Potato soil core microbiomes are regionally variable across the continental US

Authors: KLASEK, SCOTT - University Of Minnesota; CRANTS, JAMES - University Of Minnesota; ABBAS, TOUQEER - University Of Minnesota; ASHLEY, KATHERINE - University Of Maine; BOLTON, MARIAN - University Of Minnesota; CELOVSKY, MADELYN - Michigan State University; GUDMESTEAD, NEIL - North Dakota State University; HAO, JIANJUN - University Of Maine; IBARRA CABALLERO, JORGE - Colorado State University; JAHN, COURTNEY - Colorado State University; KAMGAN NKUEKAM, GILBERT - University Of Idaho; LANKAU, RICHARD - University Of Wisconsin; Larkin, Robert - Bob; LOPEZ-ECHARTEA, EGLANTINA - North Dakota State University; MILLER, JEFF - Miller Research, Inc; MOORE, AMBER - Oregon State University; PASCHE, JULIE - North Dakota State University; RUARK, MATTHEW - University Of Wisconsin; SCHROEDER, BRENDA - University Of Idaho; SHAN, SHAN - University Of Wisconsin; SKILLMAN, VICTORIA - Oregon State University; Srour, Ali; STASKO, ANNA - North Dakota State University; STEINKE, KURT - Michigan State University; STEWART, JANE - Colorado State University; THORNTON, MIKE - University Of Idaho; ZITNICK-ANDERSON, KIM - North Dakota State University; FROST, KENNETH - Oregon State University; ROSEN, CARL - University Of Minnesota; KINKEL, LINDA - University Of Minnesota

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/13/2023
Publication Date: 1/12/2024
Citation: Klasek, S.A., Crants, J.E., Abbas, T., Ashley, K., Bolton, M.L., Celovsky, M., Gudmestead, N.C., Hao, J., Ibarra Caballero, J.R., Jahn, C.E., Kamgan Nkuekam, G., Lankau, R.A., Larkin, R.P., Lopez-Echartea, E., Miller, J., Moore, A., Pasche, J.S., Ruark, M.D., Schroeder, B.K., Shan, S., Skillman, V.P., Srour, A.Y., Stasko, A.K., Steinke, K., Stewart, J.E., Thornton, M., Zitnick-Anderson, K., Frost, K.E., Rosen, C.J., Kinkel, L.L. 2024. Potato soil core microbiomes are regionally variable across the continental US. Phytobiomes Journal. 8(2):168-178. https://doi.org/10.1094/PBIOMES-07-23-0060-R.
DOI: https://doi.org/10.1094/PBIOMES-07-23-0060-R

Interpretive Summary: The soil microbiome consists of all the various microorganisms that occur within the soil ecosystem, including bacteria, fungi, archea, and protists. Soil microbiomes play crucial roles in pathogen suppression, nutrient mobilization, and maintenance of plant health. Their complexity and variability across location and time provide challenges for identifying appropriate management practices in different regional agricultural systems. To understand how soil microbiomes vary across potato growing regions and identify commonly distributed microbial components among them, we compiled a continental-scale bacterial and fungal dataset of over 1300 communities with corresponding physical and chemical measurements from nine US field sites. Field site explained most of the variance across bacterial and fungal communities, while pH, organic matter, and NPK concentrations also varied with community structure. Bacterial and fungal potato soil microbiomes show consistent basic level composition across locations at the continental scale, with regional-scale differences evident at finer taxonomic compositions. Core community analysis indicated common soil components across all locations, as well as potential functional variations that may be involved in maintaining soil health across regionally variable systems. These results demonstrate consistencies and variation in potato soil microbiomes in regions across the US. This research advances our understanding of the role of soil microbiomes in soil health and potato production, and is useful for scientists, extension personnel, and growers in the development of improved production practices.

Technical 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 soil microbiomes vary across potato 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.