Changes in bacterial, archaeal, and fungal communities from saline soils cultivated with tomatoes in Italy

Background and Aims Soil salinization is a major concern in modern agriculture. In southern Italy, the climate change scenario is challenging tomato crops, especially because of increased average temperature, irregular precipitation patterns, and scarcity of irrigation fresh water. Apulia ranks among the top Italian regions producing processing tomatoes, but certain areas are being subjected to salinization, especially near the coast. Methods Physical-chemical and metagenomic analyses were conducted to compare Apulian saline and non-saline soils. Four fields from three areas were sampled during the tomato cropping cycle. Results Saline and non-saline soils differed for several chemical properties, especially exchangeable sodium, which increased over time, suggesting that soil salinization depended on irrigation water quality rather than pedoclimatic conditions. The amount of DNA extracted from soil samples, as well as the number of sequencing reads, were unexpectedly low at post-transplanting compared to the other two time points, indicating that the establishment of microbiomes in the rhizosphere takes place as the crop develops. In the three considered kingdoms, i.e., Bacteria, Archaea, and Fungi, differential operational taxonomic units (OTUs) were identified in saline and non-saline soils, including both dominant and rare taxa. Conclusions This will lead to the identification of taxa with a better fitness under high salinity, which could be considered for searching for new plantbeneficial microbes sustaining tomato crops cultivated in salinized soils. Acknowledgments. This work was funded by the research project MiCroResi, within the framework “4th EU-LAC Multi-thematic Joint Call for collaborative projects from Europe, Latin-America and the Caribbean Countries”.