Elucidation of the metabolic pathway for dibenzothiophene desulphurization by Rhodococcus sp. strain IGTS8 (ATCC 53968)

The Role of Dioxygen in Microbial Bio-Oxygenation: Challenging Biochemistry, Illustrated by a Short History of a Long Misunderstood Enzyme

A Special Issue of Microorganisms devoted to 'Microbial Biocatalysis and Biodegradation' would be incomplete without some form of acknowledgement of the many important roles that dioxygen-dependent enzymes (principally mono- and dioxygenases) play in relevant aspects of bio-oxygenation. This is reflected by the multiple strategic roles that dioxygen -dependent microbial enzymes play both in generating valuable synthons for chemoenzymatic synthesis and in facilitating reactions that help to drive the global geochemical carbon cycle. A useful insight into this can be gained by reviewing the evolution of the current status of 2,5-diketocamphane 1,2-monooxygenase (EC 1.14.14.108) from (+)-camphor-grown Pseudomonas putida ATCC 17453, the key enzyme that promotes the initial ring cleavage of this natural bicyclic terpene. Over the last sixty years, the perceived nature of this monooxygenase has transmogrified significantly. Commencing in the 1960s, extensive initial studies consistently reported that the enzyme was a monomeric true flavoprotein dependent on both FMNH2 and nonheme iron as bound cofactors. However, over the last decade, all those criteria have changed absolutely, and the enzyme is currently acknowledged to be a metal ion-independent homodimeric flavin-dependent two-component mono-oxygenase deploying FMNH2 as a cosubstrate. That transition is a paradigm of the ever evolving nature of scientific knowledge.

Biodegradation of vulcanized rubber by a gut bacterium from plastic-eating mealworms

The disposal of vulcanized rubber waste is difficult due to the presence of three-dimensional crosslinking network structure. Here, we report that a bacterium Acinetobacter sp. BIT-H3, isolated from the gut of plastic-eating mealworm, can grow on and degrade vulcanized poly(cis-1,4-isoprene) rubber (vPR). Scanning electronic microscopy (SEM) shows that strain BIT-H3 can penetrate into the vPR and produce craters and cracks. The tensile strength and the crosslink density of vPR decreased by 53.2% and 29.3% after ten weeks' incubation, respectively. The results of Horikx analysis, attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, and X-ray absorption near-edge structure (XANES) spectroscopy reveal that strain BIT-H3 can break down both sulfide bridges and double bonds of polymeric backbone within vPR. Sulfate and oligo(cis-1,4 isoprene) with terminal aldehyde and keto groups were identified as metabolic products released during vPR degradation. Through genomic and transcriptional analyses, five enzymes of dszA, dszC1, dszC2, Laccase2147, and Peroxidase1232 were found to be responsible for vPR degradation. Based on the chemical structure characterizations and molecular analyses, a vPR biodegradation pathway was proposed for strain BIT-H3. These findings pave a way for exploiting vulcanized rubber-degrading microorganisms from insect gut and contribute to establish a biodegradation method for vulcanized rubber waste disposal.

Assessment of the dibenzothiophene desulfurization potential of indigenously isolated bacterial consortium IQMJ-5: a different approach to safeguard the environment

Biodesulfurization is emerging as a valuable technology for the desulfurization of dibenzothiophene (DBT) and its alkylated substitutes, which are otherwise regarded as refractory to other physical and chemical desulfurizing techniques. The inability of the currently identified pure cultures and artificial microbial consortia due to lower desulfurization rate and product inhibition issues has compelled the researcher to look for an alternative solution. Thus, in the present study, an indigenously isolated microbial consortium was employed to tackle the desulfurization issue. Herein, we isolated several kinds of DBT desulfurizing natural microbial consortia from hydrocarbon-contaminated soil samples by conventional enrichment technique. The most effective desulfurizing microbial consortium was sequenced through illumine sequencing technique. Finally, the effect of the products of the desulfurizing pathway (such as 2-hydroxybiphenyl (2-HBP) and sulfate (SO₄^-2) was evaluated on the growth and desulfurization capability of the isolated consortium. The outcomes of Gibb's assay analysis showed that six isolates followed the "4S" pathway and converted DBT to 2-HBP. Among the isolates, I5 showed maximum growth rate (1.078 g/L dry cell weight) and desulfurization activity (about 77% as indicated by HPLC analysis) and was considered for further in-depth experimentation. The analysis of 16S rRNA by high-throughput sequencing approach of the I5 isolate revealed five types of bacterial phyla including Proteobacteria, Bacteroidetes, Firmicutes, Patescibacteria, and Actinobacteria (in order of abundance). The isolate showed significant tolerance to the inhibitory effect of both 2-HBP and SO₄^-2 and maintained growth in the presence of even about 1.0 mM initial concentration of both products. This clearly suggests that the isolate can be an efficient candidate for future in-depth desulfurization studies of coal and other fossil fuels.

Improvement in desulfurization of dibenzothiophene and dibenzothiophene sulfone by Paenibacillus strains using immobilization or nanoparticle coating

AIMS

Biodesulfurization of fossil fuels is a promising technology for deep desulfurization. Previously we have shown that Paenibacillus strains 32O-W and 32O-Y can desulfurize dibenzothiophene (DBT) and DBT sulfone (DBTS) effectively. In this work, improvements in DBT and DBTS desulfurization by these strains were investigated through immobilization and nanoparticle coating of cells.

METHODS AND RESULTS

Paenibacillus strains 32O-W and 32O-Y immobilized in alginate gel beads or coated with Fe₃ O₄ magnetite nanoparticles were grown at various concentrations (0.1-2 mmol l^-1 ) of DBT or DBTS for 96 h. The production of 2-hydroxybiphenyl (2-HBP) from 4S pathway biotransformation of DBT or DBTS was measured. The highest amounts of 2-HBP production occurred at concentrations of 0.1 and 0.5 mmol l^-1 . Compared to planktonic cultures maximum 2-HBP production increased by 54 % for DBT and 90 % for DBTS desulfurization with immobilized strains, and 44 % for DBT and 66% for DBTS desulfurization by nanoparticle coated strains.

CONCLUSIONS

Nanoparticle coated and immobilized cells may be of use in efforts to increase the efficiency of biodesulfurization.

SIGNIFICANCE AND IMPACT OF STUDY

Alginate immobilization or nanoparticle coating of bacterial cells may be useful approaches for enhancement of biodesulfurization for eventual use at an industrial scale.

A Pseudomonas sp. strain uniquely degrades PAHs and heterocyclic derivatives via lateral dioxygenation pathways

Polycyclic aromatic hydrocarbons (PAHs) and heterocyclic derivatives are organic pollutants that pose a serious health risk to human beings. In this study, a newly isolated Pseudomonas brassicacearum strain MPDS could effectively degrade PAHs and heterocyclic derivatives, including naphthalene, fluorene, dibenzofuran (DBF) and dibenzothiophene (DBT). Notably, strain MPDS is able to degrade fluorene, DBF and DBT uniquely via a lateral dioxygenation pathway, while most reported strains degrade fluorene, DBF and DBT via an angular dioxygenation pathway or co-metabolize them via a lateral dioxygenation pathway. Strain MPDS completely degraded 50 mg naphthalene (in 50 mL medium) in 84 h, and OD₆₀₀ reached 1.0-1.1; while, it stabilized at OD₆₀₀ 0.5-0.6 with 5 mg fluorene or DBF or DBT. Meanwhile, 65.7% DBF and 32.1% DBT were degraded in 96 h, and 40.3% fluorene was degraded in 72 h, respectively. Through genomic and transcriptomic analyses, and comparative genomic analysis with another DBF degradation strain, relevant gene clusters were predicted, and a naphthalene-degrading gene cluster was identified. This study provides understanding of degradation of PAHs and their heterocyclic derivatives, as well as new insights into the lateral dioxygenation pathway of relevant contaminants.

Combining co-culturing of Paenibacillus strains and Vitreoscilla hemoglobin expression as a strategy to improve biodesulfurization

Enhancement of the desulfurization activities of Paenibacillus strains 32O-W and 32O-Y were investigated using dibenzothiophene (DBT) and DBT sulfone (DBTS) as sources of sulphur in growth experiments. Strains 32O-W, 32O-Y and their co-culture (32O-W plus 32O-Y), and Vitreoscilla hemoglobin (VHb) expressing recombinant strain 32O-Yvgb and its co-culture with strain 32O-W were grown at varying concentrations (0·1-2 mmol l^-1 ) of DBT or DBTS for 96 h, and desulfurization measured by production of 2-hydroxybiphenyl (2-HBP) and disappearance of DBT or DBTS. Of the four cultures grown with DBT as sulphur source, the best growth occurred for the 32O-Yvgb plus 32O-W co-culture at 0·1 and 0·5 mmol l^-1 DBT. Although the presence of vgb provided no consistent advantage regarding growth on DBTS, strain 32O-W, as predicted by previous work, was shown to contain a partial 4S desulfurization pathway allowing it to metabolize this 4S pathway intermediate.

Diesel-born organosulfur compounds stimulate community re-structuring in a diesel-biodesulfurizing consortium

We enriched and characterized a biodesulfurizing consortium (designated as MG1). The MG1 consortium reduced the total sulfur of diesel by 25 % and utilized each of the diesel-born compounds dibenzothiophene (DBT), benzothiophene (BT), 4-methyldibenzothiophene (4-MDBT) and 4, 6-dimethyldibenzothiophene (4, 6-DMDBT) as a sole sulfur source. MiSeq analysis revealed compositional shifts in the MG1 community according to the type of the sulfur source. A DBT-grown MG1 culture had Klebsiella, Pseudomonas, Rhodococcus and Sphingomonas as the most abundant genera. When diesel or 4, 6-DMDBT was provided as a sole sulfur source, Klebsiella and Pseudomonas spp. were the most abundant. In the BT culture, Rhodococcus spp. were the key biodesulfurizers, while Klebsiella, Pseudomonas and Sphingomonas spp. dominated the 4-MDBT-grown consortium. MG1 also utilized 2-hydroxybiphenyl (the product of the 4S biodesulfurization pathway) where Pseudomonas spp. uniquely dominated the consortium. The data improves our understanding of the sulfur source-driven structural adaptability of biodesulfurizing consortia.

Bacterial and enzymatic degradation of poly(cis-1,4-isoprene) rubber: Novel biotechnological applications

Poly(cis-1,4-isoprene) rubber is a highly demanded elastomeric material mainly used for the manufacturing of tires. The end-cycle of rubber-made products is creating serious environmental concern and, therefore, different recycling processes have been proposed. However, the current physical-chemical processes include the use of hazardous chemical solvents, large amounts of energy, and possibly generations of unhealthy micro-plastics. Under this scenario, eco-friendly alternatives are needed and biotechnological rubber treatments are demonstrating huge potential. The cleavage mechanisms and the biochemical pathways for the uptake of poly(cis-1,4-isoprene) rubber have been extensively reported. Likewise, novel bacterial strains able to degrade the polymer have been studied and the involved structural and functional enzymes have been analyzed. Considering the fundamentals, biotechnological approaches have been proposed considering process optimization, cost-effective methods and larger-scale experiments in the search for practical and realistic applications. In this work, the latest research in the rubber biodegradation field is shown and discussed, aiming to analyze the combination of detoxification, devulcanization and polymer-cleavage mechanisms to achieve better degradation yields. The modified superficial structure of rubber materials after biological treatments might be an interesting way to reuse old rubber for re-vulcanization or to find new materials.

Characterization of sludge reduction and bacterial community dynamics in a pilot-scale multi-stage digester system with prolonged sludge retention time

Sludge reduction performance and bacterial community dynamics in a pilot-scale multi-stage digester system with prolonged sludge retention time were characterized. Throughout the operation period of 281 days, the total loading sludge and the total digested sludge were 4700 and 3300 kg-MLSS. After 114 days of operation, the residual MLSS (RMLSS) in the reactors for sludge treatment was maintained at 18-25 kg-RMLSS m^-3, and the sludge reduction efficiency achieved 95% under the F/M ratio (kg-loading MLSS kg-RMLSS^-1) of less than 0.018. Also, among the sludge components, both fixed suspended solids and volatile suspended solids were reduced. Based on the sludge reduction performance and the RNA-based bacterial community characteristics, the combined action of the maintenance metabolism, lysis-cryptic growth, and particulate inorganic matter is proposed as the sludge reduction mechanism in the multi-stage sludge treatment process.

Biodegradation of dibenzothiophene by efficient Pseudomonas sp. LKY-5 with the production of a biosurfactant

A potent bacterial strain capable of degrading dibenzothiophene (DBT) was isolated and evaluated for its characteristics. The strain, designated as LKY-5, is rod-shaped, gram-negative, and occurs mainly in clusters. It was identified as belonging to the Pseudomonas genus based on the 16S rDNA sequence and phylogenic analysis. Determination of its DBT depletion efficiency by gas chromatography revealed that the isolate was able to completely degrade up to 100 mg L^-1 DBT within 144 h. The pH values, DBT concentrations, and biomasses in the medium varied significantly in the initial 24 h. A biosurfactant produced by LKY-5 was extracted and identified as a di-rhamnolipid with the formula Rha-Rha-C₈-C_8:1 by HPLC-ESI-MS/MS. There were 26 metabolites in the DBT degradation process. Pseudomonas sp. LKY-5 exhibited unusually high DBT degradation efficiency via multiple metabolic pathways. Compared with the reported 4S and Kodama pathways, two more expanded metabolic pathways for the degradation of DBT are proposed. The polycyclic aromatic sulfur heterocycles (PASHs) in diesel, such as C₁-DBT, C₂-DBT, C₃-DBT, 4,6-DMDBT, and 2,4,6-TMDBT, can also be degraded with 28.2-42.3% efficiency. The results showed that LKY-5 is an excellent bacterial candidate for the bioremediation of PASH-contaminated sites and sediments.

An overview of conventional and alternative technologies for the production of ultra-low-sulfur fuels

Environmental concerns have given a great deal of attention for the production of ultra-low-sulfur fuels. The conventional hydrodesulfurization (HDS) process has high operating cost and also encounters difficulty in removing sulfur compound with steric hindrance. Consequently, various research efforts have been made to overcome the limitation of conventional HDS process and exploring the alternative technologies for deep desulfurization. The alternative processes being explored for the production of ultra-low-sulfur content fuel are adsorptive desulfurization (ADS), biodesulfurization (BDS), oxidative desulfurization (ODS), and extractive desulfurization (EDS). The present article provided the comprehensive information on the basic principle, reaction mechanism, workability, advantages, and disadvantages of conventional and alternative technologies. This review article aims to provide valuable insight into the recent advances made in conventional HDS process and alternative techniques. For deep desulfurization of liquid fuels, integration of conventional HDS with an alternative technique is also proposed.

Contribution of the Kodama and 4S pathways to the dibenzothiophene biodegradation in different coastal wetlands under different C/N ratios

Dibenzothiophene (DBT) degradation mechanisms and the transformation of pathways during the incubation of three types of coastal sediments with C/N ratios ranging from 1 to 9 were investigated. The DBT degradation efficiencies were clearly improved with increasing C/N ratio in reed wetland sediments, tidal wetlands sediments and estuary wetland sediments. The quantitative response relationships between DBT degradation rates and related functional genes demonstrate that the Kodama pathway-related gene groups were dominant factors at low C/N ratios, while the 4S-related gene groups mainly determined the degradation rate when the C/N ratio was up to 5. Network analysis also shows that the pathway shifts from the Kodama pathway to the 4S pathway occurred through changes in the connections between functional genomes and rates. Furthermore, there were competition and collaboration between the Kodama and 4S pathways. The 4S pathway-related bacteria were more active in estuary wetland sediments compared with reed wetland sediments and tidal wetland sediments. The higher degradation efficiency in estuary wetland sediments may indicate the greater participation of the 4S pathway in the DBT biodegradation reaction. And the effects of ring cleavage of Kodama pathway caused more complete metabolizing of DBT.

Assimilation of alternative sulfur sources in fungi

Fungi are well known for their metabolic versatility, whether it is the degradation of complex organic substrates or the biosynthesis of intricate secondary metabolites. The vast majority of studies concerning fungal metabolic pathways for sulfur assimilation have focused on conventional sources of sulfur such as inorganic sulfur ions and sulfur-containing biomolecules. Less is known about the metabolic pathways involved in the assimilation of so-called “alternative” sulfur sources such as sulfides, sulfoxides, sulfones, sulfonates, sulfate esters and sulfamates. This review summarizes our current knowledge regarding the structural diversity of sulfur compounds assimilated by fungi as well as the biochemistry and genetics of metabolic pathways involved in this process. Shared sequence homology between bacterial and fungal sulfur assimilation genes have lead to the identification of several candidate genes in fungi while other enzyme activities and pathways so far appear to be specific to the fungal kingdom. Increased knowledge of how fungi catabolize this group of compounds will ultimately contribute to a more complete understanding of sulfur cycling in nature as well as the environmental fate of sulfur-containing xenobiotics.

Structural and Biochemical Characterization of BdsA from Bacillus subtilis WU-S2B, a Key Enzyme in the "4S" Desulfurization Pathway

Dibenzothiophene (DBT) and their derivatives, accounting for the major part of the sulfur components in crude oil, make one of the most significant pollution sources. The DBT sulfone monooxygenase BdsA, one of the key enzymes in the “4S” desulfurization pathway, catalyzes the oxidation of DBT sulfone to 2′-hydroxybiphenyl 2-sulfonic acid (HBPSi). Here, we determined the crystal structure of BdsA from Bacillus subtilis WU-S2B, at the resolution of 2.2 Å, and the structure of the BdsA-FMN complex at 2.4 Å. BdsA and the BdsA-FMN complex exist as tetramers. DBT sulfone was placed into the active site by molecular docking. Seven residues (Phe12, His20, Phe56, Phe246, Val248, His316, and Val372) are found to be involved in the binding of DBT sulfone. The importance of these residues is supported by the study of the catalytic activity of the active site variants. Structural analysis and enzyme activity assay confirmed the importance of the right position and orientation of FMN and DBT sulfone, as well as the involvement of Ser139 as a nucleophile in catalysis. This work combined with our previous structure of DszC provides a systematic structural basis for the development of engineered desulfurization enzymes with higher efficiency and stability.

A Novel Aerobic Degradation Pathway for Thiobencarb Is Initiated by the TmoAB Two-Component Flavin Mononucleotide-Dependent Monooxygenase System in Acidovorax sp. Strain T1

Thiobencarb is a thiocarbamate herbicide used in rice paddies worldwide. Microbial degradation plays a crucial role in the dissipation of thiobencarb in the environment. However, the physiological and genetic mechanisms underlying thiobencarb degradation remain unknown. In this study, a novel thiobencarb degradation pathway was proposed in Acidovorax sp. strain T1. Thiobencarb was oxidized and cleaved at the C-S bond, generating diethylcarbamothioic S-acid and 4-chlorobenzaldehyde (4CDA). 4CDA was then oxidized to 4-chlorobenzoic acid (4CBA) and hydrolytically dechlorinated to 4-hydroxybenzoic acid (4HBA). The identification of catabolic genes suggested further hydroxylation to protocatechuic acid (PCA) and finally degradation through the protocatechuate 4,5-dioxygenase pathway. A novel two-component monooxygenase system identified in the strain, TmoAB, was responsible for the initial catabolic reaction. TmoA shared 28 to 32% identity with the oxygenase components of pyrimidine monooxygenase from Agrobacterium fabrum, alkanesulfonate monooxygenase from Pseudomonas savastanoi, and dibenzothiophene monooxygenase from Rhodococcus sp. TmoB shared 25 to 37% identity with reported flavin reductases and oxidized NADH but not NADPH. TmoAB is a flavin mononucleotide (FMN)-dependent monooxygenase and catalyzed the C-S bond cleavage of thiobencarb. Introduction of tmoAB into cells of the thiobencarb degradation-deficient mutant T1m restored its ability to degrade and utilize thiobencarb. A dehydrogenase gene, tmoC, was located 7,129 bp downstream of tmoAB, and its transcription was clearly induced by thiobencarb. The purified TmoC catalyzed the dehydrogenation of 4CDA to 4CBA using NAD⁺ as a cofactor. A gene cluster responsible for the complete 4CBA metabolic pathway was also cloned, and its involvement in thiobencarb degradation was preliminarily verified by transcriptional analysis.IMPORTANCE Microbial degradation is the main factor in thiobencarb dissipation in soil. In previous studies, thiobencarb was degraded initially via N-deethylation, sulfoxidation, hydroxylation, and dechlorination. However, enzymes and genes involved in the microbial degradation of thiobencarb have not been studied. This study revealed a new thiobencarb degradation pathway in Acidovorax sp. strain T1 and identified a novel two-component FMN-dependent monooxygenase system, TmoAB. Under TmoAB-mediated catalysis, thiobencarb was cleaved at the C-S bond, producing diethylcarbamothioic S-acid and 4CDA. Furthermore, the downstream degradation pathway of thiobencarb was proposed. Our study provides the physiological, biochemical, and genetic foundation of thiobencarb degradation in this microorganism.

Ralstonia eutropha as a biocatalyst for desulfurization of dibenzothiophene

The potential of Ralstonia eutropha as a biocatalyst for desulfurization of dibenzothiophene (DBT) was studied in growing and resting cell conditions. The results of both conditions showed that sulfur was removed from DBT which accompanied by the formation of 2-hydroxybiphenyl (2-HBP). In growing cell experiments, glucose was used as an energy supplying substrate in initial concentrations of 55 mM (energy-limited) and 111 mM (energy-sufficient). The growing cell behaviors were quantitatively described using the logistic equation and maintenance concept. The results indicated that 2-HBP production was higher for the energy-sufficient cultures, while the values of the specific growth rate and the maintenance coefficient for these media were lower than those of the energy-limited cultures. Additionally, the kinetic studies showed that the half-saturation constant for the energy-limited cultures was 2 times higher than the energy-sufficient ones where the inhibition constant (0.08 mM) and the maximum specific DBT desulfurization rate (0.002 mmol g_cell^-1 h^-1) were almost constant. By defining desulfurizing capacity (D _DBT) including both the biomass concentration and time to reach a particular percentage of DBT conversion, the best condition for desulfurizing cell was determined at 23% g_cell L^-1 h^-1 which corresponded with the resting cells that were harvested at the mid-exponential growth phase.

Biodesulphurization of gasoline by Rhodococcus erythropolis supported on polyvinyl alcohol

A new biodesulphurization (BDS) method has been considered using Rhodococcus erythropolis supported on polyvinyl alcohol (PVA) for BDS of thiophene as a gasoline sulphur model compound in n-hexane as the solvent, subsequently this biocatalyst has been applied to BDS of gasoline samples. The obtained results according to UV-Spectrophotometer analysis at 240 nm showed that 97·41% of thiophene at the optimum condition of primary concentration 80 mg l^-1 , pH = 7, by 0·1 g of biocatalyst in 30°C and after 20 h of contact time has been degraded. These optimum conditions have been applied to gasoline BDS and the biodegradation of gasoline thiophenic compounds have been investigated by gas chromatography-mass spectrometry (GC-MS). According to GC-MS, thiophene and its 2-methyl, 3-methyl and 2- ethyl derivatives had acceptable biodegradation efficiencies of about 26·67, 21·03, 23·62% respectively. Also, benzothiophene that has been detected in a gasoline sample had 38·89% biodegradation efficiency at optimum conditions, so biomodification of PVA by R. erythropolis produces biocatalysts with an active metabolism that facilitates the interaction of bacterial strain with gasoline thiophenic compounds. The morphology and surface functional groups of supported R. erythropolis on PVA have been investigated by scanning electron microscope (SEM) and FT-IR spectroscopy respectively. SEM images suggest some regular layered shape for the supported bacteria. FT-IR spectra indicate a desirable interaction between bacterial cells and polymer supports. Also, the recovery of biocatalyst has been investigated and after three times of using in BDS activity, its biocatalytic ability had no significant decreases.

SIGNIFICANCE AND IMPACT OF THE STUDY

The biomodification of polyvinyl alcohol by Rhodococcus erythropolis described herein produces a new biocatalyst which can be used for significantly reducing the thiophenic compounds of gasoline and other fossil fuels. The immobilization process is to increase the biodegradation efficiency of cells and accelerating the biodesulphurization process.

Initial investigations of C4a-(hydro)peroxyflavin intermediate formation by dibenzothiophene monooxygenase

Dibenzothiophene monooxygenase is the initiating enzyme in the Rhodococcus 4S biodesulfurization pathway. A member of the Class D flavin monooxygenases, it uses FMN to activate molecular oxygen for oxygenation of the substrate, dibenzothiophene. Here, we have used stopped-flow spectrophotometry to show that DszC forms a peroxyflavin intermediate in the absence of substrate. Mutagenesis of Ser163 and His391 to Ala appears to decrease the binding affinity for reduced FMN and eliminates the enzyme's ability to stabilize the peroxyflavin intermediate.

Engineering synthetic bacterial consortia for enhanced desulfurization and revalorization of oil sulfur compounds

The 4S pathway is the most studied bioprocess for the removal of the recalcitrant sulfur of aromatic heterocycles present in fuels. It consists of three sequential functional units, encoded by the dszABCD genes, through which the model compound dibenzothiophene (DBT) is transformed into the sulfur-free 2-hydroxybiphenyl (2HBP) molecule. In this work, a set of synthetic dsz cassettes were implanted in Pseudomonas putida KT2440, a model bacterial "chassis" for metabolic engineering studies. The complete dszB1A1C1-D1 cassette behaved as an attractive alternative - to the previously constructed recombinant dsz cassettes - for the conversion of DBT into 2HBP. Refactoring the 4S pathway by the use of synthetic dsz modules encoding individual 4S pathway reactions revealed unanticipated traits, e.g., the 4S intermediate 2HBP-sulfinate (HBPS) behaves as an inhibitor of the Dsz monooxygenases, and once secreted from the cells it cannot be further taken up. That issue should be addressed for the rational design of more efficient biocatalysts for DBT bioconversions. In this sense, the construction of synthetic bacterial consortia to compartmentalize the 4S pathway into different cell factories for individual optimization was shown to enhance the conversion of DBT into 2HBP, overcome the inhibition of the Dsz enzymes by the 4S intermediates, and enable efficient production of unattainable high added value intermediates, e.g., HBPS, that are difficult to obtain using the current monocultures.

Influence of oxygen transfer on Pseudomonas putida effects on growth rate and biodesulfurization capacity

The growth rate and desulfurization capacity accumulated by the cells during the growth of Pseudomonas putida KTH2 under different oxygen transfer conditions in a stirred and sparged tank bioreactor have been studied. Hydrodynamic conditions were changed using different agitation conditions. During the culture, several magnitudes associated to growth, such as the specific growth rate, the dissolved oxygen concentration and the carbon source consumption have been measured. Experimental results indicate that cultures are influenced by the fluid dynamic conditions into the bioreactor. An increase in the stirrer speed from 400 to 700 rpm has a positive influence on the cell growth rate. Nevertheless, the increase of agitation from 700 to 2000 rpm hardly has any influence on the growth rate. The effect of fluid dynamics on the cells development of the biodesulfurization (BDS) capacity of the cells during growth is different. The activities of the intracellular enzymes involved in the 4S pathway change with dissolved oxygen concentration. The enzyme activities have been evaluated in cells at several growth time and different hydrodynamic conditions. An increase of the agitation from 100 to 300 rpm has a positive influence on the development of the overall BDS capacity of the cells during growth. This capacity shows a decrease for higher stirrer speeds and the activity of the enzymes monooxygenases DszC and DszA decreases dramatically. The highest value of the activity of DszB enzyme was obtained with cells cultured at 100 rpm, while this activity decreases when the stirrer speed was increased higher than this value.

Advances in the Reduction of the Costs Inherent to Fossil Fuels' Biodesulfurization towards Its Potential Industrial Application

Biodesulfurization (BDS) process consists on the use of microorganisms for the removal of sulfur from fossil fuels. Through BDS it is possible to treat most of the organosulfur compounds recalcitrant to the conventional hydrodesulfurization (HDS), the petroleum industry's solution, at mild operating conditions, without the need for molecular hydrogen or metal catalysts. This technique results in lower emissions, smaller residue production and less energy consumption, which makes BDS an eco-friendly process that can complement HDS making it more efficient. BDS has been extensively studied and much is already known about the process. Clearly, BDS presents advantages as a complementary technique to HDS; however its commercial use has been delayed by several limitations both upstream and downstream the process. This study will comprehensively review and discuss key issues, like reduction of the BDS costs, advances and/or challenges for a competitive BDS towards its potential industrial application aiming ultra low sulfur fuels.

Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance

In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.

L-Methionine repressible promoters for tuneable gene expression in Trichoderma reesei

BACKGROUND

Trichoderma reesei is the main producer of lignocellulolytic enzymes that are required for plant biomass hydrolysis in the biorefinery industry. Although the molecular toolbox for T. reesei is already well developed, repressible promoters for strain engineering and functional genomics studies are still lacking. One such promoter that is widely employed for yeasts is that of the L-methionine repressible MET3 gene, encoding ATP sulphurylase.

RESULTS

We show that the MET3 system can only be applied for T. reesei when the cellulase inducing carbon source lactose is used but not when wheat straw, a relevant lignocellulosic substrate for enzyme production, is employed. We therefore performed a transcriptomic screen for genes that are L-methionine repressible in a wheat straw culture. This analysis retrieved 50 differentially regulated genes of which 33 were downregulated. Among these, genes encoding transport proteins as well as iron containing DszA like monooxygenases and TauD like dioxygenases were strongly overrepresented. We show that the promoter region of one of these dioxygenases can be used for the strongly repressible expression of the Aspergillus niger sucA encoded extracellular invertase in T. reesei wheat straw cultures. This system is also portable to other carbon sources including D-glucose and glycerol as demonstrated by the repressible expression of the Escherichia coli lacZ encoded ß-galactosidase in T. reesei.

CONCLUSION

We describe a novel, versatile set of promoters for T. reesei that can be used to drive recombinant gene expression in wheat straw cultures at different expression strengths and in an L-methionine repressible manner. The dioxygenase promoter that we studied in detail is furthermore compatible with different carbon sources and therefore applicable for manipulating protein production as well as functional genomics with T. reesei.

Ultrasound assisted biodesulfurization of liquid fuel using free and immobilized cells of Rhodococcus rhodochrous MTCC 3552: A mechanistic investigation

This paper attempts to gain mechanistic insight into enhancement effect of sonication on biodesulfurization. The approach has been to fit Haldane kinetics model to dibenzothiophene (DBT) metabolism and analyze trends in model parameters concurrently with simulations of cavitation bubble dynamics. Mechanistic synergy between sonication and biodesulfurization is revealed to be of both physical and chemical nature. Generation of micro-turbulence in medium by sonication leads to fine emulsification and enhancement of DBT transport across organic/aqueous interphase. Microturbulence also enhances transport of substrate and product across cell wall that increases reaction velocity (Vmax). Michaelis constant (Km) and inhibition constant (KI), being intrinsic parameters, remain unaffected by sonication. Radicals produced by transient cavitation oxidize DBT to DBT-sulfoxide and DBT-sulfone (intermediates of metabolism), which contributes enhancement of biodesulfurization. However, high shear generated by ultrasound and cavitation has adverse effect on action of surfactant β-cyclodextrin for enhancement of interphase transport of DBT.

Biocatalytic desulfurization of thiophenic compounds and crude oil by newly isolated bacteria

Microorganisms possess enormous highly specific metabolic activities, which enable them to utilize and transform nearly every known chemical class present in crude oil. In this context, one of the most studied biocatalytic processes is the biodesulfurization (BDS) of thiophenic sulfur-containing compounds such as benzothiophene (BT) and dibenzothiophene (DBT) in crude oils and refinery streams. Three newly isolated bacterial strains, which were affiliated as Rhodococcus sp. strain SA11, Stenotrophomonas sp. strain SA21, and Rhodococcus sp. strain SA31, were enriched from oil contaminated soil in the presence of DBT as the sole S source. GC-FID analysis of DBT-grown cultures showed consumption of DBT, transient formation of DBT sulfone (DBTO₂) and accumulation of 2-hydroxybiphenyl (2-HBP). Molecular detection of the plasmid-borne dsz operon, which codes for the DBT desulfurization activity, revealed the presence of dszA, dszB, and dszC genes. These results point to the operation of the known 4S pathway in the BDS of DBT. The maximum consumption rate of DBT was 11 μmol/g dry cell weight (DCW)/h and the maximum formation rate of 2-HBP formation was 4 μmol/g DCW/h. Inhibition of both cell growth and DBT consumption by 2-HBP was observed for all isolates but SA11 isolate was the least affected. The isolated biocatalysts desulfurized other model DBT alkylated homologs. SA11 isolate was capable of desulfurizing BT as well. Resting cells of SA11 exhibited 10% reduction in total sulfur present in heavy crude oil and 18% reduction in total sulfur present in the hexane-soluble fraction of the heavy crude oil. The capabilities of the isolated bacteria to survive and desulfurize a wide range of S compounds present in crude oil are desirable traits for the development of a robust BDS biocatalyst to upgrade crude oils and refinery streams.

Crystal structures of apo-DszC and FMN-bound DszC from Rhodococcus erythropolis D-1

The release of SO2 from petroleum products derived from crude oil, which contains sulfur compounds such as dibenzothiophene (DBT), leads to air pollution. The '4S' metabolic pathway catalyzes the sequential conversion of DBT to 2-hydroxybiphenyl via three enzymes encoded by the dsz operon in several bacterial species. DszC (DBT monooxygenase), from Rhodococcus erythropolis D-1 is involved in the first two steps of the '4S' pathway. Here, we determined the first crystal structure of FMN-bound DszC, and found that two distinct conformations occur in the loop region (residues 131-142) adjacent to the active site. On the basis of the DszC-FMN structure and the previously reported apo structures of DszC homologs, the binding site for DBT and DBT sulfoxide is proposed.

DATABASE

The atomic coordinates and structure factors for apo-DszC (PDB code: 3X0X) and DszC-FMN (PDB code: 3X0Y) have been deposited in the Protein Data Bank (http://www.rcsb.org).

Improvement of Dibenzothiophene Desulfurization Activity by Removing the Gene Overlap in thedszOperon

Dibenzothiophene (DBT) and its derivatives can be microbially desulfurized by Dsz enzymes. We investigated the expressional characteristics of the dsz operon. The result revealed that the ratio of mRNA quantity of dszA, dszB, and dszC was 11:3.3:1; however, western blot analysis indicated that the expression level of dszB is far lower than that of dszC. Gene analysis revealed that the termination codon of dszA and the initiation codon of dszB overlapped, whereas there was a 13-bp gap between dszB and dszC. In order to get a better, steady expression of DszB, we removed this structure by overlap polymerase chain reaction (PCR) and expressed the redesigned dsz operon in Rhodococcus erythropolis. The desulfurization activity of resting cells prepared from R. erythropolis DR-2, which held the redesigned dsz operon, was about five-fold higher than that of R. erythropolis DR-1, which held the original dsz operon.

Crystal structure of DszC from Rhodococcus sp. XP at 1.79 Å

The dibenzothiophene (DBT) monooxygenase DszC, which is the key initiating enzyme in "4S" metabolic pathway, catalyzes sequential sulphoxidation reaction of DBT to DBT sulfoxide (DBTO), then DBT sulfone (DBTO2). Here, we report the crystal structure of DszC from Rhodococcus sp. XP at 1.79 Å. Intriguingly, two distinct conformations occur in the flexible lid loops adjacent to the active site (residue 280-295, between α9 and α10). They are named "open"' and "closed" state respectively, and might show the status of the free and ligand-bound DszC. The molecular docking results suggest that the reduced FMN reacts with an oxygen molecule at C4a position of the isoalloxazine ring, producing the C4a-(hydro)peroxyflavin intermediate which is stabilized by H391 and S163. H391 may contribute to the formation of the C4a-(hydro)peroxyflavin by acting as a proton donor to the proximal peroxy oxygen, and it might also be involved in the protonation process of the C4a-(hydro)xyflavin. Site-directed mutagenesis study shows that mutations in the residues involved either in catalysis or in flavin or substrate-binding result in a complete loss of enzyme activity, suggesting that the accurate positions of flavin and substrate are crucial for the enzyme activity.

The hydrocarbon-degrading marine bacterium Cobetia sp. strain MM1IDA2H-1 produces a biosurfactant that interferes with quorum sensing of fish pathogens by signal hijacking

Biosurfactants are produced by hydrocarbon-degrading marine bacteria in response to the presence of water-insoluble hydrocarbons. This is believed to facilitate the uptake of hydrocarbons by bacteria. However, these diffusible amphiphilic surface-active molecules are involved in several other biological functions such as microbial competition and intra-or inter-species communication. We report the isolation and characterization of a marine bacterial strain identified as Cobetia sp. MM1IDA2H-1, which can grow using the sulfur-containing heterocyclic aromatic hydrocarbon dibenzothiophene (DBT). As with DBT, when the isolated strain is grown in the presence of a microbial competitor, it produces a biosurfactant. Because the obtained biosurfactant was formed by hydroxy fatty acids and extracellular lipidic structures were observed during bacterial growth, we investigated whether the biosurfactant at its critical micelle concentration can interfere with bacterial communication systems such as quorum sensing. We focused on Aeromonas salmonicida subsp. salmonicida, a fish pathogen whose virulence relies on quorum sensing signals. Using biosensors for quorum sensing based on Chromobacterium violaceum and Vibrio anguillarum, we showed that when the purified biosurfactant was mixed with N-acyl homoserine lactones produced by A. salmonicida, quorum sensing was inhibited, although bacterial growth was not affected. In addition, the transcriptional activities of A. salmonicida virulence genes that are controlled by quorum sensing were repressed by both the purified biosurfactant and the growth in the presence of Cobetia sp. MM1IDA2H-1. We propose that the biosurfactant, or the lipid structures interact with the N-acyl homoserine lactones, inhibiting their function. This could be used as a strategy to interfere with the quorum sensing systems of bacterial fish pathogens, which represents an attractive alternative to classical antimicrobial therapies in fish aquaculture.

Biomimetic Sulfide Oxidation by the Means of Immobilized Fe(III)-5,10,15,20-tetrakis(pentafluorophenyl)porphin under Mild Experimental Conditions

This paper describes the oxidation of inorganic sulfide to sulfate, minimizing the formation of elemental sulfur. The described catalytic reaction uses dilute hydrogen peroxide at nearly neutral pH values in the presence of a bioinspired, heterogenized, and commercial ferriporphin. A substantial increase of the percentage of sulfide converted to sulfate is obtained in comparison with the yields obtained when working with hydrogen peroxide alone. The biomimetic catalyst also proved to be a much more efficient catalyst than horseradish peroxidase. Accordingly, it could be suitable for large-scale applications. Further studies are in progress to drive sulfate yields up to nearly quantitative.

Thermophilic desulfurization of dibenzothiophene and different petroleum oils by Klebsiella sp. 13T

PURPOSE

Biodesulfurization (BDS) has the potential to desulfurize dibenzothiophene (DBT) and its alkylated derivatives, the compounds that are otherwise refractory to hydrodesulfurization (HDS). Thermophilic microorganisms are more appropriate to be used for BDS applications following HDS. The aim of the present study was to isolate a thermophilic microorganism and to explore its commercial relevance for BDS process.

METHODS

The desulfurizing thermophilic strain was isolated and enriched from various soil and water samples using sulfur free medium (SFM) supplemented with DBT. Microbiological and genomic approach was used to characterize the strain. Desulfurization reactions were carried out using DBT and petroleum oils at 45°C followed by different analytical procedures.

RESULTS

We report the isolation of a thermophilic bacterium Klebsiella sp. 13T from contaminated soils collected from petroleum refinery. HPLC analysis revealed that Klebsiella sp. 13T could desulfurize DBT to 2-hydroxybiphenyl (2-HBP) at 45°C through 4S pathway. In addition, adapted cells of Klebsiella sp. 13T were found to remove 22-53% of sulfur from different petroleum oils with highest sulfur removal from light crude oil.

CONCLUSION

Klebsiella sp. 13T is a potential candidate for BDS because of its thermophilic nature and capability to desulfurize petroleum oils.