Site and Organ-Specific Culture-Dependent Endophytic Diversity of Crocus sativus L. (Saffron) in Kashmir Himalaya, India

The endophytic diversity of a host plant has been shown to vary across various spatio-temporal scales and between different organs of a plant, but no such study has been carried out on the economically important plant Crocus sativus (saffron). To fill this knowledge gap, the present study was undertaken to document the diversity of culturable bacterial, actinomycete and fungal endophytes at multiple sites from vegetative and reproductive organs of C. sativus . A total of 1170 culturable endophytic isolates were recovered from 6480 tissue segments of C. sativus collected from six different study sites in Pampore region of Kashmir valley in India. These isolates were identified using 16S and ITS (internal transcribed spacer) rDNA barcode sequence analysis and were classified into 84 operational taxonomic units (OTUs), including 52 bacterial OTUs, 7 actinomycete OTUs and 25 fungal OTUs. The phylogenetic analysis of sequences separated them into four phyla, namely, Firmicutes (46%), Ascomycota (30%), Proteobacteria (16%) and Actinobacteria (8%). Significant differences were observed in the diversity of endophytic assemblages across various study sites and different plant organs ( P ≤ 0.001). Species richness was highest at the Baroosa site and lowest at the Chandhar site while the Shannon index was highest at the Baroosa site and lowest at the Letpur site. Among organs, species richness was highest in stigma and lowest in leaf. Similarly, Shannon index was highest for root and lowest for leaf. Further, 15 culturable endophytic OTUs showed organ specificity. The present study is the first comprehensive report that not only brings out differences in the diversity of endophytes associated with different organs and at different sites but also highlights the complexity of host-endophyte interaction at multiple scales.