Title Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches
Author Shin Ae Lee1, Jiyoung Park1, Bora Chu1, Jeong Myeong Kim1, Jae-Ho Joa2, Mee Kyung Sang1, Jaekyeong Song1, and Hang-Yeon Weon1*
Address 1Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju 55365, Republic of Korea, 2Research Institute of Climate Change and Agriculture, National Institute of Horticultural & Herbal Science, RDA, Jeju 63240, Republic of Korea
Bibliography Journal of Microbiology, 54(12),823-831, 2016,
DOI 10.1007/s12275-016-6410-3
Key Words tomato rhizosphere, bacteria, diversity, culture collection, antibiotics
Abstract 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.