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.
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