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

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.

本研究报道了苯降解反硝化连续培养物中参与好氧与厌氧苯降解通路的基因转录情况。与肽球菌科（Peptococcaceae）相关的转录本在所有样本中均占据主导地位，相对丰度达21%~36%，表明该类群在菌群中发挥关键作用。我们发现一个高转录活性的基因簇，其编码推定的厌氧苯羧化酶（AbcA与AbcD）以及苯甲酸辅酶A连接酶（BzlA）。预测的基因产物与此前报道的对应苯降解基因簇的氨基酸序列一致性均超过96%，且基因排列顺序相似，为厌氧苯通过羧化作用激活提供了进一步证据。针对后续的苯甲酰辅酶A脱芳构化过程，培养物中转录了与其他严格厌氧菌中同源的bam家族基因；而参与下游苯甲酰辅酶A降解的基因转录本，则大多与兼性厌氧菌中报道的序列相似。同时，编码加氧酶介导的好氧苯降解相关酶的基因发生转录，这表明培养物中存在氧气——这类氧气可能通过近期发现的一氧化氮歧化酶（nitric oxide dismutase，Nod）生成。尽管我们未检测到编码一氧化氮歧化酶的基因转录，但向连续培养物中添加亚硝酸盐与甲酸盐后，观测到了氧气生成的迹象。这种氧气生成过程可使好氧微生物在缺氧、含硝酸盐且受烃类污染的地下环境中存活并繁衍。