On the Adaptation and Evolution of Sulfonamide-Subsisting Bacteria

The catabolic genes conferring antibiotics assimilation in bacteria, dubbed as subsistome, can provide a source of potential resistance determinants. Additionally, the distribution of such machinery may detoxicate the micro-environment inhabited by these bacteria, benefiting susceptible pathogens sharing that surroundings.

Using founding microbial communities collected from different municipal sewage, we examined the adaptation and evolution of sulfadiazine-subsisting bacteria occurring across both microbial community level and gene level in laboratory microcosms. By metagenomic assembly of enrichment cultures collected from three alternative stable states (spanning 334 days), in which recurrent complete mineralization of sulfadiazine as sole carbon source were recorded, we uncovered > 9000 bacterial genomes that are recapitulated in 511 species. In line with 16S rRNA gene amplicon analysis, analysis based on genome bins showed that microbial composition of sulfadiazine-subsisting community was contingent on founding populations on pre-assembly states, not only because of compositional variance across founding populations, but also because of inconsistent selection of adaptive species from the initial bacterial pool. Selected populations possess both plastic and evolved adaptation strategies.

Despite evidences based on short-read metagenomic sequencing indicated that genomic capacity for sulfadiazine subsistence was discovered in phylogenetic diverse genome bins, by using long-read sequencing, we validated that the canonic sulfadiazine metabolic gene clusters have assembled primarily vertically in sulfadiazine-subsisting communities, and it sweep to be fixed in Micrococcaceae lineage. We further isolated individual strains of Micrococcaceae across multiple communities and illustrated two representative configurations of sulfadiazine metabolic gene clusters, which can reside next to each other on the same chromosome or locate separately either on chromosome or extra-chromosomal mobile genetic elements, documenting the adaptive radiation in the specialist sulfadiazine-subsisting bacterial lineage.