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

• Published in: Environmental microbiology Vol. 24; no. 11; pp. 5105 - 5122
• Main Authors: Vasileiadis, Sotirios, Perruchon, Chiara, Scheer, Benjamin, Adrian, Lorenz, Steinbach, Nicole, Trevisan, Marco, Plaza‐Bolaños, Patricia, Agüera, Ana, Chatzinotas, Antonis, Karpouzas, Dimitrios G.
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01.11.2022; Wiley Subscription Services, Inc
• Subjects: Auxotrophy; Bacteria - genetics; Bacteria - metabolism; Biodegradation; Biodegradation, Environmental; Carbazole; Carbazoles; Carbazoles - metabolism; Catechol; Cleavage; Consortia; Degradation; Deoxyribonucleic acid; Detoxification; Dioxygenase; Dioxygenases - metabolism; DNA; Environmental impact; Fungicides; Fungicides, Industrial - metabolism; Gene expression; Genetic transformation; Genomes; Hydrogenophaga; Mass spectrometry; Mass spectroscopy; Metagenomics; Microorganisms; Proteomics; Sequence analysis; Sphingomonas; Sphingomonas - genetics; Sphingomonas - metabolism; Stable isotopes; Thiabendazole; Thiabendazole - metabolism; Transcriptomics; Vitamin B 12 - metabolism; Vitamin B12
• ISSN: 1462-2912; 1462-2920
• DOI: 10.1111/1462-2920.16116

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.