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

Abstract

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),...

Demonstration of Carbon Catabolite Repression in Naphthalene Degrading Soil Bacteria via Raman Spectroscopy Based Stable Isotope Probing

“…54 Other processes which may be of relevance in this observation are metabolite toxicity and depletion of electron acceptors associated with glucose utilization. 55 Reverse CCR has been observed previously in some bacteria for example in Pseudomonas putida CSV86 which resulted in the suppression of enzymes needed for the utilization of glucose by aromatic compounds. 7,56,57 However, to the best of our knowledge this is the first time this process has been observed in this particular species C. basilensis in a binary combination of glucose and naphthalene.…”

Expanding the current knowledge and biotechnological applications of the oxygen‐independent ortho‐phthalate degradation pathway

“…6A). In this sense, it should be mentioned that although strain JMP134 contains a box cluster in its genome, this cluster might not encode a functional box pathway since it lacks the boxD gene (Gescher et al ., 2006; Pérez‐Pantoja et al ., 2008) and does not allow growth on benzoate to a JMP134Δ benA mutant strain (Donoso et al ., 2011; Pérez‐Pantoja et al ., 2015).…”

Anaerobic Degradation of <b><i>p</i></b>-Alkylated Benzoates and Toluenes

“…The preference of strain pMbN1 for benzoate over 4-methylbenzoate may result from the benzoyl-CoA pathway representing the most widely used central 'hub' for a large variety of aromatic compounds, while the 4-methylbenzoyl-CoA pathway has most likely a very narrow substrate range. Likewise, in the aerobic Betaproteobacterium Cupriavidus pinatubonensis strain JMP134 (formerly described amongst others as Alcaligenes eutrophus ), benzoate is preferentially utilized against a background of seven other aromatic acids by transcriptional repression of the alternative degradation pathways [Pérez-Pantoja et al, 2015].…”