Microbial communities associated with blueberry plants: insights from microcosm, greenhouse and field experiments

Climate change and continuous population growth represent two of the greatest global challenges, further exacerbated by extreme weather events and the intensive use of chemical fertilizers and pesticides. These issues call for new strategies to optimize agricultural systems and promote more efficient, sustainable, and environmentally friendly practices. In this context, plant-associated microorganisms, including bacteria, fungi, and viruses, play a crucial role in supporting plant growth, health, and stress tolerance. Their application as bioformulated products represents a promising approach for sustainable agriculture, though it requires a deeper understanding of crop-associated microbial communities. Blueberry plants (Vaccinium spp.), both wild and cultivated, have gained major commercial importance due to the nutritional and health-promoting properties of their fruits. These plants typically grow in acidic, nutrient-poor soils, where survival largely depends on their ability to establish endosymbiotic associations with ericoid mycorrhizal (ErM) fungi. These versatile fungi act as both saprotrophs and symbionts, producing extracellular enzymes that enable them to exploit complex organic substrates. Despite the economic relevance of blueberry crops, limited information is available on their associated microbiota. One of the main aims of this PhD project was to provide an integrative overview of the microbial communities associated with Vaccinium corymbosum, to isolate novel ErM strains, and to evaluate their potential as plant growth-promoting microorganisms (PGPM). Fungal and bacterial communities were characterized in three plant compartments, bulk soil, rhizosphere, and endosphere, from two orchards with distinct soil properties. A culture-dependent approach targeting root-associated fungi was also conducted, leading to the isolation of two new Hyaloscypha hepaticicola strains. These isolates were tested in field trials and demonstrated promising plant growth promotion effects. A second goal of the project was to explore the ecological functions of ErM fungi, particularly their involvement in soil carbon and nitrogen dynamics and their interactions with other microbial communities. To investigate their ability to degrade recalcitrant substrates and promote plant growth in complex environments, a controlled microcosm system was established with various plant–fungus combinations, including V. corymbosum, V. myrtillus, and Pinus sylvestris, inoculated with O. maius, H. hepaticicola, or Paxillus involutus. Results showed that H. hepaticicola significantly enhanced biomass production in both host and non-host plants compared to O. maius-inoculated and uninoculated controls. Mycelial quantification by qPCR revealed no significant differences in fungal biomass among treatments, suggesting that the observed growth effect was not directly linked to fungal abundance but rather to the physiological and enzymatic adaptations of H. hepaticicola to the peat-rich substrate. RNA-Seq transcriptomic analyses confirmed this hypothesis, revealing the upregulation of genes encoding oxidoreductases, CAZymes, and transporters in root samples from H. hepaticicola-inoculated microcosms. These genes are likely involved in the degradation of complex organic substrates and the enhancement of nutrient availability, thereby supporting efficient plant–fungus nutrient exchange. Overall, this work provides new insights into the composition and function of blueberry-associated microbiota and highlights the ecological versatility of ErM fungi. The remarkable growth-promoting effects of H. hepaticicola underline its potential as a bioresource for developing sustainable agricultural systems and improving crop productivity in nutrient-poor soils.