The stakes are considerable. Strawberry is a hybrid of two American species, Fragaria virginiana and F. chiloensis, that was created in Europe and has since become a global crop with a market value projected to exceed 43 billion US dollars by 2028. Yet the modern industry rests on a fragile chemical foundation. Growers may apply up to 36 pesticide treatments per year, roughly 18 kilograms of plant protectants per hectare, and strawberries consistently rank near the top of the so-called Dirty Dozen list of pesticide-contaminated produce. Climate change compounds the problem: warming temperatures are pushing pests and pathogens toward higher latitudes and elevations, and Europe alone recorded 142 novel pathogen introductions between 2012 and 2022, including viruses, bacteria, and fungi.

The review’s central claim is that strawberry’s unusual biology creates an equally unusual microbiome, and that this microbiome can be harnessed for protection. Unlike most dicotyledonous plants, strawberry builds its root system around a compact crown from which short-lived adventitious and lateral roots continuously emerge and die. This rapid root turnover generates a dynamic rhizosphere in which microbial colonization and succession repeat in cycles, potentially producing microbial assemblages distinct from those of other crops. The plant also propagates vegetatively through stolons, the runners that connect mother plants to daughter plants, providing a physical route for microbes to pass between generations.

That stolon pathway cuts both ways. Researchers have documented identical endophytic bacteria, including Pseudomonas fluorescens and Pantoea species, in both stolons and seeds, and the beneficial nitrogen-fixing bacterium Azospirillum brasilense has been shown microscopically to migrate from mother to daughter plants. But pathogens exploit the same corridor: Fusarium oxysporum f. sp. fragariae, the cause of Fusarium wilt, and the bacterium responsible for strawberry marginal chlorosis both move through stolons. Understanding which microbes ride the runners, the authors argue, could be key to establishing stable, disease-resistant microbial communities in the next generation of plants.

The rhizosphere emerges as the front line of this microbial battlefield. Survey data show the strawberry root zone is dominated by Proteobacteria, followed by Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes, with fungal communities dominated by Ascomycota. A landmark 2015 study identified a South Korean field that had maintained remarkably low Fusarium wilt incidence despite fifteen years of continuous strawberry monoculture. The secret lay in the soil: a high relative abundance of Actinobacteria, and in particular a Streptomyces strain designated S4-7, which produces a thiopeptide antibiotic called conprimycin that disrupts cell wall biosynthesis in the Fusarium pathogen by targeting its cell wall remodeling kinase PKC1 and the Golgi transporter SBE2.

Subsequent work has shown that pathogen attack itself reshapes the root community in ways that depend on the plant’s genetic background. Inoculation with the charcoal rot pathogen Macrophomina phaseolina reduced microbial diversity, while Verticillium dahliae increased it. Cultivars resistant to Verticillium consistently enriched Actinobacteria such as Arthrobacter, Nocardioides, and Gaiella, alongside Acidobacteria, taxa presumed to suppress the fungus through antifungal compounds and cell wall-degrading enzymes like chitinase. Even airborne infections leave fingerprints below ground: foliar challenge with the gray mold pathogen Botrytis cinerea enriched Actinobacteria in the rhizosphere, while Colletotrichum infection depleted beneficial genera including Streptomyces, Bacillus, Azospirillum, and Trichoderma. Whether these shifts represent a plant-driven recruitment of defenders or pathogen-mediated sabotage remains an open question the review highlights as a research priority.

Beneficial microbes can also be introduced deliberately, and the evidence suggests they work as ecosystem engineers rather than simple replacements. When researchers applied a consortium of plant growth-promoting rhizobacteria comprising Bacillus subtilis, Bacillus amyloliquefaciens, and Pseudomonas monteilii to field-grown strawberries, the treatment selectively enriched functional taxa involved in nitrogen fixation, nutrient cycling, and pathogen suppression, even though overall diversity measures barely changed. Similarly, a commercial fermented soil amendment called VESTA increased the abundance of Betaproteobacteria involved in nitrogen and sulfur cycling, yet most of the enriched taxa were not even present in the formulation, indicating the product rewired existing microbial networks through plant-microbe interactions rather than displacing the native community.

Above ground, the phyllosphere tells a story of movement and exchange. A core bacterial community dominated by Sphingomonas, Pseudomonas, Bacillus, Methylobacterium, and Flavobacterium persists across cultivars, but its composition varies with genotype. More strikingly, the aerial surfaces of strawberry plants function as ecological crossroads with insects. Predatory mites introduced to greenhouse crops enriched Sphingomonas, Methylobacterium, and Pseudomonas on the leaves, while pollinating bees delivered the bacterial genera Snodgrasella and Gilliamella. In one remarkable case documented in Nature Communications, the beneficial bacterium Streptomyces globisporus SP6C4, first found in the strawberry phyllosphere, spreads among plants via pollinator movement, suppresses fungal diseases, and even protects bees from entomopathogenic fungi, forming a bacteria-plant-insect tripartite alliance. Leaf microbes, meanwhile, are transferred to developing fruit at rates of 38 to 80 percent for bacteria and 50 to 99 percent for fungi, making the phyllosphere a key reservoir for fruit health and postharvest quality.

The practical payoff comes in the form of biological control agents, and the review catalogs an impressive arsenal. Bacillus velezensis strains reduced Fusarium wilt incidence by up to 69.2 percent in field conditions, while a bioorganic fertilizer containing Bacillus licheniformis and B. methylotrophicus suppressed the disease by 80 percent. The microalga Chlorella fusca cut disease severity by 70.4 percent, and combinations of Pseudomonas fluorescens strains producing the antimicrobials 2,4-diacetylphloroglucinol and phenazine-1-carboxylic acid reduced Phytophthora root rot by up to 80 percent. Against foliar anthracnose, Paenibacillus polymyxa TP3 induced systemic resistance that reduced lesion size by 56.8 percent, and, notably, the defense priming was transmitted through stolons to daughter plants, suggesting induced immunity can persist across clonal generations. For postharvest gray mold, the yeast Rhodotorula glutinis cut disease incidence by more than 94 percent, and the mycoparasitic fungus Clonostachys rosea reduced flower and fruit infection rates by roughly 80 percent under field conditions.

Looking forward, the authors outline a roadmap that moves beyond single-strain biocontrol. Synthetic microbial communities, or SynComs, composed of complementary strains for growth promotion, resistance induction, and pathogen inhibition represent the next generation of microbiome manipulation, but their design is hampered by a shortage of high-resolution, function-oriented metagenomic data for strawberry. Artificial intelligence and explainable machine learning could identify keystone taxa and model the interactions within these consortia, while precision agriculture tools such as wearable volatile sensors, hyperspectral imaging, and LED-modulated lighting could create closed-cycle production systems tailored to microbiome health. The authors also propose microbiome-assisted breeding that selects for the plant’s ability to recruit beneficial microbes, a trait they frame through the plant social networking system model, and even raise the provocative possibility that strawberry-associated microbes such as Pseudomonas, Sphingomonas, and Methylobacterium, which have been detected in the human gut at low abundances, may make the fruit not just a source of nutrients but an ecologically meaningful microbial carrier. If the holobiome concept delivers on its promise, the future of strawberry farming may be written less in pesticide labels than in the grammar of microbial communities.

Subject of Research: The strawberry holobiome and its role in biotic stress tolerance and disease suppression

Article Title: Protective holobiome promotes strawberry tolerance of biotic stresses

Article References: Son, J.-S., Lee, S. Y., Sang, M. K., Spinelli, F., & Ryu, C.-M. (2026). Protective holobiome promotes strawberry tolerance of biotic stresses. Stress Biology, 6(1), Article 23. https://doi.org/10.1007/s44154-026-00294-5

Image Credits: AI Generated

DOI: 10.1007/s44154-026-00294-5

Keywords: strawberry, holobiome, microbiome, biological control, plant pathogens, rhizosphere, phyllosphere, induced systemic resistance, SynComs, Fusarium wilt, Botrytis cinerea, sustainable agriculture