Catabolic task division between two near‐isogenic subpopulations co‐existing in a herbicide‐degrading bacterial consortium: consequences for the interspecies consortium metabolic model

Abstract

SummaryVariovorax sp. WDL1 mediates hydrolysis of the herbicide linuron into 3,4-dichloroaniline (DCA) and N,Odimethylhydroxylamine in a tripartite bacterial consortium with Comamonas testosteroni WDL7 and Hyphomicrobium sulfonivorans WDL6. Although strain WDL1 contains the dcaQTA1A2B operon for DCA oxidation, this conversion is mainly performed by WDL7. Phenotypic diversification observed in WDL1 cultures and scrutiny of the WDL1 genome suggest that WDL1 cultures consist of two dedicated subpopulations, i.e., a linuron-hydrolysing subpopulation (Lin 1 DCA-) and a DCA-oxidizing subpopulation (Lin-DCA1). Whole genome analysis of strains representing the respective subpopulations revealed that they are identical, aside from the presence of hylA (in Lin 1 DCA-cells) and the dcaQ-TA1A2B gene cluster (in Lin-DCA1 cells), and that these catabolic gene modules replace each other at exactly the same locus on a 1380 kb extrachromosomal element that shows plasmid gene functions including genes for transferability by conjugation. Both subpopulations proliferate in consortium biofilms fed with linuron, but Lin 1 DCAcells compose the main WDL1 subpopulation. Our observations instigated revisiting the interactions within the consortium and suggest that the physical separation of two essential linuron catabolic gene clusters in WDL1 by mutually exclusive integration in the same mobile genetic element is key to the existence of WDL1 in a consortium mode.

Proma Plasmids are Instrumental in the Dissemination of Linuron Catabolic Genes between Different Genera

“…pEN1 on the other hand carries a hylA - dcaQ junction identical to that on pWDL1-1, the Variovorax sp. WDL1 megaplasmid that carries the linuron degradation genes of this bacterium (Albers et al, 2018; Öztürk et al, 2019). As previously reported for pWDL1-1 and pPBS-H4-2, the catabolic clusters on the newly-sequenced PromA plasmids are flanked by IS 1071 -class II insertion elements, forming putative composite transposons.…”

“…The insertion site of the pEN1 IS 1071 element is an exception among the PromA plasmids. The insertion site of this IS 1071 element, associated with the hylA gene and adjacent ORFs (Albers et al, 2018; Öztürk et al, 2019), lies between the backbone genes repB and mobA . This site is located before the first insertion site of the other catabolic plasmids relative to repA , and exists in other PromA γ plasmids, but with four nucleotide differences.…”

“…Isogenic subpopulations carrying either hylA or dca genes were reported for Variovorax sp. WDL1 before (Albers et al, 2018). It was proposed that the existence of two subpopulations may be an adaptation to linuron degradation in a consortium, where linuron is degraded to DCA hylA -carrying consortium member, while the DCA degradation is performed by the other consortium members (Albers et al, 2018).…”

“…WDL1 before (Albers et al, 2018). It was proposed that the existence of two subpopulations may be an adaptation to linuron degradation in a consortium, where linuron is degraded to DCA hylA -carrying consortium member, while the DCA degradation is performed by the other consortium members (Albers et al, 2018). Indeed, PBL-H3 indeed tends to accumulate DCA when growing on linuron on its own, and performed much better in a consortium with other DCA degraders (Breugelmans et al, 2007).…”

“…qPCR reactions were performed with the ABsolute QPCR Mix (Thermo Fisher) on a Roche LightCycler 480 II. The qPCRs for 16S rRNA gene (Lopez-Gutierrez et al, 2004), hylA (Horemans et al, 2016) and dcaQ (Albers et al, 2018) quantification were performed as previously described. qPCR targeting korB was performed as previously-described, except that the Taqman probe was omitted (Jechalke et al, 2013).…”