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ARS Home » Pacific West Area » Pullman, Washington » WHGQ » Research » Publications at this Location » Publication #375247
Research Project: Biology, Ecology, and Genomics of Pathogenic and Beneficial Microorganisms of Wheat, Barley, and Biofuel Brassicas

Location: Wheat Health, Genetics, and Quality Research

Title: Global landscape of phenazine biosynthesis and biodegradation reveals species-specific colonization patterns in agricultural soils and crop microbiomes

Author
item DAR, DANIEL - California Institute Of Technology
item Thomashow, Linda
item Weller, David
item NEWMAN, DIANNE - California Institute Of Technology

Submitted to: eLife
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/2/2020
Publication Date: 9/15/2020
Citation: Dar, D., Thomashow, L.S., Weller, D.M., Newman, D.K. 2020. Global landscape of phenazine biosynthesis and biodegradation reveals species-specific colonization patterns in agricultural soils and crop microbiomes. eLife. https://doi.org/10.7554/eLife.59726.
DOI: https://doi.org/10.7554/eLife.59726

Interpretive Summary: Phenazines are bacterially produced antibiotics that can protect crops from disease. However, for most crops, it is not known which producers and specific phenazine compounds are involved in nature, and whether phenazine degraders can interfere with their effects. We therefore developed and tested a computational method to test for phenazine synthesis and degradation genes in more than 800 soil and plant-associated environmental samples. We found that phenazine biosynthesis genes are enriched in many plant microbiomes, but that phenazine biodegradation genes were less common. The bbacterium Dyella japonica, a phenazine producer frequently detected in our analysis of soils associated with crop roots, produced increased amounts of phenazine compounds iunder conditions of limited phosphate availability and was a strong colonizer of corn seedling roots.This study provides the first global and quantitative picture of phenazine production and biodegradation potential in agricultural and natural soils and highlights new plant-microbe associations for focused studies. Our metagenomic approach may be extended to other metabolites and functional traits in diverse ecosystems.

Technical Abstract: Phenazines are bacterially produced redox-active metabolites that can protect crops from disease. However, for most crops it is unknown which producers and specific phenazines are ecologically relevant, and whether phenazine biodegradation can potentially interfere with their effects. Towards this end, we developed and environmentally validated a quantitative metagenomic approach to mine for phenazine biosynthesis and biodegradation genes, applying it to >800 soil and plant-associated shotgun-metagenomes. Phenazine biosynthesis genes are enriched in diverse plant microbiomes, yet phenazine biodegradation genes are less common. Dyella japonica, a putative phenazine producer frequently detected in our analysis of crop rhizospheres, upregulates phenazine biosynthesis during phosphate limitation and robustly colonizes maize seedling roots. This study provides the first global and quantitative picture of phenazine production and biodegradation potential in agricultural and natural soils and highlights new plant-microbe associations for focused studies. Our metagenomic approach may be extended to other metabolites and functional traits in diverse ecosystems.