Diversity and Community Structure of Endophytic Bacteria in the Bark and Stem of Cryptocarya massoy Revealed by 16S rRNA Amplicon Sequencing

Abstract

The masoi tree (Cryptocarya massoy), endemic to Papua, is valued for its essential oils rich in massoia lactone. However, conventional extraction methods raise sustainability concerns, highlighting the need for alternative sources of bioactive compounds. This study investigated the diversity and community structure of endophytic bacteria in different tissues of C. massoy using 16S rRNA amplicon sequencing. Bark (KBP), inner stem (BP), and twig bark (KRC) samples were collected and surface-sterilized before genomic DNA extraction. The full-length 16S rRNA gene was amplified and sequenced using the Oxford Nanopore Technologies (ONT) platform. Sequencing reads were quality-filtered, taxonomically classified against the NCBI database, and analyzed to characterize bacterial diversity and community composition. Agarose gel electrophoresis confirmed successful amplification of the approximately 1,500 bp target gene. BP yielded the highest sequencing output (192 Mbp), whereas KRC showed the highest proportion of reads with quality scores above Q15 (69.8%). Alpha diversity analysis indicated that BP harbored the richest and most diverse bacterial community, followed by KRC and KBP. Taxonomic profiling revealed that Pantoea dominated all three samples, particularly KRC. In contrast, BP exhibited a more diverse community, with notable contributions from Pseudomonas, Paraflimonas, Erwinia, and Paraburkholderia. These findings demonstrate tissue-associated variation in endophytic bacterial community composition, with the inner stem harboring greater bacterial diversity. This study provides information on the endophytic bacterial diversity of C. massoy and offers their possible roles in the biotransformation of plant derived compounds.