Kinetic analysis of microbial desulfurization of model and light gas oils containing multiple alkyl dibenzothiophenes

Mapping the knowledge domain of microbial desulfurization application in fuels and ores for sustainable industry

Direct application of high-sulfur fuels and ores can cause environmental pollution (such as air pollution and acid rain) and, in serious cases, endanger human health and contribute to property damage. In the background of preserving the environment, microbial desulfurization technologies for high-sulfur fuels and ores are rapidly developed. This paper aims to reveal the progress of microbial desulfurization research on fuels and ores using bibliometric analysis. 910 publications on microbial desulfurization of fuels and ores from web core databases were collected in this work, spanning 39 years. Through 910 retrieved documents, collaborative networks of authors, institutions and countries were mapped by this work, the sources of highly cited articles and cited documents were statistically analyzed, and keyword development from different perspectives was discussed. The results of the study provide a reference for microbial desulfurization research and benefit environmental protection and energy green applications.

Bacterial Biological Factories Intended for the Desulfurization of Petroleum Products in Refineries

The removal of sulfur by deep hydrodesulfurization is expensive and environmentally unfriendly. Additionally, sulfur is not separated completely from heterocyclic poly-aromatic compounds. In nature, several microorganisms (Rhodococcus erythropolis IGTS8, Gordonia sp., Bacillus sp., Mycobacterium sp., Paenibacillus sp. A11-2 etc.) have been reported to remove sulfur from petroleum fractions. All these microbes remove sulfur from recalcitrant organosulfur compounds via the 4S pathway, showing potential for some organosulfur compounds only. Activity up to 100 µM/g dry cell weights is needed to meet the current demand for desulfurization. The present review describes the desulfurization capability of various microorganisms acting on several kinds of sulfur sources. Genetic engineering approaches on Gordonia sp. and other species have revealed a variety of good substrate ranges of desulfurization, both for aliphatic and aromatic organosulfur compounds. Whole genome sequence analysis and 4S pathway inhibition by a pTeR group inhibitor have also been discussed. Now, emphasis is being placed on how to commercialize the microbes for industrial-level applications by incorporating biodesulfurization into hydrodesulfurization systems. Thus, this review summarizes the potentialities of microbes for desulfurization of petroleum. The information included in this review could be useful for researchers as well as the economical commercialization of bacteria in petroleum industries.

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.

Biodesulfurization of refractory sulfur compounds in petro-diesel by a novel hydrocarbon tolerable strain Paenibacillus glucanolyticus HN4

One of the main precursors of air pollution and acid rains is the presence of the recalcitrant thiophenic compounds, for example dibenzothiophene (DBT) and its derivatives in transportation fuels. In an attempt to achieve the worldwide regulations of ultra-low sulfur transportation fuels without affecting its hydrocarbon skeleton, a biphasic medium containing 100 mg/L DBT dissolved in n-hexadecane (1/4 oil/water v/v) used for enrichment and isolation of selective biodesulfurizing bacterium from an oil-polluted sediment sample collected from Egyptian Red Sea shoreline. The isolated bacterium is facultative anaerobe, motile, spore-former, and mesophile. It is genetically identified as Paenibacillus glucanolyticus strain HN4 (NCBI Gene Bank Accession No. MT645230). HN4 desulfurized DBT as a model of the recalcitrant thiophenic compounds without affecting its hydrocarbon skeleton via the 4S-pathway producing 2-hydroxybiphenyl (2-HBP) as a dead end product. HN4 substantiated to be a hydrocarbon tolerant, biosurfactants(s) producer, and endorsed unique enzymatic system capable of desulfurizing broad range of thiophenic compounds and expressed an efficient desulfurization activity against the recalcitrant alkylated DBTs. As far our knowledge, it is the first reported BDS study using P. glucanolyticus. Statistical optimization based on One-Factor-At-A-Time (OFAT) technique and response surface methodology (RSM) applied for elucidation of mathematical model correlations describing and optimizing the effect of different physicochemical parameters on batch biphasic BDS process. That illustrated an approximate increase in BDS efficiency by 1.34 fold and recorded 94% sulfur removal in biphasic batch process at optimum operation conditions of 120 h, 0.14 wt% S-content model oil (DBT dissolved in n-hexadecane), 33.5 °C, pH7 and 1/1 oil/water phase ratio, and 147 rpm. Resting cells of HN4 in a biphasic reactor (1/1 v/v) decreased the sulfur content of a refractory thiophenic model oil (thiophene, benzothiophene, DBT, and alkylated DBT dissolved in n-hexadecane) from 0.14 to 0.027 wt%, and petro-diesel from 0.2 to 0.04 wt%, within 120 h, keeping the calorific value of the treated fuel intact. Consequently, that novel strain could be recommended as a promising candidate for BDS as complementary to hydrodesulfurization process in oil refinery.

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.

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.

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.

A novel Bacillus pumilus-related strain from tropical landfarm soil is capable of rapid dibenzothiophene degradation and biodesulfurization

BACKGROUND

The presence of organic sulfur-containing compounds in the environment is harmful to animals and human health. The combustion of these compounds in fossil fuels tends to release sulfur dioxide in the atmosphere, which leads to acid rain, corrosion, damage to crops, and an array of other problems. The process of biodesulfurization rationally exploits the ability of certain microorganisms in the removal of sulfur prior to fuel burning, without loss of calorific value. In this sense, we hypothesized that bacterial isolates from tropical landfarm soils can demonstrate the ability to degrade dibenzothiophene (DBT), the major sulfur-containing compound present in fuels.

RESULTS

Nine bacterial isolates previously obtained from a tropical landfarm soil were tested for their ability to degrade dibenzothiophene (DBT). An isolate labeled as RR-3 has shown the best performance and was further characterized in the present study. Based on physiological aspects and 16 s rDNA sequencing, this isolate was found to be very closely related to the Bacillus pumillus species. During its growth, high levels of DBT were removed in the first 24 hours, and a rapid DBT degradation within the first hour of incubation was observed when resting cells were used. Detection of 2-hydroxybiphenyl (HBP), a marker for the 4S pathway, suggests this strain has metabolical capability for DBT desulfurization. The presence of MgSO4 in growth medium as an additional sulfur source has interfered with DBT degradation.

CONCLUSIONS

To our knowledge, this is the first study showing that a Bacillus strain can metabolize DBT via the 4S pathway. However, further evidences suggest RR-3 can also use DBT (and/or its derivative metabolites) as carbon/sulfur source through another type of metabolism. Compared to other reported DBT-degrading strains, the RR-3 isolate showed the highest capacity for DBT degradation ever described in quantitative terms. The potential application of this isolate for the biodesulfurization of this sulfur-containing compound in fuels prior to combustion was discussed.

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.

Rate-limiting step analysis of the microbial desulfurization of dibenzothiophene in a model oil system

A mechanistic analysis of the various mass transport and kinetic steps in the microbial desulfurization of dibenzothiophene (DBT) by Rhodococcus erythropolis IGTS8 in a model biphasic (oil-water), small-scale system was performed. The biocatalyst was distributed into three populations, free cells in the aqueous phase, cell aggregates and oil-adhered cells, and the fraction of cells in each population was measured. The power input per volume (P/V) and the impeller tip speed (vtip ) were identified as key operating parameters in determining whether the system is mass transport controlled or kinetically controlled. Oil-water DBT mass transport was found to not be limiting under the conditions tested. Experimental results at both the 100 mL and 4 L (bioreactor) scales suggest that agitation leading to P/V greater than 10,000 W/ m(3) and/or vtip greater than 0.67 m/s is sufficient to overcome the major mass transport limitation in the system, which was the diffusion of DBT within the biocatalyst aggregates.

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.

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 alkylated forms of dibenzothiophene and benzothiophene by Sphingomonas subarctica T7b

Sphingomonas subarctica T7b was isolated from soil in Toyotomi, Hokkaido, Japan as an organism capable of desulfurizing aromatic hydrocarbons in light gas oil (LGO) through enrichment culture. S. subarctica T7b could grow on mineral salt sulfur-free (MSSF) medium with the n-tetradecane oil phase containing dibenzothiophene (DBT), alkyl dibenzothiophenes (alkyl DBTs) or alkyl benzothiophenes (alkyl BTs) as the sole sulfur source and desulfurize these compounds, but could not utilize the tetradecane as a carbon source. This is the first report of a gram-negative bacterium which can desulfurize 4,6-dibutyl DBT and 4,6-dipentyl DBT. The desulfurized product of DBT produced by this strain was 2-hydroxybiphenyl, as in the case of other DBT-desulfurizing bacteria. S. subarctica T7b could desulfurize LGO and the sulfur content was decreased to 41% within 36 h.

Isolation of a recombinant desulfurizing 4,6-diproply dibenzothiophene in n-tetradecane

Rhodococcus erythropolis strain KA2-5-1 is unable to desulfurize 4,6-dipropyl dibenzothiophene (DBT) in the oil phase. The dsz desulfurization gene cluster from R. erythropolis strain KA2-5-1 was transferred into 22 rhodococcal and mycobacterial strains using a transposon-transposase complex. The recombinant strain MR65, from Mycobacterium sp. NCIMB10403, was able to grow on a minimal medium supplemented with 1.0 mM 4,6-dipropyl DBT in n-tetradecane (50%, v v ) as the sole sulfur source. Resting cells of recombinant strain MR65 could desulfurize 68 mg l- of sulfur in light gas oil (LGO) containing 126 mg sulfur l-. Strain MR65 had about 1.5-times the LGO desulfurization activity of R. erythropolis strain KA2-5-1. The application of a recombinant, which is able to utilize 4,6-dipropyl DBT in the oil phase, was effective in enhancing LGO biodesulfurization.

Biodesulfurization using Pseudomonas delafieldii in magnetic polyvinyl alcohol beads

AIMS

To immobilize Pseudomonas delafieldii R-8 cells in magnetic polyvinyl alcohol (PVA) beads for biodesulfurization.

METHODS AND RESULTS

Magnetic PVA beads were prepared by a freezing-thawing technique under liquid nitrogen. The beads have distinct super-paramagnetic properties and their saturation magnetization is 8.02 emu g(-1). The desulfurization rate of the immobilized cells could reach 40.2 mmol kg(-1) h(-1). Desulfurization patterns of dibenzothiophene in model oil with the immobilized and free cells were represented by the Michaelis-Menten equation. The Michaelis constant for both immobilized and free cells was 1.3 mmol l(-1).

CONCLUSIONS

The cells immobilized in magnetic PVA beads could be stably stored and be repeatedly used over 12 times for biodesulfurization. The immobilized cells could be easily separated by magnetic field.

SIGNIFICANCE AND IMPACT OF THE STUDY

Magnetic PVA beads are easy to prepare. The immobilization process in the paper is to increase the efficiency of cells and to decrease the cost of operations.

Can whole genome analysis refine the taxonomy of the genus Rhodococcus?

The current systematics of the genus Rhodococcus is unclear, partly because many members were originally included before the application of a polyphasic taxonomic approach, central to which is the acquisition of 16S rRNA sequence data. This has resulted in the reclassification and description of many new species. Hence, the literature is replete with new species names that have not been brought together in an organized and easily interpreted form. This taxonomic confusion has been compounded by assigning many xenobiotic degrading isolates with phylogenetic positions but without formal taxonomic descriptions. In order to provide a framework for a taxonomic approach based on multiple genetic loci, a survey was undertaken of the known genome characteristics of members of the genus Rhodococcus including: (i) genetics of cell envelope biosynthesis; (ii) virulence genes; (iii) gene clusters involved in metabolic degradation and industrially relevant pathways; (iv) genetic analysis tools; (v) rapid identification of bacteria including rhodococci with specific gene RFLPs; (vi) genomic organization of rrn operons. Genes encoding virulence factors have been characterized for Rhodococcus equi and Rhodococcus fascians. Based on peptide signature comparisons deduced from gene sequences for cytochrome P-450, mono- and dioxygenases, alkane degradation, nitrile metabolism, proteasomes and desulfurization, phylogenetic relationships can be deduced for Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus ruber and a number of undesignated Rhodococcus spp. that may distinguish the genus Rhodococcus into two further genera. The linear genome topologies that exist in some Rhodococcus species may alter a previously proposed model for the analysis of genomic fingerprinting techniques used in bacterial systematics.

Analyses of microbial desulfurization reaction of alkylated dibenzothiophenes dissolved in oil phase

The kinetics of the oil/water two-phase reaction system was analyzed, and the reaction was carried out with the desulfurization of alkylated dibenzothiophenes (Cx-DBTs) using the desulfurizing microorganism Mycobacterium sp. G3. In the water-phase reaction system, the desulfurization activities were constant with respect to species of Cx-DBTs as substrates. However, the desulfurization activities in the oil/water two-phase reaction system against DBT, 4,6-dimethyl DBT, 4,6-diethyl DBT, 4,6-dipropyl DBT, and 4,6-dibutyl DBT were 49.0, 45.9, 11.5, 1.35, and 0.00 micromol g DCW(-1) h(-1), respectively. The kinetic parameters for the degradation of DBT, 4,6-dimethyl DBT, and 4,6-diethyl DBT were also obtained (V(max) values 90.0, 68.7, and 22.7 micromol g DCW(-1) h(-1) and K(m) values 0.21, 0.70, and 3.03 mM, respectively). The reason for the decrease in activity against Cx-DBTs of high molecular weight was a decrease in the V(max) value and an increase in the K(m) value, the latter being a particularly serious problem. Furthermore, the hydrophobicity of the substrate was evaluated as the capacity factor measured by high-performance liquid chromatography (HPLC). The correlation between substrate hydrophobicity and desulfurization activity indicated that the desulfurization reaction in the oil/water two-phase reaction system is greatly influenced by the hydrophobicity of the substrates. In addition, the influence of the solvent on desulfurization activity was examined, and it was found that not only the hydrophobicity of substrates, but also that of solvents, affected the desulfurization reaction.

Chemostat approach for the directed evolution of biodesulfurization gain-of-function mutants

Chemostat enrichment is a classical microbiological method that is well suited for use in directed-evolution strategies. We used a two-phase sulfur-limited chemostat to select for gain-of-function mutants with mutations in the biodesulfurization (Dsz) system of Rhodococcus erythropolis IGTS8, enriching for growth in the presence of organosulfur compounds that could not support growth of the wild-type strain. Mutations arose that allowed growth with octyl sulfide and 5-methylbenzothiophene as sole sulfur sources. An isolate from the evolved chemostat population was genetically characterized and found to contain mutations in two genes, dszA and dszC. A transversion (G to T) in dszC codon 261 resulted in a V261F mutation that was determined to be responsible for the 5-methylbenzothiophene gain-of-function phenotype. By using a modified RACHITT (random chimeragenesis on transient templates) method, mutant DszC proteins containing all possible amino acids at that position were generated, and this mutant set was assayed for the ability to metabolize 5-methylbenzothiophene, alkyl thiophenes, and dibenzothiophene. No mutant with further improvements in these catalytic activities was identified, but several clones lost all activity, confirming the importance of codon 261 for enzyme activity.