Impact of domestication on root microbiota: a comparison between cultivated and wild varieties biodiversity

Abstract presented at the Advancing Soil Knowledge for a Sustainable Future:.the VII EUROSOIL Meeting 8-12 de septiembre de 2025, Sevilla

Understanding how domestication has shaped the rhizosphere microbiota is essential to clarify the ecological consequences of plant breeding and to harness beneficial microbes for sustainable agriculture. Despite increasing interest, the extent and nature of microbial changes induced by domestication remain unclear, partly due to limited comparative data between wild and cultivated plant taxa across different soil environments. To address this gap, we conducted a metabarcoding-based analysis of rhizosphere and bulk soil microbiota from 128 samples collected in agricultural and natural environments in the Trentino region. Domestication and intensive cultivation greatly influence the interaction between plants and their root-associated microbiota (Bulgarelli et al., 2013). However, the effect on rhizosphere microbiota composition and function remains unclear. Studies suggest reduced microbial diversity, but outcomes vary depending on selected plant traits, agronomic practices, and species, and the underlying mechanisms are poorly understood. Our taxonomic analysis revealed genera such as Geomyces and Penicillium, known soil decomposers; Geomyces is particularly associated with cold environments. Mortierella and Solicoccozyma were identified as plant growth-promoting fungi (Carvajal et al., 2024; Ozimek & Hanaka, 2021). Alpha diversity indices showed cultivated plants host significantly richer and more diverse microbial communities, with higher species richness in cultivated roots suggesting a more permissive or selective rhizosphere environment (Tkacz et al., 2015). Beta diversity analysis revealed clear separation between cultivated and wild groups, with cultivated samples forming distinct clusters. These results indicate that domestication shapes not only plant genomes but also root-associated microbial communities, confirming that microbial structure is influenced by domestication, agronomic practices, and soil management (Pérez-Jaramillo et al., 2018). ACKNOWLEDGEMENTS This paper and related research have been conducted during and with the support of the Italian national inter-university PhD course in Sustainable Development and Climate change (link: http://www.phd-sdc.it).

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This study was supported by the Agritech National Research Center and received funding from the European Union Next-Generation EU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR)—MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4—D.D. 1032 17/06/2022, CN00000022).

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