Community-driven Metadata Standards for Agricultural Microbiome Research

Authors

J. P. Dundore-Arias, California State University, Monterey BayFollow
E. A. Eloe-Fadrosh, Lawrence Berkeley National Laboratory
L. M. Schriml, University of Maryland School of Medicine
G. A. Beattie, Iowa State University
F. P. Brennan, Teagasc, Department of Environment Soils and Land-Use
P. E. Busby, Oregon State University
R. B. Calderon, Louisiana State University at Baton Rouge
S. C. Castle, U.S. Department of Agriculture-Agriculture Research Service
J. B. Emerson, University of California, Davis
S. E. Everhart, University of Nebraska - Lincoln
K. Eversole, International Alliance for Phytobiomes Research
K. E. Frost, Oregon State University
J. R. Herr, University of Nebraska - Lincoln
A. I. Huerta, North Carolina State University at Raleigh
A. S. Iyer-Pascuzzi, Purdue University
A. K. Kalil, Williston Research Extension Center
J. E. Leach, Colorado State University - Fort Collins
J. Leonard, Louisiana State University at Baton Rouge
J. E. Maul, U.S. Department of Agriculture
B. Prithiviraj, Brooklyn College of the City University of New York
M. Potrykus, Medical University of Gdansk
N. R. Redekar, Oregon State University
J. A. Rojas, University of Arkansas, Fayetteville
K. A. T. Silverstein, Minnesota Supercomputing Institute for Advanced Computational Research
D. J. Tomso, AgBiome
S. G. Tringe, Lawrence Berkeley National Laboratory
B. A. Vinatzer, Virginia Polytechnic Institute and State University
L. L. Kinkel, University of Minnesota

Document Type

Article

Publication Date

2020

Publication Title

Phytobiomes Journal

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.

Comments

© 2020 The American Phytopathological Society.

Published in Phytobiomes Journal by The American Phytopathological Society. Available via doi: 10.1094/PBIOMES-09-19-0051-P.

Recommended Citation

Dundore-Arias, J. P.; Eloe-Fadrosh, E. A.; Schriml, L. M.; Beattie, G. A.; Brennan, F. P.; Busby, P. E.; Calderon, R. B.; Castle, S. C.; Emerson, J. B.; Everhart, S. E.; Eversole, K.; Frost, K. E.; Herr, J. R.; Huerta, A. I.; Iyer-Pascuzzi, A. S.; Kalil, A. K.; Leach, J. E.; Leonard, J.; Maul, J. E.; Prithiviraj, B.; Potrykus, M.; Redekar, N. R.; Rojas, J. A.; Silverstein, K. A. T.; Tomso, D. J.; Tringe, S. G.; Vinatzer, B. A.; and Kinkel, L. L., "Community-driven Metadata Standards for Agricultural Microbiome Research" (2020). Biology and Chemistry Faculty Publications and Presentations. 6.
https://digitalcommons.csumb.edu/biochem_fac/6