Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches
2016
Lee, S.A., National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, Republic of Korea | Park, J., National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, Republic of Korea | Chu, B., National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, Republic of Korea | Kim, J.M., National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, Republic of Korea | Joa, J.H., Nationa Institute of Horticultural and Herbal Science, RDA, Jeju, Republic of Korea | Sang, M.K., National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, Republic of Korea | Song, J., National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, Republic of Korea | Weon, H.Y., National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, Republic of Korea
The microbiome in the rhizosphere the region surrounding plant roots plays a key role in plant growth and health, enhancing nutrient availability and protecting plants from biotic and abiotic stresses. To assess bacterial diversity in the tomato rhizosphere, we performed two contrasting approaches: culture-dependent and -independent. In the culturedependent approach, two culture media (Reasoner's 2A agar and soil extract agar) were supplemented with 12 antibiotics for isolating diverse bacteria from the tomato rhizosphere by inhibiting predominant bacteria. A total of 689 bacterial isolates were clustered into 164 operational taxonomic units (OTUs) at 97% sequence similarity, and these were found to belong to five bacterial phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes). Of these, 122 OTUs were retrieved from the antibiotic-containing media, and 80 OTUs were recovered by one specific antibiotic-containing medium. In the culture-independent approach, we conducted Illumina MiSeq amplicon sequencing of the 16S rRNA gene and obtained 19,215 high-quality sequences, which clustered into 478 OTUs belonging to 16 phyla. Among the total OTUs from the MiSeq dataset, 22% were recovered in the culture collection, whereas 41% of OTUs in the culture collection were not captured by MiSeq sequencing. These results showed that antibiotics were effective in isolating various taxa that were not readily isolated on antibiotic-free media, and that both contrasting approaches provided complementary information to characterize bacterial diversity in the tomato rhizosphere.
Show more [+] Less [-]AGROVOC Keywords
Bibliographic information
This bibliographic record has been provided by Korea Agricultural Science Digital Library
