ArticleJournal of microbiology (Seoul, Korea)2016
Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches.
Article in Journal of microbiology (Seoul, Korea), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Linking microbiome structure to functional analysis identifies resilientFrontiers in microbiology · 2026Article
- Community assembly and potential function analysis of the endophyte in Eucommia ulmoides.BMC microbiology · 2024Article
- Metagenomic evaluation of peanut rhizosphere microbiome from the farms of Saurashtra regions of Gujarat, India.Scientific reports · 2024Article
- Diversity and Functionality of Bacteria Associated with Different Tissues of Spider Heteropoda venatoria Revealed through Integration of High-Throughput Sequencing and Culturomics Approaches.Microbial ecology · 2024Article
- Structure and ecological function of the soil microbiome associated with 'Sanghuang' mushrooms suffering from fungal diseases.BMC microbiology · 2023Article
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- Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees.Plants (Basel, Switzerland) · 2023Review
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- Soil and Soilless Tomato Cultivation Promote Different Microbial Communities That Provide New Models for Future Crop Interventions.International journal of molecular sciences · 2022Article
- Cultivating the Bacterial Microbiota ofmSystems · 2021Article
- Manure-Based Amendments Influence Surface-Associated Bacteria and Markers of Antibiotic Resistance on Radishes Grown in Soils with Different Textures.Applied and environmental microbiology · 2021Article
- Bioprospecting of Beneficial Bacteria Traits Associated With Tomato Root in Greenhouse Environment Reveals That Sampling Sites Impact More Than the Root Compartment.Frontiers in plant science · 2021Article
- Formation, characterization and modeling of emergent synthetic microbial communities.Computational and structural biotechnology journal · 2021Article
- Article
- Phylogenetic farming: Can evolutionary history predict crop rotation via the soil microbiome?Evolutionary applications · 2020Article
- Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application.Journal of experimental botany · 2020Review
- Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota.Microorganisms · 2020Article
- Testing the Two-Step Model of Plant Root Microbiome Acquisition Under Multiple Plant Species and Soil Sources.Frontiers in microbiology · 2020Article
- Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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