UD students look at possible contamination of irrigation water

November 21, 2013 under CANR News

students look for contaminants in irrigation waterStudents in the University of Delaware College of Agriculture and Natural Resources (CANR) are using a plot of land on the campus farm to help study possible contaminants in soil and irrigation water used to grow leafy greens and tomatoes in order to help inform new regulations on growers that will be going into effect next year as part of the Food Safety Modernization Act.

The study is part of a $9 million U.S. Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) Specialty Crops Research Initiative (SCRI) grant titled “Developing Consensus Produce Safety Metrics for Leafy Greens and Tomatoes.” The project is led by the University of Maryland and is taking place at seven different universities and industry liaisons across the country.

Signed into law in 2011 by President Barack Obama, the food safety act has been implemented in stages over the past two years.

Kali Kniel, associate professor of animal and food sciences, explained that part of the law includes regulations for growers of fruits and vegetables, noting that this is the first time there have ever been specific regulations for growing fruits and vegetables.

“There have been guidelines and marketing agreements before but not regulations in terms of environmental aspects that are difficult to control,” Kniel said, “so growers are anxious and nervous about this.”

The rules are not yet finalized and include some fairly complicated aspects in terms of metrics, use of irrigation water and soil amendments. Delaware extension agents have been working with growers over the past two years to make the transition more manageable.

To help inform these regulations, researchers from the seven universities will meet with representatives of the Food and Drug Administration (FDA) to report on their findings.

UD research team

At UD, the research team used a plot of land next to the Allen Laboratory and has been growing tomatoes, romaine lettuce and spinach on the plot for the past two years.

Angela Ferelli, a senior double majoring in biochemistry and food science, worked on the project during the first summer and said that it was interesting to get hands-on experience outside of the lab.

Because it was her first time working in a garden and growing plants for a project, she said that it was a “labor of love. We really wanted to tackle it head on and we didn’t know what the best way was to keep the weeds out and keep the plants growing and happy. And if you looked down the rows the first time we planted, we had four rows — they started out straight and then they went crooked, but you could definitely tell that we were doing it, and it was great.”

Ferelli said that the next year, the group tested a new variable plasticulture for tomatoes, putting down plastic tarps to keep the weeds out. This is also a means of potential control for splash from rainfall for growing produce and for the protection from plant contact with soil.

Patrick Spanninger, a doctoral student in Kniel’s lab who has been working on the project since the beginning, explained that after the students grew the plants, they ran trials by pouring water mixed with manure that contained different levels of E. coli on the plants to monitor bacterial persistence on the fruit. “We wanted to see if the bacteria in the manure that we started with survived after we put it on the plants,” said Spanninger. This is a controlled way modeling how irrigation water may become naturally contaminated in real-life situations.

The students then harvested the tomatoes and leafy greens by hand and used random sampling strategies to look at the levels of generic E. coli on the plants.

Explaining that because the outdoors is a complicated, unsterile environment, Kniel said that they tested for generic E. coli because it is an indicator organism, meaning that if increased levels of generic E. coli show up, there could be a potential risk associated with the irrigation water. This is the current industry standard and part of a grower’s best practices.

The problem with rain

Another part of the research on which the students worked was the development of water safety metrics to help decide how many generic bacteria — nonpathogenic bacteria — can be found in water used for irrigation.

students look for contaminants in rain water“They’re associating the levels of bacteria in the water with climactic changes with rainfall and wind and relative humidity and temperatures to try and understand what puts produce at risk for having higher bacterial levels or potential pathogens,” said Kniel.

Ultimately, Kniel said that rainfall more than anything else poses a problem for growers when it comes to bacterial contamination on fruit that may have originated in irrigation water. Using DNA fingerprint analysis on the recovered E. coli, Spanninger was able to trace bacteria coming from the manure through the tomatoes on different plants.

“We actually are seeing that the initial amounts of generic bacteria in the water are not really the biggest issue. Bacterial decay on plants occurs within a couple of days. Rainfall seems to really affect fresh produce,” Kniel said. “We think that rain close to harvest dates is an important consideration and should be part of a Food Safety Plan, so we’re sharing with the FDA that aspects other than strict water metrics should be considered. At this time meeting the water standards the FDA is suggesting is difficult for produce growers around the country, in particular those that use surface water for irrigation.”

Spanninger agreed with that assessment. “From what we saw, the greatest influence on bacterial presence and persistence was big rain events, which we’ve been getting more of in recent years.” He explained that the research was conducted last fall during Hurricane Sandy and in the summer when the area was doused with a large amount of rainfall.

Spanninger also added that possible contamination from animals — such as geese, dogs, and groundhogs in the field — is another issue that the group is investigating. Wildlife intrusion into produce fields is an important area of study along with irrigation water standards.

In addition to looking for E. coli, the group — along with the research teams at other universities involved in the project — also set out to identify potential hot spots for growers, areas where they would have the most success growing crops without high risk of contamination.

Ferelli explained, “The overarching implications of this research are going to be for the growers to be able to have a better grip on where the risk is in the field. So if a grower goes out now with this risk in mind and he or she see’s there has been a rain event, or observes that an animal has come in and left it’s signature, instead of just taking out that one plant that has been affected, the grower will be better equipped with knowledge to recognize the possibility to section off several plants in that area.’”

Article by Adam Thomas

This article can also be viewed on UDaily.

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UD plant and soil sciences researcher receives two USDA grants

October 7, 2013 under CANR News

Yan Jin is awarded two USDA grantsThe University of Delaware’s Yan Jin has received two awards from the U.S. Department of Agriculture for her studies on wetlands waters and for cross-disciplinary research on fresh produce and microbial contaminants.

The funding for both projects is being provided through the USDA National Institute of Food and Agriculture’s Agriculture and Food Initiative (AFRI) Competitive Grants Program.

Jin, professor of soil science and an environmental physicist in the Department of Plant and Soil Sciences in UD’s College of Agriculture and Natural Resources (CANR) said the four-year wetlands project is funded under AFRI’s Renewable Energy, Natural Resources and Environment program area and is titled “Colloid Mobilization and Biogeochemical Cycling of Organic Carbon, Nitrogen and Phosphorous in Wetlands.”

This is a new collaboration developed with Bruce Vasilas, UD professor of plant and soil sciences and a hydric soil scientist with extensive research experience in wetland hydrology and water chemistry.

The project design incorporates extensive sampling of both ground and surface waters at three wetland sites with complementary laboratory experiments.

Wetlands are vital components to the ecosystem because they can remove nutrients and pollutants before those can enter downstream waters. Jin’s research will ultimately focus on how the mobilization of colloidal particles within the soil can influence the transport, retention and cycling of essential nutrients such as nitrogen, phosphorus and dissolved organic matter.

A comprehensive assessment of wetlands and a clear understanding of their geochemical and hydrological mechanisms controlling nutrient retention/removal and carbon cycling is valuable in developing integrated management strategies of water resources at the urban-ecological interface.

Jin said she is very excited about the opportunity to team with Vasilas, who is a nationally recognized expert on wetlands and has well-established field sites for which long-term monitoring data of hydrological, water chemistry and soil properties are already available.

She is confident that their work will generate a better understanding of the role colloids might play in natural wetlands in the cycling of essential nutrients and carbon.

“We are a nice match in terms of us having very different skills. My expertise is in the lab while his is in the field,” said Jin. “By working together and combining field measurements and laboratory investigations we will understand things each one of us individually could not understand as well.”

Produce research

The second grant, awarded by AFRI’s Food Safety, Nutrition, and Health Program, evaluates the processes contributing to the microbial contamination of fresh produce. “Receiving this award is very encouraging, and a bit surprising because this is the first time we applied and we are being funded by a program that is outside of our discipline. The project is a new cross-discipline attempt to link environmental physics to the field of food safety,” Jin said.

With the increasing association of food-borne illness outbreaks with fruits and vegetables, the mechanisms allowing pathogens to attach and colonize on these surfaces has come into question. The goal of the project will be to link crop surface properties, physics of small-scale water organization and subsequent nutrient availability with the attachment, growth and colonization of bacteria.

The three-year project will be a joint effort with two young scientists, Volha Lazouskaya, a former Ph.D. student and postdoctoral researcher in Jin’s group, and Gang Wang, who will join Jin’s group early next year from the Swiss Federal Institute of Technology.

John Xiao, professor of physics in UD’s Department of Physics and Astronomy, and Kali Kniel, professor of food microbiology in CANR’s Department of Animal and Food Sciences, will also participate in the project. The goal of this research is to provide insight to improve risk assessment methods and pathogen control protocols of produce contamination.

Jin’s work takes a systematic approach and applies physics and colloidal theories. “In this project, we will apply our knowledge of colloid/bacteria attachment and transport processes in porous media to understand how microbial pathogens attach and colonize to fruit and vegetable surfaces,” she said. “We will use natural produce surfaces and create model surfaces using state-of-the-art nanofabrication techniques to mimic surface features such as roughness, hydrophobicity and water distribution, which affects bacterial attachment, colonization and growth.

“We will compare those properties across different produces to evaluate their vulnerability to pathogenic contamination. We also expect to develop a computational model, which will provide a quantitative and predictive tool for addressing the key biophysical factors influencing bacterial attachment, survival and colonization on fresh produce.”

Although Jin’s office is currently located in Townsend Hall, she soon will be making the move to UD’s new Interdisciplinary Science and Engineering Laboratory (ISE Lab), where she will utilize state of the art technologies during her projects.

Research group

The Jin group’s general research interest is in measurement, modeling and interpretation of mass and energy flow and transformation in soil and groundwater. A special focus in the last decade has been on the behavior of colloids, microscopic particles that include natural soil mineral and organic particles, manufactured nanoparticles, and biocolloids or viruses and bacteria.

The basic and systematic nature of their investigation on the mechanisms of colloid mobilization, attachment, and transport from their previous research built a strong foundation that led to the award of the two new NIFA grants. The new projects will allow Jin’s group and their collaborators to apply their fundamental knowledge of colloid behavior to address larger scale environmental issues and to new systems they had never worked with before.

Article by Angela Carcione

Photo by Danielle Quigley

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University’s Kniel, Everts join study of produce safety

December 9, 2011 under CANR News, Cooperative Extension

Researchers at the University of Delaware are participating in a project that is focused on increasing produce safety and delivering more trustworthy salad fixings.

Total funding for the University of Maryland-led project amounts to $9 million, with $5.4 million in contributions coming from the U.S. Department of Agriculture’s National Institute of Food and Agriculture and substantial industry funds.

The three-year study promises to be one of the most comprehensive studies of fresh produce safety ever conducted.

Produce safety has been a hot topic ever since 2006, when a deadly batch of spinach killed three people and sickened hundreds of Americans. The project will involve extensive testing and data collection by industry, supplemented by field experiments involving eight other university and federal laboratories around the country.

Kali Kniel, associate professor in UD’s Department of Animal and Food Sciences, and Kathryne Everts, professor and Cooperative Extension specialist in plant pathology at Maryland with a joint appointment at UD, are part of the University of Delaware team.

“Since the large outbreak of E. coli in 2006 which was traced back to spinach grown in the Salinas Valley of California, produce commodities have been under great scrutiny,” Kniel said of the project. “As we all know fresh fruits and vegetables are grown outside, which puts them at great risk for coming in contact with biological hazards like pathogenic bacteria and viruses. There are some processes that growers and packers can do to reduce the risk but the science is still not there to completely understand what those are. This project will help to resolve that for very important and ‘high-risk’ products, including leafy greens and tomatoes.”

Kniel explained the role that she and Everts will play in the study, saying, “Dr. Everts and I will be working with the farmers and packers to both develop metrics and to disseminate the science-based results of the project.  I am particularly looking forward to working with regional growers and packers to help them deal with the food safety challenges including increased biological testing and best practices for safe compost and water use.”

Robert Buchanan, a University of Maryland professor and director of its Center for Food Safety and Security Systems, is heading the research initiative.

In addition to UD and Maryland, other universities involved include Ohio State University, Rutgers University, the University of California Davis, the University of Florida and the University of Maryland Eastern Shore. The USDA and the Food and Drug Administration (FDA) will be involved in the research as well.

The initiative’s industry partners — representing more than 90 percent of the leafy greens and tomato production in the United States — will conduct about 200,000 separate tests during the project to measure the presence of pathogens.

“This project is very unique in that it has the support of the industry on a significant scale. We have a great team of scientists and great industry support,” Kniel said.

The research aims to create the scientific basis for detailed safe, hygienic practices in farming, packing, transporting and storing fresh produce.

The idea is to prevent water, air or ground sources of pathogen contamination by setting standards or benchmarks that can be applied in a variety of growing regions and countries.

The study will examine questions such as how far apart do you need to keep a lettuce patch from pigs or other farm animals to prevent bacterial contamination and what kinds of barriers are needed to prevent contaminated water from reaching crops?

Members of the research team said they believe the project will give regulators, farmers, packers and others along the supply chain the scientific and technological knowledge needed to develop and defend produce safety protocols, or “metrics” as the industry calls them.

At the production stage, the research will focus on air, water and other environmental factors related to potential contamination by pathogens; risks during harvesting, packing, and processing; as well as temperature and other handling concerns as produce moves to market.

Photos by Ambre Alexander

This story can also be viewed on UDaily > >

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UD’s Wisser receives USDA grant to study genetic barriers in corn

November 15, 2011 under CANR News

When it comes to crops in the U.S., corn is king. Just because it is king, however, does not mean that breeders and in turn growers are using corn to its fullest potential.

With this in mind, the University of Delaware’s Randall Wisser and a group of six fellow researchers have received a five-year $4.2 million grant from the U.S. Department of Agriculture’s National Institute of Food and Agriculture (USDA-NIFA) to study the genetics of adaptation and crop improvement.

Wisser, assistant professor in the Department of Plant and Soil Sciences, said that “there is a great deal of diversity in corn, or maize, particularly in the tropics, which has generally been underutilized in the U.S.” This is because tropical sources of maize are unadapted to North American environments.

Wisser added, “It is virtually impossible to realize the potential breeding value of maladapted materials; finding ways to efficiently adapt crops to new environments is a frontier of agricultural genetics research.”

Populations that lack genetic diversity can fall prey to climate change or other stressors by not having an array of genes on which to draw from. Breeding-based solutions to addressing abiotic and biotic challenges require access to genetic diversity. “If you’re drawing from a limited sample of diversity, the likelihood that you’ve got the necessary genes is less,” Wisser said.

Through its research, the team aims to help plant breeders increase breeding efficiency and access more genetic diversity, increasing their capability of responding to current and future challenges in food production.

Wide-ranging study

The research team is conducting a range of studies that combine field and controlled environment testing with genome sequence analysis and analytics.

In one avenue of research, they are working to better understand the genetics underlying how environment variables such as temperature and day lengths influence plant maturity, a primary barrier to adaptation.

When tropical maize is grown in a North American environment, like Delaware, where summer day lengths can reach up to 15 hours (compared to 10-12 hour days in the tropics), the plants are not receiving the appropriate signals that tell them to flower. They just keep growing, getting very tall and producing lots of leaves, flowering very late or not at all. The plants are out of synch with the growing season and get damaged by frosts or produce no seeds.

Maize that now grows in the U.S. has been adapted over hundreds of years with increasing selection intensities. Through many generations of breeding, an elite pool of maize plants have been developed for North American farmers that are insensitive to long days and flourish in these climates.

“In the process of intense selection, there’s been a big loss in potentially valuable genetic diversity,” Wisser said. “We are thinking about ways to recoup some of what has been lost to help deal with the complex problems of the future”

In another study of the project, the team will test if there are common regions in which the corn genome is associated with broad environmental adaptation or in which genetic barriers are created.

The group will track the flow of genes across generations of selection in the same tropical population adapted to a broad range of environments from Wisconsin to Puerto Rico.

“If adaptation is achieved through one or a few genetic tracks, then existing methods can be used to more quickly adapt tropical maize to different environments,” Wisser said. “If, on the other hand, there are multiple independent genetic tracks to adaptation then a different set of solutions will be needed.”

Wisser said he is hopeful that by studying the adaptation process researchers can pinpoint the barriers that limit use of tropical genetic diversity for North American maize improvement and “open the flood gates” for accessing maize diversity.

The research team

Other investigators in the study are Sherry Flint-Garcia from the USDA-Agricultural Research Services (ARS) and University of Missouri; James B. Holland from the USDA-ARS and North Carolina State University; Nick Lauter from the USDA-ARS and Iowa State University; Natalia deLeon from the University of Wisconsin-Madison; and Seth Murray and Wenwei Xu from Texas A&M University.

Further information about the Maize ATLAS (Adaptation Through Latitudinal Artificial Selection) project can be found at this website.

The study is funded by the USDA Climate Change Mitigation and Adaptation in Agriculture program, which also funded research by Carl Schmidt, associate professor of animal and food sciences and biological sciences at the University of Delaware, concerning heat stress in poultry. For more on that story, see the earlier UDaily article.

Article by Adam Thomas

Photo by Danielle Quigley

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UD’s Schmidt takes look back to study heat stress in poultry

August 12, 2011 under CANR News

To help the chickens of the future, Carl Schmidt is looking to the chickens of the past. Schmidt, associate professor of animal and food sciences and biological sciences at the University of Delaware, has been awarded a grant to study heat stress on chickens — both those that would have been around in the grocery stores of the 1950s and those that are found in supermarkets today.

Totaling $4.7 million, the five-year grant is funded through the Climate Change Initiative of the United States Department of Agriculture’s National Institute of Food and Agriculture (USDA-NIFA).

Schmidt said of the research, “The basic thought is that with climate change, it’s not so much the fact that the average temperature is going to go up a couple of degrees; it’s more the anticipation that there will be more heat waves, they will be hotter and they will last longer. And that is a problem for poultry production.”

By studying poultry from the 1950s, or “heritage” chickens, Schmidt is trying to see if any specific alleles — or individual gene variances — have been bred out of modern chickens that might make them less resistant to heat stress.

“Our hope is to identify particular alleles, variances in the population of genes, that help them survive heat stress. The thought is that if we can identify these alleles, industry could attempt to breed the alleles into their production lines,” he said.

The heritage chickens used by the University of Delaware in the study have been provided by the University of Illinois. In 1956, Illinois scientists set aside a male and female line of chickens and stopped selecting them for improved meat production. Those lines have been maintained, unselected, throughout the years, allowing researchers to study the chickens much as they would have been found in the 1950s.

One of the differences between the two types of chickens is that whereas the modern chicken goes to market in six weeks, the heritage bird would not go to market for 16 weeks. The modern chicken is also a lot larger than the heritage chicken.

Schmidt said, “Given the focus of this, we’re very curious, and we’ve really just started to ask the question: Do these birds response differently to heat stress?”

Explaining his research, Schmidt said, “We heat stress the birds and then we have a controlled population that we don’t heat stress. We then look at response and at gene expression patterns. We’re just doing our first trial but the heritage birds actually are using their drinker — the implement from which they get water — to get wet, whereas the modern chicken hasn’t used that yet.”

Two indicators that will help determine the two breeds’ levels of heat stress will be survival rate and production traits. “In many ways, since these are meat birds, breast muscle yield would be the thing really relevant to that,” Schmidt said. “The anticipation would be that by having to deal with the heat stress, perhaps diverting energy into dumping heat or whatever, they don’t have the final production yields of the control birds.”

Schmidt also said that he is personally interested to see how human selection and evolution has impacted the various traits of the chicken. “How did selection pull out alleles of genes that for example made the breast muscle like three times bigger? That’s the kind of thing that really excites me.”

Schmidt is collaborating on the research with Susan Lamont and Max Rothschild from Iowa State University and Chris Ashwell from North Carolina State University.

In addition to the professors from other universities, students from UD will also help conduct the research. Those students involved include Janet de Mena, Schmidt’s associate and a UD graduate; Liang Sun, a doctoral student in animal sciences in the College of Agriculture and Natural Resources; and Shurnevia Strickland, a master’s degree student in animal sciences.

This article can also be viewed on UDaily > >

Article by Adam Thomas

Photos by Danielle Quigley

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Kniel part of USDA-NIFA Food Virology Collaborative study on norovirus

August 4, 2011 under CANR News

Kali Kniel, associate professor in the University of Delaware’s Department of Animal and Food Sciences, is part of a national team led by North Carolina State University that has received a $25 million grant from the U.S. Department of Agriculture’s (USDA) National Institute of Food and Agriculture (NIFA) to strengthen food safety by studying human noroviruses across the food supply chain in an effort to design effective control measures and reduce the number of virus-caused food-borne illnesses.

Human noroviruses are the most common cause of food-borne disease, responsible for more than 5 million cases in the United States each year. Noroviruses spread from person to person, through contaminated food or water, and by touching contaminated surfaces.

The five-year project is led by Lee-Ann Jaykus, a professor in the Department of Food, Bioprocessing and Nutrition Sciences at North Carolina State University. The group, called the USDA-NIFA Food Virology Collaborative, consists of a team of more than 30 collaborators from academia, industry and government.

The team will work to increase understanding of the viruses; educate producers, processors and food handlers on safe handling and preparation of food; and develop control and management strategies to reduce food contamination before and after harvesting.

The project has six core objectives:

• Develop improved methods of studying human noroviruses and their role in food-borne illnesses.

• Develop and validate rapid and practical methods to detect human noroviruses.

• Collect and analyze data on viral food-borne illnesses – including how they are transmitted – and provide risk and cost analyses.

• Improve understanding of how human noroviruses behave in the food-safety chain in order to develop scientifically justifiable control measures.

• Develop online courses and curricula for food safety and health professionals and food service workers, and provide information to fresh produce and shellfish producers and processors on the risks, management and control of food-borne viruses.

• Develop a public literature database, build virus research capabilities in state public health laboratories, and develop graduate-level curricula to educate masters and doctoral students trained in food virology.

Other institutions involved include Clemson University, Baylor College of Medicine, Emory University, Research Triangle Institute, the U.S. Centers for Disease Control and Prevention, the University of Georgia, North Carolina A&T State University, North Carolina Central University, and the Institute for Food Safety and Health at the Illinois Institute of Technology.

Other key collaborators hail from Ohio State University, Louisiana State University, the U.S. Food and Drug Administration (FDA) and USDA Agricultural Research Service, Arizona State University, New Mexico State University, Cincinnati Children’s Hospital and Rutgers University. Various industrial and government stakeholders will serve the collaborative in advisory capacity.

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CANR researchers Chen, Kniel receive funds to fight foodborne illness

July 27, 2011 under CANR News

Researchers in the University of Delaware College of Agriculture and Natural Resources (CANR) have received funds to continue the fight against foodborne illness in the form of two grants totaling more than $5 million from the U.S. Department of Agriculture’s National Institute of Food and Agriculture.

Haiqiang Chen, associate professor in the Department of Animal and Food Sciences, will serve as the project director for a team of researchers who received a $4,997,078 grant focusing on the “Inactivation of Enteric Foodborne Viruses in High Risk Foods by Non-Thermal Processing Technologies.”

The study will focus mainly on human noroviruses, which cause acute gastroenteritis and account for more than 50 percent of foodborne disease outbreaks. Other enteric foodborne viruses such as hepatitis A virus and rotavirus will also be studied.

The overall goal of the study is to identify effective non-thermal processing technologies to destroy the viruses in high-risk foods, such as shellfish and produce, and disseminate the knowledge through education and outreach.

While thermal processing technologies, which involve heating food to a high temperature to kill microorganisms and enzymes, is the most commonly used processing technology in the food industry, scientists have been working on non-thermal processing technologies for the past three decades.

According to Chen, non-thermal processing technologies can still kill microorganisms and enzymes while, at the same time, better maintaining the raw characteristics of processed foods.

The efficiency of those non-thermal technologies will be tested, as will the effect of processing technologies on the quality of high-risk foods.

“This grant will help us to understand the mechanism of viral inactivation by non-thermal processing technologies, potentially develop a culture system to assess the survival of human norovirus and develop effective processing technologies that potentially could be used by the food industry to control foodborne viruses in high risk foods,” Chen said.

Kali Kniel, associate professor of animal and food sciences, along with Manan Sharma of the USDA-Agricultural Research Service Environmental Microbiology and Food Safety Laboratory and Jeri Barak of the University of Wisconsin, Madison, have received a grant of more than $444,949 to study “Plant Responses to Foodborne Bacteria and Viruses.”

“We are working together to investigate the growing problem of fresh produce contamination by microbial pathogens,” said Kniel. “This is the first time all three pathogens of high importance are being investigated using novel approaches.”

The three pathogens the group will be looking at are norovirus, pathogenic E. coli, and salmonella. The long-term goal of the their research is to understand and characterize the mechanisms that allow foodborne pathogens to attach to and colonize plants.

The researchers said they are hoping that this will eventually lead them to the more effective use of antimicrobials and good agricultural practices, which will reduce the number of illnesses and harmful effects on public health.

Article by Adam Thomas

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