Orchid Mycorrhizal Fungi Found Living Inside Stems, Leaves and Seeds

Mycorrhizal fungi, long thought to travel from soil into orchid roots and stop there, have now been detected throughout the bodies of three European orchid species. In a study published in Environmental Microbiome, researchers report that fungi belonging to the so-called rhizoctonia complex were found not only in the roots of Spiranthes spiralis, Serapias vomeracea and Neottia ovata, but also in their stems, leaves, seed capsules and, in one species, in the seeds themselves. The finding challenges a basic assumption about how these plant-fungus partnerships work.

Orchids are among the largest plant families on Earth, and their dependence on fungal partners is unusually intimate. Unlike most plants, orchid seeds contain almost no stored nutrients and cannot germinate without a fungus supplying carbon and other resources. For most green orchids, the fungi that make this possible belong to the rhizoctonia complex, a polyphyletic group that spans the families Tulasnellaceae, Ceratobasidiaceae, Serendipitaceae and Sebacinaceae within the subphylum Agaricomycotina. These fungi have generally been assumed to colonize orchid roots from the soil, where they live as saprotrophs, decomposing organic matter.

That assumption has had a persistent problem. Some rhizoctonia orchid mycorrhizal fungi have only rarely been detected by metabarcoding in soil samples taken around orchid roots. If the fungi are scarce or absent in the surrounding soil, the standard model of root colonization from soil becomes difficult to sustain. The research team, led by Jacopo Calevo with colleagues including Pasquale Alibrandi, Samuele Voyron, Mariangela Girlanda and Silvia Perotto, tested an alternative hypothesis: that adult orchid plants themselves may serve as a habitat for these fungi, harboring them not just in roots but in other organs as well.

To investigate, the researchers used metabarcoding, a DNA-based method that identifies fungal species present in a sample by sequencing genetic markers. They examined three terrestrial orchid species and screened tissues from roots, stems and leaves. The results were striking. In all three orchid species, a broad majority of the putative orchid mycorrhizal fungi found in roots was also detected in either the stems or the leaves of the same plant. This means the fungi were not confined to underground tissues but had spread systemically through the plant body.

The survey went further. Putative orchid mycorrhizal fungi were also detected in the seed capsules of all three species, and in seeds of Spiranthes spiralis. The presence of these fungi in reproductive structures raises the possibility that orchid-fungus associations may be transmitted in ways that do not depend entirely on soil, though the study reports occurrence rather than demonstrating a mechanism of transmission.

The authors describe the systemic occurrence of mycorrhizal fungi in plants as a novel finding. In their conclusions, they note that identifying orchid mycorrhizal symbionts in all orchid tissues raises important questions about the nature of the plant-fungus relationship in aerial organs. What these fungi are doing inside stems and leaves is not yet established. They may be passive residents, or they may play active roles in the nutrition and health of above-ground tissues, but the study does not resolve that question.

The technical significance lies partly in what metabarcoding revealed about fungal distribution. Because the method detects DNA signatures rather than requiring cultivation of the fungi, it can reveal organisms that would be missed by traditional isolation techniques. Applying it across multiple organ types from the same individual plants allowed the researchers to match fungal communities between roots and aerial tissues, showing that the same putative orchid mycorrhizal fungi occupied both.

For orchid biology, the results suggest that the root-centered view of orchid mycorrhizal symbiosis is incomplete. If rhizoctonia fungi inhabit the entire plant, ecological studies that sample only soil and roots may underestimate where these fungi live and how they persist. The rarity of rhizoctonia detections in soil around orchid roots, combined with their abundance inside plant tissues, hints that adult orchids could function as reservoirs for these fungi in the environment.

The study was published as a brief report in the journal Environmental Microbiome on 3 November 2026 and is available as an open-access article. As the authors conclude, the identification of orchid mycorrhizal symbionts in all orchid tissues opens a new line of inquiry into how these essential fungal partners interact with their hosts beyond the root zone, and what that means for one of the most distinctive plant-fungus partnerships in nature.

Subject of Research: Systemic occurrence of orchid mycorrhizal rhizoctonia fungi in roots, stems, leaves and reproductive tissues of three European orchid species

Article Title: Breaking boundaries: fungi in the “rhizoctonia” complex occur systemically in three European orchid species

Article References: Jacopo, C., Pasquale, A., Samuele, V., Mariangela, G., & Silvia, P. (2026). Breaking boundaries: fungi in the “rhizoctonia” complex occur systemically in three European orchid species. Environmental Microbiome. https://doi.org/10.1186/s40793-026-00965-w

Image Credits: AI Generated

DOI: 10.1186/s40793-026-00965-w

Keywords: orchids, mycorrhizal fungi, rhizoctonia, metabarcoding, Spiranthes spiralis, Serapias vomeracea, Neottia ovata, plant-fungus symbiosis, Environmental Microbiome, fungal ecology, orchid seeds, systemic colonization