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

Abstract

In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (21-36% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.

Figure 1

Taxonomic comparison of active microbial communities at mRNA level. Samples 1–4 are from white biofilms and sample 5–6 are from the brown biofilms.

Figure 2

Gene transcripts identified in reactor samples corresponding to known or hypothesized enzymes involved in anaerobic (A) and aerobic (B) benzene degradation in different microbes and their relative abundances (%) (C). Gene transcripts that could not be distinguished due to overlapping assignment with similar genes in the pathway are shown with question marks (full list is given in Table 1). Note that only the substrate and products of each enzymatic reaction are given for clarity. The bar showing the number of relative abundance was log scaled and 0 values were removed.