The study set out to answer a deceptively simple question. Both vermicompost and Piriformospora indica, a root-colonizing endophytic fungus sometimes classified in the genus Serendipita, are known individually to promote plant growth and reshape soil microbial populations. What remained largely unknown was what happens when the two are applied together, and whether their combined effect on apple seedlings is simply additive or something more synergistic. To find out, the researchers grew apple seedlings under four regimes: an untreated control, vermicompost alone, fungal inoculation alone, and the two combined. They then measured everything from seedling biomass and root architecture to photosynthetic capacity, soil chemistry, enzyme activity, and the composition of the rhizosphere microbiome—the teeming microbial ecosystem hugging the root surface.

The results were striking in their consistency. Every treatment that included either vermicompost or the fungus promoted seedling growth, encouraged root development, and enhanced photosynthetic capacity compared with untreated controls. But the combination outperformed both single treatments, delivering the strongest gains across nearly every metric the team tracked. Seedlings receiving both the fungus and the worm castings grew larger, built more extensive root systems, and photosynthesized more efficiently than their counterparts in any other group. For orchardists and nursery operators, the implication is that these two inputs, often marketed and applied separately, may work best as a paired prescription.

Nutrient uptake told a more nuanced story. The combined treatment significantly increased both the uptake fluxes—the rate at which phosphorus and potassium streamed into the roots—and the total contents of those two essential macronutrients in plant tissue. Vermicompost alone, by contrast, was the standout for nitrogen uptake, improving the seedlings’ acquisition of that nutrient without the fungus needing to be present. This divergence suggests that the two amendments operate through partially distinct physiological channels: the fungus appears to amplify phosphorus and potassium mobilization, while the organic matter in vermicompost feeds the nitrogen cycle directly. Growers tailoring fertilization strategies to specific nutrient deficiencies could, in principle, select one or both inputs accordingly.

Soil health metrics followed a similar pattern. Both vermicompost and the combined treatment improved soil fertility and boosted the activity of soil enzymes, the biological catalysts that drive decomposition, nutrient mineralization, and organic matter turnover. Notably, the fungus on its own showed no significant benefit to these soil properties. That asymmetry is scientifically telling: it implies that Piriformospora indica does not so much improve the soil directly as it reprograms the plant and its microbial entourage to exploit the soil more effectively. The vermicompost, meanwhile, supplies the raw biochemical substrate—the carbon, nitrogen, and micronutrients—that enzymes and microbes need to do their work. Together, the two create a feedback loop in which better soil feeds better roots, and better roots cultivate better soil.

The heart of the study, however, lies in its microbiome analysis. Using high-throughput sequencing of rhizosphere soil, the researchers found that all three treatments enriched taxa classified as plant-growth-promoting, or PGP, microbes—organisms known to fix nitrogen, solubilize minerals, produce plant hormones, or suppress pathogens. But which of these enriched taxa actually mattered for the growth response? To move beyond correlation, the team deployed random-forest analysis, a machine-learning method that ranks microbial features by their predictive power for a given outcome. The algorithm’s verdict was unambiguous: the bacterial phylum Actinobacteriota, and within it especially the genus Streptomyces, emerged as the key contributor distinguishing high-performing seedlings from the rest.

Streptomyces are the workhorses of the actinomycete world, famous both for their earthy smell in freshly turned soil and for their prodigious output of antibiotics, including the compounds behind many clinical drugs. In the rhizosphere, they are prized for their ability to solubilize phosphorus, produce indole-3-acetic acid and other auxin-type hormones that stimulate root growth, and outcompete pathogens. The Shanxi team did not stop at statistical association. In a crucial experimental step, they isolated four Streptomyces strains directly from fresh vermicompost and inoculated apple seedlings with them. The purified bacteria reproduced the growth-promoting effects observed with the full vermicompost treatment, enhancing seedling vigor and soil fertility on their own. That causal demonstration elevates the finding from an intriguing correlation to a functional mechanism: actinomycetes recruited or enriched by vermicompost and the fungus are not passive bystanders but active agents of plant growth.

The study’s design reflects a broader shift in plant science toward viewing crops as holobionts—plants plus their associated microbiomes—as integrated biological units. Earlier work cited by the authors has shown that vermicompost can suppress apple replant disease, that Piriformospora indica reshapes rhizosphere communities in willows and other species, and that specific bacterial strains such as Pseudomonas sp. CM11 can induce lateral root formation in apple rootstocks. What this new research adds is a mechanistic bridge: a specific bacterial taxon, identifiable by machine-learning analysis and verifiable through strain isolation, that links a widely used organic amendment and a model endophytic fungus to concrete physiological outcomes in a major fruit crop. The four Streptomyces strains have been deposited in GenBank, and the full microbiome dataset is available in the NCBI Sequence Read Archive, giving other researchers the raw material to build on the work.

The practical implications extend well beyond the apple orchard. Vermicompost is already a cornerstone of organic and low-input agriculture worldwide, valued for improving soil structure, water retention, and nutrient availability. Piriformospora indica, meanwhile, is increasingly marketed as a biostimulant for horticultural crops, prized for its broad host range and its capacity to confer tolerance to drought, salinity, and heavy metals. If the growth benefits of both depend substantially on recruiting actinomycetes, then management practices that favor these bacteria—such as maintaining organic matter inputs, minimizing disruptive tillage, and avoiding broad-spectrum biocides—could amplify the returns on either investment. Conversely, the finding that the fungus alone did not improve soil fertility cautions against expecting microbial inoculants to substitute for organic amendments; the two appear to be complements, not substitutes.

There are, of course, caveats. The experiments were conducted on apple seedlings under controlled conditions, and translating seedling responses to mature orchard trees across seasons and variable field soils remains a challenge that the authors themselves acknowledge in framing their conclusions. The random-forest approach identifies predictive taxa but cannot fully disentangle whether Streptomyces abundance is a cause or a consequence of vigorous growth, though the strain-inoculation experiment goes a long way toward resolving that ambiguity. Still, the convergence of evidence—community profiling, machine-learning attribution, and functional validation with isolated strains—makes a compelling case that actinomycetes are central players in vermicompost- and fungus-mediated plant growth. For a discipline often accused of cataloging microbes without explaining them, the study offers a template: find the keystone taxon, isolate it, and prove it works. In the rhizosphere of a young apple tree, at least, the earthworm’s gift and the fungus’s partnership appear to converge on the same microscopic allies, quietly manufacturing the growth that growers see above ground.

Subject of Research: The role of rhizosphere Actinomycetes in vermicompost- and Piriformospora indica-mediated apple seedling growth and nutrient uptake

Article Title: Rhizosphere microbiome analysis revealed the role of Actinomycetes in vermicompost- and Piriformospora indica-mediated apple growth

Article References: Zhao, Q., Li, Q., Ma, X., Li, H., Qin, M., Zhang, Y., Chen, M., Cheng, C., & Li, L. (2026). Rhizosphere microbiome analysis revealed the role of Actinomycetes in vermicompost- and Piriformospora indica-mediated apple growth. Plant and Soil. https://doi.org/10.1007/s11104-026-09099-x

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09099-x

Keywords: apple, vermicompost, Piriformospora indica, rhizosphere microbiome, Actinomycetes, Streptomyces, plant growth promotion, soil fertility, nutrient uptake, soil enzymes, endophytic fungus, random forest analysis