Vitali Francesco, Trzciński Paweł, Manfredini Andrea, Olimi Expedito, Bigiotti Gaia, Ptaszek Magdalena, Sas-Paszt Lidia, Bickel Samuel, Berg Gabriele, Canfora Loredana, Malusà Eligio, Mocali Stefano
Research Centre for Agriculture and Environment, Council for Agricultural Research and Economics (CREA-AA), Via di Lanciola, 12/A, Firenze, 50125, Italy.
The National Institute of Horticultural Research, Skierniewice, 96-100, Poland.
Sci Rep. 2025 Sep 29;15(1):33487. doi: 10.1038/s41598-025-15862-4.
The application of beneficial microorganisms with biostimulant, biofertilizer, and/or biopesticide properties represents an alternative to the use of chemicals in agriculture. Nevertheless, bioproducts' selection and application efficacy under field condition need to be improved. A deeper understanding of the bioinoculant strains at genomic and phenomic level, would advance selection process and field application. The objective of this manuscript was to develop a combined genomic-phenomic approach for the characterization of bioproducts, and to demonstrate its application with a real use-case scenario. At the genomic level, the presence of several functional genes supporting plant nutrition (e.g., nitrate conversion into ammonia, phosphorous solubilization, siderophore production), improving plant growth (e.g., plant hormones) or promoting plant health through antagonism to plant pathogens, pointed to the multifunctionality of the strain. The phenomic analysis showed various carbon, nitrogen, phosphate, and sulfur utilization patterns, and confirmed the expression of the associated metabolic pathways. Our analysis approach encompasses as many aspects of the genome and phenome as possible for understanding the complexities of a microorganism, enabling the generation of greater value compared to the individual technologies. The proposed approach unlocks data-driven decision making in bioproduct optimisation, as such should be routinely included in screening programs.
应用具有生物刺激素、生物肥料和/或生物农药特性的有益微生物是农业中使用化学物质的一种替代方法。然而，生物产品在田间条件下的选择和应用效果仍需提高。在基因组和表型水平上更深入地了解生物接种菌株，将推动选择过程和田间应用。本手稿的目的是开发一种用于生物产品表征的基因组-表型联合方法，并通过实际应用案例展示其应用。在基因组水平上，存在几个支持植物营养（例如，硝酸盐转化为氨、磷溶解、铁载体产生）、促进植物生长（例如，植物激素）或通过拮抗植物病原体促进植物健康的功能基因，这表明了该菌株的多功能性。表型分析显示了各种碳、氮、磷和硫的利用模式，并证实了相关代谢途径的表达。我们的分析方法涵盖了基因组和表型的尽可能多的方面，以了解微生物的复杂性，与单独的技术相比能够产生更大的价值。所提出的方法开启了生物产品优化中数据驱动的决策，因此应常规纳入筛选程序。
