Cimminella, Carmen (2026) Microbial Biodiversity: a Source for Sustainable Plant Growth and Protection to Reduce Environment and Human Health Risks. [Tesi di dottorato]

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Abstract

The continuous growth of the global population, together with increasing pressures from climate change, soil degradation, water scarcity, and biodiversity loss, poses major challenges to modern agriculture. Conventional cropping systems, largely dependent on synthetic fertilizers and chemical plant protection products (PPPs), have significantly increased yields; however, long term use has resulted in serious environmental and ecological consequences, including soil and water contamination, negative effects on non-target organisms, disruption of soil microbial communities, and the emergence of resistant plant pathogens. Copper-based PPPs are frequently applied in conventional and organic farming for disease control, however, this element is non degradable and accumulates in the environment, where it can negatively affect soil fertility, microbial biodiversity and ecosystem functions. The European Union has introduced increasingly restrictive regulations on PPPs use to reduce risks to the environment and human health by promoting Integrated Pest Management (IPM) strategies and sustainable biologically based alternatives. Limitations have been imposed for copper use in the future, and it is designated for substitution. Within this framework, microbial-based bioformulations can be considered as valid alternatives to chemical PPPs due to their target specificity, biodegradability and limited persistence, resulting in lower risks to the environment, operators and consumers, with minimal impacts on non-target organisms. Plant-associated microbial communities contribute to nutrient cycling, plant growth, stress tolerance, and disease suppression. Therefore, exploiting microbial biodiversity to harness the plant beneficial activities can offer promising strategies to reduce chemical inputs while maintaining crop productivity and health, thus contributing to the biodiversity, resilience and sustainability of agroecosystems. The aim of this PhD research was to investigate the development of innovative and sustainable plant production-protection strategies that exploit microbial biodiversity to reduce environmental impact, while safeguarding environmental health and consumer well-being for use in agricultural and urban green management. The selection of suitable microorganism candidates was conducted based on the use of Bacillus and Trichoderma, since these bacteria and fungi include species widely studied and commercialized as plant growth-promoting microorganisms (PGPMs) and biological control agents (BCAs). Many of these taxa exhibit multiple and complementary mechanisms resulting in plant beneficial activities, including antagonism of pathogenic organisms, increased tolerance to abiotic stress, production of antimicrobial metabolites, manipulation of nutrient availability-uptake, competition for ecological niches, anti-biofilm activity, induction of systemic resistance, and phytohormone modulation. Microbial strains were identified and selected by functional characterization to assess their plant growth-promoting and biocontrol potential under controlled laboratory conditions, growth chambers, and greenhouse experiments. Studies focused on the screening and development of microbial consortia, based on their compatibility, functional complementation, and ecological stability, which that demonstrated greater consistency and broader efficacy than single-strain applications as plant biostimulants and biological control agents. An innovative aspect of the research included the screening of Bacillus and Trichoderma strains for compatibility with copper and the development of integrated formulations containing low copper doses combined with the microbial consortium to maintain disease control activities similar to the copper-based product. Effects of copper were also investigated in soils of an organically managed vineyard, where copper accumulation and impacts on microbial communities were analyzed using metagenomic approaches. Furthermore, novel protocols were developed by employing advanced in vitro phenotyping and imaging techniques to quantitatively assess plant growth, stress responses, and disease progression, thereby obtaining a more precise, rapid, and reproducible characterization of microbial effects on treated plants. These methodologies contribute to the standardization of monitoring and screening of numerous potential biostimulant and biocontrol microbial candidates that support the translation of laboratory findings to future greenhouse and field applications. In summary, a progressive experimental framework was adopted, integrating in vitro screening, greenhouse and growth chamber trials, advanced phenotyping approaches, and field analyses of soil microorganisms to achieve a comprehensive understanding of microbe-plant-soil interactions. Overall, the results of this PhD thesis demonstrated that beneficial microorganisms, particularly Bacillus and Trichoderma spp., used individually or as part of carefully designed consortia, can significantly contribute to sustainable crop management. The integration of microbial-based solutions with reduced chemical inputs offers a viable pathway to decrease reliance on conventional pesticides, preserve soil biodiversity, enhance plant resilience to biotic and abiotic stresses, and comply with evolving regulatory frameworks. Finally, this PhD thesis provides a robust scientific basis for the development of innovative plant protection and biostimulation strategies based on beneficial microorganisms that corresponds to the One Health approach, integrating plant health, environmental sustainability, biodiversity conservation, and human well being.

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