Culturomics and amplicon-based insights into the endophytic microbiome of Kalmegh (Andrographis paniculata (Burm.f.) Nees) and its implications in plant growth promotion.

Abstract

Leaf and stem endophytic microorganisms play an important role in plant physiology and secondary metabolite biosynthesis of plants, particularly in medicinal plants. Kalmegh (Andrographis paniculata (Burm.f.) Nees) is an important medicinal plant with liver-protective, anti-inflammatory, ovicidal, larvicidal, and anti-urolithatic properties. The medicinal activities are due to presence of andrographolides. This study investigated the culture-independent diversity of endophytic bacteria associated with Kalmegh at nursery, vegetative, and flowering stages using a metagenomic approach. The results revealed that Sphingomonas was the dominant bacterial genus during nursery and vegetative stages, whereas Halobacterium predominated during the flowering stage. Microbial abundance was highest in the nursery stage, followed by flowering and vegetative stages. Functional analysis showed that flowering stage endophytes were enriched with specialized carbon metabolism and aromatic compound degradation pathways, potentially influencing andrographolide biosynthesis. Chemical analysis supported these findings, showing the highest andrographolide content in leaves during flowering (3.1%). Gene expression analysis further demonstrated that increased andrographolide accumulation was associated with upregulation of methyl erythritol phosphate pathway (MEP) pathway and diterpene biosynthetic genes. Bacterial endophytes isolated from flowering-stage leaves exhibited plant growth-promotion, antifungal, and seed germination-enhancing activities. In vitro assays against Fusarium wilt and Rhizoctonia disease showed that Bacillus cereus strains KL11, KL12, and KL5 inhibited pathogen growth by 60-65%. Biopriming with strains KL3 and KL5 of Bacillus cereus improved seed germination and plant growth. Pot trials with Micrococcus luteus KES1 increased herbage yield, plant height, and andrographolide content by 43%. These findings highlight the potential of leaf and stem endophytes for sustainable improvement of Kalmegh productivity and andrographolide content in the plant.