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

Abstract

Endohyphal microbial communities, composed of bacteria and viruses residing within fungal hyphae, play important roles in shaping fungal phenotypes, host interactions, and ecological functions. While endohyphal bacteria have been shown to influence fungal pathogenicity, secondary metabolism, and adaptability, much remains unknown about their diversity and host specificity. Even less is known about endohyphal viruses, whose ecological roles and evolutionary dynamics are poorly understood. This study integrates genomic and transcriptomic approaches to (1) characterize the diversity of endohyphal bacterial and viral communities in fungal endophytes isolated from Fagus grandifolia leaves, and (2) assess potential host specialization through phylogenetic signal analyses. We analyzed 19 fungal isolates spanning eight fungal orders (Amphisphaeriales, Botryosphaeriales, Diaporthales, Glomerellales, Mucorales, Pleosporales, Sordariales, and Xylariales). Bacterial communities were highly diverse and showed significant phylogenetic signal, with core taxa—such as Bacillales, Burkholderiales, Enterobacterales, Hyphomicrobiales, and Pseudomonadales—shared across hosts. Several bacterial groups were associated with specific fungal orders, suggesting host specialization, Moraxellales, Sphingomonadales, and Streptosporangiaceae in Amphisphaeriales; Enterobacterales, Hyphomicrobiales, and Micrococcales in Glomerellales; and Cytophagales in Diaporthales. In contrast, viral communities were less diverse and dominated by double-stranded DNA viruses, primarily Bamfordvirae and Heunggongvirae. No core viral taxa were detected in metatranscriptomic data, and only a few reads of double-stranded RNA viruses were found. Overall, our results indicate potential host specialization in bacterial endophytes and limited viral diversity in fungal hosts, with dsDNA viruses dominating the endohyphal virome. These findings provide new insights into the ecological and evolutionary dynamics of fungal-associated microbiota. Future work expanding taxonomic reference databases and exploring the functional roles of these microbial symbionts will be essential to understanding their contributions to fungal biology, host interactions, and broader ecosystem processes.

Marcelo Araya-Salas

Research Associate

My research interests include evolutionary behavioral ecology, cultural evolution, scientific programming and all possible combinations of them.