California Ag Network

Tag: USDA ARS

  • ComBase Bioinformatic Tool Reduces Scourge of Foodborne Illness

    For many, the science of food preservation is not terribly exciting, but each year researchers save thousands of lives and countless belly aches. Although the United States has one of the world’s safest food supplies, the Centers for Disease Control and Prevention says foodborne illness affects about 48 million Americans each year, resulting in 128,000 hospitalizations and 3,000 deaths. Food poisoning is most often caused by eating food that’s been contaminated by bacteria or other pathogens.

    No one can control how private citizens prepare and store their own food, but America’s commercial food industry is closely monitored by several state and federal agencies. These agencies have many tools to accomplish that mission, including something called ComBase.

    ComBase is an online quantitative food microbiology database that contains more than 65,000 records collected from research organizations and published scientific articles. The information includes graphical data on how microbes grow, survive, and die under specific conditions, such as temperature and acidity. ComBase also contains food and broth models that predict the growth or inactivation – death – of microorganisms in food.

    ComBase was created in 2003 from a collaboration among the Agricultural Research Service (ARS), the United Kingdom’s Institute of Food Research, and Australia’s University of Tasmania. Since 2020, ComBase has been managed by ARS and hosted by the Eastern Regional Research Center (ERCC), in Wyndmoor, PA.

    “Representatives from the regulatory agencies, food companies, allied industry, academic institutions, and consumers in the United States and foreign countries help identify types of information needed to better predict and manage food safety,” said Vijay Juneja, ARS microbiologist at ERCC.

    ComBase data allows food companies to use predictive microbiology to help them design and implement food safety programs, document regulatory compliance, and test new model interfaces. Predictive microbiology states that microbial behavior, under a specific set of environmental conditions, is reproducible and can be predicted with mathematical equations. “In other words,” Juneja said, “it uses mathematics to describe how microorganisms will respond to specific environmental conditions.”

    For example, a food safety professional can search ComBase and retrieve specific information on the growth of a pathogen found in the food. This information could then be used to determine whether the food is safe to sell or consume; all without the need for an expensive and untimely microbiological test.

    “The result,” Juneja said, “is safer food, less foodborne illness, better public health, fewer product recalls, less litigation, and greater consumer confidence, health, and well-being.

    “ComBase saves the food industry millions of dollars a year in testing and other associated costs, as well as helping to prevent recalls and foodborne illness,” Juneja said. — By Scott Elliott, USDA-ARS Office of Communications

  • Study Shows Amygdalin in Almond Nectar can Reduce Viruses & Gut Parasites in Honey Bees

    Researchers at the U.S. Department of Agriculture’s (USDA) Agricultural Research Service (ARS) have found that a component in almond nectar and pollen can reduce honey bee viruses and gut parasites, which are some of the leading threats to bee health and colonies.

    The study, published in the journal Insects, showed amygdalin – a naturally-occurring chemical compound found in the nectar and pollen of almond trees – decreased levels of chronic bee paralysis virus, black queen cell virus and deformed wing virus. The bees also showed increased levels of beneficial gut bacteria and lower levels of the gut parasite Lotmaria passim.

    “We have found nectar chemicals can work as an antibiotic in bees, even against important viruses,” said Jay Evans, USDA-ARS research entomologist. “We were interested in amygdalin as a possible inhibitor of bee disease, because it is so important to the diet of honey bees.”

    The bees were fed natural concentrations of amygdalin over a two-month period as part of the study conducted in a bee yard at the Bee Research Laboratory in Beltsville, MD. In the treatment group, bees received a sugar solution supplemented with dissolved amygdalin from a supplier. The control group just received sugar water.

    The findings showed that amygdalin, which was previously reported to cause malaise in bees when fed sugar syrup, did not cause any negative effects to bee behavior.

    Amygdalin is not only found in the nectar and pollen of almond trees, but in a variety of other crops, such as cherries, nectarines and apples. During almond pollination season, western honey bees inevitably consume the natural compound since almond crops are almost exclusively pollinated by honey bees.

    The Agricultural Research Service is the U.S. Department of Agriculture’s chief scientific in-house research agency. Daily, ARS focuses on solutions to agricultural problems affecting America. Each dollar invested in agricultural research results in $17 of economic impact.

  • Numerous Health Benefits Found in Summer-Favorite Watermelon

    No summer barbecue is complete without fresh watermelon. As the nation moves towards the summer grilling season, you may want to consider how watermelon’s fruit chemistry can affect your overall health. Researchers in the USDA’s Agricultural Research Service (ARS) recently identified over 1,500 small molecules of diverse chemical characters in the fruit, known as phytochemicals. They concluded that eating watermelon is an excellent way to increase your intake of antioxidants, non-protein amino acids and lycopene. This means that every time you eat watermelon, you’ll be improving the health of your cells, organs and nervous system.

    The research specifically finds that the antioxidants in watermelon can help your body fight free radicals and slow down cell damage. The fruit’s non-protein amino acids will also help to repair your body tissue, break down food from other meals, and even regulate your blood pressure.

    “Watermelon could be part of the refreshing and healthy fruit options on your summer picnic table,” said USDA-ARS scientist Larry Parnell. “The fruit has gone through many years of evolution, domestication, and selection for desirable qualities—mainly those associated with flesh color, texture and nutrient and sugar content. But our research continues to find that the fruit contains a wide range of nutrients that improve your overall health.”

    Most Americans purchase the sweet dessert watermelon species, Citrullus lanatus, at their local grocery store or farmer’s market.  This species is among the most important vegetable crops grown and consumed throughout the world, with over 100 million tons in annual global production.  The fruit also has more lycopene than a raw tomato, which is linked to healthy eyes, overall heart health and protection against certain cancers. Other nutrients, like carotenoids, flavonoids, carbohydrates and alkaloids, are also found in the flesh, seed, and rind.

    “I worked with Dr. Parnell and the team to develop a pioneering concept of using big data and computational biology to identify and catalog all of the phytochemicals that exist in edible fruit,” said ARS researcher Amnon Levi. “The research to identify the metabolic pathways and genome sequence of genes involved in the production of beneficial phytochemicals could be highly useful for plant scientists and breeders aiming to improve nutrient content in fruits and vegetables.”

    The watermelon’s phytochemicals are human-cell-protecting compounds found in fruit, vegetables, grains and beans. All of these nutrients can contribute to your overall health in numerous ways.

    Watermelon was introduced to Europe via Moorish Spain in the 10th century. Since then, watermelon has been cultivated successfully in warmer Mediterranean regions before being brought to the Americas by European colonists during the 16th century. Today, watermelon is grown in 44 U.S. states, while major production is centered in California, Florida, Georgia and Texas.

    Fruits and vegetables are a part of a healthy, balanced diet, with the recommendation being 1.5 to 2 cups of fruit and 2 to 3 cups of vegetables per day.

    The Agricultural Research Service is the U.S. Department of Agriculture’s chief scientific in-house research agency. Daily, ARS focuses on solutions to agricultural problems affecting America. Each dollar invested in agricultural research results in $17 of economic impact.

  • Healthy Roots, Healthy Trees: HLB & Soil Microbes

    The rhizosphere, defined as the soil environment that surrounds the plant roots, is a rich and diverse habitat for microbes. Some members of the rhizosphere microbiome (or collection of microbes), are good, others bad while many are just there and don’t provide any benefits or harm to the host. One function of the good microbes in the rhizosphere is to help facilitate the availability and assimilation of nutrients and water from the rhizosphere. Just like the human gut, the plant rhizosphere conveys key nutritional functions and the analogy was made that “plants wear their gut on the outside”. One example is the symbiotic relationship between legumes (peas, beans) and rhizobia. Those bacteria help the plant fix atmospheric nitrogen in exchange for carbon supply. Another example is the symbiotic relationship between the plant and mycorrhizal fungi, whereby the mycorrhizae receive carbon from the plant in exchange for increased nutrient uptake (principally phosphorus and nitrogen). There is undeniable evidence that plants have developed a mechanism for recruiting good microbes to cope with environmental stress such as protection against opportunistic pathogens or drought. The rise of ‘omics’ technologies have helped profile entire microbial communities associated with plants and shed light in their biological functions. This research has fueled the development of novel commercial bioproducts to address the increasing consumer’s demand of environmentally-friendly products. As a result, there has been several commercial ‘probiotics’ and ‘prebiotics’ that have been marketed for agricultural use including many biocontrol agents such as fungal- (e.g., Trichoderma) and bacterial- based (e.g., Bacillus, Streptomyces, or Pseudomonas) bioproducts.

    One goal of my research program is to identify beneficial microbes for tree and vines crops, promote practices that support the presence and abundance of beneficial microbes and figure out how good microbes help combat pathogens and support plant health. As part of a collaborative project (UC Riverside, University of Florida, USDA-ARS) funded by the California Citrus Research Board and the USDA-NIFA, we profiled the microbiome of citrus trees in the context of Huanglongbing disease (or HLB). HLB is a highly destructive and lethal disease to all commercial citrus cultivars making it a threat to citrus production globally. Finding strategies that do not only rely exclusively on management of the insect vector of the bacterium (the Asian Citrus Psyllid), is a priority to the citrus industry. In our research, we found that there were significant tissue-specific microbial shifts occurring within the citrus microbiome as trees get sicker, especially in the root compartment. As HLB progressed, there were depletions of beneficial species in roots, such as mycorrhizal fungi, and enrichments of parasitic microorganisms, such as Fusarium and Phytophthora (see Figure). HLB-affected trees decline because of the clogging the phloem sieve tubes, which limit movement of sap and translocation of sugar to the roots, hence leading to feeder root collapse. Once tree is weakened, it becomes more susceptible to pathogens such as Phytophthora which further weakens the trees and exacerbate above ground HLB symptoms. In addition, several studies from Florida suggested that cultural practices that supported root health and rhizosphere microbiome richness and diversity limited root collapse.

    Figure: Citrus decline caused by HLB (https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-04-20-0027- R – Ginnan et al. 2020. Phytobiomes); canopy thinning, wood dieback, feeder roots decline, collapse of beneficial microbes and enrichment of pathogens in roots.

    Our group was recently awarded another research funding by the USDA-NIFA Emergency Citrus Disease Research and Extension program (project director, M.C. Roper, Microbiology and Plant Pathology, UC Riverside). This research effort in collaboration with UC Agricultural and Natural Resources, UC Davis, University of Florida, and the USDA-ARS aims at investigating the root collapse associated with HLB- impacted trees and finding ways to mitigate it by promoting root health. In the proposed work, we will test how different sectors of the root microbiome contribute to or lessen fibrous root loss and if soil amendments (e.g., humic acid treatment, mulching) and planting of HLB tolerant rootstocks (Poncirus trifoliata and P. trifoliata hybrids) can be used to mitigate root loss associated with HLB in Florida, and how tree respond to those practices under a HLB free environment in California. While these approaches will not cure trees from HLB, it will provide a science-based information for strategies that support root and tree health and sustain orchard longevity until remedies are discovered. — By Philippe Rolsausen, Professor in Cooperative Extension, UC Riverside

  • Genome to Phenome: ARS Research in Precision Agriculture

    How do you build a better dairy cow? Use a tool designed to study the human genome, of course.

    Working alongside international research partners in the Agricultural Genome to Phenome Initiative (AG2PI), Agricultural Research Service (ARS) scientists are using technology to meet the challenges of the increasing global population and ever-changing environmental stressors. The goal of AG2PI is to better understand how genetics and the environment together influence the performance of plants and animals. This is easier said than done because regional environmental differences can vary the results of seeds from the same plant.

    “We know that nature (genotype) and nurture (environment and management) are both important factors in agricultural production (phenotype),” said Caird Rexroad III, ARS national program leader for animal production and protection in Beltsville, MD. “We need to better understand exactly how they affect production to develop optimal production strategies that are tailored to the diversity of genetics and environments that make up U.S. and world agriculture.”

    To achieve this goal, AG2PI reaches across kingdoms (scientific classifications) to examine genome-to-phenome challenges. Scientists in the various specialties work together to identify and fill in similar research gaps, access advanced cyberinfrastructure, and share data and new technology, such as sensors, robotics, and imaging platforms.

    “AG2PI is a community of scientists who share a passion for agricultural research and developing technologies that improve our ability to produce a safe, abundant, healthy, and affordable food supply,” Rexroad said. “This platform is inclusive of many scientific disciplines that may not have interacted in the past, such as breeders, engineers, economists, social scientists, etc., and works by sharing ideas, providing trainings on state-of-the-art technologies, and enhancing communication and collaboration.”

    One example of how ARS scientists used AG2PI to avoid research “stovepipes” (the term used to describe how one group may isolate its information from other unrelated groups) involves the international research to improve dairy cattle.

    “The Genome-to-Phenome Initiative began for us in 2007,” said Curt Van Tassell, research geneticist at the ARS Animal Genomics and Improvements Laboratory in Beltsville. According to Van Tassell, the landmark study used existing technology from one scientific discipline and applied it to another; in this case, technology was developed for the human genome and adapted for use in the cow by designing a DNA chip to characterize the whole genome of the cow.

    “We worked closely with dairy genetics industry partners to implement genome-enabled genetic improvement with dramatic impact in the dairy industry,” Van Tassell said. “With the help of our partners, we revolutionized the world of genetic improvement in livestock in one fell swoop.”

    While AG2PI is not in itself a scientific project, it supports all agricultural research that will benefit farmers, ranchers, and consumers, Rexroad said. “Farmers and ranchers will have access to genetics and management practices that will increase yields, improve crop and animal health and well-being, increase production efficiency or product value, and improve sustainability in the production system,” he said.

    “AG2PI is all about agricultural research, and it is inclusive of many scientific disciplines, and that ties into the ARS goal of finding solutions to agricultural problems that affect Americans everyday from farm to table,” Rexroad said. – By Scott Elliott, USDA-ARS Office of Communications

  • Growers Refine Date Palm Irrigation with UCANR Research

    California’s $86 million date industry produces more than half of the nation’s dates. Most of the fruit is grown in the arid Coachella Valley. Despite efforts by growers to conserve water, data was lacking on date palms’ actual water use to refine the best irrigation management for the crop until a recent research project led by Ali Montazar, UC Cooperative Extension irrigation and water management advisor for Imperial and Riverside counties.

    New research provides data California date growers need to apply a more precise amount of irrigation water to meet the trees’ needs to produce a healthy crop (photo by Ali Montazar).

    “California dates are grown in the hottest and most arid climate in North America and require substantial amounts of water in order to bring a successful crop to fruition,” Albert Keck, Coachella Valley date grower and chairman of the California Date Commission, wrote in a letter of support for this project. “In addition, there is scant modern research specifically and technically focused on growing dates in North America.”

    Montazar said there is a lack of irrigation management information on date palms worldwide.

    “The information developed in this study is expected to have a worldwide impact,” he said.

    To determine the evapotranspiration rate and crop coefficients for California date palms, Montazar teamed up with scientists at UC Davis, California Department of Water Resources, USDA Agricultural Research Service, and USDA Salinity Laboratory.

    The experiment was carried out in six date orchards in the Coachella and Imperial valleys. The sites represent various soil types and conditions, irrigation management practices, canopy characteristics, and the most common date cultivars in the region.

    “The findings of the project indicate that there is considerable variability in date palm consumptive water use, both spatially and temporally,” Montazar said. In other words, the amount of water the trees use varies considerably depending on each site’s growing conditions.

    He estimated the water needs for date palms planted in different soil types in the low desert region.

    “Growers will be able to use the science-based information and tools developed by this project to determine their date palm water needs and optimize the efficiency of water and fertilizer use in their groves,” Montazar said.

    Fruit bags protect date from insect damage and dust and prevent the fruit from falling to the ground (photo by Ali Montazar).

    The peer-reviewed article “Determination of Actual Evapotranspiration and Crop Coefficients of California Date Palms Using the Residual of Energy Balance Approach” is published in the journal MDPI Waterat https://www.mdpi.com/2073-4441/12/8/2253.

    “With a large quantity of new date plantings in the region, coupled with increasingly limited water resources in the Colorado River Basin Watershed, the knowledge anticipated to be developed by this research project has the potential to yield large dividends through not only improved water use efficiency, but also best management practices and crop quality,” said Keck of the California Date Commission.

    Although the research focused on Coachella Valley dates, Montazar said the results are likely to be useful to growers who have orchards with similar varieties, irrigation practices, and canopy and soil features in other locations.

    Montazar’s co-authors are Robert Krueger of the USDA-ARS National Clonal Germplasm Repository for Citrus and Dates; Dennis Corwin of USDA-ARS U.S. Salinity Laboratory; Alireza Pourreza UC Cooperative Extension specialist based at UC Davis Department of Biological and Agricultural Engineering; Cayle Little of California Department of Water Resources; Sonia Rios, UC Cooperative Extension advisor in Riverside County; and Richard L. Snyder UC Cooperative Extension specialist emeritus in the UC Davis Department of Land, Air and Water Resources.

    The date palm irrigation project was funded by the CDFA Specialty Crop Block Grant Program. — By Pamela Kan-Rice, UCANR

  • Drink Your Peas, Please!

    USDA Agricultural Research Service (ARS) scientist and director of the Western Regional Research Center (Albany, CA), Tara McHugh and her team in the Healthy Processed Foods Research Unit are experts at solving food-manufacturing problems. Using cutting-edge processing technologies, they have helped numerous small businesses, such as Ripple Foods, turn ideas into products for the consumer.

    ARS is helping Ripple Foods optimize its current pea protein drying process to make it more efficient and to further improve its products. The company manufactures its own pea protein by processing yellow split peas into a liquid form and then isolating, purifying, and drying the protein. The pea protein is then made into non-dairy milks, protein shakes, half and half, ice cream, and other products.

    The drying step is necessary because producing this clean-tasting plant protein in a wet state comes with challenges: It’s difficult to transport, has a greater risk for microbial spoilage, and has handling issues, McHugh said.

    “It’s also expensive to ship all over the country, so we are working to optimize the drying process—looking at a way to dehydrate it so it can be rehydrated to save expenses,” she said. “The drying process also may even improve the quality and flavor of the final product.”

    Ripple Foods has a cooperative research and development agreement with ARS, which assists the company in data gathering and analysis on different aspects of its pea beverage. “Ripple’s mission is to make plant-based foods delicious,” said Aminah Johnston, a process engineer with the company. “We are always looking for ways to make our protein and products better. Our collaboration with ARS has been extremely helpful.”

    This kind of research not only supports small businesses and U.S. growers, but also reduces waste and increases consumption of healthy foods.—By Sandra Avant, formerly with USDA-ARS Office of Communications.

  • Using Satellites to Improve Sustainability, Yield

    Two of the nation’s great agricultural regions are the focus of new research that aims to head off emerging threats and improve sustainability.

    Scientists with the Agricultural Research Service (ARS) are joining colleagues to create and use artificial intelligence to help farmers in the Colorado River Basin and Salinas Valley, CA, improve their management of irrigation, fertilization, and pests. USDA’s National Institute of Food and Agriculture funded the University of California, Riverside-led project with a 5-year, $10 million grant.

    “This project will integrate multiple satellite and meteorological data sets to help farmers in the Southwestern United States,” said Ray Anderson, a research soil scientist with the ARS Agricultural Water Efficiency and Salinity Research Unit in Riverside. Anderson leads the ARS portion of the study, working with ARS scientists Todd Skaggs and Andrew French.

    ARS has three primary roles in the project: To calculate project area crop water use and anomalies with crop water use across the entire region; develop tools that help growers avoid salinity damage while minimizing the leaching of fertilizer; and to gather field data to validate satellite algorithms.

    Researchers will take advantage of advanced satellite technology to provide more frequent, detailed information to farmers than ever before. The plan is to integrate high-resolution commercial satellite data with established government satellite platforms and meteorological data.

    A major advance with this work will be the use of daily, high-resolution (12-foot) satellite imagery, Anderson said. Previously, data have only been available every 1-2 weeks at 60- to 100-foot resolution and were too infrequent or coarse to provide timely and actionable information to farmers.

    “By combining the new satellite data with artificial intelligence, we will be able to discover and create tools that will help farmers pinpoint areas that need better irrigation, nutrient, and pest management,” Anderson said.

    “One of the major advantages to this project is that the outputs – recommendations and highlights on a smartphone app – will be accessible to all farmers,” he said. “Previously, farmers had to pay for aircraft and specialized processing to get this level of imagery and detail. Soon, high resolution satellite imagery, machine learning, and cloud processing will be available to smaller producers in one easy-to-use tool. These algorithms will help farmers with their field scouting so that they can catch problems early, before significant yield reductions occur.”

    Agriculture in the Colorado River Basin and Salinas Valley employs more than 500,000 people and generates roughly $12 billion annually in revenue. Farmers in the regions grow fruits and vegetables that are shipped around the country all year round, particularly in winter.

    Water availability and use top the researchers’ priority list because prolonged drought has reduced agricultural water availability in the southwestern United States.

    “These valleys consume large amounts of irrigation water, but the amount and quality of irrigation water is decreasing,” Anderson said. “It is important to use existing supplies more efficiently and to protect water sources from nutrient and salinity contamination that can come from poor irrigation management.” — By Scott Elliott, USDA-ARS Office of Communications.

  • Keeping Up with the Evolving Navel Orangeworm Pest Pressure

    So how bad can Navel Orangeworm damage get in our tree nut orchards? Hopefully we won’t have to find out this season, as growers are equipped with more tools and practices to control the pest. Watch this brief interview with Research Entomologist Joel Siegel as he shares some evolving trends in pest pressure across the state, and read more about it in Pacific Nut Producer Magazine.