Nutritional inter‐dependencies and a carbazole‐dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazole

Abstract

Thiabendazole (TBZ), is a persistent fungicide/anthelminthic and a serious environmental threat. We previously enriched a TBZ‐degrading bacterial consortium and provided first evidence for a Sphingomonas involvement in TBZ transformation. Here, using a multi‐omic approach combined with DNA‐stable isotope probing (SIP) we verified the key degrading role of Sphingomonas and identify potential microbial interactions governing consortium functioning. SIP and amplicon sequencing analysis of the heavy and light DNA fraction of cultures grown on 13C‐labelled versus 12C‐TBZ showed that 66% of the 13C‐labelled TBZ was assimilated by Sphingomonas. Metagenomic analysis retrieved 18 metagenome‐assembled genomes with the dominant belonging to Sphingomonas, Sinobacteriaceae, Bradyrhizobium, Filimonas and Hydrogenophaga. Meta‐transcriptomics/‐proteomics and non‐target mass spectrometry suggested TBZ transformation by Sphingomonas via initial cleavage by a carbazole dioxygenase (car) to thiazole‐4‐carboxamidine (terminal compound) and catechol or a cleaved benzyl ring derivative, further transformed through an ortho‐cleavage (cat) pathway. Microbial co‐occurrence and gene expression networks suggested strong interactions between Sphingomonas and a Hydrogenophaga. The latter activated its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway to satisfy its B12 auxotrophy. Our findings indicate microbial interactions aligning with the ‘black queen hypothesis’ where Sphingomonas (detoxifier, B12 recipient) and Hydrogenophaga (B12 producer, enjoying detoxification) act as both helpers and beneficiaries.

β-Ketoadipic acid production from poly(ethylene terephthalate) waste via chemobiological upcycling

“… 14 For pKE112-catABCpcaD, DNA fragments from each gene were cloned sequentially using EcoRI , KpnI , BamHI , SbfI , and HindIII restriction enzymes. 15 pKM212-tphBAabc was also created by inserting four genes into five restriction enzyme sites. The synthesized aroY was digested with BamHI and SbfI before being ligated into pKA312 and digested with the same restriction enzymes.…”

Metagenomic and proteomic insights into the self‐adaptive cell surface hydrophobicity of Sphingomonas sp. strain PAH02 reducing the migration of cadmium‐phenanthrene co‐pollutant in rice

“…More importantly, knowledge gaps regarding what critical genes and proteins mediate the self‐adaptive CSH changes of Sphingomonas sp. still exist so far, which should thus be systemically elucidated (Chang et al, 2022; Vasileiadis et al, 2022). Recent advances in metagenome assembly and Tandem Mass Tag (TMT) proteome technologies would be greatly expected to peek into the subtle interaction mechanisms therein and can provide a comprehensive view of how bacteria adapt to environmental stresses at the gene and protein level (Zhang et al, 2022).…”

Analysis of predation-driven inoculum loss and carbon flow in bioaugmented soils through DNA-SIP

“…Stable isotope probing (SIP) of DNA can assess trophic linkages between microbes or identify their contributions to specific functions in the environment [28]. SIP has been widely applied to trace carbon transfer in soil food webs [29][30][31][32], and to identify microbial degraders in bioremediation processes [33][34][35][36][37][38]. Most commonly, a labelled substrate is added to the soil to follow its fate as it is consumed by the soil biota.…”