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 1300 communities with corresponding edaphic measurements from nine US field sites. Field site explained most of the variance across bacterial and eukaryotic (predominantly fungal) communities, while pH, organic matter, and NPK concentrations also varied with community structure. Bacterial and eukaryotic potato soil microbiomes show 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 that were present, but unequally distributed, across all nine field sites. Many of these core ASVs belong to common soil genera, such as Bacillus and Mortierella, which may reveal functional potential involved in maintaining soil health across regionally variable soil systems.

Potato Microbiome: Relationship with Environmental Factors and Approaches for Microbiome Modulation

“…The authors reported a substantial regional variation in the microbial communities, which was contrasted with consistency between seasonal and cultivar factors. Three major phyla were reported among the bacteria: Pseudomonadota, Acidobacteriota and Actinomycetota, which was consistent with previous studies cited above [10,21], but on lower layers of taxonomy the arising details complicated the overall picture [22]. Typically, the colonization of potato tubers from soil involves bacteria from the rhizosphere penetrating into the roots of potato plants, passing through the roots, and reaching the cortex or endoderm cell layer.…”

“…It is formed in the process of evolutionary mechanisms by the selection of microbial taxa containing the necessary genes [20]. The main representatives of the potato core microbiome are Bradyrhizobium, Sphingobium and Microvirga, and the most abundant genera in the rhizosphere are Lentzea and Streptomyces [10,21], which is confirmed by a very recent largescale microbiome study across the US regions [22]. Additionally, Custer et al reported that in the rhizosphere, members of the phyla Actinomycetota and Pseudomonadota showed the highest relative abundances, with Lentzea and Streptomyces being the most abundant genera [23].…”

“…The investigations of the relationship between microbiome composition and soil type were constrained by a lack of large-scale research. Recently, a study of core microbiomes in several regions of the US (nine field sites total) was published by Klasek et al [22]. The authors reported a substantial regional variation in the microbial communities, which was contrasted with consistency between seasonal and cultivar factors.…”

“…The main representatives of the potato core microbiome are Bradyrhizobium, Sphingobium and Microvirga; the most abundant genera in the rhizosphere are Lentzea and Streptomyces [10,[21][22][23] Growth stages Specific bacterial genera were consistently present during the flowering stage of potato plant development [53,54] Soil type influence…”