Deciphering the endomicrobiome of Podophyllum hexandrum to reveal the endophytic bacterial-association of in-planta podophyllotoxin biosynthesis.

Understanding the change in plant-associated microbial diversity and secondary metabolite biosynthesis in medicinal plants due to their cultivation in non-natural habitat (NNH) is important to maintain their therapeutic importance. Here, the bacterial endomicrobiome of Podophyllum hexandrum plants of natural habitat (NH; Kardang and Triloknath locations) and NNH (Palampur location) was identified and its association with the biosynthesis of podophyllotoxin (PTOX) was revealed. Rhizomes (source of PTOX) of plants of NH had highest endophytic bacterial diversity compared to NNH-plants. Presence of plant-location and tissue-specific distinct and common taxa were also identified. Acinetobacter, Ralstonia and Pseudomonas were identified as core taxa, present in plants of both NH and NNH. Predictive functional analysis of endophytic communities revealed abundant presence of genes encoding initial enzymes of PTOX biosynthesis and plant growth promotion in the rhizomes and roots of Kardang locations. Higher accumulations of secondary metabolites such as PTOX (2.78 and 2.11 folds in Kardang and Triloknath rhizomes, respectively; 1.48 and 1.71 fold in Kardang and Triloknath roots, respectively), Picropodophyllotoxin (3.08 fold in Kardang rhizomes), Quercetin (1.65 fold in Kardang and 1.32 fold in Triloknath rhizomes; 3.07-fold in Kardang and 1.60 fold in Triloknath roots) and Kaempferol (1.66 and 1.24-fold in Kardang and Triloknath rhizomes, respectively; 2.91 and 1.94-fold in Kardang and Triloknath roots, respectively) were also found in NH compared to NNH. This study provides novel insight into the change in the endomicrobiome of NH and NNH-plants and their correlation to secondary metabolites biosynthesis, and that must be considered for cultivation practices.