Genome Study Of Beneficial Microbe May Help Boost Plant Health

The research provides clues to better explain how the helpful microbe, Pseudomonas fluorescens Pf-5, naturally safeguards roots and seeds from infection by harmful microbes that cause plant diseases. The genome paper will be published in Nature Biotechnology and was scheduled to be posted online on June 26.

"The genome sequence has helped us identify new chemical pathways that the microbe apparently uses to create what are known as 'secondary metabolites' -- possibly including new antibiotic compounds," says Ian Paulsen. He led the sequencing at The Institute for Genomic Research (TIGR), Rockville, Md., and is the study's first author.

The use of naturally-occurring, beneficial microbes such as P. fluorescens to control plant pathogens is called "biological control." That method is gaining momentum as a way to grow healthy plants without using synthetic fungicides. In all, about three dozen beneficial microbes are currently used as an environmentally-friendly way to fight plant diseases.

Joyce E. Loper, senior author of the genome paper and an expert on P. fluorescens Pf-5, predicts that the new genomic data will help scientists more quickly develop new ways to boost the effectiveness of beneficial microbes in fighting plant diseases.

"This genomic sequence reveals previously unknown traits of P. fluorescens that increase its potential for biological control," says Loper. She is a plant pathologist with USDA's Agricultural Research Service (ARS) and is based at Oregon State University, Corvallis. The P. fluorescens genome was sequenced at TIGR and analyzed by scientists there and at ARS and Oregon State University, with contributions by researchers at Rutgers, Washington State University and the University of Arizona. The project was funded by a grant from the USDA's Cooperative State Research, Education and Extension Service.

The article in Nature Biotechnology presents the first complete genome sequence of a biological control agent for combating plant diseases.

P. fluorescens Pf-5 was discovered two decades ago by Charles R. Howell, a plant pathologist with the ARS in Texas, who showed that the microbe suppressed two major cotton diseases. Since then, plant pathologists around the world have used this strain as a laboratory model to study beneficial microbes.

Paulsen says the P. fluorescens project also pioneered a new methodology. This novel approach relies on the analysis of repeated regions of the DNA sequence to help identify segments of the genome that appear to have been transferred from other microbes or viruses, known as phages, that infect bacteria.

Says Paulsen: "We found exciting evidence that P. fluorescens may have acquired new clusters of genes, called genomic islands, by means of lateral transfer from phages or other microbes."

The Institute for Genomic Research (TIGR) is a not-for-profit research institute based in Rockville, Maryland. TIGR, which sequenced the first complete genome of a free-living organism in 1995, has been at the forefront of the genomic revolution since the institute was founded in 1992. TIGR conducts research involving the structural, functional, and comparative analysis of genomes and gene products in viruses, bacteria, archaea, and eukaryotes.

As the principal in-house research arm of the U.S. Department of Agriculture, the Agricultural Research Service (ARS) conducts research to develop and transfer solutions to agricultural problems of high national priority and provides information access and dissemination to ensure high-quality, safe food and other agricultural products, assess the nutritional needs of Americans, sustain a competitive agricultural economy, enhance the natural resource base and the environment, and provide economic opportunities for rural citizens, communities, and society as a whole.

Oregon State University is known nationally and internationally for the quality of its academic programs, its research excellence and its service and outreach. OSU is one of only two universities in the nation that are designated land grant, sea grant, space grant and sun grant institutions.