Endophytic bacterial diversity in the roots of medicinal rice in Kerala

This investigation was an attempt to assess the root endophytic bacterial diversity in three distinct rice varieties: Black Njavara, Rakthasali, and Vaishak. The collaboration between plants and bacteria, forming a holobiont, is vital for plant health and resilience. The study employed metagenomics, specifically targeting the V ₃ -V ₄ regions of the 16S rRNA gene, to analyze the microbial diversity within the roots of these rice varieties. Surface sterilization and metagenomic DNA isolation protocols were optimized to ensure high-quality DNA devoid of epiphyte contamination. The metagenomic DNA was then subjected to 16S rRNA gene amplification and Next Generation Sequencing using the Illumina platform. Bioinformatics analysis, performed with QIIME2, revealed the taxonomic composition of the microbial communities. The results showcase significant diversity at different taxonomic levels. Cyanobacteria, Proteobacteria, and OD1 emerged as major phyla, with distinct abundance patterns in the three varieties. Genus-level analysis identified key players like Azospirillum , Sphingomonas , Caulobacter , and Novosphingobium , suggesting potential roles in plant growth promotion, nitrogen fixation, and stress tolerance. Moreover, a few genera such as Magnetospirillum, Sulfurospirillum, Agrobacterium, Rhodoblastus, Asticcacaulis , Elstera , Mycoplana , Asteroleplasma, Clostridium and Bdellovibrio were found exclusively in medicinal rice varieties, indicating potential role in production of pharmacologically active compounds. This research not only contributes to understanding plant-microbe interactions but also unveils potential applications in sustainable farming, human welfare and ecological welfare. The findings may pave the way for harnessing these microbial communities for improved agricultural practices, medicinal advancements, and ecosystem health.