Posts Tagged: Sciences
Google Weed View? Professor trains computer to spot invasive weed
Algorithm for AI enables low-cost tracking of invasive plant
To manage johnsongrass, a noxious weed that crowds out cotton and sickens horses, farmers have tried herbicides, burning and hand-pulling. Now, researchers at University of California, Davis, have developed a more high-tech weapon against the invasive weed: artificial intelligence and machine learning.
Using photos from Google's Street View database, UC Davis researchers have tracked down over 2,000 cases of johnsongrass in the Western United States for a fraction of the cost and time that it would take to do drive-by or other in-person surveys. They call their tool Google Weed View.
The advancement could help land managers easily and quickly survey for other problem plants.
“Once the model is trained, you can just go and run it on millions of images from Google Street View,” said Mohsen Mesgaran, an assistant professor in the Department of Plant Sciences at UC Davis. “We have huge flexibility, and its capability can be scaled up very quickly.”
The technique can easily be extended to other plant species. All that is needed is to label the new item in Street View photos and train the algorithm to identify that object in the images.
By providing location information, Google Weed View also offers an opportunity to examine how climate affects the growth and spread of weeds and invasive plants at very large scales.
“I think it can be both useful for management and for people with interests in more basic questions in ecology,” Mesgaran said.
A colleague's query
Mesgaran began looking at using Google's photo database of roadways, streets and highways after Kassim Al-Khatib, a professor of Cooperative Extension in the same department, asked if he could survey Western states for johnsongrass.
Al-Khatib studies where johnsongrass grows, ways to manage it and how this perennial has evolved to be so prevalent and resilient. He's also working with scientists at the University of Georgia to decode the genome of johnsongrass, which is one of the top 10 most invasive weeds worldwide.
Johnsongrass can crowd out native plants, harbor pathogens and affect agriculture. It grows up to 7 feet tall with flowers that are green, violet, dark red or purplish brown depending on maturity, according to a UC Statewide Integrated Pest Management Program briefing page.
“Johnsongrass is a major weed not just in California but worldwide,” Al-Khatib said. “It's very difficult to control. It's a problem on vineyards. It's a problem for cultivated crops. It's a problem on orchards.”
Google Weed View allows for rapid, convenient scanning. It is continuously updated via everyday users with compatible cameras and images collected by Google. “Instead of a day of in-person driving, we can use AI to determine if johnsongrass is in a county or not,” Al-Khatib said.
Setting the parameters
To find the weeds, Mesgaran went to Google Street View, which hosts billions of panoramic photos. It didn't take long to find johnsongrass.
“The pictures are really good quality,” he said. “You can see plants and flowers.”
Street View's photos offer a 360-degree view, so in his request Mesgaran set parameters, based on street direction (bearing), to only see the side view. He also specified latitude and longitude, and other factors. To train the deep, or machine learning model, he chose Texas, where johnsongrass is prevalent.
A student sorted through over 20,000 images from that request to find pictures with johnsongrass and drew rectangular shapes around the weeds. They located 1,000 images.
The labeled photos were fed into a computer to train a deep learning algorithm capable of identifying johnsongrass in Google's images. The model was run again to capture potentially more images containing johnsongrass. These additional images were then labeled and used to further refine the model. With each iteration, the algorithm learned and became more accurate.
“This deep learning model was trained by these images,” Mesgaran said. “Once we had a semi-working model, we ran it against about 300,000 images.”
For Al-Khatib's request, researchers focused on 84,000 miles of main roads in California, Nevada, Oregon and Washington states. The team discovered 2,000 locations with johnsongrass.
Google Weed View cost less than $2,000 to purchase the images and teach the model. A traditional car survey to cover the same area would cost an estimated $40,000 in gas, hotel, food and other costs.
“In a matter of months, we came up with 2,000 records and I can do it for the whole U.S.,” Mesgaran said.
Next up? The entire United States.
This story was originally published on the UC Davis College of Agricultural and Environmental Sciences news site.
No-till annual wheat better for soil health in California’s climate
One more reason to adopt sustainable cultivation
California wheat farmers could both maintain their yields and improve soil health by growing annual wheat without tilling the soil year after year.
This could be one more encouragement to farmers to adopt a sustainable practice commonly called conservation tillage, no-till or minimum-till cultivation, impacting how we grow a grain that supplies about 20 percent of the calories and protein for people around the world.
A new study, by a team led by Mark Lundy, University of California Cooperative Extension specialist in UC Davis' Department of Plant Sciences, offers new insight for decades-long discussions around soil conservation, sustainable agriculture and climate-warming emissions related to growing our food. The study has been published in the journal Soil and Tillage Research. For the first time, researchers have shown that annual wheat that is not tilled each year is better for stashing carbon in the soil than perennial wheatgrass, while still yielding more crop in Central California.
Previous studies have looked at annual wheat that is tilled each year, annual wheat that is not tilled, and a cousin species, perennial intermediate wheatgrass (trademarked Kernza), which also is not tilled. But until now, no one has looked at all of the benefits and trade-offs together. Most importantly, “no one has ever controlled for tillage,” Lundy said. “And, no one has compared annual wheat to perennial intermediate wheatgrass over multiple years in a Mediterranean climate, which is what we have in California.”
This study also is unique because it delves into the deeper question of what is going on in the soil that drives the different results for carbon there. Soil carbon reflects various processes linked to plant activity and soil health. Measuring the different forms of soil carbon may also signal whether a farming system is accumulating carbon in the soil over time – a plus for reducing climate-warming gases in the atmosphere.
“Measuring soil carbon is complex and nuanced,” said Kalyn Taylor, the lead author on the paper. “We started this experiment because we wanted to know whether and how plant activity and tilling or not tilling would affect the carbon story belowground in California's climate.”
“When we started this study, we thought the crop being perennial or annual would drive the differences in carbon storage in the soil,” Lundy added. Specifically, they had expected perennial wheatgrass would lead to more carbon in the soil because of its deeper, better-established root system. “But that's not what we found,” he went on. “What we found was, it was the lack of tillage, plus the level of productivity of common annual wheat, that made the difference in soil carbon here in California.”
Soil carbon in annual vs. perennial grain
In 2017, Lundy, then-graduate-student Taylor, UC Davis Professor Emeritus Kate Scow and others on the team started measuring different forms of soil carbon in test plots at Russell Ranch, west of campus. Plots were planted with annual wheat that was tilled each spring, annual wheat that was not tilled and perennial intermediate wheatgrass (Kernza) that also was not tilled.
Each year, the researchers measured the carbon present in the soil, the amount of soil organisms (which have carbon in their bodies) and the amount of material the plants created.
At the end of three growing seasons, they found that land planted with no-till, common, annual wheat had the highest amount of soil organisms, measured as biomass, of the three treatments.
The researchers also found soil carbon is more likely to remain stable in the no-till, annual plots, compared to both tilled wheat and wheatgrass.
In addition, the no-till, annual wheat produced plant material more consistently than the perennial wheatgrass across the three years, which saw variation in rainfall.
“Overall, annual wheat grown without soil disturbance or tillage had both higher productivity and higher potential for storing carbon in the topsoil than perennial wheatgrass in our Mediterranean climate,” Lundy said.
Related research
“No-till annual wheat increases plant productivity, soil microbial biomass, and soil carbon stabilization relative to intermediate wheatgrass in a Mediterranean climate,” is online now and will be published in the January 2024 edition of Soil and Tillage Research.
The team also found that tilled annual wheat vs. Kernza stores total carbon at different depths in the soil profile and hosts distinct soil fungal communities, primarily in the root zone and topsoil: Taylor, K., Samaddar, S., Schmidt, R., Lundy, M. and Scow, K., 2023. Soil carbon storage and compositional responses of soil microbial communities under perennial grain IWG vs. annual wheat. Soil Biology and Biochemistry, p.109111.
Previous work comparing the perennial grain known as intermediate wheatgrass (trademarked Kernza) to annual wheat had not distinguished the extent to which soil health benefits are a function of the perennial nature of the crop. Read the story here.
This story was originally published on the UC Davis News site.
/h3>/h3>/h3>UC Davis to build new $5.25M greenhouse to protect U.S. grapevine collection
Project designed to prevent red blotch and other grapevine diseases
A new, $5.25 million greenhouse is being built on the University of California, Davis, campus to safeguard an important grapevine collection from red blotch disease and other pathogens.
The 14,400-square-foot greenhouse will have a vestibuled entry, be insect-proof and provide another level of disease protection. It is being spearheaded by Foundation Plant Services, or FPS, which provides the U.S. grape industry with high-quality, virus-tested grapevine plant material.
The program serves as the primary source for grapevine plant material distributed to nurseries under the California Department of Agriculture's Grapevine Registration and Certification Program, which provides the majority of grapevines planted in the United States. For the grape industry, it is essential to protect this material from disease-carrying insects and guarantee fast access to clean plant material.
“The program is considered the largest quarantine center for the grapevine industry in the United States,” said Maher Al Rwahnih, a plant pathologist and FPS director. “This is kind of a game changer for us.”
A history of serving the grapevine industry
FPS has maintained healthy grapevine planting stock on the UC Davis campus for more than 70 years in open fields at the Classic and Russell Ranch foundation vineyards. FPS scientists first detected grapevine red blotch virus at Russell Ranch in 2017. By 2021, an estimated 51.6% of the crop there was infected. Material from that vineyard is not being sold, and the site is now part of an epidemiological study to try to pinpoint how the disease is transmitted.
FPS pathologists have detected red blotch on less than 1% of the Classic vineyard crop. But it may not always be that way in the future.
“We don't know how long the Classic vineyard will remain clean,” Al Rwahnih said. “Every testing season, this is what keeps me up at night. We're not sure why it's happening in Russell Ranch and not the Classic vineyard.”
Once the greenhouse is operating, grapevines propagated from plant material from the Classic vineyard will be moved into the greenhouse, tested and verified as clean from disease. From there it will be sold to nurseries, which will grow additional plants to sell to growers.
Two greenhouses part of plan
Normally the foundation has 4,000 vines available, but the greenhouse will only house 2,000 vines, so inventory will be cut in half.
“This phase is just a starting phase,” Al Rwahnih said. “It's not sufficient for our needs.”
FPS plans to build another greenhouse in the next two to three years to increase capacity.
Industry groups and FPS identified greenhouses as the best way to protect the plants from red blotch and other pathogens transmitted by insects. They are also consulting with those same people on the grape varieties to include in the greenhouse.
“We have a large selection, and we need to make sure all the varieties that are important to industry are contained,” he said.
The first greenhouse is expected to be finished by the end of 2023.
Funding for the first greenhouse is coming from a variety of sources. The California Fruit Tree, Nut Tree and Grapevine Improvement Advisory Board, managed by the California Department of Food and Agriculture, contributed $4 million to the project. The California Grape Rootstock Research Foundation gave $500,000, Foundation Plant Services with UC Davis is funding $450,000, and the California Grape Rootstock Commission gave $100,000.
“This is crucial for the grapevine industry, and we are very grateful for the support,” Al Rwahnih said.
/h3>/h3>/h3>Should there be more microbes on your plate?
Scientists make the first large-scale estimate of live microorganisms consumed in the U.S. diet
Our diets provide us with the building blocks we need to stay healthy and fight disease. The nutrients in foods and beverages can be tallied up to know if we are getting what our bodies need. Yet what if a nutrient has been overlooked? For instance, friendly microbes in raw and fermented foods have not been measured as part of our diets — until now.
“Ultimately we want to understand if there should be a recommended daily intake of these microbes to keep us healthy, either through the foods or from probiotic supplements,” said Maria Marco, a professor in the food science and technology department at UC Davis. “In order to do that, we need to first quantify the number of live microorganisms we consume today in our diets.”
Marco co-authored a new study with a group of scientists that examined the number of living microbes per gram of more than 9,000 different foods consumed by nearly 75,000 adults and children. It found that around 20% of children and 26% of adults consumed foods with high levels of live microorganisms in their diet. Both children and adults increased their consumption of these foods over the 18-year study period. The study, published in the Journal of Nutrition, is the first large-scale estimate of how many live microbes are consumed by Americans every day.
“This trend is going in the right direction. Exposure to friendly microorganisms in our foods can be good for promoting a healthy immune system.” said Marco.
Foods for gut health
Study authors examined the National Health and Nutrition Examination Survey to create the estimate. The health and dietary database contains extensive information on the foods consumed by Americans daily. Food science and fermentation experts assigned each food an estimated range of live microbes per gram, creating categories of foods with low, medium and high levels of live microbes. Foods in the high category included fermented dairy foods such as yogurt, fermented pickles and kimchi. Fresh, uncooked fruits and vegetables were also good sources of live microorganisms, represented in the medium category.
The analysis was funded by a grant from the International Scientific Association for Probiotics and Prebiotics, or ISAPP. The microorganisms quantified in this study are not necessarily probiotics.
“By definition, a probiotic must be well-defined and have a demonstrated health benefit at a quantified dose. Live microbes associated with food as a category, however, do not generally meet the criteria of a probiotic,” said corresponding author Mary Ellen Sanders, executive science officer for the ISAPP.
The publication is part of a larger global effort to determine how live dietary microbes might contribute to health.
“There is no doubt that the microbes we eat affect our health. When we think of microbes in our food, we often think of either foodborne pathogens that cause disease or probiotics that provide a documented health benefit,” said co-author Colin Hill, a professor of microbial food safety with University College Cork, Ireland. “But it's important to also explore dietary microbes that we consume in fermented and uncooked foods. It is very timely to estimate the daily intake of microbes by individuals in modern society as a first step towards a scientific evaluation of the importance of dietary microbes in human health and well-being.”
Other scientists co-authoring the paper were ISAPP board members Robert Hutkins, Dan Merenstein, Daniel J. Tancredi, Christopher J. Cifelli, Jaime Gahche, Joanne L. Slavin and Victor L. Fulgoni III.
Editor's note: Maria Marco is affiliated with UC Agriculture and Natural Resources as an Agricultural Experiment Station faculty member.
/h3>/h3>Can vines speed urban cooling?
Study explores cooling benefits of fast-growing vines as trees take their time
Perhaps trees aren't the only green solution when it comes to cooling urban spaces and reducing energy costs. Honeysuckle, Virginia creeper, pink trumpet and other vines could be a fast-growing substitute in climate-smart cities of the future.
Researchers from UC Davis are leading a nearly $880,000 federal grant to study how vines may provide cooling and shade in Western states in less time than it takes a tree to grow tall.
“Vines can quickly shade buildings and reduce energy consumption while trees slowly grow to maturity,” said Alessandro Ossola, an assistant professor of plant sciences who is a principal investigator for the project. “We believe vines can be an effective and cheap measure to help cities accelerating climate change adaptation.”
The grant from the U.S. Department of Agriculture's Agricultural Marketing Service will fund work to plant and monitor at least 10 types of vines on trellises in five locations in different climate zones over three years. California Department of Food and Agriculture is administering the grant.
Using less water
Water conservation will be vital as populations rise, climate extremes become more prevalent and the demand for agricultural and drinking water increases. The goal of this research is to identify vines that can help save energy by providing cooling and reduce the need for irrigated water.
“In addition to rapid growth rates, vines can be easily integrated with structures to maximize potential cooling effects,” said Loren Oki, a Cooperative Extension specialist with Department of Plant Sciences, who is the project lead. “But we need to understand the relationships between low water-use plants and their ability to reduce thermal loads on buildings.”
The vines will be planted, supported by a trellis and watered regularly during the first growing season to establish deep roots and healthy shoots. Over the next two years, the vines will experience low, moderate and high water allocations.
The vines will be rated on aesthetics, foliage quality, floral quantity, pest and disease resistance, appearance and other factors. Thermal images of trellis coverage and other environmental measurements will also be taken to assess shading and cooling potential, according to grant documents.
Many vines can be grown along cables and wire nets that are actually detached from walls to avoid direct contact and still provide shade, Ossola said.
“We want to understand which vine characteristics relate to fast growth, reduced water use and increased aesthetic appeal,” he added.
Outreach and education
The findings will enable recommendations to be developed for regions, planners, the landscape industry and the public. It could lead to plants being designated as “water-wise,” “low-water use,” “energy-saving” or “cooling.”
Extensive engagement and outreach will also publicize the information.
“Climate change is a great opportunity for the horticultural industry to innovate and promote climate-ready plant productions,” Ossola said.
USDA funding supports research across state lines to find innovative solutions to regional and national problems, USDA Under Secretary for Marketing and Regulatory Programs Jenny Lester Moffitt said in a news release announcing this and other grants.
“This year's funded projects will address a range of those challenges, from energy and water saving in vine plants, finding cost-effective solutions for heat tolerance and drought, to addressing food safety risks for produce,” Moffitt said.
Scientists from the University of Arizona, University of Washington, Utah State University and the South Coast Research and Extension Center at UC Agricultural and Natural Resources are contributing to the research and will be overseeing vine sites in their states.
This article is reprinted from the UC Davis College of Agricultural and Environmental (CA&ES) website, where it is titled "Could Vines Be the Answers to Speeding Urban Cooling, Water Reduction in the West?"