Genome-based characterization and pathway elucidation of dibenzothiophene and 4-methyldibenzothiophene desulfurization in a thiophenic compound desulfurizing Rhodococcus sp. SB1D.

Microorganisms can metabolize or transform a range of known chemical compounds present in fossil fuels by naturally having highly specific metabolic activities. In this context, the microbial desulfurization of fuels is an attractive and alternative process to the conventional hydrodesulfurization (HDS) process, since the thiophenic sulfur containing compounds such as dibenzothiophene (DBT) and benzothiophene (BT) cannot be removed by HDS. A DBT desulfurizing mesophilic bacterium, identified on the basis of 16S rRNA gene sequence as Gordonia sp. HS126-4N (source: periphery soil of a coal heap) has been evaluated for its biodesulfurization traits and potential to desulfurize the thiophenic compounds. The HPLC and LC/MS analyses of the metabolites produced from DBT desulfurization and PCR-based nucleotide sequence confirmation of the key desulfurizing genes (dszA/dszB/dszC) proved that HS126-4N could convert DBT to 2-hydroxybiphenyl (2-HBP) via the 4S pathway. The isolate could convert 0.2mM of DBT to 2-HBP within 48h and was reasonably tolerant against the inhibitory effect of 2-HBP (retained 70% of growth at 0.5mM 2-HBP). The isolated biocatalyst desulfurized/degraded 100% of 0.2mM of 4-methyl DBT, 2,8-dimethyl DBT, BT and 3-methyl BT within 108h. The capabilities to survive and desulfurize a broad range of thiophenic sulfur containing substrates as well as less inhibition by the 2-HBP suggest that HS126-4N could be a potential candidate for improved biodesulfurization/organic sulfur removal from fossil fuels.

Adsorption of sulfur compoundsby porous materials is an effective way to produce cleaner diesel fuel.In this study, adsorption of refractory thiophenic sulfur compounds, i.e., benzothiophene (BT), dibenzothiophene (DBT), and 4,6-dimethyldibenzothiophene (4,6-DMDBT) in single-solute systems from n-hexane solutions onto metal-impregnated activated carbons was investigated. A hydrogen-treated activated carbon fiber was selectively loaded with Ni, NiO, Cu, Cu2O, and CuO species to systematically assess the impact of each metal species on the adsorption of thiophenic compounds (TC). Metal-loaded adsorbents had the same total metal contents and similar microporosities, but contained different types of copper or nickel species. All metal-loaded adsorbents showed enhanced adsorption of tested TC. Cu2O- or NiO-loaded adsorbents exhibited the highest uptakes, due to more specific interactions between Cu+ or Ni2+ species and TC molecules. The theoretical monolyer coverage of TC on the exposed Cu+ sites was estimated and compared with that calculated from the experimental data. Results suggested catalytic conversion of TC molecules to other compounds on the Cu+ sites, followed by adsorption of reaction products onto the carbon surface or multilayer accumulation of TC molecules on the Cu+sites. TC adsorption uptake of the majority of adsorbents followed the order of: 4,6-DMDBT > DBT > BT due to higher intensity of specific and non-specific interactions of larger TC molecules with adsorbents.

To deepen the understanding the interactions of thiophenic compounds in ionic liquids, we have performed a systemic study on the electronic structures, and topological properties of interactions between N-ethyl-N-ethylimidazolium diethyl phosphate ([EEIM][DEP]) ionic liquid and 3-methylthiophene (3-MT), benzothiophene (BT), or dibenzothiophene (DBT) using density functional theory. From NBO atomic charges and electrostatic potential analyses, most of the positive charge is located on C2–H2 in the [EEIM] cation, and the negative charge is focused on oxygen atoms in [DEP] anion, implying oxygen atoms in [DEP] should easily attack C2–H2 in [EEIM]. The electrostatic interaction between anion and cation may be dominant for the formation of the [EEIM]–[DEP] ion pair. The large stabilizing effect is due to the strong orbital interactions between the antibonding orbital of proton donor σ*(C2–H2) in [EEIM] cation and the lone pairs of proton acceptor LP(O) in [DEP] anion. A common feature of [EEIM][DEP], [EEIM][DEP]-3-MT/BT/DBT complexes is the presence of hydrogen bonds between [EEIM] cation and [DEP] anion. This work has also given the interacting mechanism of 3-MT, BT, and DBT adsorption on [EEIM][DEP] ionic liquid. Both [EEIM] cation and [DEP] anion are shown to play important roles in interactions between 3-MT, BT, DBT and [EEIM][DEP], which has been corroborated by NBO and AIM analyses. The π···π, π···C–H and hydrogen bonding interactions occur between [EEIM][DEP] and 3-MT, BT, DBT. The strength of sulfur involved interactions between 3-MT, BT, DBT and [EEIM][DEP] follows the order of 3-MT > BT > DBT. The order of interaction energies between [EEIM][DEP] and 3-MT, BT, DBT is 3-MT BT > 3-MT) in terms of sulfur partition coefficients.

Two-dimensional gas chromatography with sulfur chemiluminescence detection (GC × GC-SCD) is applied to understand the changes in alkylated thiophenes, benzothiophenes (BTs), and dibenzothiophenes (DBTs) during supercritical water (SCW) upgrading of Arabian Heavy crude oil. It is shown that SCW treatment of heavy crude oil has several important effects: (1) The amount of BTs and DBTs in the distillate range increase, primarily due to cracking of heavier compounds. (2) Most of the long side chains on the thiophenes, BTs, and DBTs crack to form the corresponding thiophenic compounds with shorter side chains. (3) A small amount of the alkylated thiophenes undergo ring closure to form BTs during SCW treatment, and a small amount of the alkylated BTs appear to form DBTs in a similar way. As reported earlier, SCW treatment removes some of the sulfur from the oil phase, presumably as hydrogen sulfide (H2S). Distilling the heavy crude oil into light and heavy fractions and treating these fractions individually wit...

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.

Deep-desulfurization of dibenzothiophene and its derivatives present in diesel oil by a newly isolated bacterium Achromobacter sp. to reduce the environmental pollution from fossil fuel combustion

Thiophenic compounds are the refractory organosulfur compounds remaining in the transportation fuels, and their removal from liquid fuels has become increasingly important. In this work, adsorption isotherms of thiophene (T), benzothiophene (BT), and dibenzothiophene (DBT) in isooctane onto a metal–organic framework (Cu-BTC) were measured for (293.15 to 313.15) K and equilibrium sulfur concentrations up to 370 ppmw-S (ppmw of sulfur). The adsorption capacity followed the order of BT < T < DBT under the investigated sulfur concentrations and temperatures. The adsorption isotherms of T and DBT are highly favorable. The isotherm data were well-correlated using a multitemperature Langmuir model, and three parameters were extracted for each thiophenic compound. The multitemperature Langmuir model has predictive ability for the adsorption of T, BT, and DBT within the sulfur concentration range and the temperature range studied. The heat of adsorption (ΔH) of T, BT, and DBT is (−21.99, −14.23, and −37.34) kJ·mol...

A Gram-stain-negative, light yellow pigmented, non-motile and aerobic bacterial strain, designated HHUE2-1T, was isolated from a surface seawater sample. The 16S rRNA gene sequence analysis indicated that HHUE2-1T shared the highest sequence similarity to the type strain Qipengyuania gaetbuli DSM 16225T (96.90%), which belongs to the family Erythrobacteraceae. Combined phylogeny of 288 single-copy orthologous gene clusters, analysis of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), average amino acid identity (AAI) and evolutionary distances suggested that HHUE2-1T can be considered as a member of the genus Altererythrobacter based on the recently proposed standard for defining genera of Erythrobacteraceae. Strain HHUE2-1T grew at 15-35°C and pH 5.0-8.0, with optimum growth at 28°C and pH 7.0. Tolerance to NaCl was up to 4% (w/v) with optimum growth in 2-3% NaCl. The major fatty acids (> 10%) were C18:1ω7c11-methyl, summed feature 3 (C16:1ω7c and/or C16:1ω6c), and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The predominant isoprenoid quinone was ubiquinone-10. The genomic G + C content was 57.40%. On the basis of the phenotypic, phylogenetic and chemotaxonomic characterizations, HHUE2-1T represents a novel species of the genus Altererythrobacter, for which the name Altererythrobacter flava sp. nov. is proposed. The type strain is HHUE2-1T (= CGMCC 1.17394T = KCTC 72835T = MCCC 1K04226T).

Effects of aromatics on desulfurization of liquid fuel by π-complexation and carbon adsorbents

The genus Gordonia is well known for its catabolic diversity and ability to transform several compounds including the various recalcitrant polyaromatic sulfur heterocycles (PASHs) found in the fossil fuels. In fact, some strains offer the unique ability to desulfurize even benzothiophene (BT) and other thiophenic compounds, which most of the commonly studied rhodococci strains cannot. In this work, we present the first genome scale metabolic model for G. alkanivorans, a desulfurizing strain, to enable a holistic study of its metabolism and comparison with R. erythropolis. Our model consists of 881 unique metabolites and 922 reactions associated with 568 ORFs/genes and 544 unique enzymes. It successfully predicts the growth rates from experimental studies and quantitatively elucidates the pathways for the desulfurization of the commonly studied sulfur compounds, namely dibenzothiophene (DBT) and benzothiophene (BT). Using our model, we identify the minimal media for G. alkanivorans, and show the significant effect of carbon sources on desulfurization with ethanol as the best source. Our model shows that the sulfur-containing amino acids such as cysteine and methionine decrease desulfurization activity, and G. alkanivorans prefers BT over DBT as a sulfur source. It also suggests that this preference may be driven by the lower NADH requirements for BT metabolism rather than the higher affinity of the transport system for BT. Our in silico comparison of R. erythropolis and G. alkanivorans suggests the latter to be a better desulfurizing strain due to its versatility for both BT and DBT, higher desulfurization activity, and higher growth rate.

A novel bacterium, Gordonia alkanivorans strain 1B, was isolated from hydrocarbon-contaminated soil. Assessment of the biodegradation of distinct organic sulfur-compounds, such as dibenzothiophene (DBT), benzothiophene (BT), DBT sulfone, and alkylated tiophenic compounds, as the sole source of sulfur was investigated. G. alkanivorans strain 1B was able to remove selectively the sulfur from DBT while keeping intact the remaining carbon-carbon structure. Orthophenyl phenol (2-hydroxybiphenyl) was the only detected metabolic product. The bacterial desulfurization activity was repressed by sulfate. G. alkanivorans strain 1B consumed 310 microM DBT after 120 h of cultivation, corresponding to a specific desulfurization rate of 1.03 micromol/(g of dry cells x h). When an equimolar mixture of DBT/BT was used as a source of sulfur in the growth medium, G. alkanivorans strain 1B assimilated both compounds in a sequential manner, with BT as the preferred source of sulfur. Only when BT concentration was decreased to a very low level was DBT utilized as the source of sulfur for bacterial growth. The specific desulfurization overall rates of BT and DBT obtained were 0.954 and 0.813 micromol/(g of dry cells x h), respectively. The newly isolated G. alkanivorans strain 1B has good potential for application in the biodesulfurization of fossil fuels.

The order Methylococcales constitutes the methanotrophs – bacteria that can metabolize methane, a potent greenhouse gas, as their sole source of energy. These bacteria are significant players in the global carbon cycle and can produce value-added products from methane, such as biopolymers, biofuels, and single-cell proteins for animal feed, among others. Previous studies using single-gene phylogenies have shown inconsistencies in the currently established taxonomic structure of this group. This study aimed to determine and resolve these issues by using whole-genome sequence analyses. Phylogenomic analysis and the use of similarity indexes for genomic comparisons – average amino acid identity, digital DNA–DNA hybridization (dDDH), and average nucleotide identity (ANI) – were performed on 91 Methylococcales genomes. Results suggest the reclassification of members at the genus and species levels. Firstly, to resolve polyphyly of the genus Methylomicrobium, Methylomicrobium alcaliphilum, “Methylomicrobium buryatense,” Methylomicrobium japanense, Methylomicrobium kenyense, and Methylomicrobium pelagicum are reclassified to a newly proposed genus, Methylotuvimicrobium gen. nov.; they are therefore renamed to Methylotuvimicrobium alcaliphilum comb. nov., “Methylotuvimicrobium buryatense” comb. nov., Methylotuvimicrobium japanense comb. nov., Methylotuvimicrobium kenyense comb. nov., and Methylotuvimicrobium pelagicum comb. nov., respectively. Secondly, due to the phylogenetic affinity and phenotypic similarities of Methylosarcina lacus with Methylomicrobium agile and Methylomicrobium album, the reclassification of the former species to Methylomicrobium lacus comb. nov. is proposed. Thirdly, using established same-species delineation thresholds (70% dDDH and 95% ANI), Methylobacter whittenburyi is proposed to be a later heterotypic synonym of Methylobacter marinus (89% dDDH and 99% ANI). Also, the effectively but not validly published “Methylomonas denitrificans” was identified as Methylomonas methanica (92% dDDH and 100% ANI), indicating that the former is a later heterotypic synonym of the latter. Lastly, strains MC09, R-45363, and R-45371, currently identified as M. methanica, each represent a putative novel species of the genus Methylomonas (21–35% dDDH and 74–88% ANI against M. methanica) and were reclassified as Methylomonas sp. strains. It is imperative to resolve taxonomic inconsistencies within this group, first and foremost, to avoid confusion with ecological and evolutionary interpretations in subsequent studies.

Three bacterial strains, C9, H5 and TLL-A3, were isolated from fecal pellets of conventionally raised C57BL/6J mice. Analysis of 16S rRNA genes indicated that the strains belonged to the Muribaculaceae, and shared 91.6-99.9 % sequence identity with the recently described Duncaniella muris DSM 103720T. Genome-sequencing of the isolates was performed to compare average nucleotide identities (ANI) between strains. The ANI analysis revealed that all isolates shared highest ANI with D. muris DSM 103720T, with strain C9 being most similar (ANI: 98.0 %) followed by strains H5 (ANI: 76.4 %) and TLL-A3 (ANI: 74.4 %). Likewise, digital DNA-DNA hybridization (dDDH) indicated high similarity of strain C9 (dDDH: 86.6 %) to D. muris DSM 103720T, but strains H5 and TLL-A3 showed lower similarity (dDDH <35 %) to either of the three type species of the Muribaculaceae (Muribaculum intestinale DSM 28989T , Paramuribaculum intestinale DSM 100749T, D. muris DSM 103720T). MK-10 and MK-11 were abundant in all three isolates, but concentrations varied between species. Based on genotypic, phylogenetic and phenotypic differences, the strains TLL-A3 and H5 are considered to represent novel species of the genus Duncaniella, for which the names Duncaniella freteri sp. nov., and Duncaniella dubosii sp. nov., are proposed. The respective type strains are TLL-A3T (=DSM 108168T=KCTC 15769T), and H5T (=DSM 107170T=KCTC 15734T). Strain C9 reveals limited sequence dissimilarity and minor differences in morphological properties with Duncaniella muris DSM 103720T and is therefore proposed to belong to the same species. The respective strain is C9 (=DSM 107165=KCTC 15733).

Currently, bacterial classification at the species level relies on the 95-96% average nucleotide identity (ANI) value that is known to be equivalent to a 70% digital DNA-DNA hybridization (dDDH) value. However, during the routine identification of bacteria in the uteri of camels with a history of conception failure, we found that four out of the seven strains (2298A, 2569A, 2652, 2571B, 1103A, 2571A, and 335C) could not be assigned to any valid Corynebacterium species. Furthermore, a 70% dDDH value did not correspond to a 95-96% ANI value in strain 2569A. Thus, we aimed to classify these strains and explain the mechanisms underlying gene repertoire diversity and the disagreement we found between the ANI and dDDH cutoff values. For this study, we extracted information from the genomes of 150 Corynebacterium-type species and seven sequenced genomes of uterine Corynebacterium isolates. We found that the 96.67% OrthoANI value should be used in place of the generally accepted 95-96% ANI threshold in order to obtain an equivalent 70% dDDH value. Phylogenomic analysis determined the evolutionary position of each uterine strain. Then, strains 2652 and 2571B were classified as C. camporealensis based on the ANI value (98.44% and 98.72%) and dDDH value (85.8% and 88.5%). Strain 2569A had a 96.58% ANI and a 69.4% dDDH value and was classified as C. urogenitale. The strains 335C, 1103A, 2571A, and 2298A were classified as novel Corynebacterium based on the ANI value (77.12, 94.01%, 94.26%, and 94.03%) and dDDH value (21.3%, 54.1%, 54.9%, and 51.3%), respectively. Genes for menaquinone biosynthesis and the saturation of chains were detected in uterine strains and their closely related type strains. Gene gain predominates as a source of variation in the gene repertoire. Most of these genes are gained by horizontal gene transfer, driven by genomic islands and prophage. In summary, we refined the ANI cutoff value for an accurate diagnosis of Corynebacterium. Moreover, we clarified the mechanism underlying the diversity of the gene repertoire and expanded the number of Corynebacterium species isolated from the camel uterus.

Investigation of genomic characteristics and carbohydrates’ metabolic activity of Lactococcus lactis subsp. lactis during ripening of a Swiss-type cheese