Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP

Abstract

BackgroundMicrobial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified.ResultsPrevious studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements.ConclusionsComparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.

Antibiotrophy: Key Function for Antibiotic-Resistant Bacteria to Colonize Soils—Case of Sulfamethazine-Degrading Microbacterium sp. C448

“…Although previous studies have indicated that sadA is potentially mobile in other antibiotroph strains (Ricken et al, 2017;Reis et al, 2019), our results did not show any increase in the sadA/groL ratio (data not shown), suggesting an absence of horizontal gene transfer. This is consistent with the chromosomic localization of sadA, which makes its mobility via a horizontal gene transfer event unlikely (whole genome sequencing of Microbacterium sp.…”

Profiling trace organic chemical biotransformation genes, enzymes and associated bacteria in microbial model communities

“…For example, SadA had a wider pocket than its homolog XiaF, and Leucobacter strain GP containing SadA showed better sulfonamide removal than Microbacterium sp. BR1 containing XiaF 76 .…”

Subsistence and complexity of antimicrobial resistance on a community‐wide level

“…This strain was actually the first bacterium for which the genes and enzymes involved in the use of an antibiotic as a carbon and energy source had been characterized. The sad cluster is flanked by sequences encoding for mobile genetic elements (Ricken et al, 2017), as was also the case for Candidatus Leucobacter sulfamidivorax, where multiple copies of sadA were found to be flanked by single IS1380 family transposases (Reis et al, 2019). Moreover, the sulfonamide-resistant gene sul1 is commonly found in class 1 integrons and therefore known to be easily disseminated (Gillings, 2014).…”