Identification of genes specifically required for the anaerobic metabolism of benzene in Geobacter metallireducens

Abstract

Although the biochemical pathways for the anaerobic degradation of many of the hydrocarbon constituents in petroleum reservoirs have been elucidated, the mechanisms for anaerobic activation of benzene, a very stable molecule, are not known. Previous studies have demonstrated that Geobacter metallireducens can anaerobically oxidize benzene to carbon dioxide with Fe(III) as the sole electron acceptor and that phenol is an intermediate in benzene oxidation. In an attempt to identify enzymes that might be involved in the conversion of benzene to phenol, whole-genome gene transcript abundance was compared in cells metabolizing benzene and cells metabolizing phenol. Eleven genes had significantly higher transcript abundance in benzene-metabolizing cells. Five of these genes had annotations suggesting that they did not encode proteins that could be involved in benzene metabolism and were not further studied. Strains were constructed in which one of the remaining six genes was deleted. The strain in which the monocistronic gene Gmet 0232 was deleted metabolized phenol, but not benzene. Transcript abundance of the adjacent monocistronic gene, Gmet 0231, predicted to encode a zinc-containing oxidoreductase, was elevated in cells metabolizing benzene, although not at a statistically significant level. However, deleting Gmet 0231 also yielded a strain that could metabolize phenol, but not benzene. Although homologs of Gmet 0231 and Gmet 0232 are found in microorganisms not known to anaerobically metabolize benzene, the adjacent localization of these genes is unique to G. metallireducens. The discovery of genes that are specifically required for the metabolism of benzene, but not phenol in G. metallireducens is an important step in potentially identifying the mechanisms for anaerobic benzene activation.

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

“…In contrast to many aerobic benzene-degrading pure cultures, only few anaerobic benzene-degrading axenic cultures have been described. The hyperthermophilic archaeon Ferroglobus placidus was proposed to employ a putative UbiD-related carboxylase in anaerobic benzene activation 17 , and anaerobic benzene oxidation in Geobacter metallireducens was shown to proceed via hydroxylation to phenol 18 , 19 . In contrast to these strictly anaerobic iron-reducers that employ oxygen-independent activation routes, the chlorate-reducing Alicycliphilus denitrificans strain BC 20 was shown to degrade benzene via an oxygenase-mediated pathway 21 .…”

Opportunities for groundwater microbial electro‐remediation

“…Some years later, anaerobic benzene oxidation by Geobacter was successfully proven (Zhang et al ., ). And even the genes for anaerobic benzene oxidation were identified for Geobacter metallireducens (Zhang et al ., ). Thus, it was not surprising that one of the first MET experiences on aromatics removal evaluated the ability of Geobacter metallireducens to oxidize toluene, benzene or naphthalene to carbon dioxide using a graphite electrode as electron sink (Zhang et al ., ).…”

Application of Diagnostic Tools to Evaluate Remediation Performance at Petroleum Hydrocarbon‐Impacted Sites

“…Assessment of ethylbenzene, xylene, and naphthalene degradation can also occur via metabolite analysis. For benzene, a compound‐specific metabolite has been identified for aerobic conditions (Gibson and Parales ), but the few identified anaerobic metabolites produced from benzene, that is, benzoic acid and phenol (Abu Laban et al ; Zhang et al ; Zhang et al ), can have many sources and therefore, are considered ambiguous biomarkers. As such, detection of benzoic acid and phenol by itself is not sufficient to demonstrate anaerobic benzene biodegradation.…”

“…It is important to note that the information in Table is evolving because ongoing research continues to reveal new findings on how microorganisms metabolize contaminants. For example (Zhang et al ; Zhang et al ) have recently confirmed that phenol is an early metabolite during anaerobic benzene biodegradation, whereas Dong et al () recently identified benzoyl‐CoA as a metabolite of anaerobic benzene degradation.…”