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UC scientist gives orchards a whole new color scheme

For centuries, farmers have used all the colors of the rainbow to assess their orchards: The bright pink of blossoms in springtime, the vibrant green of heathy leaves, the red blush on fruit ready to harvest.

However, there are wavelengths beyond what a typical human eye can see that also provide valuable information about the crop – including tree vigor, plant stress, water use and fertilizer needs.

UC Cooperative Extension agricultural engineering advisor Ali Pourreza is peering into these previously invisible colorations to create a virtual orchard that will quickly, easily and inexpensively allow farmers and scientists to manage orchards for optimum production.

To develop his first virtual orchards, Pourreza launched a camera-equipped drone over an orchard at the UC Kearney Agricultural Research and Extension Center in Parlier. As the drone flies over the trees, it snaps thousands of photos and, using photogrammetry and software that stiches the images together, makes a three-dimensional point cloud model of the orchard.

A computer program can make colors that are invisible to the human eye – such as near infrared, red edge and ultraviolet – into imagery that illuminates key crop health indicators. Near infrared indicates the amount of healthy foliage, plant vigor and crop type. If the trees have low near infrared values, it means the plants are under stress. Red edge indicates plant stress and nitrogen content. High red edge values indicate nitrogen stress and low water content in plant tissues.

UCCE ag engineer Ali Pourreza views the virtual orchard on his computer.

Patrick Brown, a pomology professor at UC Davis, is planning to use the virtual orchard to map nitrogen use in citrus.

“We are currently working on developing models to help growers determine their fertilization demands and have been contrasting the results from real orchards with the virtual orchard,” Brown said. “We have already utilized the approach to contrast the estimates of tree growth and yield with whole tree excavations and harvests to help validate the virtual approach and provide a more accurate estimate of tree nitrogen demand.”

Ultimately, Brown hopes to develop a way for growers to rapidly and cheaply estimate the nitrogen demand of their orchards, monitor the status of their orchards and manage nitrogen fertilizer applications.

The drone hovers over an orchard at the UC Kearney Agricultural Research and Extension Center.

In addition to the color variations brought to light by the virtual orchard, the system provides detailed data on other aspects of the crop development.

“We can learn canopy height and width, the spacing between the trees, total leaf area, canopy density and the amount of shaded area in the orchard,” Poureza said.

This data is of interest to scientists studying plant development, soil health and irrigation.

For example, UCCE agricultural water management specialist Daniele Zaccaria is researching the impact of soil-water salinity on water use by pistachio trees in the San Joaquin Valley.

“In our on-going research study we are characterizing the functional relationships between soil-water salinity, canopy size and density and evapotranspiration of pistachio trees through the light interception by the canopy,” Zaccaria said. “We plan to work with Ali to see how the virtual orchard approach can represent that and simulate the physical process of soil evaporation and tree transpiration as a result of different canopy sizes and densities intercepting different amounts of solar radiation.”

Zaccaria said he also plans to deploy a similar approach to understand how different canopy sizes, planting densities and row orientations found in commercial citrus orchards in the San Joaquin Valley – from navel oranges, to mandarins and lemons – can affect the citrus water demand and use.

In addition to the rich data that scientists can glean from the virtual technology, Pourreza envisions many applications of this technology for farmers, including yield forecasting, blossom mapping, variable pesticide application and robotic harvesting.

Ali Pourreza with the drone he uses to create virtual orchards.
View a video on YouTube produced by the scientist, Ali Pourreza. The video shows images of the virtual orchard.
Posted on Tuesday, July 25, 2017 at 11:10 AM
Tags: Ali Pourreza (1), drone (1), virtual orchard (1)

UC puts high science online in easy-to-read citrus research updates

California citrus farmers have their ears perked for all news related to Asian citrus psyllid (ACP) and huanglongbing (HLB) disease, but the very latest advances have been available only in highly technical research journals, often by subscription only.

UC Cooperative Extension scientists are now translating the high science into readable summaries and posting them on a new website called Science for Citrus Health to inform farmers, the media and interested members of the public.

“The future of the California citrus depends on scientists finding a solution to this pest and disease before they destroy the industry,” said Beth Grafton-Cardwell, UC Cooperative Extension citrus entomology specialist. “Our farmers want to stay on top of all the efforts to stop this threat.”

The new 'Science for Citrus Health' website can be found at http://ucanr.edu/sites/scienceforcitrushealth/

Grafton-Cardwell and UC Cooperative Extension biotechnology specialist Peggy Lemaux are the two scientists behind the new website. When scientists make progress toward their goals, Grafton-Cardwell and Lemaux craft one-page summaries with graphics and pictures to provide readers with the basics.

For example, the website outlines scientific endeavors aimed at stopping the spread of huanglongbing disease by eliminating the psyllid's ability to transfer the bacterial infection. This section is titled NuPsyllid, and contains summaries of three research papers including one by UC Davis plant pathologist Bryce Falk.

Falk is collecting viruses found in Asian citrus psyllid; so far he has identified five. He is looking into the potential to utilize one of the viruses as is or modify one of the viruses to block the psyllid's ability to transmit the bacterium.  For example, the virus might out compete the bacterium in the psyllid's body.   

Another focus of the website is HLB early detection techniques (EDTs). If HLB-infected trees are found and destroyed before they show symptoms, ACP is less likely to spread the disease to other trees. EDT research described on the website includes efforts to detect subtle changes in the tree that take place soon after infection, such as alterations in the scents that waft from the tree (studied by UC Davis engineer Cristina Davis), changes in the proteins in the tree (studied by UC Davis food scientist Carolyn Slupsky) and starch accumulation in the leaves (studied by UC farm advisor Ali Pourreza).

Other research areas on the Science for Citrus Health website are solutions for established orchards and replants.

As more research is published, more one-page descriptions will be added to the website. The website contains a feedback form to comment on the science and the summaries.

UC Cooperative Extension specialist Beth Grafton-Cardwell is one of two UC ANR scientists who have developed the Science for Citrus Health website.
Posted on Tuesday, July 18, 2017 at 8:54 AM

Caging kids! The next generation of wildlife biologists

Mikayla McWilliams shows a tiny frog at the Sustainable You Summer Camp, UC Hopland Research and Extension Center.

As 10-year-old Dominic Vargas crouched on the ground, in a cage not much larger than himself, trying to forage for tasty treats (candy) on the woodland floor...CRASH! The cage door came falling down and he realized that he had inadvertently tripped a tiny fishing line in his efforts to reach that candy - he was now trapped. Dominic seemed to accept his fate with good humor, shrugging, smiling and getting to work on that candy. Wildlife biologist, Jessie Roughgarden, commented that Dominic will now be collared, tagged and measured before returning him to the wild ... or in this case his parents.

This seemingly terrifying experience is in fact all part of the new "Sustainable You - 4-H Summer Camp" held at the UC Hopland Research and Extension Center. Sustainable You is a five-day camp allowing students to experience science and nature while learning about ways in which to conserve the land, water, air and energy.

View Dominic's experience in this 44-second video:

The camp is conducted at three of the UC Agriculture and Natural Resources' Research and Extension Centers across the state and each center tweaks the curriculum to suit their landscape and the kinds of research conducted at their sites. At Hopland this means getting the chance to meet with wildlife biologists from the UC Berkeley "Brashares Lab," led by professor Justin Brashares. It's an amazing opportunity for these kids to meet and ask questions of scientists conducting experiments in the countryside that surrounds them. Dominic may not be collared, but more than 10 deer on the property went through the same experience last week (minus the candy) as they were carefully captured by researchers and fitted with collars to better understand their movements and population across the 5,358-acre center.

The young team of scientists enjoying summer camp were also working to understand what wildlife shares the landscape with them by setting wildlife cameras daily and improving their positioning and locations each day. Advice from Brashares and Jessie Roughgarden helped the students improve their chance of catching footage of raccoons, foxes and maybe even a mountain lion. Day one  produced fox video footage and shots of raccoons feeling around in the last pools of creek water to catch some of the tiny young frogs currently in residence.

Hear what Ahmae saw on her wildlife camera in the 59-second video below:

A raccoon captured on one of the wildlife cameras set up by campers.

Exposure for these kids not only to hands-on activities exploring sustainability, but also to wildlife biologists, young researchers and professors working on today's wildlife and land management challenges, gives them an open door to explore their own future careers and interests.

Local Americorps watershed steward Alejandara Prendergast disects a salmon with campers

As 9-year-old Ahmae Munday so sweetly put it, when asked what her favorite part of the Sustainable You Summer Camp was, "Everything! Especially the cameras."

The UC ANR network of Research and Extension Centers provide the perfect location to offer exposure to youth and communities to better understand and interact with the science going on in their own back yards and to inspire the next generation of researchers - as camp attendee and scholarship recipient Kaiden Stalnaker described in his scholarship application, "When I grow up I dream of a career in science and your camp would be a boost in the right direction."

Thanks to the researchers, camp counselors and students who have allowed the Sustainable You summer camp to inspire young people like Kaiden.

Campers enjoy a woodland hike and discover slender salamanders and a discarded lizard skin.
Posted on Monday, July 17, 2017 at 9:19 AM

A quiet carnivore recovery

California land managers and wildlife experts are increasingly tasked with managing the return of long-suppressed predators to the landscape, including wolves, mountain lions, badgers, foxes, coyotes, bobcats, and bears. As a result, California is poised to see growing numbers of complex human-wildlife interactions, said Justin Brashares, UC Berkeley professor and UC ANR researcher. 

State and federal policies once incentivized the removal of large carnivores, even offering bounty payments, Brashares said. The last California grizzly became a victim of such practices in 1922. The gray wolf was exterminated shortly thereafter, only to make a historic return 90 years later in the form of a single young male called OR-7, who has been followed into California by several other wolves.

Wolf OR-7 is the first wolf to live in California since their extinction in the 1920. (Photo: California Department of Fish and Wildlife, 2012)

Beginning in the 1970s with the federal Endangered Species Act and the banning of bounties, things began to change. Poisons and leghold traps were prohibited in 1998. Next came an end to the sport hunting of mountain lions in 1990, bear hunting with dogs in 2012, and bobcat trapping in 2015. The cumulative result of these actions, which eased centuries of pressure on wild animals treated as pests, has been a “quiet carnivore recovery” happening across our state, Brashares said. And depending on whom you ask, that may be a great thing or a terrible thing.

An ecologist or environmentalist might emphasize the role of carnivores in maintaining healthy ecosystems.

“What we're seeing across the state, particularly over the last 10 years, is arguably an unprecedented recovery of our wildlife communities,” Brashares said.

A livestock rancher, meanwhile, might view the development with dread.

“They're the ones most likely to be negatively impacted by the return of these animals.” A similar divide, he notes, exists between urban and rural dwellers.

“Those who face the challenges of coexistence with carnivores on a day-to-day basis tend to be more negative about their return,” he says.

The rest of us tend to view the return of carnivores — particularly large, charismatic ones — much more favorably.

Mountain lions are considered charismatic wildlife. (Photo: U.S. Fish and Wildlife)

“In more-urban communities, we often have the luxury of interacting with carnivores on our own terms, by going out and seeking them in wild settings, away from our safe living and work environments, in places like Yosemite National Park,” Brashares said.

But anyone who has lost a dog or cat to a mountain lion, let alone commercial ranchers trying to protect their livelihood from hungry coyotes and wolves, may feel differently. Even so, he said, reliance on lethal control as the primary strategy for managing predators in the state is becoming a thing of the past.

How to behave instead is, in part, a question for science — and one that Brashares is working to answer through ongoing research at the University of California's Hopland Research and Extension Center (HREC), in southern Mendocino County. There the university owns a 5,300-acre parcel with oak woodland, grassland, chaparral, and riparian environments — and, according to recent surveys, wildlife densities on par with those in Yellowstone and Yosemite. Linked to the massive Mendocino and Shasta-Trinity National Forests, it's part of a corridor of undeveloped and protected land extending all the way to the Canadian border. As such, it commonly hosts coyotes, bobcats, mountain lions and black bears.

The facility is also home to more than 500 sheep, on-site since the 1950s for the study of sustainable agricultural practices. But sheep, open space, and carnivores spell conflict, and the flock has regularly suffered significant losses to coyote predation. The coyotes, in turn, have traditionally been shot on sight, in line with established wildlife management practices in agricultural settings.

Good fencing is one tool that allows coyotes and sheep to share the open range.

In 2014 alone, nearly 50 lambs were killed by coyotes at HREC, and another 178 went unaccounted for. Meanwhile, 26 coyotes were killed to prevent further losses to the flock. Toward the end of the year, when Kim Rodrigues became director of HREC, she realized the current system wasn't working and set about to fix it.

Rodrigues brought on more guard dogs and a new shepherd; she improved fencing, and changed the rules about shooting coyotes and other predators. She also initiated a number of research efforts, in which Brashares now plays a lead role, to critically evaluate the effectiveness of tools like dogs, fences, and “fox lights,” which are randomly lit on the fields to scare off predators. Brashares and Rodrigues are also studying how to better use technology like GPS, drones, and tagging to understand the often-mysterious behavior and movement of carnivores and their prey, in hopes of gaining new insights for human-wildlife coexistence.

After Rodrigues instituted some of these changes, the numbers of lamb and coyote deaths at HREC began to decrease dramatically. In 2016, fewer than five lambs were believed to have been killed by coyotes, with another eight unaccounted for, and just seven coyotes were shot.

Professor Justin Brashares (center) and members of his lab utilize tagging, drones, and GPS technologies to track the movement of carnivores and their prey. (Jim Block)

In a bid to make HREC a statewide hub for cutting-edge research and discussion around human-wildlife interactions, Rodrigues enlisted Brashares's help in December 2015 in hosting a community conversation with stakeholders about the management of wildlife and livestock using nonlethal methods. A second discussion is planned for this June.

“My research and extension focus is now on how we can start to explore standard operating procedures that actually have a stated goal to protect both the livestock and the wildlife, and not one or the other,” Rodrigues says. “It's changing the either/or conundrum to thinking about how we really value both on the landscapes that we're managing.”

Excerpted from the Spring 2017 issue of Breakthroughs, the magazine of the College of Natural Resources at the University of California, Berkeley. Read the full article.

Posted on Friday, June 30, 2017 at 9:03 AM

Citrus farmers bracing to battle huanglongbing

Two more trees infected with huanglongbing (HLB) disease were identified and destroyed in the days before UC Cooperative Extension and the Citrus Research Board kicked off their spring Citrus Growers Education Seminar in Exeter June 27. The new infections raise the total number of HLB-infected trees in Los Angeles and Orange counties to 73.

The latest statistic set the stage for spirited discussions about a looming threat that cut Florida citrus production by 60 percent in 15 years. The devastating citrus losses in Florida were recounted by Ed Stover, a plant breeder with USDA Agricultural Research Service in Fort Pierce. 

An abandoned orange grove in Florida. (Photo: USDA)

"One of the benefits of coming here is I am reminded how beautiful citrus is," Stover said. "In Florida, there are more than 130,000 acres of abandoned groves." He showed slides of trees with thin canopies, pale leaves and green fruit; in one image the trees were skeletons among tall weeds.

Huanglongbing disease is an incurable condition spread by Asian citrus psyllid (ACP). The psyllid, native of Pakistan, Afghanistan and other Asian regions, was first detected in California in 2008. Everywhere ACP is found, the pests find and spread HLB.

Stover and his colleagues are searching for citrus cultivars that have natural tolerance for the bacteria that causes HLB, but progress is slow. Transgenic citrus, he said, is the best bet for developing citrus with HLB immunity.

"In my opinion, commercial genetically engineered citrus is inevitable, and GE crop concerns will likely decline with time," he said. 

In California, the aggressive push to keep psyllid populations low, regulations to limit the spread of psyllids when trucking the fruit, and active scouting for and removal of HLB infected trees in residential areas could buy time for researchers to find a solution before California suffers the fate of Florida citrus growers.

"Be vigilant," Stover said. "As long as you are still making a good return, there is almost no investment too great if it keeps HLB out of California."

UCCE specialist Beth Grafton-Cardwell outlines research underway to detect huanglongbing disease of citrus.

Beth Grafton-Cardwell, UCCE citrus entomology specialist and director of the UC Lindcove Research and Extension Center near Exeter, said the prime research in the San Joaquin Valley is aimed at early detection techniques.

Once a tree is infected, it takes nine months to two years for the bacteria to spread throughout the tree, so that when leaves are selected for testing, they detect the bacteria. Capturing and testing psyllids is one way to to find the disease early. Other early detection techniques focus on the microbes, proteins and aromas produced by sick trees.

"These can be measured with leaf test, a VOC (volatile organic compound) sniffer, swab or even dogs," Grafton-Cardwell said. "Scientists are studying every conceivable way to stop the disease."

In the meantime, growers were encouraged to carefully monitor for and treat psyllid populations in their orchards with pesticides. Pesticide treatment recommendations are available on Grafton-Cardwell's Asian Citrus Psyllid Distribution and Management websitehttp://ucanr.edu/acp.

"We have lots of challenges," Grafton-Cardwell conceded. "We hate disrupting our beautiful integrated pest management program. But monitor your own groves, apply the most effective treatments and remove suspected (infected) trees. Going through the pain up front will save us in the long run."

The Citrus Research Board presented UCCE entomology specialist Joseph Morse, center, with a specially commissioned painting for his retirement June 30. Morse spoke at the Exeter meeting about citrus thrips, fuller rose beetle, and avocado thrips.


UCCE citrus advisor Greg Douhan, center in plaid shirt, spoke at the well-attended Exeter meeting about the frequency of citrus tree deaths due to dry root rot. Citrus Growers Educational Seminars are also being held June 28 in Santa Paula and June 29 in Temecula.
The city of Exeter in Tulare County is in the heart of the San Joaquin Valley's citrus belt.
Posted on Wednesday, June 28, 2017 at 11:10 AM

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