Uncovering the microbial diversity of Chak-hao rice: Isolation and characterisation of indigenous beneficial microbes in Manipur

Abstract

Chak-hao (Oryza sativa L.), an aromatic black glutinous rice native to Manipur, is valued for its unique fragrance and high nutraceutical value, including iron, vitamin E and antioxidants. The present study aimed to isolate and characterise beneficial rhizospheric and endophytic microbes that could enhance Chak-hao rice cultivation. A total of 170 bacterial and 55 fungal isolates were obtained from different Chak-hao varieties collected from the farmers’ fields across four districts of Manipur. These isolates were screened for plant growth-promoting traits such as phosphate solubilisation, indole-3-acetic acid (IAA) production, nitrogen fixation and antagonistic activity against harmful fungal pathogens. The study showed 51.94 % phosphate solubilisation, 41.26 % produced IAA and 9.2 % exhibited nitrogen-fixing ability. Based on multiple plant growth promoting traits, 11 promising isolates were selected for molecular characterisation. The 16S ribosomal DNA (16S rDNA) sequencing identified these isolates as belonging to Bacillus, Enterobacter and Pseudomonas genera, with Bacillus species being predominant. Microbial inoculation significantly improved grain yield, straw yield and aroma-associated compounds compared to the untreated control (p ≤ 0.05, Duncan’s multiple range test). The study reveals the potential of indigenous beneficial microbes as eco-friendly biofertilisers and biocontrol agents for sustainable Chak-hao rice cultivation, quality grain improvement and conservation of unique Chak-hao rice germplasm Manipur.