Abstract
The proteobacteria Variovorax sp. WDL1, Comamonas testosteroni WDL7, and Hyphomicrobium sulfonivorans WDL6 compose a triple‐species consortium that synergistically degrades and grows on the phenylurea herbicide linuron. To acquire a better insight into the interactions between the consortium members and the underlying molecular mechanisms, we compared the transcriptomes of the key biodegrading strains WDL7 and WDL1 grown as biofilms in either isolation or consortium conditions by differential RNAseq analysis. Differentially expressed pathways and cellular systems were inferred using the network‐based algorithm PheNetic. Coculturing affected mainly metabolism in WDL1. Significantly enhanced expression of hylA encoding linuron hydrolase was observed. Moreover, differential expression of several pathways involved in carbohydrate, amino acid, nitrogen, and sulfur metabolism was observed indicating that WDL1 gains carbon and energy from linuron indirectly by consuming excretion products from WDL7 and/or WDL6. Moreover, in consortium conditions, WDL1 showed a pronounced stress response and overexpression of cell to cell interaction systems such as quorum sensing, contact‐dependent inhibition, and Type VI secretion. Since the latter two systems can mediate interference competition, it prompts the question if synergistic linuron degradation is the result of true adaptive cooperation or rather a facultative interaction between bacteria that coincidentally occupy complementary metabolic niches.
Highlights
Mineralization of organic xenobiotic compounds is often performed by microbial consortia by means of metabolic association in which one organism in the consortium converts the organic xenobiotic into metabolites that are degraded by other consortium members (Horemans, Albers, & Springael, 2016)
Using a differential transcriptomic approach, we revealed that next to metabolic association between the members of a linuron-degrading consortium, additional cross-feeding interactions are expected to be present and that amino acids are one type of metabolites exchanged between the consortium members that in particular are used by WDL1 for growth
In comparison to WDL7, WDL1 shows a more extensive response upon coculturing with WDL6 and WDL7, including the increased expression of hylA encoding linuron hydrolase which can be directly linked with enhanced linuron degradation and a stress response
Summary
Mineralization of organic xenobiotic compounds is often performed by microbial consortia by means of metabolic association in which one organism in the consortium converts the organic xenobiotic into metabolites that are degraded by other consortium members (Horemans, Albers, & Springael, 2016). When the consortium is grown as a biofilm on linuron as the sole carbon, nitrogen, and energy source, the removal of 3,4-DCA by WDL7 increases the rate of linuron hydrolysis by strain WDL1, whereas N,O-DMHA degradation by WDL6 has no effect on linuron hydrolysis. Metabolic association during linuron degradation appears the major driving force of the consortium composition and functionality, we do not know whether other interactions underlie the synergistic degradation of linuron It is not yet clear which carbon source(s) support the growth of the primary linuron degrader strain WDL1 in the consortium. In its first application to scrutinize an organic xenobiotic-degrading consortium, we used differential RNAseq to identify molecular mechanisms mediating synergistic interactions between the members of the linuron-degrading consortium consisting of Variovorax sp. Focus was on mutualistic partners WDL1 and WDL7 for which gene expression was compared between consortium and monoculture biofilms fed with linuron or 3,4-DCA as the sole carbon and energy source
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