Data Sheet 1_Farming system shapes rhizosphere microbiota and root gene expression in common bean.pdf

A study integrating metabarcoding and RNA-seq data compares rhizosphere microbiota and root gene expression in common bean under organic and conventional farming systems. It identifies 5511 differentially expressed genes and reports 2961 vs. 1532 bacterial ASVs and 372 vs. 321 fungal ASVs across the two systems. The research by Marta Suarez-Fernandez provides a basis for investigating plant-microbe interactions and cultivar breeding.

Use Cases

• Analyze correlations between beneficial fungal taxa like Funneliformis and Metarhizium and the induction of genes related to plant growth and defense.
• Identify differentially expressed genes (DEGs) with |log2FC| ≥ 2, such as those involved in secondary metabolism and nodulation, to understand farming system impacts.
• Compare the fungi-to-prokaryote ratio and ASV counts for bacterial (2961 vs. 1532) and fungal (372 vs. 321) communities between organic and conventional systems.
• Examine DEGs involved in the synthesis of root exudate metabolites, including fatty acids and indolic compounds, for their role in microbial recruitment.

Strengths

• Integrates two high-resolution molecular methods: metabarcoding (16S rRNA and ITS) and RNA sequencing (RNA-seq).
• Reports specific quantitative findings, including 5511 differentially expressed genes and distinct Amplicon Sequence Variant (ASV) counts for bacterial and fungal communities.
• Provides detailed taxonomic and functional insights, identifying promoted microbial genera and enriched gene functions per farming system.

Limitations

• Data is presented in a PDF report (1.7 MB), not in a structured, machine-readable tabular format, limiting direct computational analysis.
• Sample size and specific row/column counts for underlying sequencing data are unknown from the provided description.
• The study's geographic location and specific temporal coverage for sample collection are not specified.

Provenance

Source

Marta Suarez-Fernandez via figshare.

Collection Method

Integration of metabarcoding (16S rRNA and ITS) and RNA sequencing (RNA-seq) approaches on common bean plants grown under organic and conventional systems.

Time Range

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Freshness

Last updated March 2026.

Geography

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