A microbiome survey of contrasting potato terroirs using 16S rRNA long-read sequencing

Abstract

Aims As a consequence of the increasing impact of climate change on crop production and food security worldwide, the need to explore agricultural systems in a sustainable manner is also intensified. The improvement of long-read metagenomics approaches might give valuable information not only on soil microbial communities, but also on their potential effects on plant phenotypes. Soil properties, climate conditions, and agricultural techniques are the main factors shaping microbial communities found in the soil and on the surface of the potatoes, influencing plant health and performance. The objective of this study was to decipher the bacterial communities in contrasting potato terroirs using long-read sequencing of the 16S rRNA gene. Methods To do so, 18 soil samples were taken from different potato fields in the island of Naxos (Island Terroir) and Northern Greece (Continental Terroir). Differences in soil properties and climatic conditions were also regarded to explore the possible motif of microbial structure and diversity in each region. Results Our results highlighted that contrasting potato terroirs strongly affected microbial community composition and diversity. A richer microbial composition in the island terroir was evident. A wide range of soil bacteria were identified, including Vicinamibacter, Neobacillus, Povalibacter, Microvirga, Thermoanaerobaculum, Arenimonas, and Rubrobacter, with different distribution patterns that resulted in characteristic microbial footprints. Conclusions In combination with soil analysis, microbial mapping might be a valuable tool, not only for gaining a deeper knowledge of their impact on potato production, but also for developing biomarkers that would uniquely define and characterize each potato habitat.