California Ag Network

Tag: UC Riverside

  • 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

  • $1.7 million Grant to Unlock Barley’s Genetic Superpowers

    Barley is important for more than beer. A UC Riverside geneticist has won $1.7 million to study how one of the world’s staple foods might survive climate change.

    The National Science Foundation CAREER Award to Daniel Koenig, an assistant professor in the Department of Botany and Plant Sciences, will reveal details about genetic adaptations barley has made in the past to enable its survival over thousands of years. These details will also help steer its future as weather becomes more extreme.

    In addition to alcoholic beverages, barley is used as a major crop for feeding both animals and humans. It ranks fourth among cereals in terms of total world production. After it was domesticated as a crop over 10,000 years ago, it spread rapidly to environments as different as hot, dry Egypt and cold, wet Minnesota.

    Koenig, who studies plant evolution, wonders how the plant has been able to successfully adapt to these wildly different places.

    “Though we have the tools to compare the DNA of plants collected in different countries, our challenge is understanding which genes evolved in response to weather and which evolved over time in response to other pressures, like diseases,” Koenig said.

    Since only one generation of a plant can be grown per year, the process of observing adaptation real-time is lengthy. To speed up progress, Koenig’s lab is making use of an experiment started in the 1920s. Breeders took barley varieties collected from all over the world and have grown them over the last century in Davis, Calif., and Bozeman, Mont.

    “We can analyze the genes of these varieties, watch as they continue to adapt, and identify the genes that might be responsible for their survival,” Koenig said.

    The NSF CAREER Award is a competitive grant for promising new faculty to help them improve their integration of research and teaching. In this case, Koenig is going to use the award to train undergraduates to compare genes from the beginning of the 1920s experiment with those from today.

    Students will learn to use both traditional molecular biology and newer, computational techniques for this project. The process of identifying survival genes in barley can also be repeated for other crops, helping to ensure the future of other foods as well.

    Growing up in the Central Valley surrounded by agriculture, and attending graduate school at UC Davis, Koenig is excited to expose a new generation of students to food science.

    “This grant will provide an opportunity for students, especially those who grew up in urban environments, to learn about agriculture and give them the basis for possible careers in agricultural science,” Koenig said. — By Jules Bernstein, UC Riverside

  • Protein Discovery Could Help Enable Eco-Friendly Fungicides

    New research reveals an essential step in scientists’ quest to create targeted, more eco-friendly fungicides that protect food crops.

    Scientists have known for decades that biological cells manufacture tiny, round structures called extracellular vesicles. However, their pivotal roles in communication between invading microorganisms and their hosts were recognized only recently.

    UC Riverside geneticist Hailing Jin and her team found plants use these vesicles to launch RNA molecules at fungal invaders, suppressing the genes that make the fungi dangerous.  

    ​Infection of an Arabidopsis plant by the fungus that causes white mold disease. (Anna Schroll/Max Planck Institute for Chemical Ecology)

    “These vesicles shuttle small RNAs between cells, like tiny Trojan horses with weapons hidden inside,” said Jin, a professor of genetics and the Cy Mouradick Chair in the Department of Plant Pathology and Microbiology. “They can silence pathogenic fungal gene expression.”

    Using extracellular vesicles and small RNAs has several advantages over conventional fungicides. They’re more eco-friendly because they are similar to naturally occurring products. Eventually, they degrade and do not leave toxic residues in the soil. Also, Jin explained, this method of fighting fungi is less likely to breed drug-resistant pathogens.

    A sticking point for scientists in creating these fungicides has been figuring out how to load their desired small RNAs into the vesicles.

    “We’ve wondered how these weaponized small RNAs get into the bubbles,” Jin said. “Now, we think we have an answer.”

    Her laboratory has identified several proteins that serve as binding agents, helping to select and load small RNAs into the vesicles. The lab’s research is detailed in a new Nature Plants journal article.

    The Jin laboratory has been working for several years on the development of gene-silencing RNA fungicides. Work toward this goal led to the team’s landmark discovery in 2013 that gene-silencing RNA messages can be sent from the fungal pathogen to the plant host to suppress host immunity. Later, the team learned small RNAs can move both ways — from plants into pathogenic invader cells as well. In 2018, the team worked out that extracellular vesicles were the major delivery system for these small RNAs. They observed that Arabidopsis plants secrete extracellular vesicles into Botrytis cinerea, a fungus that causes grey mold disease and destroys millions of crops every year.

    “This was the first example of a host using these vesicles to deliver small RNAs to another organism,” Jin said. “Previously we saw movement of RNA, but didn’t know how the small RNA are selected and transported.”

    Now, she and her colleagues have identified several RNA-binding proteins in Arabidopsis that bind to specific small RNA molecules and load them into extracellular vesicles. This suggests the proteins play an important role in loading and stabilizing small RNAs in the vesicles. The finding can help increase the payload of gene-silencing RNAs that make it into vesicles and enhance the efficiency of disease control.

    Some scientists have taken inspiration from the RNA communication in plant vesicles to design human therapies. For example, some are attempting to load anti-cancer RNAs and drugs into extracellular vesicles in fruits or vegetables, so people can eat or drink them. Jin is hopeful that her lab’s discovery can aid these efforts. — By Jules Bernstein, UC Riverside

  • Novel Treatment Causes Killer Citrus Disease to Leak & Die

    New research affirms a unique peptide found in an Australian plant can destroy the No. 1 killer of citrus trees worldwide and help prevent infection. Huanglongbing, HLB, or citrus greening has multiple names, but one ultimate result: bitter and worthless citrus fruits. It has wiped out citrus orchards across the globe, causing billions in annual production losses.

    Untreated citrus plants on the left, as compared to treated ones on the right. (Hailing Jin/UCR)

    All commercially important citrus varieties are susceptible to it, and there is no effective tool to treat HLB-positive trees, or to prevent new infections. However, new UC Riverside research shows that a naturally occurring peptide found in HLB-tolerant citrus relatives, such as Australian finger lime, can not only kill the bacteria that causes the disease, it can also activate the plant’s own immune system to inhibit new HLB infection. Few treatments can do both.

    Research demonstrating the effectiveness of the peptide in greenhouse experiments has just been published in the Proceedings of the National Academy of Sciences.

    The disease is caused by a bacterium called CLas that is transmitted to trees by a flying insect. One of the most effective ways to treat it may be through the use of this antimicrobial peptide found in Australian finger lime, a fruit that is a close relative of citrus plants.

    “The peptide’s corkscrew-like helix structure can quickly puncture the bacterium, causing it to leak fluid and die within half an hour, much faster than antibiotics,” explained Hailing Jin, the UCR geneticist who led the research.

    When the research team injected the peptide into plants already sick with HLB, the plants survived and grew healthy new shoots. Infected plants that went untreated became sicker and some eventually died.

    Arrows point to areas of fluid leakage from the bacterial cell after treatment with the antimicrobial peptide. (Hailing Jin/UCR)

    “The treated trees had very low bacteria counts, and one had no detectable bacteria anymore,” Jin said. “This shows the peptide can rescue infected plants, which is important as so many trees are already positive.”

    The team also tested applying the peptide by spraying it. For this experiment, researchers took healthy sweet orange trees and infected them with HLB-positive citrus psyllids — the insect that transmits CLas.

    After spraying at regular intervals, only three of 10 treated trees tested positive for the disease, and none of them died. By comparison, nine of 10 untreated trees became positive, and four of them died.

    In addition to its efficacy against the bacterium, the stable anti-microbial peptide, or SAMP, offers a number of benefits over current control methods. For one, as the name implies, it remains stable and active even when used in 130-degree heat, unlike most antibiotic sprays that are heat sensitive — an important attribute for citrus orchards in hot climates like Florida and parts of California.

    In addition, the peptide is much safer for the environment than other synthetic treatments. “Because it’s in the finger lime fruit, people have eaten this peptide for hundreds of years,” Jin said.

    Hailing Jin, research leading UC Riverside geneticist

    Researchers also identified that one half of the peptide’s helix structure is responsible for most of its antimicrobial activity. Since it is only necessary to synthesize half the peptide, this is likely to reduce the cost of large-scale manufacturing.

    The SAMP technology has already been licensed by Invaio Sciences, whose proprietary injection technology will further enhance the treatment.

    Following the successful greenhouse experiments, the researchers have started field tests of the peptides in Florida. They are also studying whether the peptide can inhibit diseases caused by the same family of bacteria that affect other crops, such as potato and tomato.

    “The potential for this discovery to solve such devastating problems with our food supply is extremely exciting,” Jin said. — By Jules Bernstein, UC Riverside

  • A New Microscopic Almond Pest of Concern

    Another pest in almonds? Just what we needed, right? Only this one you can’t see.  Almond growers have been dealing with nematodes for a long time; however, the peach root knot nematode is new to California almond orchards.  Watch this brief interview with UC Riverside Nematologist Andreas Westphal as he explains and read more about it in Pacific Nut Producer Magazine.

    Please thank this video’s sponsor Trece for their industry support.

  • Root Bacteria Could Help Defeat Fatal Citrus Disease

    A UC Riverside-led team is looking at tiny underground microorganisms for a way to prevent a huge problem — Huanglongbing, a disease with no cure that has decimated citrus orchards worldwide.

    The disease, also known as HLB or citrus greening, has multiple names but the same ultimate result: bitter and worthless citrus fruits. By some estimates, the end of citrus orchards in California and Florida could amount to $14 billion in lost commercial revenue.

    Fruit affected by Huanglongbing. (UCR)

    “Often times, it is thought of as an above-ground disease of the fruits, leaves, and stems,” said Caroline Roper, plant pathology professor and director of the new research effort. “However, we have seen the roots of trees decline with infection, and we want to understand why.”

    The National Institute of Food and Agriculture has awarded the UCR-led team $10 million over the next five years to investigate the role of soil and root microbes in the disease.

    Roper said data from previous studies shows the microbiome of the infected tree — which includes bacteria and fungi as well as protozoa and viruses — plays a role in the disease.

    “We have seen a shift in the root microbiome as trees get sicker,” she said.

    The microbiomes shift to contain more potentially parasitic organisms that may act as secondary invaders to a tree that is suffering from HLB, according to Roper. The invasion of these root pathogens may be causing trees to die faster when they have HLB.

    Part of this new research effort will test whether soil amendments like manure and compost might suppress parasitic microorganisms in the roots as well as the soil, and give the trees more strength to combat diseases including HLB.

    In addition, the research team will try to determine the molecular basis of HLB resistance shown by citrus root stocks developed in Florida. They’ll then see how those rootstocks perform in California, which has different soil and climate conditions.

    The research team will examine both younger trees, because a lot of citrus growers have had to re-plant their orchards after infection, as well as older trees to see if mature groves can recover.

    It will also be important to note how well root stocks from Florida, where there has been a heavy infestation of HLB, perform in California, where much less of the disease has been detected.

    “One of the great things about this grant is that we’re able to leverage existing field trials being done by our collaborators in Florida and at the UC’s Lindcove Research and Extension Center in central California,” Roper said. “This may lead to faster results than we’d otherwise have had.”

    Collaborators on the project include UC Davis; California State University, Sacramento; the University of Florida; and the U.S. Department of Agriculture’s Agricultural Research Service in Ft. Pierce, Florida. — By Jules Bernstein, UC Riverside

  • $6.3 Million to Help UC Riverside Save Avocado Orchards

    New grants totaling $6.3 million will help UC Riverside solve problems facing American avocado orchards, including a lethal fungal disease called Laurel Wilt.

    Laurel Wilt can destroy an entire avocado orchard in a couple of weeks once symptoms develop. It is already present in Florida. Without effective treatments, it will inevitably spread to California, which is the nation’s leading producer of avocados.

    Laurel Wilt is caused by a fungus, Raffaelea lauricola, that the non-native redbay ambrosia beetle introduces in trees of the Laurel family, which includes avocado.

    The non-native redbay ambrosia beetle, which carries the fungus causing deadly Laurel Wilt. (UCR)

    “When the beetle attacks, the fungus enters and colonizes the tree’s vascular system, and within weeks, the tree wilts and dies if not managed properly,” said Patricia Manosalva, director of this project as well as UCR’s Avocado Rootstock Breeding Program.

    In addition to Laurel Wilt, avocado growers face numerous production challenges including devastating diseases such as Phytophthora root rot, or, PRR, and soil salinity, which in combination cause severe reduction in fruit yield and quality. This combination can also completely destroy avocado orchards.

    Avocado roots darkened and killed by Phytophthora root rot. (David Rosen/UCR)

    Avocado is also highly sensitive to salinity. Increasing levels of salinity in water and soil due to drought and the use of reclaimed water for crop irrigation purposes threatens avocado production worldwide.

    To combat the threats, the USDA’s National Institute of Food and Agriculture Specialty Crop Research Initiative has awarded UC Riverside $4.4 million. The grant will enable the development of next-generation technological solutions to these problems over the next four years in partnership with scientists at the universities of Hawaii, Florida, Texas, and Milan.

    The same grant will enable research on both short- and long-term solutions for managing avocado PRR, the major hindrance for avocado production worldwide, Manosalva said.

    “Under this grant we will select rootstocks harboring resistance to the current pathogen population and we will register new fungicides with different modes of actions to reduce avocado losses to this destructive oomycete pathogen,” Manosalva said.

    The UCR rootstock breeding program has already identified advanced rootstock lines that are tolerant to salinity and P. cinnamomi, the pathogen that causes PRR. These rootstocks may also confer resistance or tolerance to Laurel Wilt when grafted with different varieties. Field trials of these rootstocks will be conducted in California, Florida, Texas, Hawaii and Puerto Rico and will be screened for resistance at University of Florida.

    Another approach to mitigating avocado threats will be the further development of remote field sensors that can detect and differentiate drought from high salinity and Phytophthora root rot. UCR initially developed prototypes of these sensors and tested them in greenhouses. This grant will enable researchers to improve the sensors and test them in fields.

    Manosalva notes that UC Riverside is unique in having a highly recognized avocado breeding program first developed 70 years ago.

    “We’ve been developing agricultural science for a long time,” she said. “This grant will allow us to keep moving the UCR rootstock breeding program forward and continue developing hearty avocado rootstocks.”

    Through the Office of Technology Partnerships, UCR currently has three rootstocks available for licensing in the U.S. and may have up to five new rootstocks available in the next few years. The new rootstocks could provide increased tolerance to diseases, drought, heat, and soil salinity.

    In a related grant, the USDA’s National Institute of Food and Agriculture, Organic Agriculture Research and Extension Initiative awarded $1.9 million to a team of 15 scientists from five universities and the USDA Agricultural Research Service, or USDA-ARS. The grant will allow the researchers to study whether essential oils can help suppress certain pathogens and pests.

    Researchers from the University of Florida, Clemson University, the University of Georgia, the University of Hawaii at Manoa and the USDA-ARS as well as UC Riverside will collaborate on the project.

    Producers of essential oils claim their products may be able to treat plant pathogens such as gray mold, powdery mildew, algal stem blotch and brown rot as well as insects including mites, thrips and scales. This grant will enable the team to evaluate those claims.

    Manosalva said both grants underscore the importance of funding basic research in agricultural science. “California’s produce feeds the nation, and the world,” she said. “Our science will help feed people and empower growers everywhere.” — By Jules Bernstein, UC Riverside

    About UC Riverside

    The University of California, Riverside (www.ucr.edu) is a doctoral research university, a living laboratory for groundbreaking exploration of issues critical to Inland Southern California, the state and communities around the world. Reflecting California’s diverse culture, UCR’s enrollment is more than 24,000 students. The campus opened a medical school in 2013 and has reached the heart of the Coachella Valley by way of the UCR Palm Desert Center. The campus has an annual statewide economic impact of almost $2 billion. To learn more, email news@ucr.edu.

  • Autonomous Robot to Sample Leaves and Measure Water Potential

    Every backyard gardener knows how hard it can be to tell when to water the plants. Multiply that by tens or hundreds of acres and it’s easy to see the challenges growers face keeping their crops healthy while managing water resources wisely.

    To determine water needs accurately, growers hand-pluck individual leaves from plants, put them in pressure chambers, and apply air pressure to see when water begins to leak from the leaf stems. That kind of testing is time consuming and means growers can only reach so many areas of a field each day and cannot test as frequently as needed to accurately determine optimal irrigation scheduling patterns.

    A group of researchers from UC Riverside and UC Merced have received a grant for more than $1 million from the U.S. Department of Agriculture through the National Science Foundation’s National Robotics Initiative to address these challenges. From UC Riverside are Assistant Professor Konstantinos Karydis and Professor Amit K. Roy-Chowdhury, both from the Department of Electrical and Computer Engineering. UC Merced, which leads the effort, is represented by Stefano Carpin, professor of computer science; and Joshua Viers, professor of environmental engineering.

    UC Riverside Assistant Professor Konstantinos Karydis

    As part of the project, the group is developing a robotic pressure chamber that can autonomously sample leaves and immediately test them on site to provide the freshest data. The system will work to gather data even in large fields, and over a period of time, rather than just providing a snapshot.

    Frequently updated data can help growers better plan irrigation schedules to conserve water, optimize the time and effort spent by crop specialists tasked with determining and analyzing lead water potential, and help decrease some of the costs in the food-production chain.

    UC Riverside Professor Amit K. Roy-Chowdhury

    Current measuring techniques involve collecting leaf samples and transporting them to an off-site location, where testers can use very accurate, expensive pressure chambers; or sampling and analyzing leaf samples in the field using hand-held pressure chambers.

    “In the first category, leaf samples can get mixed up, making it impossible to track them back to the specific areas of the field they came from, Karydis said. “In addition, the properties of the leaf might vary given the time elapsed between being sampled and being analyzed, which in turn may yield misleading results.”

    Hand-held instruments in the field can be less accurate, but testing can be done multiple times with different leaves from the same plants. This method is time- and labor-intensive, and must be undertaken by specially trained personnel.

    Carpin has already worked with colleagues at UC Davis and UC Berkeley to create the Robot-Assisted Precision Irrigation Delivery, or RAPID, system, which travels along rows of crops adjusting irrigation flows according to sensor data that tells the robot precisely what’s needed for each plant.

    The project will use the same mobile base robot as in RAPID but equip it with a custom-made robotic leaf sampler and pressure chamber being designed by the researchers at UC Riverside, and pair it with drones that can survey the fields and direct the robot to areas of interest.

    “Using this process, growers could survey plants all day long, even in large fields,” Carpin said.

    The four-year project will support graduate students as well as summer research opportunities for undergraduates. The project has four phases: development of the chamber; developing machine vision so the robot can “see” the water coming from the leaf stems; coordinating multiple robots — in the air and on the ground; and evaluation.

    The researchers plan to have the first set of automated pressure chamber prototypes fabricated by spring 2021, and to evaluate their performance and refine designs in controlled settings over spring and summer 2021. They expect to have a completed setup by winter 2022, so they can begin controlled field testing.

    “We have to be quick about it because if we miss a peak growing season, we have to wait another nine months for the next one,” Carpin said. “We’d like to be able to start testing next summer and test every summer, and we need to be able to maximize the tests.”

    When all of the components have been designed, the designs and code will be made open source, and all the data collected during the project will be made available to the scientific community, the researchers wrote in their proposal.

    The project came about after Carpin and Viers, director of the Center for Information Technology Research in the Interest of Society, or CITRIS, at UC Merced, had been talking with area farmers about the challenges of growing almonds and grapes. Karydis and Roy-Chowdhury had been hearing the same challenges from citrus and avocado growers in the Riverside area, so the four partnered up.

    “California agriculture presents a challenge in terms of scalability,” Carpin said. “But this an exciting collaboration because we’ll get to develop a system that will work on different kinds of crops.” — By Holly Ober, UC Riverside

  • New Targets for Huanglongbing Treatments

    Scientists are closer to gaining the upper hand on a disease that has wiped out citrus orchards across the globe. New models of the bacterium linked to the disease reveal control methods that were previously unavailable.

    Metabolic models of organisms are like road maps of cities. “They show you all the biological processes, and how they work together,” said UC Riverside microbiology professor James Borneman. “They also show you which molecular pathways, if blocked, will kill the organism.” 

    Simplified metabolic model and its striking similarity to a road map. (Metallo&Vander Heiden)

    In this case, researchers created the first models of the bacterium associated with Huanglongbing or HLB, also known as citrus greening disease. The team’s work is described in a new paper published in Nature’s npj Systems Biology and Applications.

    The research team made models for six different strains of the bacterium known as CLas and doing so enabled them to identify as many as 94 enzymes essential for the bacterium’s survival. These enzymes can now be considered targets for the creation of new antibacterial treatments.

    In addition, the team identified metabolites required for the bacteria to grow.

    “Just like when humans break down the food they eat into small components called metabolites, which feed our cells, bacterial cells also require metabolites for their growth,” Borneman said.

    Knowing the metabolites needed for CLas’ growth could enable scientists to cultivate it in a laboratory setting. It is not currently possible to grow CLas on its own, hindering scientists’ ability to study it and ultimately to manage it.

    This research project involved a collaboration between UC Riverside, UC San Diego, Texas A&M University, and the U.S. Department of Agriculture. In addition to Borneman, members of the modeling team included UCR plant pathologist Georgios Vidalakis and UCSD systems biologist Karsten Zengler.

    UC Riverside is at the forefront of efforts to combat Huanglongbing. Other important areas of research include antibacterial development and delivery, immune system fortification in citrus, engineering resistant citrus via a detailed understanding of host-microbe interactions, breeding resistant citrus, and insect management, among others.

    Because microbes tend to mutate and acquire resistance mechanisms in response to drugs and other efforts to thwart them, Borneman cautions that any one solution to the problem may be short-lived.

    Transmission electron microscope image of CLas bacterium. (J.M. Bové/INRA)

    “Microbes almost always adapt to control measures, perpetuating the ‘arms race’ between pathogens and hosts,” Borneman said. “There won’t be one thing that will fix this disease. We likely will need to address all three components associated with the disease — the bacterium, the insect that transmits it, and the citrus plants — to find a long-lasting solution.”

    To that end, the research team is constructing metabolic models of citrus and the insect, the Asian citrus psyllid.

    “We expect that this multiorganism modeling endeavor will provide new insights into the mechanisms underlying this disease, which will lead to effective and sustainable Huanglongbing management strategies,” Borneman said. — By Jules Bernstein, UC Riverside

  • UCR Wins $10 Million to Develop AI for Sustainable Ag

    Digital Agriculture Team Principal Investigator Elia Scudiero. (Elia Scudiero/UCR)

    The University of California, Riverside, has won a $10 million grant to develop artificial intelligence that will increase the environmental and economic stability of agriculture in the Western U.S. 

    This Sustainable Agricultural Systems grant is one of nine given by the U.S. Department of Agriculture’s National Institute of Food and Agriculture, or NIFA, annually to shape the future of U.S. agriculture toward environmental, economic, and socially sustainable food production. It is the third-largest grant in UCR history.

    This project will focus on the Colorado River Basin and Salinas River Valley areas, which employ more than 500,000 people and generate roughly $12 billion annually in revenue.

    Despite its productivity, the region has experienced major, prolonged droughts over the past 20 years, and is increasingly under attack by weed, pathogen, and insect invasions worsened by climate change. In addition to insufficient water, soil and water degradation from excessive salt and chemicals is also a threat. This project will develop solutions to these problems in the form of new data science tools, a new multistate cooperative extension program for growers, and a fellowship to educate future agriculture leaders.

    Elia Scudiero, a professional researcher in UCR’s Department of Environmental Sciences, is the project’s principal investigator. Scudiero is an expert in soil, plant, and water relationships, and received NIFA’s New Investigator Award in 2019.

    In addition to Scudiero, the following UC Riverside scientists are involved: Hoori Ajami, Ahmed Eldawy, Milt McGiffen, Connie Nugent, Vagelis Papalexakis, Alexander Putman, Monique Rivera, and Kurt Schwabe. Partner institutions include UC Agriculture and Natural Resources, USDA Agricultural Research Service, University of Arizona, Duke University, Colorado State University, and University of Georgia.

    Leaders of the UC Riverside Digital Agriculture Team. (Elia Scudiero/UCR)

    One of the major challenges of this project will be teaching AI algorithms to synthesize massive amounts of data from a wide variety of sources. Vagelis Papalexakis, assistant professor of computer science and engineering, explained there is currently no one prevailing method for combining such radically different types of data.

    The crux of the solution, he said, will involve inventing new statistical and algebraic models that find repeated and generalizable patterns between seemingly different types of data.

    “This will be an endeavor that will help make field management more efficient, reduce costs for growers, and make food more accessible,” Papalexakis said. “This by itself is an amazing prospect. But the lessons learned from this project also have the potential to advance core AI techniques for combining large, disparate data sets, which extend to a wide variety of real-life applications.”

    A key piece of advancing the agriculture industry will be supplying it with the next generation of growers, managers, and scientists. According to the USDA, the average age of farmers in California went from 56.8 in 2002 to 60.1 in 2012. There is a need to recruit more young people into the workforce, and this project represents an opportunity to do so.

    Funds from this grant will establish a Digital Agriculture Fellowship program that will recruit more than 50 students over the next five years.

    Data, environmental, or agricultural science students will mostly come from UCR, while some will come from partnering institutions. Those coming from other universities will spend summers at UCR participating in career development activities.

    Students will be paired with faculty mentors to develop unique research projects they’ll undertake throughout their 1.5 years as fellows. Internships with key commercial partners are also a focal feature of the program.

    “This program will not only provide intensive professional training for the students, it will also spread awareness of big challenges facing American food growers when students present at academic and professional conferences,” said Connie Nugent, Divisional Dean for Student Academic Affairs.

    The UCR College of Natural and Agricultural Sciences has a track record of success in managing undergraduate research and mentorship programs. The Digital Agriculture Fellowship is an adjunct to UCR’s Research in Science and Engineering, or RISE program, offering long-term guidance for undergraduate success, preparation for graduate school, and careers as leaders in the agricultural sector.

    Scudiero is excited for the project to begin in September this year.

    “This work is very relevant not only for California, but for the entire U.S. Southwest because of water scarcity and other environmental challenges facing us all,” Scudiero said. “We hope to bring transformative changes to the entire farming system in this area of the country and engage students, as well as the research and farming communities in the process.” — By Jules Bernstein, UC Riverside