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Genomic insights reveal community structure and phylogenetic associations of endohyphal bacteria and viruses in fungal endophytes

Summary

Fungi living inside healthy plant leaves contain communities of bacteria and viruses. Researchers studied these microbial passengers in fungi from American beech leaves and found that bacteria show patterns of preference for specific fungal types, while viruses are less diverse and mostly DNA-based rather than RNA-based. Understanding these microbial relationships helps explain how fungi interact with plants and could potentially improve biological control strategies.

Background

Endohyphal microbial communities composed of bacteria and viruses residing within fungal hyphae play important roles in shaping fungal phenotypes and ecological functions. While endohyphal bacteria have been shown to influence fungal pathogenicity and secondary metabolism, much remains unknown about their diversity, host specificity, and viral associations.

Objective

This study aimed to characterize the diversity of endohyphal bacterial and viral communities in fungal endophytes isolated from Fagus grandifolia leaves using genomic and transcriptomic approaches, and to assess potential host specialization through phylogenetic signal analyses.

Results

Bacterial communities were highly diverse with significant phylogenetic signal and core taxa shared across hosts, including Bacillales, Burkholderiales, Enterobacterales, Hyphomicrobiales, and Pseudomonadales. Several bacterial groups showed host specialization with specific fungal orders. Viral communities were less diverse and dominated by double-stranded DNA viruses, primarily Bamfordvirae and Heunggongvirae, with no core viral taxa detected.

Conclusion

The results indicate potential host specialization in bacterial endophytes and limited viral diversity in fungal hosts. Double-stranded DNA viruses dominate the endohyphal virome, providing new insights into ecological and evolutionary dynamics of fungal-associated microbiota.
  • Published in:Environmental Microbiome,
  • Study Type:Observational Study,
  • Source: PMID: 40713930, DOI: 10.1186/s40793-025-00757-8
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