Farming system shapes rhizosphere microbiota and root gene expression in common bean

Area of Science:

• Plant-microbe interactions
• Agricultural ecology
• Molecular biology

Background:

• The rhizosphere is a critical zone for plant-microbe communication and nutrient exchange.
• Farming practices significantly influence the composition of rhizosphere microbial communities and plant responses.
• Understanding these interactions is key to sustainable agriculture and crop improvement.

Purpose of the Study:

• To investigate the impact of organic versus conventional farming on common bean rhizosphere microbiota.
• To analyze root gene expression changes in response to different farming systems.
• To correlate microbial community shifts with plant molecular responses.

Main Methods:

• Integrated metabarcoding (16S rRNA and ITS sequencing) for microbial community profiling.
• RNA sequencing (RNA-seq) for comprehensive root gene expression analysis.
• Bioinformatic and statistical analyses to link microbial and transcriptomic data.

Main Results:

• Organic farming showed higher fungal diversity and a greater fungi-to-prokaryote ratio, promoting beneficial taxa like Rhizobium.
• Conventional farming exhibited higher bacterial diversity, favoring distinct microbial groups.
• Transcriptomic analysis revealed significant upregulation of genes involved in secondary metabolism, hormone signaling, and nutrient transport under organic conditions, with correlations to beneficial fungi.

Conclusions:

• Organic farming practices foster a more beneficial rhizosphere microbiome and induce advantageous gene expression in common bean roots.
• Specific microbial taxa are associated with the induction of plant genes related to growth, defense, and symbiosis.
• This study provides insights into molecular mechanisms underlying plant-microbe interactions, aiding future breeding programs for enhanced crop resilience.