ArticleJournal of visualized experiments : JoVE2018
Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere.
Article in Journal of visualized experiments : JoVE, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
41 citing papers in PubMed.
- Isoprene-Emitting Transgenic Tobacco Shapes Root Microbiome and Enhances Growth of Co-Cultivated Non-Emitting Plants.Plant, cell & environment · 2026Article
- Distinct Defence Mechanisms of Allelopathic Rice Against Quinclorac-Susceptible and -Resistant Barnyardgrass: Involvement of Specific Metabolites and Rhizosheath Microbiota.Plant biotechnology journal · 2026Article
- Biomass Seedling Trays Drive Rhizosphere Microbiome Restructuring and PGPR Enrichment in Tomato.Plants (Basel, Switzerland) · 2026Article
- Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits.The ISME journal · 2026Article
- Root-associated bacterial and fungal communities of the endangered páramo bromeliad Puya goudotiana.PloS one · 2026Article
- Microbial community characterization in semi-hydroponic systems of Starbor kale (Current research in microbial sciences · 2026Article
- Microbial community composition and diversity in nodules and rhizosphere soil of bitter white lupine (Frontiers in microbiology · 2026Article
- Digging for meaningful connections: associations between root phenotypes and rhizosphere microbial diversity in maize.Plant and soil · 2026Article
- Locating the microbes along the maize root system under nitrogen limitation: a root phenotypic approach.Annals of botany · 2025Article
- Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Article
- Water Deficit Stress Alters the Microbial Community Assembly, Structure, and Sources in Corn and Sugar Beet.Environmental microbiology · 2025Article
- Underground guardians: how collagen and chitin amendments shape soil microbiome structure and function for Meloidogyne enterolobii control.Microbiome · 2025Article
- Deciphering Soil Microbial Dynamics in Northeastern American Grasslands with Goldenrods (Solidago sp.).Microbial ecology · 2025Article
- Characterizing the Soil Microbial Community Associated with the Fungal PathogenJournal of fungi (Basel, Switzerland) · 2025Article
- Comparative metagenomics of wild and cultivatedCurrent research in microbial sciences · 2025Article
- Transforming Agricultural and Sulfur Waste into Fertilizer: Assessing the Short-Term Effects on Microbial Biodiversity via a Metagenomic Approach.Life (Basel, Switzerland) · 2024Article
- Climate change and plant rhizosphere microbiomes: an experiential course-embedded research project.Journal of microbiology & biology education · 2024Article
- Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora.Nature communications · 2024Article
- Inoculum and pH effects on ammonium removal and microbial community dynamics in aquaponics systems.iScience · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The intimate interaction between plant host and associated microorganisms is crucial in determining plant fitness, and can foster improved tolerance to abiotic stresses and diseases. As the plant microbiome can be highly complex, low-cost, high-throughput methods such as amplicon-based sequencing of the 16S rRNA gene are often preferred for characterizing its microbial composition and diversity. However, the selection of appropriate methodology when conducting such experiments is critical for reducing biases that can make analysis and comparisons between samples and studies difficult. This protocol describes in detail a standardized methodology for the collection and extraction of DNA from soil, rhizosphere, and root samples. Additionally, we highlight a well-established 16S rRNA amplicon sequencing pipeline that allows for the exploration of the composition of bacterial communities in these samples, and can easily be adapted for other marker genes. This pipeline has been validated for a variety of plant species, including sorghum, maize, wheat, strawberry, and agave, and can help overcome issues associated with the contamination from plant organelles.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.