Metatranscriptomic profiling of active endophytic microbiome functions across diverse Musa cultivars

ABSTRACT 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. IMPORTANCE Endophytic microbiomes can influence plant health, but their active roles inside banana tissues remain poorly characterized. Here, we used metatranscriptomic profiling of culture-free enriched endophytic microbiomes from seven Musa cultivars to identify microbial taxa and functional pathways detected across sampled tissues. Metatranscriptomic data characterized pathways related to metabolism, transport, microbial signaling, biofilm formation, nutrient cycling, and secondary metabolism, suggesting potential variation in active microbiome profiles among sampled plants. This work provides a pilot resource for banana endophyte research and may help guide future studies on how plant-associated microbiomes interact with their hosts, how microbes function together inside plant tissues, and how these relationships could be used for microbiome-based crop improvement.