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

Phenazines are natural bacterial antibiotics 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 counter their effects. To better understand their ecology, we developed...

Full description

Saved in:
Bibliographic Details
Published in:eLife 2020-09, Vol.9
Main Authors: Dar, Daniel, Thomashow, Linda S, Weller, David M, Newman, Dianne K
Format: Article
Language:English
Subjects:
Agricultural industry
Agriculture
Antibiotics
Bacteria
Biodegradation
Biodegradation, Environmental
Crops, Agricultural - microbiology
Dyella japonica
Ecology
Ecosystems
Gammaproteobacteria - physiology
Metagenomics
Microbiology and Infectious Disease
Microbiota
phenazines
Phenazines - metabolism
Physiological aspects
Soil - chemistry
Soil Microbiology
Soil Pollutants - metabolism
Soils
Species Specificity
Up-Regulation
Zea mays - microbiology
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Phenazines are natural bacterial antibiotics 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 counter their effects. To better understand their ecology, 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. We discover novel producer-crop associations and demonstrate that phenazine biosynthesis is prevalent across habitats and preferentially enriched in rhizospheres, whereas biodegrading bacteria are rare. We validate an association between maize and , a putative producer abundant in crop microbiomes. upregulates phenazine biosynthesis during phosphate limitation and robustly colonizes maize seedling roots. This work provides a global picture of phenazines in natural environments and highlights plant-microbe associations of agricultural potential. Our metagenomic approach may be extended to other metabolites and functional traits in diverse ecosystems.
ISSN:2050-084X
2050-084X
DOI:10.7554/eLife.59726