Community-Driven Metadata Standards for Agricultural Microbiome Research

Author:

Dundore-Arias J. P.1ORCID,Eloe-Fadrosh E. A.2,Schriml L. M.3,Beattie G. A.4,Brennan F. P.5,Busby P. E.6,Calderon R. B.7,Castle S. C.8,Emerson J. B.9,Everhart S. E.10ORCID,Eversole K.11,Frost K. E.12ORCID,Herr J. R.13ORCID,Huerta A. I.14,Iyer-Pascuzzi A. S.15,Kalil A. K.16ORCID,Leach J. E.17ORCID,Leonard J.18,Maul J. E.19,Prithiviraj B.20ORCID,Potrykus M.21,Redekar N. R.22ORCID,Rojas J. A.23ORCID,Silverstein K. A. T.24,Tomso D. J.25,Tringe S. G.2,Vinatzer B. A.26ORCID,Kinkel L. L.27ORCID

Affiliation:

1. California State University Monterey Bay, Biology and Chemistry, 100 Campus Center, Seaside, CA 93955, U.S.A.

2. Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, U.S.A.

3. University of Maryland School of Medicine, Department of Epidemiology and Public Health, Institute for Genome Sciences, Baltimore, MD, U.S.A.

4. Iowa State University, Department of Plant Pathology, 207 Science I, Ames, IA 50011-3211, U.S.A.

5. Teagasc, Department of Environment Soils and Land-Use, Wexford, Johnstown Castle, Ireland

6. Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR, U.S.A.

7. Louisiana State University, Department of Plant Pathology and Crop Physiology, Baton Rouge, LA, U.S.A.; and Benguet State University, Benguet, La Trinidad, Philippines

8. U.S. Department of Agriculture-Agriculture Research Service, Plant Science Research Unit, Saint Paul, MN, U.S.A.

9. University of California Davis, Department of Plant Pathology, Davis, CA, U.S.A.

10. University of Nebraska, Plant Pathology, 406G PLSH 1875 N 38th St., Lincoln, NE 68510, U.S.A.

11. International Alliance for Phytobiomes Research, Lee’s Summit, MO, U.S.A.

12. Oregon State University, Botany and Plant Pathology, 2121 S 1st St., Hermiston, OR 97838, U.S.A.

13. University of Nebraska-Lincoln, Department of Plant Pathology and Center for Plant Science Innovation, 422 Plant Sciences Hall, Lincoln, NE 68588, U.S.A.

14. North Carolina State University College of Agriculture and Life Sciences, Department of Entomology and Plant Pathology, Raleigh, NC, U.S.A.

15. Purdue University, Department of Botany and Plant Pathology and Center for Plant Biology, West Lafayette, IN, U.S.A.

16. Williston Research Extension Center, Williston, ND, U.S.A.

17. Colorado State University, Bioagricultural Sciences and Pest Management, 1177 Campus Delivery, Fort Collins, CO 80523-1177, U.S.A.

18. Louisiana State University, AgCenter and Department of Plant Pathology and Crop Physiology, Baton Rouge, LA, U.S.A.

19. U.S. Department of Agriculture-Agricultural Research Service Administrative and Financial Management, Sustainable Agricultural Systems Laboratory, Beltsville, MD, U.S.A.

20. Brooklyn College of the City University of New York, Department of Biology, Brooklyn, NY, U.S.A.

21. Medical University of Gdansk, Department of Environmental Toxicology, Gdansk, Poland

22. Oregon State University, Crop and Soil Science, 109 Crop Science Building, 3050 SW Campus Way, Corvallis, OR 97331-4501, U.S.A.

23. University of Arkansas Fayetteville, Plant Pathology, 495 N. Campus Drive PTSC 217, Fayetteville, AR 72703, U.S.A.

24. Minnesota Supercomputing Institute for Advanced Computational Research, Minneapolis, MN, U.S.A.

25. AgBiome, 104 TW Alexander Drive Building 1, RTP, NC 27709, U.S.A.

26. Virginia Polytechnic Institute and State University, PPWS, Latham Hall AgQuad Lane Room 551, Blacksburg, VA 24061-0131, U.S.A.

27. University of Minnesota, Plant Pathology, 495 Borlaug Hall 1991 Upper Buford Circle, Saint Paul, MN 55108, U.S.A.

Abstract

Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require transdisciplinary studies, comparisons among datasets, and synthetic analyses of research from diverse crop management contexts. However, despite the widespread availability of crop-associated microbiome data, variation in field sampling and laboratory processing methodologies, as well as metadata collection and reporting, significantly constrains the potential for integrative and comparative analyses. Here we discuss the need for agriculture-specific metadata standards for microbiome research, and propose a list of “required” and “desirable” metadata categories and ontologies essential to be included in a future minimum information metadata standards checklist for describing agricultural microbiome studies. We begin by briefly reviewing existing metadata standards relevant to agricultural microbiome research, and describe ongoing efforts to enhance the potential for integration of data across research studies. Our goal is not to delineate a fixed list of metadata requirements. Instead, we hope to advance the field by providing a starting point for discussion, and inspire researchers to adopt standardized procedures for collecting and reporting consistent and well-annotated metadata for agricultural microbiome research.

Funder

National Science Foundation

Publisher

Scientific Societies

Subject

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

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