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United States Department of Agriculture

Agricultural Research Service

Research Project: Antibiotics and Their Biosynthetic Intermediates: Inter-Cellular Messengers Mediating Genome-Wide Transcriptional Effects in Soil Bacteria

Location: Horticultural Crops Research

2011 Annual Report


1a.Objectives (from AD-416)
1. Determine the influence of purified antibiotics on the transcriptome of P. fluorescens Pf-5. 2. Determine the influence of antibiotic-mediated cell to cell signaling on the expression of antibiotic-biosynthesis genes and biocontrol activity of P. fluorescens.


1b.Approach (from AD-416)
1. Characterize the transcriptome of P. fluorescens Pf-5 by strand-specific direct RNA sequencing, employing bioinformatic and computational tools to identify the genome-wide distribution of transcripts and small RNAs. 2. Focusing on antibiotics produced by Pf-5 and other biocontrol strains of Pseudomonas sp. (examples: 2,4-diacetylphloroglucinol, pyoluteorin, pyrrolnitrin, orfamide A, rhizoxin analogs, phenazine-1-carboxylate), evaluate the influence of purified compounds on a) the transcriptome and b) antibiotic production profiles of Pf-5 grown in culture. 3. Evaluate the influence of purified antibiotics on the transcriptome of Pf-5 on seed surfaces. 4. Determine the influence of antibiotic-producing bacterial co-inhabitants on a) the expression of biocontrol genes by Pf-5 in the rhizosphere or spermosphere of plants grown in soil, and b) biological control of Pythium damping-off. These experiments will employ a combination of well-characterized mutants and reporter gene constructs to assess gene expression and biocontrol in natural field soils.


3.Progress Report

Biological control offers an attractive complement to existing practices for management of plant disease and therefore can contribute to the productivity and sustainability of U.S. agriculture in the future. Unfortunately, its widespread use in agriculture is impeded by unexplained variations in the efficacy of biocontrol organisms. One source of this variation is in the inconsistent expression of biocontrol traits by antagonists inhabiting soil or plant surfaces where they suppress target plant pathogens. The goal of this project is to test the hypothesis that antibiotics serve as chemical messengers that influence the physiology and gene expression of the producing organism. We will evaluate the effect of antibiotics on the genome-wide expression profiles of the soil bacterium Pseudomonas fluorescens Pf-5, a well-characterized biocontrol strain. We anticipate gaining new insight into factors influencing gene expression by biological control bacteria, including their expression of key biocontrol traits. Since the funds became available very recently, we began the process to set up the sub-contract and identify candidates for the postdoctoral position for this project. There is no research progress to report.


Last Modified: 10/23/2014
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