Rhizosphere Microbiota and Gene Expression in Common Bean Under Farming Systems

A study integrating metabarcoding and RNA-seq data evaluates the impact of organic and conventional farming on common bean rhizosphere microbiota and root gene expression. The analysis identified 5511 differentially expressed genes and quantified microbial diversity, reporting 2961 vs. 1532 bacterial ASVs and 372 vs. 321 fungal ASVs between farming systems. The dataset was created by Marta Suarez-Fernandez and published in 2026.

Use Cases

• Analyze correlations between farming system type and the abundance of microbial taxa like Funneliformis, Metarhizium, Chitinophaga, and Rhizobium.
• Model the relationship between differentially expressed genes (DEGs) with |log2FC| ≥ 2 and enriched functions like secondary metabolism, redox homeostasis, or hormone signaling.
• Investigate the fungi-to-prokaryote ratio as a potential indicator of farming system impact on the rhizosphere community.
• Examine links between upregulated DEGs involved in the synthesis of root exudate metabolites (fatty acids, indolic compounds, organic acids) and the recruitment of specific microbial taxa.

Strengths

• Integrates two high-throughput data types: metabarcoding (16S rRNA and ITS) and RNA sequencing (RNA-seq).
• Reports concrete microbial diversity metrics, including 2961 bacterial ASVs under conventional farming and 372 fungal ASVs under organic farming.
• Identifies 5511 differentially expressed genes, with 1085 showing strong fold-change (|log2FC| ≥ 2).

Limitations

• The dataset scale is limited to 13.2 MB, suggesting a focused experimental study rather than a large-scale survey.
• Specific sample size (number of biological replicates, plots, or rows of data) is not provided in the input.
• Geographic origin and specific temporal details of the study are not stated, limiting generalizability.

Provenance

Source

figshare, authored by Marta Suarez-Fernandez.

Collection Method

Data generated from an experimental study integrating metabarcoding and RNA-seq approaches on common bean plants under different farming systems.

Time Range

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Freshness

Last updated in March 2026.

Geography

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