title: Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches.
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 culture-dependent 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.
authors.affiliation: Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea.
authors.forename: Shin Ae
authors.initials: SA
authors.lastname: Lee
authors.affiliation: Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea.
authors.forename: Jiyoung
authors.initials: J
authors.lastname: Park
authors.affiliation: Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea.
authors.forename: Bora
authors.initials: B
authors.lastname: Chu
authors.affiliation: Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea.
authors.forename: Jeong Myeong
authors.initials: JM
authors.lastname: Kim
authors.affiliation: Research Institute of Climate Change and Agriculture, National Institute of Horticultural & Herbal Science, RDA, Jeju, 63240, Republic of Korea.
authors.forename: Jae-Ho
authors.initials: JH
authors.lastname: Joa
authors.affiliation: Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea.
authors.forename: Mee Kyung
authors.initials: MK
authors.lastname: Sang
authors.affiliation: Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea.
authors.forename: Jaekyeong
authors.initials: J
authors.lastname: Song
authors.affiliation: Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Wanju, 55365, Republic of Korea. why@korea.kr.
authors.forename: Hang-Yeon
authors.initials: HY
authors.lastname: Weon
mesh_terms: D039903:Actinobacteria / Q000235:genetics / Q000302:isolation & purification; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001419:Bacteria / Q000145:classification* / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D001431:Bacteriological Techniques; D044822:Biodiversity; D003470:Culture Media / Q000737:chemistry; D004269:DNA, Bacterial / Q000235:genetics; D018551:Solanum lycopersicum / Q000033:anatomy & histology / Q000382:microbiology; D064307:Microbiota; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology; D020560:Proteobacteria / Q000235:genetics / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S; D058441:Rhizosphere; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
chemical_list: D000900:Anti-Bacterial Agents; D003470:Culture Media; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: antibiotics; bacteria; culture collection; diversity; tomato rhizosphere