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Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities

Citation

Stapleton, Ann et al. (2020), Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities, Dryad, Dataset, https://doi.org/10.5061/dryad.7m0cfxprs

Abstract

The phyllosphere epiphytic microbiome is composed of microorganisms that colonize the external aerial portions of plants. Relationships of plant responses to specific microorganisms–both pathogenic and beneficial–have been examined, but the phyllosphere microbiome functional and metabolic profile responses are not well described. Changing crop growth conditions, such as increased drought, can have profound impacts on crop productivity. Also, epiphytic microbial communities provide a new target for crop yield optimization. We compared Zea mays leaf microbiomes collected under drought and well-watered conditions by examining functional gene annotation patterns across three physically disparate locations each with and without drought treatment, through the application of short read metagenomic sequencing. Drought samples exhibited different functional sequence compositions at each of the three field sites. Maize phyllosphere functional profiles revealed a wide variety of metabolic and regulatory processes that differed in drought and normal water conditions and provide key baseline information for future selective breeding.

Methods

Experimental design, plant growth conditions, and leaf epiphytic microbial DNA collection is described in the manuscript methods section.  Full descriptions of computational methods are available in the R notebook in the drought-metagen folder. 

Usage Notes

Metadata is included in the supplemental files folder; full details of code, simulations, and real data analysis are included in the drough-metagen folder.

Funding

National Science Foundation, Award: 1126938