Characterization of Bacterial Community in Shallow Aquifers by Dilution-to-Extinction Culturing and Culture- Independent Analyses

초록

While most of the research on groundwater microorganisms have focused on the aspects of bioremediation, pathogenic microorganisms, and microbial dark matters, cultivation of groundwater microorganisms has been less studied. Cultivation of groundwater prokaryotes, especially the uncultured, is important to understand their physiology, metabolism, and ecological roles. High-throughput-cultivation (HTC) based on dilution-to-extinction method has been proven to be highly efficient in isolating representative bacterial groups. To isolate uncultured groups of groundwater microorganisms, we investigated the microbial community of the groundwater in Yang-gu, Korea, using the seasonal HTC and 16S rRNA gene amplicon sequencing. A total of 1,042 bacterial strains were successfully cultivated using the HTC method. Phylogenetic analysis of 16S rRNA genes of the bacterial strains showed that they belong to diverse taxa such as the phyla Proteobacteria (Alpha-, Beta- and Gammaproteobacteria), Bacteroidetes, and Actinobacteria. Notably, isolates belonging to several previously uncultured lineages, such as the OPB56 and SJA-28 clade, were obtained in this study. Through the 16S rDNA amplicon sequencing analysis, the abundance and distribution of cultured bacterial groups were also determined. This study will be a valuable resource for further studies on the microbial community dwelling in groundwater environments.