New perspectives on the anaerobic degradation of BTEX: Mechanisms, pathways, and intermediates

Aromatic hydrocarbons like benzene, toluene, xylene, and ethylbenzene (BTEX) can escape into the environment from oil and gas operations and manufacturing industries posing significant health risks to humans and wildlife. Unlike conventional clean-up methods used, biological approaches such as bioremediation can provide a more energy and labour-efficient and environmentally friendly option for sensitive areas such as nature reserves and cities, protecting biodiversity and public health. BTEX contamination is often concentrated in the subsurface of these locations where oxygen is rapidly depleted, and biodegradation relies on anaerobic processes. Thus, it is critical to understand the anaerobic biodegradation characteristics as it has not been explored to a major extent. This review presents novel insights into the degradation mechanisms under anaerobic conditions and presents a detailed description and interconnection between them. BTEX degradation can follow four activation mechanisms: hydroxylation, carboxylation, methylation, and fumarate addition. Hydroxylation is one of the mechanisms that explains the transformation of benzene into phenol, toluene into benzyl alcohol or p-cresol, and ethylbenzene into 1-phenylethanol. Carboxylation to benzoate is thought to be the primary mechanism of degradation for benzene. Despite being poorly understood, benzene methylation has been also reported. Moreover, fumarate addition is the most widely reported mechanism, present in toluene, ethylbenzene, and xylene degradation. Further research efforts are required to better elucidate new and current alternative catabolic pathways. Likewise, a comprehensive analysis of the enzymes involved as well as the development of advance tools such as omic tools can reveal bottlenecks degradation steps and create more effective on-site strategies to address BTEX pollution.

Geobacter benzoatilyticus sp. nov., a novel benzoate-oxidizing, iron-reducing bacterium isolated from petroleum contaminated soil

A strictly anaerobic bacterial strain, designated Jerry-YXT, was isolated from petroleum-contaminated soil sampled in China. Strain Jerry-YXT was a Gram-stain-negative bacterium forming reddish colonies. It grew optimally at 30 °C and pH 7.0, and tolerated 1.0 % (w/v) NaCl. Strain Jerry-YXT was able to use fumarate, ferric citrate and ferrihydrite as electron acceptors, and ethanol, acetate and benzoate as electron donors. The major fatty acids of this strain were C16 : 0 and C16 : 1  ω7c/C16 : 1  ω6c (summed feature 3). The 16S rRNA gene sequence-based phylogenetic analysis placed this strain in the genus Geobacter , being most closely related to Geobacter metallireducens (98.2 % similarity), Geobacter hydrogenophilus (98.1 %) and Geobacter grbiciae (98.0 %). The DNA G+C content was 57.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of strain Jerry-YXT and G. metallireducens GS-15T were 81.8 and 35.4 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain Jerry-YXT from its closest species, which suggested that strain Jerry-YXT represents a novel species of the genus Geobacter . The name for the proposed new species is Geobacter benzoatilyticus sp. nov. The type strain is Jerry-YXT (=MCCC 1K05659T=JCM 39190T).

Anaerobic phenanthrene biodegradation by a newly isolated sulfate-reducer, strain PheS1, and exploration of the biotransformation pathway

Phenanthrene is a widespread and harmful polycyclic aromatic hydrocarbon that is difficult to anaerobically biodegrade. Current challenges in anaerobic phenanthrene bioremediation are a lack of degrading cultures and limited knowledge of biotransformation pathways. Under sulfate-reducing conditions, pure-cultures and biotransformation processes for anaerobic phenanthrene biodegradation are poorly understood. In this study, strain PheS1, which is phylogenetically closely related to Desulfotomaculum, was found to be a sulfate-reducing phenanthrene-degrading bacterium. Anaerobic phenanthrene biodegradation using PheS1 was proposed based on metabolite and genome analyses, and the initial step was identified as carboxylation based on the detection of 2-phenanthroic acid, [¹³C]-2-phenanthroic acid, and [D9]-2- phenanthroic acid when phenanthrene+HCO₃^-, phenanthrene+H¹³CO₃^-, and [D10]-phenanthrene+HCO₃^- were used as the substrate, respectively. PheS1 genome ubiD gene encoding of carboxylase putatively involved in the biodegradation was performed. Next, benzene ring reduction and cleavage that produced benzene compounds and cyclohexane derivative were reported to occur in the downstream biotransformation processes. Additionally, benzene, naphthalene, benz[a]anthracene, and anthracene can be utilised by PheS1, whereas pyrene and benz[a]pyrene cannot. We discovered a new phenanthrene-degrading sulfate-reducer and provided the anaerobic phenanthrene biotransformation pathway under sulfate-reducing conditions, which can act as a reference for practical applications in bioremediation and for studying the molecular mechanisms of phenanthrene in anaerobic zones.

Paradesulfitobacterium ferrireducens gen. nov., sp. nov., a Fe(III)-reducing bacterium from petroleum-contaminated soil and reclassification of Desulfitobacterium aromaticivorans as Paradesulfitobacterium aromaticivorans comb. nov

A strictly anaerobic bacterium, strain PLL0^T, was isolated from petroleum-contaminated soil sampled in Gansu Province, PR China. Cells were rods, non-motile and Gram-stain-positive. The strain grew at 25-37 °C (optimum, 30 °C) in the presence of 0-3 % (w/v) NaCl (optimum, 2 %). Strain PLL0^T was able to reduce ferrihydrite, Fe(III) citrate and thiosulphate. The 16S rRNA gene analysis revealed that this strain clustered with the genus Desulfitobacterium, and showed highest similarity to Desulfitobacterium aromaticivorans UKTL^T (95.4 %) followed by Desulfitobacterium chlororespirans Co23^T (93.9 %). However, strains PLL0^T and UKTL^T showed no more than 94.0 % similarity to other species of the genus Desulfitobacterium, and formed an independent group in the phylogenetic tree. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain PLL0^T and Desulfitobacterium species (except for D. aromaticivorans) were 67.4-68.5 % and 12.6-12.7 %, respectively, which are far below the threshold for delineation of a new species. Based on ANI, dDDH, average amino acid identity, phylogenetic analysis and physiologic differences from the previously described taxa, we suggest that strain PLL0^T represents a novel species of a novel genus, for which the name Paradesulfitobacterium ferrireducens gen. nov. sp. nov. is proposed. The type strain is PLL0^T (=MCCC 1K05549=KCTC 25248). We also propose the reclassification of D. aromaticivorans as Paradesulfitobacterium aromaticivorans comb. nov.

Transcriptional Regulation of the Peripheral Pathway for the Anaerobic Catabolism of Toluene and m-Xylene in Azoarcus sp. CIB

Alkylbenzenes, such as toluene and m-xylene, are an important class of contaminant hydrocarbons that are widespread and tend to accumulate in subsurface anoxic environments. The peripheral pathway for the anaerobic oxidation of toluene in bacteria consists of an initial activation catalyzed by a benzylsuccinate synthase (encoded by bss genes), and a subsequent modified β-oxidation of benzylsuccinate to benzoyl-CoA and succinyl-CoA (encoded by bbs genes). We have shown here that the bss and bbs genes, which are located within an integrative and conjugative element, are essential for anaerobic degradation of toluene but also for m-xylene oxidation in the denitrifying beta-proteobacterium Azoarcus sp. CIB. New insights into the transcriptional organization and regulation of a complete gene cluster for anaerobic catabolism of toluene/m-xylene in a single bacterial strain are presented. The bss and bbs genes are transcriptionally coupled into two large convergent catabolic operons driven by the PbssD and PbbsA promoters, respectively, whose expression is inducible when cells grow anaerobically in toluene or m-xylene. An adjacent tdiSR operon driven by the PtdiS promoter encodes a putative two-component regulatory system. TdiR behaves as a transcriptional activator of the PbssD, PbbsA, and PtdiS promoters, being benzylsuccinate/(3-methyl)benzylsuccinate, rather than toluene/m-xylene, the inducers that may trigger the TdiS-mediated activation of TdiR. In addition to the TdiSR-based specific control, the expression of the bss and bbs genes in Azoarcus sp. CIB is under an overimposed regulation that depends on certain environmental factors, such as the presence/absence of oxygen or the availability of preferred carbon sources (catabolite repression). This work paves the way for future strategies toward the reliable assessment of microbial activity in toluene/m-xylene contaminated environments.