Analysis of microbial community of soil of a ginseng field using culture- independent and culture-dependent approaches and description of the first pure-culture representative of phylum OP10

Abstract

The extent of microbial community diversity in two different types of rhizosphere of ginseng (NR & DR) and soil (NS & DS) of a ginseng field (Pocheon, KOREA) was analyzed with a culture-independent and a culture-dependent approach. As the culture-independent method, terminal restriction fragment length polymorphism (T-RFLP) and 16S RNA (SSU rRNA) gene-based approach with about 400-600 SSU rDNA clones were carried out to reveal community of bacterial operational taxonomic units (OTUs). In culture-independent method, total 268 clones were obtained. Several clones (5.2%) obtained from these analysis had sequence more than 20% different from those in the current databases, which mean putative novel phylum candidate. A few of the clones (1.5%) differed by 10-15% in sequence from the database. About 11% of the clones differed by 5-10%, 16% of the clones differed by 3-5%, and 66.5% of the clones differed by only 0-3%, and only 34% of the clones had sequences that were most closely related with cultured bacteria differed by 0-10% in sequence from the current database. This suggests that the sequences of these bacterial clones were highly diverse. Phylogenetic analysis indicated that these sequences fell into 17 of the 35-40 known phylogenetic divisions. Eight sequences had no specific association with any of the known divisions or candidate and phylogenetically divided into five novel division level groups, named after GSO1, GSO2, GSO3, GSO4, and GSO5. The phylogenetic distribution of the sequences between NS and DS samples was similar for the dominant divisions. For example, Actinobacteria was the dominant in both NS (23.0%) and DS (24.1%) samples, followed by Acidobacteria (11.5% and 16.7% for NS and DS samples), Alphaproteobacteria (10.3 and 16.7% for NS and DS samples), Betaproteobacteria (9.0 and 13.0% for NS and DS samples). The proportion of low G+C Gram positive bacteria was low in NS sample and not observed in DS sample. Cytophaga-Flexibacter-Bacteroides group...