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Boron-induced microbial filtering delays early rhizosphere establishment in agricultural soil

Preprint Created on 10 Sep 2026 bioRxiv

Excessive application of boron-based fertilizers in agriculture has led to increased boron accumulation in soil, adversely affecting microbial communities and plant species, ultimately contributing to boron-induced desertification. This study presents the first metagenome-based analysis of boron-contaminated agricultural soil in Northern West Bengal, India, providing a comprehensive profile of the soil microbiome under boron stress. Boron-amended and unamended agricultural soil samples were analyzed using metagenomics sequencing approach over 365 days under natural environmental conditions. The results revealed a significant decline in bacterial diversity in boron-amended soil, with Firmicutes emerging as the dominant phylum. Notably, all boron-tolerant bacterial strains belonged to Firmicutes, suggesting that high boron levels impose selective pressure favouring Gram-positive bacteria. The enrichment of metal-resistant and oligotrophic bacterial taxa in boron-amended soil underscores microbial adaptation to boron stress. In addition to microbial community dynamics, we investigated plant succession in boron-enriched soil, offering novel insights into the interplay between above- and below-ground ecosystems. Our findings highlight two key adaptive traits, high boron tolerance and oligotrophic survival strategies, that enable bacterial communities to persist in boron-rich environments. These results enhance our understanding of microbial resilience in chemically stressed soils and have implications for soil health and sustainable agriculture.

Sen, S., Mondal, N., Basak, C., Ghosh, W., Chakraborty, R.

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