Metatranscriptomic profiling of active endophytic microbiome functions across diverse Musa cultivars

Plant-endophyte symbioses play important roles in plant health and resilience, but the active functions of endophytic microbiomes remain less characterized than those of soil and rhizosphere microbiomes. We used metatranscriptomic profiling of culture-free enriched endophytic microbiomes from seven Musa cultivars grown under shared environmental conditions to characterize active microbial taxa and functional annotations across sampled tissues. Because each genotype and tissue combination had only one metatranscriptomic sample, this pilot study focuses on the microbial transcripts and functions detected in each sample rather than testing for cultivar or tissue differences. Culture-free enrichment produced metatranscriptomic profiles across samples, including 5,434 taxonomic annotations, and 32,694 gene annotations from expressed microbial transcripts. Functional annotations included pathways involved in secondary metabolism, energy production, environmental information processing, transport systems, oxidative phosphorylation, nitrogen metabolism, quorum sensing, biofilm formation, and xenobiotic biodegradation. Several taxa, including Bradyrhizobium sp., were detected across multiple samples and linked to diverse functional annotations. Approximately 30–35% of sequence reads were annotated as hypothetical proteins, showing that the functions of many detected transcripts are still unknown. Correlation analysis also showed sample-level associations among detected pathway profiles. Overall, this pilot metatranscriptomic data set provides a resource for banana endophyte research and identifies candidate microbial taxa and functional pathways for future studies of plant–microbiome interactions and microbe–microbe relationships.