Green agricultural innovations to face food and climate crises

Despite their crucial importance, the role of seed-borne microorganisms during germination is still largely unexplored. Agricultural crops are often treated with pest control agents. However, there is growing interest in using biodegradable, bio-based materials to replace synthetic polymers in seed treatments. Consequently, culturing methods and basic DNA approaches are likely inadequate for assessing microbial contamination or treatment effects on seed-borne microbes during germination. The main objective of this study was to develop a novel seed quality approach and a cost-effective, easy-to-use tool to elucidate interactions between seed-borne microorganisms and treated seeds during germination. The first chapter summarizes the development of a germination apparatus specifically designed to examine both seed germination and seed-borne microorganism growth. The apparatus, patent pending, was designed and produced using 3D-printing technology, fits standard single-use 50-mL centrifuge tubes, and prevents microbial contamination from external sources. The second chapter focuses on seed-borne microorganisms, particularly endophytes. The use of the germination tube was combined with traditional microbiological techniques and advanced Next Generation Sequencing (NGS) metabarcoding analysis. This approach allowed the identification of the entire fungal community recovered from corn germinating seeds. The results highlight the importance of carefully monitoring the use of fungicides in seed treatments, as they could promote the selection of microorganisms with resistance, such as Aspergillus flavus, a fungus of agricultural and medical relevance. The final chapter presents a study on using biochar in corn seed treatment to improve germination. Being a bio-based solution, the study also investigated the potential growth of a key fungus of corn seeds, Aspergillus flavus. In conclusion, the germination apparatus enabled deeper investigation of seed–microorganism interactions during germination. Findings from these studies support using this tool and NGS to assess seed quality, especially relevant given rising interest in bio-based seed treatments and beneficial microbes to enhance germination and protection.