Healthy Roots, Healthy Microbes? Metagenomic Exploration of Soil Microbiota in Contrasting Potato Fields ^†

Potato (Solanum tuberosum) is a globally significant crop due to its adaptability to various climatic conditions, nutritional value, and economic importance. As the global population rises, conventional agriculture practices relying heavily on synthetic inputs have become widespread, often resulting in environmental degradation. In response, sustainable agricultural approaches have gained prominence, particularly through the use of plant growth-promoting bacteria (PGPB), which enhance crop productivity while minimizing ecological impact.

This study aims to compare the microbial diversity and abundance of total bacterial communities and PGPB populations in agricultural fields producing either healthy or diseased potato plants. Soil and plant samples were collected from two distinct potato cultivation areas in Ödemiş, İzmir. The Ödemiş potato (known as “İzmir’s yellow girl”) has received geographical indication registration and has been certified with a designation of origin due to its unique taste, color, and composition. The fact that this is the first study to identify species diversity in both PGPB and metagenomic contexts related to this potato variety and its agricultural fields highlights the originality of the research. A total of 65 endophytic bacterial isolates were obtained, and the 10 most promising strains in terms of plant growth-promoting activity were identified using 16S rRNA gene sequencing. Additionally, a metagenomic analysis was conducted to examine the microbial composition of soils from both fields.

The metagenomic data revealed Proteobacteria (30.3% ± 0.32) as the dominant phylum, followed by Alphaproteobacteria (class, 10.66% ± 1.86), Xanthomonadales (order, 5.36% ± 1.6), Xanthomonadaceae (family, 30.3% ± 2.02), Kaistobacter (genus, 1.11% ± 0.41), and Anoxybacillus kestanbolensis (species, 0.21% ± 0.08) as the most abundant taxa. Furthermore, A. kestanbolensis was identified for the first time in a metagenomic study from a potato-growing agricultural field. These findings highlight significant differences in soil microbiota composition associated with plant health status and suggest that microbial community structure plays a critical role in disease resistance and soil functionality.

This study contributes valuable insights into the development of sustainable strategies for soil health improvement and biological disease management in potato cultivation. Understanding microbe–plant interactions is essential for ensuring food security and agricultural resilience in the face of global challenges.