Genome Sequencing Furthers Knowledge of Plant and Animal Pathogen
The various species of bacteria in the genus Enterobacter may be painfully familiar to you. Enterobacter cloacae, the best known of the genus, is a cause of various infections, including those of the lower respiratory tract, urinary tract, skin and soft tissues, wounds, and all manner of other nastiness. This indiscriminate little bug is also a cause of bulb rot in onions.
To make things even trickier, Enterobacter cloacae is not a single homogenous species but rather a complex collection of speciated populations. Each species in the group is adapted to take advantage of whatever is available in its local environment. “Genetically, the E. cloacae complex is very diverse,” said Brenda Schroeder, a plant pathologist at Washington State University who works on bacterial diseases of vegetable crops grown in Washington.
“Individual bacteria populations have variations due to their response to local environmental conditions. That’s why we needed to sequence the genome of a local strain,” Schroeder said. “There is very little known about how E. cloacae infects humans and plants. It’s a pathogen of numerous plants, including ginger, papaya, and macadamia. It’s also an opportunistic human pathogen. So contributing to the understanding of how this bacteria operates not only helps vegetable farmers, it also could potentially contribute to our understanding of human health.”
It’s the impact on onion farmers that is the immediate concern of Schroeder and her colleagues. According to the National Onion Association, Washington has more acres planted in onions than any other state. The state produces over 1.3 billion (yes, that’s a “b”) pounds of onions a year, adding more than $150 million in direct farmgate value to the Washington economy, with a total economic impact of around $1 billion per year to the state. Onions, in other words, are not small potatoes and onion health is critical to the continued economic sustainability of many Washington farm operations.
Schroeder said that, among onion pathogens that cause bulb rotting, E. cloacae is the most commonly isolated. “Over half of the time we see E. cloacae involved in bulb rotting. But we don’t know how it causes disease.”
Schroeder and her colleagues, post-doctoral scientist Jodi Humann and WSU School of Molecular Biosciences scientific assistant Mark Wildung, were able to sequence the genome of E. cloacae at WSU’s DNA sequencing facility for a mere $4,000. Schroeder pointed out that the E. cloacae genome is not very large compared to plants or humans, but the team also used some tricks to help drive the cost of sequencing down. Colleagues at the University of Florida, Eric Triplett and Jennifer Drew, shared their genomic data of another E. cloacae strain, which helped speed up the complex problem of figuring out what the raw data means.
Genome sequencing results in a soupy puzzle of genetic pieces. Some overlap, some begin where other chunks leave off. Sorting out the pieces and getting them all aligned is the computationaly intensive part of a sequencing project. Fortunately, in addition to the data from her Florida colleagues and others, Schroeder was able to call on the assistance of WSU bioinformaticist Dorrie Main. Main set the team up with local copies of other E. cloacae sequences and online analysis tools to allow rapid comparison of individual genomes and genes, highlighting similarities as well as differences.
“Doing the sequencing work is a step toward a much more important goal,” Schroeder said. “Our lab is part of a big project that is developing tools that will allow us to identify bacteria pathogens by their molecular fingerprint.”
Fingerprinting disease-causing agents is important in understanding how they work. “We really want to know what these microorganisms are doing,” Schroeder said. “We need the molecular window to get a view of how they interact as communities under various conditions, for instance, while onions are in storage.”
E. cloacae was only identified as an onion pathogen in 1991. “We know that it doesn’t have a big arsenal of invasive weapons, of ways of causing infection. What we don’t know is what mechanisms are at work to cause bulb rot.” Schroeder said that while at this point there are more unknowns than knowns, that situation is rapidly changing. “What we have here is a great window of opportunity for young scientists to solve some major problems and make some really key discoveries. There is a real excitement in the scientific community about this and related issues. That’s why some of the best plant scientists in the country are all working together to meet this challenge.”
Learn more about the research going on in Brenda Schroeder’s lab by visiting http://bit.ly/schroederlab.
Scientists Collaborate to Improve Wheat Flour
The same fondness for fluffy, soft texture that prompts Americans to prefer white flour for bread is shared by Koreans for steamed buns, pan bread and noodles. But the same health concerns that have caused more Americans to choose high-fiber, vitamin- and mineral-rich whole wheat flour also are affecting Korean preferences.
“In the United States, we are experiencing significant health problems associated with diet, such as obesity, diabetes, heart diseases, and cancer,” said Byung-Kee Baik, an associate professor and cereal chemist at Washington State University. “Those trends are the same in Korea.” Baik and his colleague, South Korean scientist Induck Choi, are embarking on a three-year project to investigate whole wheat flour processing and quality.
South Korea is developing a growing interest in consuming whole grain products, Baik said. But the products would be more popular if whole wheat flour behaved more like white flour in baking. Without large amounts of added gluten, whole wheat bread is half the size of white wheat bread, he said. Whole wheat flour requires added ingredients to enhance the volume and texture of bread.
Baik and Choi will investigate the composition of whole wheat flour and explore milling methods that affect flour particle size and processing quality. They hope to develop novel whole wheat flour processing technologies that will improve the quality of bread, noodles, and other foods. Ultimately, they intend to develop a protocol for selecting wheat varieties most suitable for making whole wheat products with more desirable sensory properties.
As a side benefit, Baik said, their work will have a positive influence on Korean domestic production of wheat, the consumption of whole wheat products, and the creation of a strategic plan for food security. Wheat is the second major staple product in Korea, but close to 99 percent of wheat consumed in Korea is imported, he said.
“This research will provide us an understanding of wheat grain and information for developing wheat varieties suitable for developing whole wheat products,” Baik said.
–Tallie Mattson, WSU News Intern
Read an earlier article about Baik’s research by visiting http://bit.ly/uuzqkC.
See You in December
It’s time again for the writers and editors at On Solid Ground to help support the Washington agricultural economy by grazing and gobbling on all manner of wonderful foodstuffs. We’ll be back in December with the next issue of On Solid Ground. If you haven’t gotten your fill and feel the need to feast on ag news, please check out our other agricultural science publications.
- Voice of the Vine – the monthly newsletter for lovers of wine… and wine science. Subscribe at http://bit.ly/aJeDG9.
- Green Times – the monthly newsletter focusing on organic and sustainable agriculture. Subscribe at http://bit.ly/ojREu3.