Functional Gene Markers for Fumarate-Adding and Dearomatizing Key Enzymes in Anaerobic Aromatic Hydrocarbon Degradation in Terrestrial Environments

Abstract

Anaerobic degradation is a key process in many environments either naturally or anthropogenically exposed to petroleum hydrocarbons. Considerable advances into the biochemistry and physiology of selected anaerobic degraders have been achieved over the last decades, especially for the degradation of aromatic hydrocarbons. However, researchers have only recently begun to explore the ecology of complex anaerobic hydrocarbon degrader communities directly in their natural habitats, as well as in complex laboratory systems using tools of molecular biology. These approaches have mainly been facilitated by the establishment of a suite of targeted marker gene assays, allowing for rapid and directed insights into the diversity as well as the identity of intrinsic degrader populations and degradation potentials established at hydrocarbon-impacted sites. These are based on genes encoding either peripheral or central key enzymes in aromatic compound breakdown, such as fumarate-adding benzylsuccinate synthases or dearomatizing aryl-coenzyme A reductases, or on aromatic ring-cleaving hydrolases. Here, we review recent advances in this field, explain the different detection methodologies applied, and discuss how the detection of site-specific catabolic gene markers has improved the understanding of processes at contaminated sites. Functional marker gene-based strategies may be vital for the development of a more elaborate population-based assessment and prediction of aromatic degradation potentials in hydrocarbon-impacted environments.

Sulfate Alters the Competition Among Microbiome Members of Sediments Chronically Exposed to Asphalt

“…Representative species of Desulfobulbus are capable of both respiratory and fermentative growth ( Laanbroek et al, 1982 ; Sass et al, 2002 ; El Houari et al, 2017 ; Kharrat et al, 2017 ) and are considered generalists, based on their metabolic flexibility. Lineages within the Desulfobulbaceae family have been previously identified as carriers of genes coding for monoaromatic degrading enzymes ( von Netzer et al, 2016 ), although the high share of Desulfobulbus did not result in an increased potential for degradation of monoaromatics as inferred via bamA gene abundance in our experiment. Members of the species Desulfobulbus rhabdoformis , found in the asphalt-exposed microcosms, is able to use small-molecular-weight compounds and has no vitamin needs, compared to other Desulfobulbus representatives ( Lien et al, 1998 ).…”

Structure and Functions of Hydrocarbon-Degrading Microbial Communities in Bioelectrochemical Systems

“…Indeed, it can be related with the fact that these two reactors share toluene as the substrate. Moreover, fumarate addition is a strategy for the anaerobic activation of aromatic hydrocarbons, which was first described for the activation of toluene catalyzed by benzylsuccinate synthase (BSS) in Thauera aromatica strain K172, but is also involved in the activation of xylenes and ethylbenzene [48].…”

“…In order to perform a deeper analysis of those genes specifically related to hydrocarbon degradation, benzylsuccinate synthase was selected, based on the KO term, as a marker for the anaerobic degradation of toluene, ethylbenzene, and xylenes [48] since it catalyzes the first step (i.e., fumarate addition) in the contaminant degradation pathway. This analysis revealed an increase in the coverage of the sequences annotated as benzylsuccinate synthase (BssA-[EC:4.1.99.11]) on the anodes of the toluene and BTEX reactors ( Figure 4A), but the presence of this enzyme was not found in the inocula nor in the phenol sample.…”

“…We searched for the genes involved in the anaerobic degradation of toluene, benzene, xylenes, ethylbenzene, and phenol. Regarding toluene and the xylenes, fumarate addition was considered the principal mechanism for the degradation of these compounds [48,52] ( Figure S3). The activation of ethylbenzene can follow the pathway of fumarate addition [47,51], but an alternative pathway (through the oxidation of ethylbenzene to benzoyl-CoA) has been proposed in denitrifying bacteria [52][53][54] (Figure S3).…”

The sequence capture by hybridization: a new approach for revealing the potential of mono‐aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer

“…Subsequently, other primer sets enabled sulphate-reducing, iron-reducing and syntrophic bacteria to be targeted (Winderl et al, 2007;Beller et al, 2008;Staats et al, 2011;Fowler et al, 2014). There was a difficulty in amplifying the bssA gene of some sulphate-reducing bacteria belonging to the Clostridia which was partly solved by the subsequent design of specific primers for this class (von Netzer et al, 2013; for the latest review on bssA-like gene diversity, see von Netzer et al, 2016).…”