Orchid Species Identity, Not Life Form, Shapes Root Bacterial Communities

The bacteria living inside orchid roots appear to be selected far more by the species of the host plant than by whether that plant grows in soil or on tree branches. A new study of ten Cymbidium orchid species, all grown side by side in the same greenhouse, found that host species identity explained nearly 60 percent of the variation in root endophytic bacterial communities, while the distinction between epiphytic and terrestrial life forms accounted for less than 7 percent.

Root bacterial communities were profiled by 16S rRNA gene amplicon sequencing. After rarefying each sample to 29,628 sequences, the team recovered 129,922 amplicon sequence variants, or ASVs, distributed across 33 phyla and 779 genera. The most abundant genera included Pseudomonas, Sphingomonas, the Burkholderia–Caballeronia–Paraburkholderia complex, Bradyrhizobium and Reyranella.

One of the most striking results was how little the bacterial communities overlapped between orchid species. This points to an extremely small interspecific core microbiome, suggesting that each Cymbidium species hosts a largely distinct set of root bacteria even when grown under identical conditions. Alpha-diversity measures told a similar story from a different angle: no diversity index differed between epiphytic and terrestrial orchids, yet the Shannon, Simpson and Pielou evenness indices all differed significantly among host species.

Statistical modeling reinforced the hierarchy of host effects. Single-factor permutational multivariate analysis showed that life form explained only 6.9 percent of community variation, infrageneric section 35.6 percent, and host species 59.9 percent. Even closely related species within the same section were significantly differentiated, with an effect size of roughly 0.51. The authors caution, however, that life form, section and species are partially confounded in this design, so these figures describe associations rather than fully independent effects. A random forest classifier independently corroborated the pattern: community composition correctly assigned all 60 samples to their host species, but life-form prediction did not generalize across species, and under leave-one-species-out cross-validation its accuracy fell to 50.0 percent, below the 60 percent majority-class baseline.

Subject of Research: Root endophytic bacterial communities of Cymbidium orchids and the relative influence of host species identity versus life form

Article Title: Host species identity outweighs life form in shaping the root endophytic bacterial communities of 10 Cymbidium species grown under uniform conditions

Article References: Chen, X., Fang, R., Zhang, T., Zhao, G., & Wang, F. (2026). Host species identity outweighs life form in shaping the root endophytic bacterial communities of 10 Cymbidium species grown under uniform conditions. Frontiers in Microbiology, 17, 1996961. https://doi.org/10.3389/fmicb.2026.1996961

Image Credits: AI Generated

DOI: 10.3389/fmicb.2026.1996961

Keywords: Cymbidium, orchid microbiome, root endophytic bacteria, 16S rRNA sequencing, host species identity, life form, community assembly, Proteobacteria, core microbiome, random forest classification, Host, species