Mitigating the impact of soil salinity on tomato crops: unveiling the role of soil microorganisms

Soil salinization poses a significant threat to modern agriculture, particularly in southern Italy, where climate change exacerbates the challenges faced by crops. This research aims to investigate the soil microbiome of three Apulian locations, including coastal (Fasano and Margherita di Savoia) and inland areas (Foggia), to identify salt-adapted microorganisms that may lead to the discovery of novel plant-beneficial taxa for sustainable tomato cultivation. Soil of the three locations differed in macro- and micronutrients content, including sodium, with the highest and lowest salinity in Fasano and Foggia, respectively. No remarkable difference occurred in texture. By a metagenomic analysis (Illumina platform), differential operational taxonomic units (OTUs) were identified in the Bacteria-, Archaea-, and Fungi-specific amplicons among locations and through three stages of the tomato cropping cycle. β-diversity indices were significantly different among locations for bacteria and fungi, and over the season for archaea. α-diversity indices indicated greater variation among the locations than among the sampling time points. Microbial isolates from some soil samples, specifically Bacillus spp., Aspergillus spp., and Penicillium spp., were evaluated in vitro for their resistance to salinity and plant growth-promoting traits. Isolates from the saline soil (Fasano) showed Effective Concentration 50 (EC50) values higher than the isolates from Foggia, suggesting that the saline environment (Fasano) selected more resistant microbial populations. Overall, fungi exhibited greater resistance to salinity than bacteria. In planta experiments are underway to assess the ability of microbial isolates to improve tomato plants’ salinity tolerance.