Integrated nanopore profiling of fungal and bacterial endophytes reveals microbiome reorganization in Catharanthus roseus under heavy metal stress

Endophytes play a crucial role in plant adaptation to environmental stress; however, their coordinated responses to heavy metal contamination remain insufficiently understood, particularly in medicinal plants. This study investigated the influence of metal-contaminated soils on the composition and structuring of endophytic communities associated with Catharanthus roseus, a pharmaceutically significant species. Plants were cultivated for 12 months in contaminated soil collected from an industrial site, Hindustan Shipyard Limited (Visakhapatnam, India), and in uncontaminated control soil from the GITAM garden. Surface-sterilized leaf and root tissues were subjected to culture-independent microbial profiling. Fungal endophytes were characterized using internal transcribed spacer (ITS) amplicon sequencing, while bacterial communities were analyzed through 16S rRNA gene sequencing using the Oxford Nanopore platform. Sequencing data were processed through established bioinformatic pipelines, with taxonomic classification performed against the UNITE and Greengenes databases. The results revealed pronounced tissue- and site-specific shifts in endophytic community composition, with root tissues exhibiting greater microbial diversity than leaves. Communities from contaminated soils displayed reduced overall diversity but selective enrichment of stress-tolerant and metal-adapted taxa, indicating strong environmental filtering. These findings demonstrate that heavy metal-stress drives restructuring of endophytic assemblages and highlight the potential of native endophytes in microbe-assisted phytoremediation and sustainable management of metal-contaminated soils.