NGS amplicon metagenomic 16S seq of soybean rhizosphere under contrasting nutrient-deficient and acidic-stress soils

Acidic and nutrient stress conditions are key limiting factors affecting
the low soybean productivity and sustainability in Indonesia. They are
closely associated with the structure and diversity of bacterial
communities in the rhizosphere, which play a crucial role in plant health
and productivity. This study aims to deeply explore the diversity and
structure of bacterial communities in the rhizosphere under acidic stress
and nutrient-deficient conditions, which are essential for rhizomicrobiome
engineering to enhance soybean productivity. The investigation using a
metagenomic approach was conducted in soybean rhizospheres under two
contrasting abiotic stress conditions: highly acidic and
nutrient-deficient soil, and slightly acidic to neutral soil with moderate
fertility. High-throughput next-generation sequencing of 16S rRNA gene
amplicons was performed to profile microbial diversity and community
composition across different pH stress gradients. The findings demonstrate
that soil acidity and nutrient deficiency significantly influence the
structure and diversity of bacterial communities in the soybean
rhizosphere. Acidic stress alters microbial composition, increasing the
relative abundance of Acidobacteriota and Patescibacteria, which are well
adapted to low pH conditions while reducing Verrucomicrobiota and
Myxococcota, which are more sensitive to acidic environments. Alpha
diversity analysis revealed greater microbial richness and evenness in
acidic soils, whereas beta diversity metrics indicated distinct clustering
patterns associated with soil pH levels. Heatmap analysis showed that
Chloroflexi were most abundant in acidic soils, whereas Myxococcota
predominated in non-acidic soils. Functional predictions suggest an
upregulation of genes associated with acid resistance, nutrient cycling,
and stress adaptation in acidic soils, highlighting the potential role of
acid-tolerant bacterial taxa in promoting sustainable soybean cultivation.
These findings contribute to a deeper understanding of the interactions
between soil acidity, nutrient availability, and microbial ecology,
providing a foundation for microbial-based strategies to enhance crop
resilience in acidic and nutrient-deficient environments.