Phylogenomics of Aerobic Bacterial Degradation of Aromatics

cCupriavidus pinatubonensis JMP134, like many other environmental bacteria, uses a range of aromatic compounds as carbon sources. Previous reports have shown a preference for benzoate when this bacterium grows on binary mixtures composed of this aromatic compound and 4-hydroxybenzoate or phenol. However, this observation has not been extended to other aromatic mixtures resembling a more archetypal context. We carried out a systematic study on the substrate preference of C. pinatubonensis JMP134 growing on representative aromatic compounds channeled through different catabolic pathways described in aerobic bacteria. Growth tests of nearly the entire set of binary combinations and in mixtures composed of 5 or 6 aromatic components showed that benzoate and phenol were always the preferred and deferred growth substrates, respectively. This pattern was supported by kinetic analyses that showed shorter times to initiate consumption of benzoate in aromatic compound mixtures. Gene expression analysis by real-time reverse transcription-PCR (RT-PCR) showed that, in all mixtures, the repression by benzoate over other catabolic pathways was exerted mainly at the transcriptional level. Additionally, inhibition of benzoate catabolism suggests that its multiple repressive actions are not mediated by a sole mechanism, as suggested by dissimilar requirements of benzoate degradation for effective repression in different aromatic compound mixtures. The hegemonic preference for benzoate over multiple aromatic carbon sources is not explained on the basis of growth rate and/or biomass yield on each single substrate or by obvious chemical or metabolic properties of these aromatic compounds.A romatic compounds (AC) are widespread in the environment, displaying a heterogeneous structural diversity. They can be naturally originated by biotic and abiotic processes or released as pollutants into the environment. AC primarily can be found as aromatic amino acids, secondary products abundantly generated by plants, structural components of the very complex lignin heteropolymer in woody plants, and xenobiotic compounds: biocides, industrial by-products, and petroleum derivatives, among others. Microorganisms may degrade hundreds of different AC using specialized biochemical pathways that allow them to grow on these carbon sources (1-3). Typically, bacteria deal with AC as part of complex mixtures in naturally occurring organic compounds, such as those found in plant exudates (4), in soils (5), and even in dissolved organic matter from freshwater and seawater (6). Therefore, microorganisms are concurrently exposed to several structurally heterogeneous AC as potential substrates, which raises the question of whether the components of these mixtures are used simultaneously or in a sequential manner. In the case of the sequential utilization pattern, characterized by diauxic growth, one compound inhibits degradation of the other by exerting metabolite toxicity (7), competitive inhibition of enzymes (8, 9), depletion of electron acceptors (10, 11),...

Section: Figmentioning

confidence: 91%

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confidence: 98%

Hierarchy of Carbon Source Utilization in Soil Bacteria: Hegemonic Preference for Benzoate in Complex Aromatic Compound Mixtures Degraded by Cupriavidus pinatubonensis Strain JMP134

Pérez‐Pantoja

Leiva-Novoa

Donoso

et al. 2015

“…Curiously, degradation of intermediate catechol proceeds via an intradiol cleavage pathway (see Fig. S2 in the supplemental material) (8), which belongs to the core genomes of most Pseudomonas strains (51). Similarly to the situation for strain ML2, dehydrogenation of intermediate cis-benzene dihydrodiol in 1YB2 and 1YdBTEX2 is catalyzed by enzymes that are not closely related to toluene cis-dihydrodiol dehydrogenases.…”

Section: Figmentioning

confidence: 99%

Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters

Lima-Morales

Chaves‐Moreno

Wos‐Oxley

et al. 2016

Pseudomonas veronii 1YdBTEX2, a benzene and toluene degrader, and Pseudomonas veronii 1YB2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. These strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. Extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydroxymuconic semialdehyde dehydrogenase necessary for benzene degradation but typically absent from isopropylbenzene dioxygenase-encoding gene clusters. The benzene dihydrodiol dehydrogenase-encoding gene was not clustered with any other aromatic degradation genes, and the encoded protein was only distantly related to dehydrogenases of aromatic degradation pathways. The involvement of the different gene clusters in the degradation pathways was suggested by real-time quantitative reverse transcription PCR.

“…Toluene can be additionally activated through oxidation of the methylsubstituent initiated by xylene monooxygenase or through toluene 4-monooxygenation with 4-methylphenol as an intermediate. Central di-or trihydroxylated intermediates are subject to ring cleavage by intradiol dioxygenases (26) or extradiol dioxygenases of the vicinal chelate superfamily, the LigB superfamily, or the cupin superfamily (25,26,69). Ring cleavage products are channelled to the tricarboxylic acid cycle via central reactions.…”

Section: Figmentioning

confidence: 99%

“…Recently, a novel catabolic array was described and successfully applied to environmental samples (25). The array is based on upgraded and manually curated databases of key aromatic catabolic genes (26,27) and thereby avoids massive numbers of misannotations. The array comprises 1,500 probes, and the design facilitates the assignment of positive signals to the respective protein subfamilies, thereby directly inferring function and substrate specificity.…”

mentioning

confidence: 99%

Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

Lima-Morales

Jáuregui

Camarinha‐Silva

et al. 2016

bThree types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched.