Investigation of Cultivable Groundwater Bacteria in Shallow Aquifers Based on Dilution to Extinction Culturing and Their Gnome Analysis

초록

Bacteria play crucial biogeochemical roles in groundwater, a water resource important for human use. Cultivation of groundwater bacteria is important to understand their ecophysiological and genomic features relevant to groundwater ecosystems. But, research on cultivation of diverse groundwater microbes has not been performed much. To expand the diversity of cultured bacterial groups in groundwater, we performed high-throughput dilution-to-extinction culturing (HTC) for water samples collected from two groundwater wells located in an agricultural area, South Korea, during four seasons. A total of 1,042 putative pure bacterial strains were successfully isolated. Phylogenetic analyses of 16S rRNA genes showed that these HTC isolates were affiliated with diverse phyla, such as Proteobacteria, Bacteroidetes, and Actinobacteria. Notably, isolates belonging to abundant but notyet or rarely-cultured bacterial groups were obtained, including the OPB56, env.OPS_17, SJA-28, KD4-96 and OM190 clades. Genome sequencing and analyses were performed for three isolates of the OPB56 clade (c_Kapabacteria; GTDB). Biosynthetic pathways for quinone and heme, essential electron carriers in aerobic respiration, were lacking, implicating either auxotrophy or facultatively anaerobic lifestyle. This culture collection of diverse groundwater bacteria would be a valuable resource for better understanding of ecophysiological and genomic characteristics of groundwater microbes relevant to their habitats.