Hidden Bacterial World Inside a Famous Yunnan Medicinal Plant Revealed

Deep in the high-altitude mountains of Yunnan, China, grows a plant that has been prized in traditional medicine for centuries. Aucklandia lappa Decne., known as one of the ten major Yunnan medicines, produces roots rich in bioactive compounds and has long been cultivated for its therapeutic value. Yet the microscopic passengers living inside its tissues have remained almost entirely a mystery. A new study published in BMC Plant Biology by Yunxia Li, Yanmei Yang and colleagues at Yunnan Agricultural University, working with partners at the Potato Seeds Research and Development Center of Xuanwei and the Luliang County Plant Protection and Quarantine Station, has now provided the first systematic look at the endophytic bacterial community inhabiting the roots of this celebrated medicinal species. The findings open a window onto a hidden microbial ecosystem that may hold keys to better cultivation, natural crop protection and even environmental cleanup.

Endophytic bacteria are microorganisms that colonize the interior tissues of plants without causing disease. Far from being passive squatters, these bacteria often engage in intimate metabolic exchanges with their hosts, supplying nutrients, modulating hormone signaling, priming immune responses and helping the plant withstand environmental stress. In medicinal plants, endophytes have attracted particular interest because some strains can influence the production of secondary metabolites, the very compounds that give medicinal plants their pharmacological value. For A. lappa, which thrives at high elevations where cold temperatures and intense ultraviolet radiation impose constant physiological challenges, the endophytic community could be especially important in underpinning the plant’s resilience. Until this study, however, no one had characterized the diversity or the functional potential of the bacteria living within its roots.

The research team took a dual approach that combined culturomics, the systematic isolation and identification of living microorganisms, with high-throughput microbiomic sequencing of the total root-associated bacterial DNA. This two-pronged strategy matters because each method captures a different slice of microbial reality. Cultivation recovers living strains that can be stored, tested and deployed, but many environmental bacteria resist growth on artificial media. Sequencing, by contrast, surveys the genetic signatures of the entire community, including species that have never been cultured in a laboratory, but it yields no living isolates. By running both approaches in parallel, the researchers could cross-validate their results and build a far more complete picture of who lives inside the roots of A. lappa and what those residents might be doing.

The culturing effort was remarkably productive. From the roots of A. lappa plants, the team isolated a total of 473 endophytic bacterial strains. To make this collection manageable for identification, they selected 157 representative strains and characterized them taxonomically. These representatives turned out to span three bacterial phyla, eighteen genera and fifty-five distinct species, a striking level of diversity for a single plant organ. Among the cultured representatives, certain taxa stood out as dominant, and notably the genera Serratia and Pseudomonas emerged as prominent members of the culturable community. The collection of 473 living strains now constitutes a preserved microbial resource bank that can be drawn upon for future experiments, breeding programs and product development aimed at this medicinal crop.

High-throughput sequencing of the root samples revealed an even broader hidden diversity. The sequencing data identified 35 bacterial phyla, 825 genera and 4,755 amplicon sequence variants, or ASVs, which are precise genetic operational units used to distinguish closely related bacterial populations. The dominant phyla detected were Pseudomonadota, Actinobacteriota and Bacillota, three of the most widespread and ecologically versatile bacterial lineages in plant-associated environments. At the genus level, Serratia and Pseudomonas again topped the abundance rankings, an important point of agreement with the culture-based results. When two independent methods converge on the same dominant taxa, confidence in the biological signal rises substantially, because the biases inherent in each technique are unlikely to produce identical artifacts. The convergence suggests that these genera are genuinely central players in the root endophytic community of A. lappa.

Identifying the residents of a microbial community is only the first step; understanding what they can do is the deeper question. To probe functional potential, the researchers applied three complementary computational prediction frameworks: PICRUSt2, FAPROTAX and BugBase. Each tool infers community functions from taxonomic composition by drawing on reference genomes and curated functional databases. PICRUSt2 predicts the metabolic pathways encoded by the community’s genes, FAPROTAX maps taxa onto known ecological functions such as degradation of specific compound classes, and BugBase assesses phenotype-level traits such as stress tolerance. The three methods together painted a coherent picture of a community equipped for plant growth promotion, the degradation of aromatic compounds and hydrocarbons, and adaptation to low temperatures.

Each of these predicted functions carries practical significance. Plant growth promotion by endophytes typically involves mechanisms such as nitrogen fixation, phosphate solubilization, siderophore production and synthesis of plant hormones, capabilities that can reduce the need for chemical fertilizers. The predicted capacity to degrade aromatic compounds and hydrocarbons points toward bioremediation potential, meaning the bacteria might help break down organic pollutants in soils where the medicinal plant is grown, a valuable trait for maintaining the purity of herbal medicine raw materials. The low-temperature adaptation signal is particularly intriguing given that A. lappa is a high-altitude species whose cultivation zones experience cold stress. Endophytes that help their host tolerate chilling could directly improve yields and quality in mountain agriculture, and the authors suggest the community may contribute to the plant’s resistance to low temperatures.

The authors are careful to note an important caveat: the functional predictions are based on in silico analyses, meaning they are computational inferences rather than experimentally demonstrated activities. Prediction tools extrapolate from what is known about related bacteria, and actual functions in the specific context of the A. lappa root environment must be confirmed through laboratory and greenhouse testing. This is a standard and appropriate limitation for a first survey of an unstudied microbiome. Nevertheless, the predicted functional landscape provides a concrete roadmap for follow-up work. Researchers can now prioritize specific strains, for example dominant Pseudomonas and Serratia isolates, for assays of growth promotion, pollutant degradation and cold tolerance, rather than screening blindly through hundreds of candidates.

The broader implications extend beyond a single medicinal species. Microbial fertilizers, biopesticides and bioremediation agents are all growth areas in sustainable agriculture, and native endophytes isolated from the crop they are meant to support are often ideal candidates for such products because they are already adapted to the host and its environment. The strain collection assembled in this study, with its 473 isolates representing 55 species across three phyla, constitutes exactly the kind of raw material from which such applications can be developed. For A. lappa specifically, whose status as a major Yunnan medicine makes it economically significant to regional agriculture, the prospect of microbiome-informed cultivation practices could improve both the sustainability and the quality of production in high-altitude farming systems.

This study also demonstrates the value of pairing culturomics with sequencing as a template for exploring the microbiomes of other understudied medicinal plants. Many traditional medicinal species grow in extreme environments, and their endophytic communities remain largely unmapped despite their potential to influence both plant health and metabolite profiles. By documenting 35 phyla, 825 genera and 4,755 ASVs in the roots of A. lappa, and by showing that culture-dependent and culture-independent methods agree on the dominant taxa, the researchers have established a baseline against which future studies can measure seasonal change, geographic variation and the effects of cultivation practices. The work, funded by the National Natural Science Foundation of China and the National Key R&D Program of China, marks the beginning rather than the end of the story, as the predicted functions await experimental validation and the isolated strains await deployment. What is already clear, however, is that inside the roots of this ancient medicinal plant lives a rich bacterial world whose secrets are only now coming to light.

Subject of Research: Diversity and functional potential of root endophytic bacterial communities in the high-altitude medicinal plant Aucklandia lappa Decne.

Article Title: Diversity and functional prediction of endophytic bacterial communities in Aucklandia lappa Decne.

Article References: Li, Y., Yang, Y., Wang, M., Wang, P., Xu, W., Liu, F., Li, Q., & Hu, X. (2026). Diversity and functional prediction of endophytic bacterial communities in Aucklandia lappa Decne.. BMC Plant Biology. https://doi.org/10.1186/s12870-026-09915-7

Image Credits: AI Generated

DOI: 10.1186/s12870-026-09915-7

Keywords: Aucklandia lappa, endophytic bacteria, microbiome, culturomics, high-throughput sequencing, Pseudomonas, Serratia, plant growth promotion, bioremediation, cold tolerance, medicinal plants, Yunnan