Recent advances in molecular biology have extended our understanding of the metabolic processes related to microbial transformation of petroleum hydrocarbons. The physiological responses of microorganisms to the presence of hydrocarbons, including cell surface alterations and adaptive mechanisms for uptake and efflux of these substrates, have been characterized. New molecular techniques have enhanced our ability to investigate the dynamics of microbial communities in petroleum-impacted ecosystems. By establishing conditions which maximize rates and extents of microbial growth, hydrocarbon access, and transformation, highly accelerated and bioreactor-based petroleum waste degradation processes have been implemented. Biofilters capable of removing and biodegrading volatile petroleum contaminants in air streams with short substrate-microbe contact times ( 2 S and sulfoxides from petrochemical waste streams. Microbes also have potential for use in removal of nitrogen from crude oil leading to reduced nitric oxide emissions provided that technical problems similar to those experienced in biodesulfurization can be solved. Enzymes are being exploited to produce added-value products from petroleum substrates, and bacterial biosensors are being used to analyze petroleum-contaminated environments.

Recent Advances in Petroleum Microbiology

Recent advances in the science and technology of ultra low sulfur diesel (ULSD) production

This paper is a selective review on design approaches and associated catalysis and chemistry for deep desulfurization and deep dearomatization (hydrogenation) of hydrocarbon fuels, particularly diesel fuels. The challenge for deep desulfurization of diesel fuels is the difficulty of removing the refractory sulfur compounds, particularly 4,6-dimethyldibenzothiophene, with conventional hydrodesulfurization processes. The problem is exacerbated by the inhibiting effect of polyaromatics and nitrogen compounds, which exist in some diesel blend stocks on deep HDS. With the new Environmental Protection Agency (EPA) Tier II regulations to cut the diesel sulfur from current 500 ppmw down to 15 ppmw by June 2006, refineries are facing major challenges to meet the fuel sulfur specification along with the required reduction of aromatics contents. The principles and problems for the existing hydrodesulfurization processes, and the concepts, advantages and disadvantages of various new approaches will be discussed. Specifically, the following new design approaches for sulfur removal will be discussed: (1) novel catalysts for ultra-deep hydrodesulfurization under conventional HDS process conditions; (2) new design concept for sulfur-tolerant noble metal catalysts for low-temperature hydrogenation; (3) new desulfurization process by sulfur adsorption and capture under H2; (4) new desulfurization process by selective adsorption at ambient temperature without H2 and a related integrated process concept; (5) oxidative desulfurization in liquid-phase; and (6) biodesulfurization.

New design approaches to ultra-clean diesel fuels by deep desulfurization and deep dearomatization

Summary: Actinobacteria constitute one of the largest phyla among Bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context.

Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum

Enzyme stability and stabilization—Aqueous and non-aqueous environment

Petroleum contains many heterocyclic organosulfur compounds refractory to conventional hydrodesulfurization carried out with chemical catalysts. Among these, dibenzothiophene (DBT) and DBTs bearing alkyl substitutions are representative compounds. Two bacterial strains, which have been identified as Paenibacillus strains and which are capable of efficiently cleaving carbon-sulfur (C--S) bonds in DBT at high temperatures, have been isolated for the first time. Upon attacking DBT and its various methylated derivatives at temperatures up to 60(deg)C, both growing and resting cells of these bacteria can release sulfur atoms as sulfate ions and leave the monohydroxylated hydrocarbon moieties intact. Moreover, when either of these paenibacilli was incubated at 50(deg)C with light gas oil previously processed through hydrodesulfurization, the total sulfur content in the oil phase clearly decreased.

https://aem.asm.org/content/aem/63/8/3164.full.pdf

Thermophilic carbon-sulfur-bond-targeted biodesulfurization.

Biodesulfurization of dibenzothiophene and its derivatives through the selective cleavage of carbon-sulfur bonds by a moderately thermophilic bacterium Bacillus subtilis WU-S2B.

Rhodococus erythropolis KA2-5-1 can desulfurize dibenzothiophene (DBT) into 2-hydroxybiphenyl. A cryptic plasmid, pRC4, which was derived from R. rhodochrous IFO3338, was combined with an Escherichia coli vector to construct an E. coli-Rhodococcus shuttle vector. The complete nucleotide sequence of 2582-bp pRC4 was analyzed. Based on the characteristics of its putative replication genes, pRC4 was assigned to the family of pAL5000-related replicons. The desulfurization gene cluster, dszABC, and the related reductase gene, dszD, cloned from KA2-5-1, were reintroduced into KA2-5-1 and efficiently expressed. The DBT desulfurization ability of the transformant carrying two dszABC clusters and one dszD on the vector was about 4-fold higher than that of the parent strain, and the transformant also showed improved desulfurization activity for light gas oil (LGO). Sulfur components in LGO before and after the reaction were analyzed with gas chromatography-atomic emission detection.

Improvement of desulfurization activity in Rhodococcus erythropolis KA2-5-1 by genetic engineering.

Thirty-five bacterial strains capable of converting dibenzothiophene into 2-hydroxybiphenyl were isolated. Among them Rhodococcus erythropolis KA2-5-1 was chosen for further characterization because of its ability to retain high desulfurization activity stably. PCR cloning and DNA sequencing of a KA2-5-1 genomic DNA fragment showed that it was practically identical with dszABC genes from Rhodococcus sp. IGTS8, a representative carbon–sulfur-bond-targeted dibenzothiophene-degrading bacterium. KA2-5-1 desulfurized a variety of alkyl dibenzothiophenes through the specific cleavage of their C–S bonds. In addition, unexpectedly, KA2-5-1 also attacked alkyl benzothiophenes in a C–S-bond-targeted fashion. The purified monooxygenase, encoded by dszC of KA2-5-1, converted benzothiophene and dibenzothiophene into benzothiophene sulfone and dibenzothiophene sulfone, respectively, with the aid of an NADH-dependent oxidoreductase. This result raises the possibility that the same enzymatic step may be involved in desulfurization of alkylated forms of both dibenzothiophene and benzothiophene in KA2-5-1 cells.

Yoshitaka Ishii

Papers

Thermophilic carbon-sulfur-bond-targeted biodesulfurization.

Biodesulfurization of dibenzothiophene and its derivatives through the selective cleavage of carbon-sulfur bonds by a moderately thermophilic bacterium Bacillus subtilis WU-S2B.

Improvement of desulfurization activity in Rhodococcus erythropolis KA2-5-1 by genetic engineering.

Desulfurization of alkylated forms of both dibenzothiophene and benzothiophene by a single bacterial strain.

Operon structure and functional analysis of the genes encoding thermophilic desulfurizing enzymes of Paenibacillus sp. A11-2.