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

Searching for bacteria able to metabolize polycyclic aromatic sulfur compounds in 12-years periodically fed bioreactor

Biodesulfurization is a promising alternative for removing sulfur molecules from the polycyclic aromatic sulfur compounds (PASC) found in petroleum. PASC consists of recalcitrant molecules that can degrade fuel quality and cause a range of health and environmental problems. Therefore, identifying bacteria capable of degrading PASC is essential for handling these recalcitrant molecules. Microorganisms in environments exposed to petroleum derivatives have evolved specific enzymatic machinery, such as the 4S pathway associated with the dszABC genes, which are directly linked to sulfur removal and utilization as nutrient sources in the biodesulfurization process. In this study, bacteria were isolated from a bioreactor containing landfarm soil that had been periodically fed with petroleum for 12 years, using a medium containing dibenzothiophene (DBT), 4.6-dimethylbenzothiophene, 4-methylbenzothiophene, or benzothiophene. This study aimed to identify microorganisms capable of degrading PASC in such environments. Among the 20 colonies isolated from an inoculum containing DBT as the sole sulfur source, only four isolates exhibited amplification of the dszA gene in the dszABC operon. The production of 2-hydroxybiphenyl (HPB) and a decrease in DBT were detected during the growth curve and resting cell assays. The isolates were identified using 16S rRNA sequencing belonging to the genera Stutzerimonas and Pseudomonas. These isolates demonstrated significant potential for biodesulfurization and/or degradation of PASC. All isolates possessed the potential to be utilized in the biotechnological processes of biodesulfurization and degradation of recalcitrant PASC molecules.

Comparative Genomic Analysis of the Hydrocarbon-Oxidizing Dibenzothiophene-Desulfurizing Gordonia Strains

A number of actinobacteria of the genus Gordonia are able to use dibenzothiophene (DBT) and its derivatives as the only source of sulfur, which makes them promising agents for the process of oil biodesulfurization. Actinobacteria assimilate sulfur from condensed thiophenes without breaking the carbon-carbon bonds, using the 4S pathway encoded by the dszABC operon-like structure. The genome of the new dibenzothiophene-degrading hydrocarbon-oxidizing bacterial strain Gordonia amicalis 6-1 was completely sequenced and the genes potentially involved in the pathways of DBT desulfurization, oxidation of alkanes and aromatic compounds, as well as in the osmoprotectant metabolism in strain 6-1 and other members of the genus Gordonia, were analyzed. The genome of G. amicalis strain 6-1 consists of a 5,105,798-bp circular chromosome (67.3% GC content) and an 86,621-bp circular plasmid, pCP86 (65.4% GC content). This paper presents a comparative bioinformatic analysis of complete genomes of strain 6-1 and dibenzothiophene-degrading Gordonia strains 1D and 135 that do not have the dsz operon. The assumption is made about the participation in this process of the region containing the sfnB gene. Genomic analysis supported the results of phenomenological studies of Gordonia strains and the possibility of their application in the bioremediation of oil-contaminated environments and in the purification of oil equipment from oil and asphalt-resin-paraffin deposits.

Enhancing biodesulfurization by engineering a synthetic dibenzothiophene mineralization pathway

A synthetic dibenzothiophene (DBT) mineralization pathway has been engineered in recombinant cells of Pseudomonas azelaica Aramco J strain for its use in biodesulfurization of thiophenic compounds and crude oil. This functional pathway consists of a combination of a recombinant 4S pathway responsible for the conversion of DBT into 2-hydroxybiphenyl (2HBP) and a 2HBP mineralization pathway that is naturally present in the parental P. azelaica Aramco J strain. This novel approach allows overcoming one of the major bottlenecks of the biodesulfurization process, i.e., the feedback inhibitory effect of 2HBP on the 4S pathway enzymes. Resting cells-based biodesulfurization assays using DBT as a sulfur source showed that the 2HBP generated from the 4S pathway is subsequently metabolized by the cell, yielding an increase of 100% in DBT removal with respect to previously optimized Pseudomonas putida biodesulfurizing strains. Moreover, the recombinant P. azelaica Aramco J strain was able to use DBT as a carbon source, representing the best characterized biocatalyst harboring a DBT mineralization pathway and constituting a suitable candidate to develop future bioremediation/bioconversion strategies for oil-contaminated sites.

Characterization and genomic analysis of Gordonia alkanivorans 135, a promising dibenzothiophene-degrading strain

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Strain 135 is first dibenzothiophene-degrading Gordonia with genome fully assembled.

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This is the first strain of Gordonia absorbing thiophene sulfur without dsz genes.

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The strain utilized 45.26 % of dibenzothiophene within 150 h of growth at 26 °C.

Sulfur is the third most abundant element in crude oil. Up to 70 % of sulfur in petroleum is found in the form of dibenzothiophene (DBT) and substituted DBTs. The aim of this work was to study the physiological, biochemical and genetical characteristics of Gordonia alkanivorans 135 capable of using DBT as the sole source of sulfur. The genome of G. alkanivorans 135 consists of a 5,039,827 bp chromosome and a 164,963 bp circular plasmid. We found the absence of dsz operon present in most DBT degrading bacteria, but discovered other genes that are presumably involved in DBT utilization by G. alkanivorans 135. The strain utilized 45.26 % of DBT within 150 h of growth at 26 °C. This is the first strain of Gordonia capable of absorbing thiophene sulfur without the aid of the dsz genes.

Enhanced Production of Biosurfactant from Bacillus subtilis Strain Al-Dhabi-130 under Solid-State Fermentation Using Date Molasses from Saudi Arabia for Bioremediation of Crude-Oil-Contaminated Soils

Crude oil and its derivatives are the most important pollutants in natural environments. Bioremediation of crude oil using bacteria has emerged as a green cleanup approach in recent years. In this study, biosurfactant-producing Bacillus subtilis strain Al-Dhabi-130 was isolated from the marine soil sediment. This organism was cultured in solid-state fermentation using agro-residues to produce cost-effective biosurfactants for the bioremediation of crude-oil contaminated environments. Date molasses improved biosurfactant production and were used for further optimization studies. The traditional “one-variable-at-a-time approach”, “two-level full factorial designs”, and a response surface methodology were used to optimize the concentrations of date molasses and nutrient supplements for surfactant production. The optimum bioprocess conditions were 79.3% (v/w) moisture, 34 h incubation period, and 8.3% (v/v) glucose in date molasses. To validate the quadratic model, the production of biosurfactant was performed in triplicate experiments, with yields of 74 mg/g substrate. These findings support the applications of date molasses for the production of biosurfactants by B. subtilis strain Al-Dhabi-130. Analytical experiments revealed that the bacterial strain degraded various aromatic hydrocarbons and n-alkanes within two weeks of culture with 1% crude oil. The crude biosurfactant produced by the B. subtilis strain Al-Dhabi-130 desorbed 89% of applied crude oil from the soil sample. To conclude, biosurfactant-producing bacterial strains can increase emulsification of crude oil and support the degradation of crude oil.

Biosurfactant production and hydrocarbon degradation activity of endophytic bacteria isolated from Chelidonium majus L

Background

The process of plant growth in the contaminated environment is often inhibited and entails the neutralization of harmful compounds. To reduce the negative impact of harmful compounds microorganisms produce unique compounds called biosurfactants. This paper describes the potential of culturable endophytic microorganisms from synanthropic plant-Chelidonium majus L. for the production of biosurfactants, as indirect plant promoting factors as well as their degradation activity. Emulsifying activity and degradation potential of tested strains were assessed by cultivation of isolates in the presence of diesel oil and waste engine oil.

Results

Ten bacterial strain were isolated. Analysis of emulsifying activity revealed that all isolates possessed the ability for biosurfactant production. However, one of the isolated endophytes—2A, identified as Bacillus pumilus, exhibited the highest emulsifying activity (OD₅₀₀ 1.96). The same strain has shown very high degradation potential, both for diesel oil and waste engine oil hydrocarbons. Results obtained with the Phytotoxkit tests revealed that the addition of biosurfactant isolated from B. pumilus 2A strain resulted in stimulation of seed germination in soil contaminated with diesel oil (137%) and waste engine oil (120%). Positive impact of the biosurfactant produced by B. pumilus 2A on the growth of Sinapis alba in hydrocarbons contaminated soil was demonstrated.

Conclusions

The endophytic strain identified as Bacillus pumilus 2A produce biosurfactant that is able to act as plant-growth promoting agent. Endophytic bacteria isolated from Chelidonium majus L. exhibit potential for hydrocarbons degradation and biosurfactant production. These properties provide promising perspectives for application of biosurfactants as potential agents for bioremediation of environment contaminated with hydrocarbons.

Differential desulfurization of dibenzothiophene by newly identified MTCC strains: Influence of Operon Array

Since the sulfur specific cleavage is vital for the organic sulfur removal from fossil fuel, we explored potential bacterial strains of MTCC (Microbial Type Culture Collection) to desulfurize the Dibenzothiophene (DBT) through C-S bond cleavage (4-S pathway). MTCC strains Rhodococcus rhodochrous (3552), Arthrobacter sulfureus (3332), Gordonia rubropertincta (289), and Rhodococcus erythropolis (3951) capable of growing in 0.5 mM DBT were examined for their desulfurization ability. The presence of dsz genes as well as the metabolites was screened by polymerase chain reaction (PCR) and HPLC, respectively. All these strains showed > 99% DBT desulfurization with 10 days of incubation in minimal salt medium. From the HPLC analysis it was further revealed that these MTCC strains show differences in the end metabolites and desulfurize DBT differently following a variation in the regular 4-S pathway. These findings are also well corroborating with their respective organization of dszABC operons and their relative abundance. The above MTCC strains are capable of desulfurizing DBT efficiently and hence can be explored for biodesulfurization of petrochemicals and coal with an eco-friendly and energy economical process.