Community-driven metadata standards for agricultural microbiome research

Authors: DUNDORE-ARIAS, J - California State University; ELOE-FADROSH, E - Department Of Energy Joint Genome; SCHRIML, L - University Of Maryland; BEATTIE, G - Iowa State University; BRENNAN, F - Teagasc (AGRICULTURE AND FOOD DEVELOPMENT AUTHORITY); BUSBY, P - Oregon State University; CALDERON, R - Louisiana State University; Castle, Sarah; EMERSON, J - University Of California; EVERHART, S - University Of Nebraska; EVERSOLE, K - International Alliance For Phytobiomes Research; FROST, K - Oregon State University; HERR, J - University Of Nebraska; HUERTA, A - North Carolina State University; IYER-PASCUZZI, A - Purdue University; KALIL, A - Williston Research Center; LEACH, J - Colorado State University; LEONARD, J - Louisiana State University; Maul, Jude; PRITHIVIRAJ, B - Brooklyn College; POTRYKUS, M - Gdansk University; REDEKAR, N - Oregon State University; ROJAS, J - University Of Arkansas; SILVERSTEIN, K A - University Of Minnesota; TOMSO, D - Agbiome; TRINGE, S - Department Of Energy Joint Genome; VINATZER, B - Virginia Polytechnic Institution & State University; KINKEL, L - University Of Minnesota

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/6/2020
Publication Date: 2/20/2020
Citation: Dundore-Arias, J.P., Eloe-Fadrosh, E., 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.T., Tomso, D.J., Tringe, S.G., Vinatzer, B.A., Kinkel, L.L. 2020. Community-driven metadata standards for agricultural microbiome research. Phytobiomes Journal. 4:115-121. https://doi.org/10.1094/PBIOMES-09-19-0051-P.
DOI: https://doi.org/10.1094/PBIOMES-09-19-0051-P

Interpretive Summary: Microbiomes have been recognized for their potential to enhance crop productivity and agroecosystem health. However, despite the widespread availability of crop-associated microbiome data, inconsistent methodologies among studies, and underreporting with respect to environmental conditions and agronomic treatments have limited our ability to make comparisons among datasets. We outline the need to collect agriculture-specific metadata for microbiome research, which will enhance the potential for integration of data, and comparison, across research studies. This information will advance agricultural microbiome science by providing a starting point for discussion and inspire researchers to adopt standardized procedures for collecting and reporting consistent and well-annotated metadata.

Technical Abstract: Accelerating the pace of microbiome science to enhance crop productivity and agroecosystem health will require trans-disciplinary 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 for agricultural microbiome researchers. 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 discussion 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.