Integrative functional profiling of rhizospheric and endophytic bacteria reveals Lelliottia aquatilis as a multifunctional PGPR in Himalayan ecosystems

Abstract

Background Plant growth-promoting (PGP) bacteria have traditionally been known to have the ability to enhance crop productivity, abiotic stress-tolerance and disease resistance and providing an environmentally-friendly alternative to the currently used chemical fertilizers and pesticides. In this study, endophytic and rhizospheric bacteria were isolated from Myrica esculenta and plants residing in termite mounds, i.e., Carissa carandas and Pyrus pashia, and analyzed for PGP properties, resistance to abiotic stress and biocontrol capabilities. Methods Bacterial isolates were screened thoroughly for PGP activities, biocontrol inhibition, biofilm production, extracellular polymeric substance production and catalase activity. Selected isolates were further tested for stress tolerance (salinity, drought and pH extremes), seed germination and growth promotion. The most efficient isolate was subjected to molecular characterization using 16S rRNA sequencing. Results Seven isolates reliably displayed a wide range of PGP characteristics: efficient phosphate solubilization (up to 12.8 µg/mL), high indole-3-acetic acid (IAA) levels (up to 16.8 µg/mL), siderophore activity and strong ammonia release. Fungal pathogens, i.e., Fusarium oxysporum, Fusarium solani and Macrophomina phaseolina were substantially inhibited by Lelliottia aquatilis strain MC3 in biocontrol experiments. Stress -tolerance tests showed strong tolerance to salt (up to 5% NaCl, survival at 10% NaCl), drought (PEG 25%) and pH extremes (5–9). Chickpea growth assays confirmed its functional relevance, with inoculation of MC3 achieving the highest shoot length enhancement. Molecular identification revealed MC3 as L. aquatilis, a taxon rarely reported as plant growth promoting rhizobacteria (PGPR). Conclusion These potential isolates are considerable candidates for biofertilizers and biocontrol developments in stress prone environments. L. aquatilis strain MC3 emerged as the most promising isolate due to its multifaceted PGP traits, strong biocontrol efficacy, abiotic stress-tolerance, and proven plant growth enhancement. To our knowledge, this is one of the first reports for identification of L. aquatilis as multifunctional PGPR from Himalayan ecosystems. This study introduces L. aquatilis strain MC3 as an emerging candidate for bioinoculant development.