Potato Soil Core Microbiomes Are Regionally Variable Across the Continental United States

Abstract

Soil microbiomes play crucial roles in pathogen suppression, nutrient mobilization, and maintenance of plant health. Their complexity and variability across spatial and temporal scales provide challenges for identifying common targets—microbial taxa or assemblages—for management in agricultural systems. To understand how microbiomes in potato production soils vary across growing regions and identify commonly distributed taxa among them, we compiled a continental-scale bacterial and eukaryotic amplicon dataset of over 1,300 communities with corresponding edaphic measurements from nine U.S. field sites. Field site explained most of the variance across bacterial and eukaryotic (predominantly fungal) communities, while pH and organic matter as well as nitrate, phosphate, and potassium concentrations also varied with community structure. Bacterial and eukaryotic potato soil microbiomes showed consistent phylum-level composition across locations at the continental scale, with regional-scale differences evident among genera and amplicon sequence variants (ASVs). Core community analysis identified 606 bacterial and 74 eukaryotic ASVs, which were present, but unequally distributed, across all nine field sites. Many of these core ASVs belonged to common soil genera, such as Bacillus and Mortierella, which may reveal the functional potential involved in maintaining soil health across regionally variable soil systems.