Magaraci, Giuseppina (2026) Harnessing beneficial microbes and biological carriers for the development of innovative bioformulations: ecological and functional evaluation for soil and plant health. [Tesi di dottorato]

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Abstract

The One Health framework highlights the strong interdependence between human, animal, and environmental health, recognizing soil ecosystems and their microbial communities as fundamental components of sustainable and resilient agricultural systems. In recent decades, agricultural intensification has relied heavily on synthetic fertilizers and chemical inputs to sustain high productivity, leading to soil degradation, biodiversity loss, nutrient inefficiencies, and environmental pollution. These challenges emphasize the urgent need for alternative strategies that can maintain crop yields while reducing chemical inputs and preserving ecosystem functionality. In this context, microbial-based biofertilizers and biostimulants represent promising tools to support sustainable agriculture, circular bioeconomy, and One Health–oriented food systems. This thesis addresses key knowledge gaps related to the development, formulation, and in situ behavior of plant growth–promoting rhizobacteria (PGPR) by integrating microbial consortium design, formulation strategies, and advanced multi-omics approaches within a unified experimental framework. Particular attention was given to actinomycetes, a metabolically versatile group of microorganisms with recognized biotechnological potential that remains underexploited in agricultural microbial consortia. A comprehensive literature review highlighted their capacity to promote plant growth through nutrient mobilization, phytohormone production, enzyme secretion, stress mitigation, and the synthesis of bioactive compounds, supporting their inclusion in multifunctional microbial formulations. Based on these insights, a microbial consortium was developed consisting of one actinomycete strain, Streptomyces thermocarboxydus C2_8A, selected in this study, and four previously characterized bacterial strains with several plant growth–promoting traits (i.e. Methylobacterium populi VP2, Azotobacter chroococcum 76A, Priestia megaterium EL5 and Kosakonia. pseudosacchari TL13). Three innovative bioformulations were produced: (i) a freeze-dried powder, (ii) a liquid formulation based on alginate and castor oil, and (iii) a granular formulation obtained via solid-state fermentation using coffee silverskin, an agro-industrial by-product. This latter approach integrated microbial delivery with waste valorization, aligning agronomic innovation with circular economy objectives. The bioformulations were first evaluated on maize under controlled conditions to assess their effects on plant growth, nutrient availability, and soil and root-associated microbial communities. Results demonstrated that formulation strategy strongly influenced PGPR performance, persistence, and microbiome modulation. Among the tested approaches, the coffee silverskin–based granular formulation consistently showed superior effects on plant biomass, nutrient cycling, and microbial functional diversity, while supporting effective rhizosphere and root colonization without phytotoxic effects. Shotgun metagenomic sequencing, combined with whole-genome sequencing, enabled strain-level tracking of inoculated microorganisms, providing robust evidence of formulation-dependent persistence and functional relevance within complex soil–plant systems. The effectiveness of the bioformulations was further validated in a mesocosm experiment on processing tomato grown under full and reduced nitrogen fertilization regimes. Under low nitrogen input, microbial inoculation maintained crop yield and, in some cases, improved fruit quality parameters, including soluble solids and bioactive compound content. Microbiome analyses revealed compartment-specific and carrier-dependent responses, particularly in the rhizosphere, highlighting the critical role of formulation and carrier selection in shaping microbial dynamics and functional outcomes. Overall, this thesis demonstrates that the successful application of PGPR in sustainable agriculture depends on the integration of well-designed microbial consortia with appropriate formulation strategies. By combining agronomic performance, soil biological fertility, and reduced fertilizer inputs, this work provides a comprehensive framework for the development of microbial-based bioformulations that support resilient, low-input agricultural systems consistent with One Health principles and circular bioeconomy goals.

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