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

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.

[Impact of Tourism on Bacterial Communities of Karst Underground River: A Case Study from Two Caves in Fengdu, Chongqing].

In this research, the bacterial community compositions of underground water in a tourist and pristine cave were studied. Xueyu Cave and Shuiming Cave are tourist and pristine caves, respectively, in the same karst cave system located in Chongqing, southwest China. To understand the impact of tourism on bacterial community compositions in underground water that flows through the caves, filtered materials from water were collected, and 16S rDNA gene sequences were obtained by high-throughput sequencing. The Shuiming Cave (the pristine cave) had less diversity than Xueyu Cave (the tourist cave) based on the Shannon's diversity index according to Illumina operational taxonomic units (OTUs). Proteobacteria, represented mostly by γ-Proteobacterium and Bacteroidetes, dominated both systems. OTUs from Shuiming Cave were dominated by 38% Proteobacteria, 24% Chlorobi, and 19% Bacteroidetes. In the Xueyu Cave, OTUs from upstream samples were comprised of 62% Proteobacteria but comprised 64% in the downstream samples. In the Xueyu Cave, Bacteroidetes accounted for 11% of the total OTUs in the upstream sample and 16% in the downstream. Among the γ-Proteobacterium and Bacteroidetes, Acinetobacter, Pseudomonas spp., and Flavobacteriaceae, which are related to potentially pathogenic species, were prevalent in the Xueyu Cave, while Methylococcaceae-uncultured, Methylomonas spp., and Methylobacter, all methane-oxidizing bacteria, had high relative abundances in the Shuiming Cave. These results revealed that potentially more pathogenic bacteria are present in the stream waters from the tourist cave, which has important implications for the protection of tourist caves. The RDA analysis of the environmental factor and bacteria community in groundwater showed that the distribution of pathogenic bacteria was positively correlated with the cave air CO2, and the Spearman correlation analysis of the two environmental factors indicated that the influence of the number of tourists on the structure of the bacterial community in the groundwater was more obvious and led to the disappearance of a large number of native bacteria. We proposed that tourist caves control the number of daily tourists and that they enter in batches and increase the import and export of closed devices to avoid the cave air exchange inside and outside. In addition, it was recommended that they increase the import and export of sterilization devices to reduce tourists with bacteria and organic matter, and avoid leaving garbage in the hole to avoid cave microbial exchange inside and outside. A reduction in the fixed lighting inside caves should be required to reduce long exposure, since the tourists can bring individual source lighting.