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Objectives  To characterize the bacterial community of Wind Cave’s Madison aquifer through whole-genome sequencing, and to better understand the bacterial ecology by identifying genes involved in acyl-homoserine lactone (AHL) based quorum-sensing (QS) systems.    Results  Genome-based taxonomic classification revealed the microbial richness present in the pristine Madison aquifer. The strains were found to span eleven genera and fourteen species, of which eight had uncertain taxonomic classifications. The genomes of strains SD129 and SD340 were found to contain the archetypical AHL QS system composed of two genes,  luxI  and  luxR . Surprisingly, the genomes of strains SD115, SD129, SD274 and SD316 were found to contain one to three  luxR  orphans (solos). Strain SD129, besides possessing an archetypical AHL QS  luxI-luxR  pair, also contained two  luxR  solos, while strain SD316 contained three LuxR solos and no  luxI-luxR  pairs. The ligand-binding domain of two LuxR solos, one each from strains SD129 and SD316, were found to contain novel substitutions not previously reported, thus may represent two LuxR orphans that detection and response to unknown self-produced signal(s), or to signal(s) produced by other organisms.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13104-021-05589-6.

bmc research notes

Genomic characterization of bacteria from the ultra-oligotrophic Madison aquifer: insight into the archetypical LuxI/LuxR and identification of novel LuxR solos