotoluene than those made from nitrobenzene dioxygenase. Comparison of these structures among themselves and with other known ROs bound to substrates reveals that the orientation of substrate binding at the active site is the primary determinant of product regio- and stereoselectivity.

Microbial degradation of sulfur, nitrogen and oxygen heterocycles

Sulfur (S), nitrogen (N) and oxygen (O) heterocycles are among the most potent environmental pollutants. Microbial degradation of these pollutants is attracting more and more attention because such bioprocesses are environmentally friendly. The biotechnological potential of these processes is being investigated, for example, to achieve better sulfur removal by immobilized biocatalysts with magnetite nanoparticles or by solvent-tolerant bacteria, and to obtain valuable intermediates from these heterocycles. Other recent advances have demonstrated the mechanisms of angular dioxygenation of nitrogen heterocycles by microbes. However, these technologies are not yet available for large-scale applications so future research must investigate proper modifications for industrial applications of these processes. This review focuses on recent progress in understanding how microbes degrade S, N and O heterocycles.

Microbial degradation of organophosphorus compounds

Synthetic organophosphorus compounds are used as pesticides, plasticizers, air fuel ingredients and chemical warfare agents. Organophosphorus compounds are the most widely used insecticides, accounting for an estimated 34% of world-wide insecticide sales. Contamination of soil from pesticides as a result of their bulk handling at the farmyard or following application in the field or accidental release may lead occasionally to contamination of surface and ground water. Several reports suggest that a wide range of water and terrestrial ecosystems may be contaminated with organophosphorus compounds. These compounds possess high mammalian toxicity and it is therefore essential to remove them from the environments. In addition, about 200,000 metric tons of nerve (chemical warfare) agents have to be destroyed world-wide under Chemical Weapons Convention (1993). Bioremediation can offer an efficient and cheap option for decontamination of polluted ecosystems and destruction of nerve agents. The first micro-organism that could degrade organophosphorus compounds was isolated in 1973 and identified as Flavobacterium sp. Since then several bacterial and a few fungal species have been isolated which can degrade a wide range of organophosphorus compounds in liquid cultures and soil systems. The biochemistry of organophosphorus compound degradation by most of the bacteria seems to be identical, in which a structurally similar enzyme called organophosphate hydrolase or phosphotriesterase catalyzes the first step of the degradation. organophosphate hydrolase encoding gene opd (organophosphate degrading) gene has been isolated from geographically different regions and taxonomically different species. This gene has been sequenced, cloned in different organisms, and altered for better activity and stability. Recently, genes with similar function but different sequences have also been isolated and characterized. Engineered microorganisms have been tested for their ability to degrade different organophosphorus pollutants, including nerve agents. In this article, we review and propose pathways for degradation of some organophosphorus compounds by microorganisms. Isolation, characterization, utilization and manipulation of the major detoxifying enzymes and the molecular basis of degradation are discussed. The major achievements and technological advancements towards bioremediation of organophosphorus compounds, limitations of available technologies and future challenge are also discussed.

Expression of Vitreoscilla hemoglobin in Gordonia amarae enhances biosurfactant production

The gene (vgb) encoding Vitreoscilla (bacterial) hemoglobin (VHb) was electroporated into Gordonia amarae, where it was stably maintained, and expressed at about 4 nmol VHb g(-1) of cells. The maximum cell mass (OD(600)) of vgb-bearing G. amarae was greater than that of untransformed G. amarae for a variety of media and aeration conditions (2.8-fold under normal aeration and 3.4-fold under limited aeration in rich medium, and 3.5-fold under normal aeration and 3.2-fold under limited aeration in mineral salts medium). The maximum level of trehalose lipid from cultures grown in rich medium plus hexadecane was also increased for the recombinant strain, by 4.0-fold in broth and 1.8-fold in cells under normal aeration and 2.1-fold in broth and 1.4-fold in cells under limited aeration. Maximum overall biosurfactant production was also increased in the engineered strain, by 1.4-fold and 2.4-fold for limited and normal aeration, respectively. The engineered strain may be an improved source for producing purified biosurfactant or an aid to microorganisms bioremediating sparingly soluble contaminants in situ.

The solvent-tolerant Pseudomonas putida S12 as host for the production of cinnamic acid from glucose

A Pseudomonas putida S12 strain was constructed that efficiently produced the fine chemical cinnamic acid from glucose or glycerol via the central metabolite phenylalanine. The gene encoding phenylalanine ammonia lyase from the yeast Rhodosporidium toruloides was introduced. Phenylalanine availability was the main bottleneck in cinnamic acid production, which could not be overcome by the overexpressing enzymes of the phenylalanine biosynthesis pathway. A successful approach in abolishing this limitation was the generation of a bank of random mutants and selection on the toxic phenylalanine anti-metabolite m-fluoro-phenylalanine. Following high-throughput screening, a mutant strain was obtained that, under optimised culture conditions, accumulated over 5 mM of cinnamic acid with a yield (Cmol%) of 6.7%.

Dynamics of an oligotrophic bacterial aquifer community during contact with a groundwater plume contaminated with benzene, toluene, ethylbenzene, and xylenes: an in situ mesocosm study

An in situ mesocosm system was designed to monitor the in situ dynamics of the microbial community in polluted aquifers. The mesocosm system consists of a permeable membrane pocket filled with aquifer material and placed within a polypropylene holder, which is inserted below groundwater level in a monitoring well. After a specific time period, the microcosm is recovered from the well and its bacterial community is analyzed. Using this system, we examined the effect of benzene, toluene, ethylbenzene, and xylene (BTEX) contamination on the response of an aquifer bacterial community by denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA genes and PCR detection of BTEX degradation genes. Mesocosms were filled with nonsterile or sterile aquifer material derived from an uncontaminated area and positioned in a well located in either the uncontaminated area or a nearby contaminated area. In the contaminated area, the bacterial community in the microcosms rapidly evolved into a stable community identical to that in the adjacent aquifer but different from that in the uncontaminated area. At the contaminated location, bacteria with tmoA- and xylM/xylE1-like BTEX catabolic genotypes colonized the aquifer, while at the uncontaminated location only tmoA-like genotypes were detected. The communities in the mesocosms and in the aquifer adjacent to the wells in the contaminated area consisted mainly of Proteobacteria. At the uncontaminated location, Actinobacteria and Proteobacteria were found. Our results indicate that communities with long-term stability in their structures follow the contamination plume and rapidly colonize downstream areas upon contamination.

MetaRouter: bioinformatics for bioremediation

Bioremediation, the exploitation of biological catalysts (mostly microorganisms) for removing pollutants from the environment, requires the integration of huge amounts of data from different sources. We have developed MetaRouter, a system for maintaining heterogeneous information related to bioremediation in a framework that allows its query, administration and mining (application of methods for extracting new knowledge). MetaRouter is an application intended for laboratories working in biodegradation and bioremediation, which need to maintain and consult public and private data, linked internally and with external databases, and to extract new information from it. Among the data-mining features is a program included for locating biodegradative pathways for chemical compounds according to a given set of constraints and requirements. The integration of biodegradation information with the corresponding protein and genome data provides a suitable framework for studying the global properties of the bioremediation network. The system can be accessed and administrated through a web interface. The full-featured system (except administration facilities) is freely available at http://pdg.cnb.uam.es/MetaRouter. Additional material: http://www.pdg.cnb.uam.es/biodeg_net/MetaRouter.