Modeling the production of a Rhodococcus erythropolis IGTS8 biocatalyst for DBT biodesulfurization: Influence of media composition

Medium composition overturns the widely accepted sulfate-dependent repression of desulfurization phenotype in Rhodococcus qingshengii IGTS8

Microbial desulfurization has been extensively studied as a promising alternative to the widely applied chemical desulfurization process. Sulfur removal from petroleum and its products becomes essential, as the environmental regulations become increasingly stringent. Rhodococcus qingshengii IGTS8 has gained ground as a naturally occurring model biocatalyst, due to its superior specific activity for desulfurization of dibenzothiophene (DBT). Recalcitrant organic sulfur compounds-DBT included-are preferentially removed by selective carbon-sulfur bond cleavage to avoid a reduction in the calorific value of the fuel. The process, however, still has not reached economically sustainable levels, as certain limitations have been identified. One of those bottlenecks is the repression of catalytic activity caused by ubiquitous sulfur sources such as inorganic sulfate, methionine, or cysteine. Herein, we report an optimized culture medium for wild-type stain IGTS8 that completely alleviates the sulfate-mediated repression of biodesulfurization activity without modification of the natural biocatalyst. Medium C not only promotes growth in the presence of several sulfur sources, including DBT, but also enhances biodesulfurization of resting cells grown in the presence of up to 5 mM sulfate. Based on the above, the present work can be considered as a step towards the development of a more viable commercial biodesulfurization process.

Deciphering the biodesulfurization potential of two novel Rhodococcus isolates from a unique Greek environment

Sustainable biodesulfurization (BDS) processes require the use of microbial biocatalysts that display high activity against the recalcitrant heterocyclic sulfur compounds and can simultaneously withstand the harsh conditions of contact with petroleum products, inherent to any industrial biphasic BDS system. In this framework, the functional microbial BDS-related diversity in a naturally oil-exposed ecosystem, was examined through a 4,6-dimethyl-dibenzothiophene based enrichment process. Two new Rhodococcus sp. strains were isolated, which during a medium optimization process revealed a significantly enhanced BDS activity profile when compared to the model strain R. qingshengii IGTS8. In biocatalyst stability studies conducted in biphasic mode using partially hydrodesulfurized diesel under various process conditions, the new strains also presented an enhanced stability phenotype. In these studies, it was also demonstrated for all strains, that the BDS activity losses were decoupled from the overall cells' viability, in addition to the fact that the use of whole-broth biocatalyst positively affected BDS performance.

Interplay between Sulfur Assimilation and Biodesulfurization Activity in Rhodococcus qingshengii IGTS8: Insights into a Regulatory Role of the Reverse Transsulfuration Pathway

Biodesulfurization is a process that selectively removes sulfur from dibenzothiophene and its derivatives. Several natural biocatalysts harboring the highly conserved desulfurization operon dszABC, which is significantly repressed by methionine, cysteine, and inorganic sulfate, have been isolated. However, the available information on the metabolic regulation of gene expression is still limited. In this study, scarless knockouts of the reverse transsulfuration pathway enzyme genes cbs and metB were constructed in the desulfurizing strain Rhodococcus sp. strain IGTS8. We provide sequence analyses and report the enzymes' involvement in the sulfate- and methionine-dependent repression of biodesulfurization activity. Sulfate addition in the bacterial culture did not repress the desulfurization activity of the Δcbs strain, whereas deletion of metB promoted a significant biodesulfurization activity for sulfate-based growth and an even higher desulfurization activity for methionine-grown cells. In contrast, growth on cysteine completely repressed the desulfurization activity of all strains. Transcript level comparison uncovered a positive effect of cbs and metB gene deletions on dsz gene expression in the presence of sulfate and methionine, but not cysteine, offering insights into a critical role of cystathionine β-synthase (CβS) and MetB in desulfurization activity regulation. IMPORTANCE Precise genome editing of the model biocatalyst Rhodococcus qingshengii IGTS8 was performed for the first time, more than 3 decades after its initial discovery. We thus gained insight into the regulation of dsz gene expression and biocatalyst activity, depending on the presence of two reverse transsulfuration enzymes, CβS and MetB. Moreover, we observed an enhancement of biodesulfurization capability in the presence of otherwise repressive sulfur sources, such as sulfate and l-methionine. The interconnection of cellular sulfur assimilation strategies was revealed and validated.

Biodesulfurization of Dibenzothiophene and Its Alkylated Derivatives in a Two-Phase Bubble Column Bioreactor by Resting Cells of Rhodococcus erythropolis IGTS8

Biodesulfurization (BDS) is considered a complementary technology to the traditional hydrodesulfurization treatment for the removal of recalcitrant sulfur compounds from petroleum products. BDS was investigated in a bubble column bioreactor using two-phase media. The effects of various process parameters, such as biocatalyst age and concentration, organic fraction percentage (OFP), and type of sulfur compound—namely, dibenzothiophene (DBT), 4-methyldibenzothiophene (4-MDBT), 4,6-dimethyldibenzothiophene (4,6-DMDBT), and 4,6-diethyldibenzothiophene (4,6-DEDBT)—were evaluated, using resting cells of Rhodococcus erythropolis IGTS8. Cells derived from the beginning of the exponential growth phase of the bacterium exhibited the highest biodesulfurization efficiency and rate. The biocatalyst performed better in an OFP of 50% v/v. The extent of DBT desulfurization was dependent on cell concentration, with the desulfurization rate reaching its maximum at intermediate cell concentrations. A new semi-empirical model for the biphasic BDS was developed, based on the overall Michaelis-Menten kinetics and taking into consideration the deactivation of the biocatalyst over time, as well as the underlying mass transfer phenomena. The model fitted experimental data on DBT consumption and 2-hydroxibyphenyl (2-HBP) accumulation in the organic phase for various initial DBT concentrations and different organosulfur compounds. For constant OFP and biocatalyst concentration, the most important parameter that affects BDS efficiency seems to be biocatalyst deactivation, while the phenomenon is controlled by the affinities of biodesulfurizing enzymes for the different organosulfur compounds. Thus, desulfurization efficiency decreased with increasing initial DBT concentration, and in inverse proportion to increases in the carbon number of alkyl substituent groups.

Elevated c-di-GMP levels promote biofilm formation and biodesulfurization capacity of Rhodococcus erythropolis

Bacterial biofilms provide high cell density and a superior adaptation and protection from stress conditions compared to planktonic cultures, making them a very promising approach for bioremediation. Several Rhodococcus strains can desulfurize dibenzothiophene (DBT), a major sulphur pollutant in fuels, reducing air pollution from fuel combustion. Despite multiple efforts to increase Rhodococcus biodesulfurization activity, there is still an urgent need to develop better biocatalysts. Here, we implemented a new approach that consisted in promoting Rhodococcus erythropolis biofilm formation through the heterologous expression of a diguanylate cyclase that led to the synthesis of the biofilm trigger molecule cyclic di-GMP (c-di-GMP). R. erythropolis biofilm cells displayed a significantly increased DBT desulfurization activity when compared to their planktonic counterparts. The improved biocatalyst formed a biofilm both under batch and continuous flow conditions which turns it into a promising candidate for the development of an efficient bioreactor for the removal of sulphur heterocycles present in fossil fuels.

Investigations in enhancement biodesulfurization of model compounds by ultrasound pre-oxidation

In this study, complicated model sulfur compounds in crude oil were biodesulfurized in a batch process by microbial consortium enriched from oil contaminated soil. Dibenzothiophene (DBT) was selected as model sulfur compounds. Ultrasonic radiation was used to pre-oxidize the model sulfur compounds before the biodesulfurization (BDS) process. The enhancement mechanism of ultrasound pre-oxidation (UPO) on the biodesulfurization of DBT was investigated. The effects of initial conditions on the biodesulfurization of DBT in UPO/BDS system such as solution initial pH, DBT initial concentration, sulfur source, biocatalyst initial concentration, and incubation temperature were discussed. The results show that the application of UPO before BDS procedure significantly improved the efficiency of the biodesulfurization and allowed sulfur removal in shorter time through oxidizing DBT to DBT sulfone, resulting in shortening the "4S" pathway for biodesulfurization from 4 steps to 2 steps, enhancement in reaction velocity and enzyme-substrate affinity as well as reduction in substrate inhibition. The concentration of 2-HBP increased fast with the use of ultrasound pre-oxidation, which was dependent on solution initial pH, DBT initial concentration, sulfur source, biocatalyst initial concentration, and incubation temperature.

Metabolic and process engineering for biodesulfurization in Gram-negative bacteria

Microbial desulfurization or biodesulfurization (BDS) is an attractive low-cost and environmentally friendly complementary technology to the hydrotreating chemical process based on the potential of certain bacteria to specifically remove sulfur from S-heterocyclic compounds of crude fuels that are recalcitrant to the chemical treatments. The 4S or Dsz sulfur specific pathway for dibenzothiophene (DBT) and alkyl-substituted DBTs, widely used as model S-heterocyclic compounds, has been extensively studied at the physiological, biochemical and genetic levels mainly in Gram-positive bacteria. Nevertheless, several Gram-negative bacteria have been also used in BDS because they are endowed with some properties, e.g., broad metabolic versatility and easy genetic and genomic manipulation, that make them suitable chassis for systems metabolic engineering strategies. A high number of recombinant bacteria, many of which are Pseudomonas strains, have been constructed to overcome the major bottlenecks of the desulfurization process, i.e., expression of the dsz operon, activity of the Dsz enzymes, retro-inhibition of the Dsz pathway, availability of reducing power, uptake-secretion of substrate and intermediates, tolerance to organic solvents and metals, and other host-specific limitations. However, to attain a BDS process with industrial applicability, it is necessary to apply all the knowledge and advances achieved at the genetic and metabolic levels to the process engineering level, i.e., kinetic modelling, scale-up of biphasic systems, enhancing mass transfer rates, biocatalyst separation, etc. The production of high-added value products derived from the organosulfur material present in oil can be regarded also as an economically viable process that has barely begun to be explored.

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.

Effect of electrokinetics on biodesulfurization of the model oil by Rhodococcus erythropolis PTCC1767 and Bacillus subtilis DSMZ 3256

Biodesulfurization of the model oil using Rhodococcus erythropolis PTCC1767 (R. erythropolis) and Bacillus subtilis DSMZ 3256 (B. subtilis) strains assisted by applying electrokinetic was investigated as a novel method for desulfurization. The yield of biodesulfurization is low because it takes long time to be completed. Electrokinetic reduces the process time and accelerates degradation of the sulfur compounds. A mixture of normal hexadecane with 10mM dibenzotiophene (DBT) was employed as the model oil. The biodesulfurization experiments were initially performed. The results represented 34% and 62% DBT conversions after 1 and 6 days by R. erythropolis and the biodesulfurization yields were 11% and 36%, respectively. However, the DBT conversions for B. subtilis strain after 1 and 6 days were 31% and 55% and the biodesulfurization yields were 9% and 31%, respectively. The electrokinetic biodesulfurization experiments were studied at different current densities and the optimum current density was selected. According to the results, DBT conversion and biodesulfurization yield for R. erythropolis after 3 days were 76% and 39%, respectively, at the current density of 7.5 mA/cm(2). At the same conditions, the DBT conversion and biodesulfurization yield for B. subtilis were 71% and 37%, respectively. The experimental results indicate that the electrokinetic significantly reduces the biodesulfurization time. The combination of electrokinetic and biodesulfurization has the potential to obtain 'zero sulfur' products.

Biodesulfurization of model compounds and de-asphalted bunker oil by mixed culture

In this study, complicated model sulfur compounds in bunker oil and de-asphalted bunker oil were biodesulfurized in a batch process by microbial consortium enriched from oil sludge. Dibenzothiophene (DBT) and benzo[b]naphtho[1,2-d]thiophene (BNT1) were selected as model sulfur compounds. The results show that the mixed culture was able to grow by utilizing DBT and BNT1 as the sole sulfur source, while the cell density was higher using DBT than BNT1 as the sulfur source. GC-MS analysis of their desulfurized metabolites indicates that both DBT and BNT1 could be desulfurized through the sulfur-specific degradation pathway with the selective cleavage of carbon-sulfur bonds. When DBT and BNT1 coexisted, the biodesulfurization efficiency of BNT1 decreased significantly as the DBT concentrations increased (>0.1 mmol/L). BNT1 desulfurization efficiency also decreased along with the increase of 2-hydroxybiphenyl as the end product of DBT desulfurization. For real bunker oil, only 2.8 % of sulfur was removed without de-asphalting after 7 days of biotreatment. After de-asphalting, the biodesulfurization efficiency was significantly improved (26.2-36.5 %), which is mainly attributed to fully mixing of the oil and water due to the decreased viscosity of bunker oil.

Reconstruction of a genome-scale metabolic network of Rhodococcus erythropolis for desulfurization studies

The remarkable catabolic diversity of Rhodococcus erythropolis makes it an interesting organism for bioremediation and fuel desulfurization. However, a model that can describe and explain the combined influence of various intracellular metabolic activities on its desulfurizing capabilities is missing from the literature. Such a model can greatly aid the development of R. erythropolis as an effective desulfurizing biocatalyst. This work reports the reconstruction of the first genome-scale metabolic model for R. erythropolis using the available genomic, experimental, and biochemical information. We have validated our in silico model by successfully predicting cell growth results and explaining several experimental observations in the literature on biodesulfurization using dibenzothiophene. We report several in silico experiments and flux balance analyses to propose minimal media, determine gene and reaction essentiality, and compare effectiveness of carbon, nitrogen, and sulfur sources. We demonstrate the usefulness of our model by studying a few in silico mutants of R. erythropolis for improved biodesulfurization, and comparing the desulfurization abilities of R. erythropolis with an in silico mutant of E. coli.

C-S targeted biodegradation of dibenzothiophene by Stenotrophomonas sp. NISOC-04

Crude oil-contaminated soil samples were gathered across Khuzestan oilfields (National Iranian South Oil Company, NISOC) consequently experienced a screening procedure for isolating C-S targeted dibenzothiophene-biodegrading microorganisms with previously optimized techniques. Among the isolates, a bacterial strain was selected due to its capability of biodegrading dibenzothiophene in a C-S targeted manner in aqueous phases and medium mostly consisting of separately biphasic water-gasoline. The 16S rDNA of the isolate was amplified using eubacterial-specific primers and then sequenced. Based on sequence data analysis, the microorganism, designated NISOC-04, clustered most closely with the members of the genus Stenotrophomonas. Gas chromatography indicated that Stenotrophomonas sp. NISOC-04 utilizes 82% of starting 0.8 mM dibenzothiophene within a 48-h-long exponential growth phase. Growth curve analysis revealed the inability of Stenotrophomonas sp. NISOC-04 to utilize dibenzothiophene (DBT) as the exclusive carbon or carbon/sulfur source. Gibbs' assay showed no 2-hydroxy biphenyl accumulation, but HPLC confirmed the presence of 2-hydroxy biphenyl as the final product of DBT desulfurization. Under sulfur starvation, Stenotrophomonas sp. NISOC-04 produced a huge biomass with untraceable sulfur and utilized atmospheric insignificant sulfur levels.

Elucidation of 2-hydroxybiphenyl effect on dibenzothiophene desulfurization by Microbacterium sp. strain ZD-M2

The effect of 2-hydroxybiphenyl (2-HBP), the end product of dibenzothiophene (DBT) desulfurization via 4S pathway, on cell growth and desulfurization activity was investigated by Microbacterium sp. The experimental results indicate that 2-HBP would inhibit the desulfurization activity. Providing 2-HBP was added in the reaction media, the DBT degradation rate decreased along with the increase of 2-HBP addition. By contrast, cell growth would be promoted in the addition of 2-HBP at a low concentration (<0.1mM). At high concentration of 2-HBP, the inhibition on the cell growth occurred. Meanwhile, the inhibitory effect of 2-HBP on DBT desulfurization activity was tested both in the oil/aqueous two-phase system and the aqueous system. A mathematical model was developed to explain the product formation kinetics with DBT as the sole sulfur source. The predicted results were close to the experimental data, it elucidated that along with the 2-HBP accumulation, the inhibitory effect of 2-HBP on DBT desulfurization and cell growth was enhanced.

Biodesulfurization of dibenzothiophene by growing cells of Pseudomonas putida CECT 5279 in biphasic media

Several studies have proven that natural or genetically modified bacteria, such as Pseudomonas putida strain, degrade recalcitrant organic sulfur compounds. However, from a practical point of view, the biodesulfurization (BDS) process has to be performed with really high proportions of organic solvents. In this work, the dibenzothiophene (DBT) was selected as recalcitrant model compound, and hexadecane as model organic solvent. It has been observed that P. putida CECT 5279 was able to desulfurize DBT even in the presence of 50% (v/v) of hexadecane. A concentration of 400 ppm of DBT was converted at a specific rate of generation of desulfurized final product, 2-hydroxybiphenyl (HBP), of 2.3 and 1.5 mg HBP L-1 (g DC L-1 h)-1 for 27% and 50% (v/v) of hexadecane, respectively. Finally, the Haldane kinetic model was used to describe the process evolution. The study is relevant as it has been proven that the strain CECT 5279 is a potential biocatalyst for developing an efficient BDS process.

Dimethyl sulfoxide (DMSO) as the sulfur source for the production of desulfurizing resting cells of Gordonia alkanivorans RIPI90A

The sulfate repression of desulfurization (Dsz) phenotype represents a major barrier to the mass production of desulfurizing resting cells. This repression can be avoided by replacing sulfate with dibenzothiophene (DBT) as the main substrate for the 4S pathway. However, mass production of biocatalyst using DBT is impractical because of its high price, low water solubility, and growth inhibition by 2-hydroxybiphenyl (2-HBP), which is the end product of the 4S pathway. In this work, the results showed that readily bioavailable sulfur compounds led to repression of the desulfurization activity of Gordonia alkanivorans RIPI90A. However, the Dsz phenotype was expressed through the 4S pathway in the presence of DMSO as the sulfur source for growth. Resting cells grown on DMSO were more active than the resting cells grown on DBT. The growth rate of strain RIPI90A on DMSO was higher than when DBT was used as the sole sulfur source. DMSO concentration significantly influenced the growth pattern of the strain, and the highest growth rate was observed at a concentration of 200 microg ml(-1). Above this concentration, the growth rate gradually decreased. DBT was found to induce the Dsz phenotype, with no observed lag period, in cells grown on DMSO as the sole sulfur source. Prior to induction, the specific activity was detected as 1.4 micromol 2-HBP (g dry cell weight)(-1) h(-1), and following incubation (5 h) the highest specific activity was observed as 5.11 micromol 2-HBP (g dry cell weight)(-1 )h(-1). This study identified that resting cells can be prepared in a two-step process. First, resting cells can be produced using DMSO as the sulfur source for growth; in the second step, improvements to their desulfurizing activity can be made using DBT as an inducer. DMSO is recommended as an appropriate sulfur source for the mass production of G. alkanivorans RIPI90A.