Potato soil core microbiomes are regionally variable across the continental US

Author:

Klasek Scott1,Crants James2,Abbas Touqeer2,Ashley Katherine A.3,Bolton Marian1,Celovsky Madelyn4,Gudmestead Neil5,Hao Jianjun6,Ibarra Caballero Jorge7,Jahn Courtney7,Kamgan Nkuekam Gilbert8,Lankau Richard9,Larkin Robert10,Lopez Echartea Eglantina11,Miller Jeff S.12,Moore Amber1314,Pasche Julie Sherman1516,Ruark Matthew17,Schroeder Brenda K.18,Shan Shan19,Skillman Victoria1314,Srour Ali20,Stasko Anna5,Steinke Kurt4,Stewart Jane E.21,Thornton Mike22,Zitnick-Anderson Kimberly23,Frost Kenneth24,Rosen Carl2,Kinkel Linda25

Affiliation:

1. University of Minnesota, Department of Plant Pathology, Saint Paul, Minnesota, United States;

2. University of Minnesota, Soil, Water, and Climate, St. Paul, Minnesota, United States;

3. University of Maine, 6250, School of Food and Agriculture, Orono, Maine, United States;

4. Michigan State University, 3078, Department of Plant, Soil, and Microbial Sciences, East Lansing, Michigan, United States;

5. North Dakota State University, 3323, Department of Plant Pathology, Fargo, North Dakota, United States;

6. University of Maine, School of Food and Agriculture, Orono, Maine, United States, ;

7. Colorado State University, 3447, Department of Agricultural Biology, Fort Collins, Colorado, United States;

8. University of Idaho, Department of Entomology, Plant Pathology and Nematology, Moscow, Idaho, United States;

9. University of Wisconsin Madison, Plant Pathology, Madison, Wisconsin, United States;

10. USDA-ARS, New England Plant, Soil, and water Lab, University of Maine, Orono, Maine, United States, 04469, , ;

11. North Dakota State University, 3323, Department of Microbiological Sciences, Van Es Hall, 1523 Centennial Blvd, Fargo, North Dakota, United States, 58102;

12. Miller Research, 426 East 200 North, Rupert, Idaho, United States, 83350, ;

13. Oregon State University, 2694, Department of Botany and Plant Pathology, Corvallis, Oregon, United States

14. Oregon State University Hermiston Agricultural Research and Extension Center, 446695, Hermiston, Oregon, United States;

15. North Dakota State University, Plant Pathology, 306 walster hall, NDSU, Fargo, North Dakota, United States, 58105,

16. United States;

17. University of Wisconsin, Department of Soil Science, Madison, Wisconsin, United States;

18. University of Idaho, Plant, Soil, and Entomological Sciences, 875 Perimeter Drive MS 2339, Moscow, Idaho, United States, 83844-2339;

19. UW-Madison, 5228, Department of Plant Pathology, Madison, Wisconsin, United States;

20. USDA-ARS, New England Plant, Soil, and Water Laboratory, Orono, Maine, United States;

21. Colorado State University, 3447, Department of Agricultural Biology, 1177 Campus Delivery, Fort Collins, Colorado, United States, 80523;

22. University of Idaho, SW Idaho R&E Center, Parma, Idaho, United States;

23. North Dakota State University, 3323, Plant Pathology, 306 Walster Hall, Fargo, North Dakota, United States, 58108-6050;

24. Oregon State University, Botany and Plant Pathology, 2121 S 1st ST, Hermiston, Oregon, United States, 97838;

25. University of Minnesota, Plant Pathology, 495 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, Minnesota, United States, 55108, , ;

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.

Publisher

Scientific Societies

Subject

Plant Science,Agronomy and Crop Science,Molecular Biology,Ecology,Ecology, Evolution, Behavior and Systematics

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