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Powers of microbes: UC Davis graduate students get creative to teach farmers about soil microbiology

If you grew up in the 1980s or 1990s (or were a child at heart during that era), the famous Powers of Ten film likely left an indelible mark in your mind.

The film starts with a couple lounging on a picnic blanket and zooms out to the outer reaches of the universe, then back in to peer into the microscopic world of the human body: from white blood cells to DNA, and finally down to the proton of a carbon atom.

In its short 9-minute run time, Powers of Ten manages to inflame an existential angst about the size of a single human life while at the same time connecting the viewer to the beauty of the universe and the human body.

As a high school student watching the video, it filled me with the same sense of awe that I felt the first time I heard Carl Sagan's famous quote that “we are all made of star stuff.” 

Powers of Ten reminds us that looking at the world from different perspectives, from the very tiny to the immensely large, helps create a better understanding of the natural world, our place within it, and how we can impact it for good.

Had Powers of Ten returned from outer space by zooming into a piece of soil rather than a the human body, it would have explored the billions of living creatures in one handful of soil, slowly scaling down from millipedes to earthworms to ants to nematodes to protozoa, and finally down to the soil's bacteria and fungi that make up the base of the soil food web.

The video might then have looked a lot like the recent workshop at the Russell Ranch Sustainable Agriculture Facility, which served as a science fair for farmers and researchers to learn about the minuscule but powerful soil microbe.

PhD student Daniel Rath teaches principles of soil aggregates at Russell Ranch's recent Soil Health Workshop
Through hands-on demonstrations using everything from soccer balls to building blocks, sponges, and food coloring as props, graduate students and postdoctoral researchers in UC Davis' Soil Microbial Ecology Lab lead by soil microbiologist and professor Kate Scow explained the role and importance of these invisible players in soil to the people who depend on direct observation for much of their work: farmers.

While farmers often have a baseline knowledge about soil microbiology and its importance on the farm, “the science is evolving so quickly at this point, that it can be hard to keep up,” said attendee Margaret Lloyd, UC Cooperative Extension advisor  who works with small-scale farmers in Yolo and Sacramento counties.

The workshop coupled foundational principles of soil microbiology with practical on-farm management situations, making the case for farmers to actively consider soil bacteria, fungi, and other micro organisms in their decision-making process.

Jessica Chiartas, a fourth-year graduate student in soil microbiology and one of the workshop organizers, is somewhat of a soil science evangelist.

Her hope was to help workshop attendees better understand that “soils are not just physical, chemical systems. A majority of the processes that take place underfoot are biologically driven. Soils are living and breathing bodies and much like us, they need to be fed, covered, and protected from disturbance” in order to function in the long term.

PhD student Jessica Chiartas demonstrates how carbon sequestration differs in different soil types

Scaling down

The scale of microbial activity in soil makes it challenging to help farmers dig into just what scientists are talking about when they talk about microbes. 

“It's important to talk about the scale of microbes,” Chiartas said. “So much of what goes on in soils is mediated by microbes and the scale that they operate on is far different than the scale we measure them at. Our typical method of soil sampling and analysis is analogous to harvesting whole fields of crops, chopping them up, throwing them in a heap and then trying to glean information about the individual plants.”

The presenters at the soil health workshop used vivid analogies to translate the abstract results of scientific research and hard-to-imagine scales into concrete, relatable concepts.

A single gram of soil may contain a billion bacteria, and several miles of fungal hyphae, the web-like growth of fungus. Translated into human scale, the numbers are mind boggling.

If a single microbe were a 6-foot-tall person, then a single millimeter of soil would be as tall as the empire state building. A typical soil bacterium contains as many DNA letters in its chromosome as two copies of “War and Peace.” A stack of copies of “War and Peace” equivalent to bacterial DNA from a single teaspoon of soil would be larger than the Great Pyramid of Giza.

Radomir Schmidt explains microbial biodiversity

A soil information revolution

The metaphors of scale are a fun thought experiment, and they could provide a jumping-off point for a discussion between farmers and scientists essential for improving our current understanding of soil as a living system. Climate change is expected to amplify the  effects of soil erosion, compaction, nutrient leaching and other issues common in our current agricultural systems.

“We need improved management that works with the soil ecosystem to increase crop production while enhancing soil health,” said Radomir Schmidt, a postdoctoral researcher and workshop organizer. ”That's going to take a concerted effort and open dialog between farmers, scientists, and citizen scientists to discover, test, and implement these methods in the real world.”

We are now in the era of “soil information revolution," Schmidt said. As our knowledge of the soil microbiome expands, implementing this knowledge in agricultural practice is more and more possible.

This graduate student cohort is well-positioned to make the necessary connections, learning from farmers while helping them zoom in to see the essential lifeforms that impact their farm, then zoom out to help make decisions that are good for the farmer, good for the crop, and good for the microbe.

Farmers in the Davis area will have another opportunity to learn soil health fundamentals at a workshop this fall hosted by the UC Sustainable Agriculture Research and Education Program and Russell Ranch Sustainable Agriculture Facility. Details about the workshop will be posted here.

Postdoctoral researcher Radomir Schmidt discusses the scale and diversity of microbes in different agricultural management systems
Posted on Wednesday, August 23, 2017 at 9:08 AM

Better soil boosts farm profit and benefits the planet

Healthy soil does much more than hold plants upright on the surface of the earth. It is a mix of mineral bits and old plant particles teeming with microbes to form a mysterious and complex web of life scientists are just beginning to understand.

While scientists use high technology to study heathy soil – painstakingly counting soil worms and bugs, sequencing the DNA of soil bacteria, for example – some farmers know intuitively whether the soil is healthy just by walking on it.

Scott Park is a first-generation Meridian, Calif., farmer. “When I step on a field and it feels like a road, something is wrong,” he said. “If it feels like a marshmallow or sponge, that's good.”

An overflow crowd at the UC West Side Research and Extension Center learns about the benefits of farming practices that promote healthy soil.

Park shared his farming experiences with 200 farmers, industry representatives, University of California Cooperative Extension scientists, Fresno State students, news media and others during a half-day UC workshop at the UC West Side Research and Extension Center in Five Points.

“The last 31 years I've been on a mission of building soil,” Park said. “I discovered it by accident and I've made lots of mistakes. But yields trend upwards every year on every crop. Being sensitive to building soil, I'm making a lot of money. And if I'm doing something for the earth, all the better.”

Park said he adds 10 to 15 tons per acre of biomass to his farm every year. He's using less fertilizer, up to 20 percent less water, and even experimenting on the farm by growing a commercial crop with just four inputs: cover crops, water, seed and sun.

“We got high-yielding, good-quality crops,” Park said. “Nobody was more shocked than I am that I got a good crop.”

Soil samples on the left break down quickly in water. On the right, healthy soil absorbs water without breaking down.

Researchers are now using the scientific method to figure out the root causes of these empirical observations.

“There's a lot going on in soil,” said Radomir Schmidt, a UC Davis soil microbiologist who spoke at the soil health field day.

A teaspoon of soil has a billion bacteria and six miles of fungal hyphae, the filaments that branch out through the soil from fungi, Schmidt said. The microbes' interaction with living plant roots, the larger pores left by decomposing vegetation and tunneling worms and insects create a system that confers resilience to unforeseen challenges – such as pest pressure, torrential rainfall and plant diseases.

The field day was held under a tent pitched adjacent to an 18-year research trial at the 320-acre facility. The trial compares four farming systems side by side:

  1. Conventional system, with annual soil tillage and no cover crops.
  2. Conservation agriculture, with no tilling whatsoever and annual winter cover crops.
  3. No-till without the cover crop.
  4. Conventional tilling with a cover crop.

“Take a look over my shoulder to see the difference,” said Jeff Mitchell, UC Cooperative Extension specialist and the study leader. “We've found the cover crops and no-till reduce water needs, cut dust, and lower costs. And there may be more benefits than we realized.”

For example, a graduate student counted the worms, bugs, beetles and other microfauna in soil samples from each of the treatments. There were double the amount in the no-till, cover crop plots compared to the conventional farming system.

Randall Southard, UC ANR soil researcher, standing in a bulldozed pit, shows the characteristics of soil beneath conservation agriculture trials at the West Side REC.

UC Cooperative Extension specialist Sloan Rice found that cover crops promote water retention in the soil after rainfall. There is very little water evaporation from the soil surface and water transportation from the cover crop plants in the winter, so little water is lost. Cover crops also promote more water infiltration below three feet.

“Cover crops for sustainable water management is particularly important considering the water supply availability and its cost,” Rice said.

Healthy soil management also shows promise in confronting global climate change by sequestering carbon in the soil, rather than depleting it.

Manager of Sano Farms in Firebaugh, Jesse Sanchez, was a speaker at the field day. He wasn't surprised by the overflow crowd.

“Farmers are more and more curious. They see some of us using cover crops, and they want to learn more,” Sanchez said. “There has been a swell of interest. I have a tremendous number of visitors every year.”

Field day participants take a close look at the soil.

For more information about soil building, see the UC Conservation Agriculture Systems Innovation website at http://casi.ucanr.edu

Posted on Monday, June 12, 2017 at 2:26 PM

International Year of Soils celebrates a life-sustaining natural resource

International Year of Soils aims to raise awareness about the vital natural resource beneath our feet. (Photo: NRCS)
In a move designed to raise awareness about a substance that is the very foundation of life on earth, 2015 has been declared the International Year of Soils by high-level national and global organizations, including the U.S. Department of Agriculture and the United Nations.

“Soil is a life-sustaining natural resource that often goes unnoticed,” said Anthony O'Geen,  UC Cooperative Extension soil specialist in the Department of Land, Air and Water Resources at UC Davis. “But soil is fundamental for production of food, animal feed, fuel and natural fiber as well as performing many critical ecosystem functions, like filtering water, cycling nutrients and maintaining biodiversity.”

Moreover, soil is an extremely limited natural resource. Three-quarters of the earth is covered by water. Half of what's left is desert, swamps, frozen solid or mountainous – areas unsuitable for agricultural production. Land that's rocky or floods annually further reduces space for growing crops, leaving just a tiny fraction of the earth's surface as arable land.

These limited areas of productive soils on earth are threatened by expanding urban development, unsustainable soil management practices, pollution and overgrazing. Other natural resources – like air and water – garner more attention as they enjoy much greater visibility, while soil is kept in the dark and treated like dirt. UC Agriculture and Natural Resources is taking part in the year-long celebration of soil to help give soil the recognition it deserves and promote policies that will protect the earth's soil for future generations.

O'Geen is the chair of the Soils and Biochemistry Graduate Group at UC Davis. As a UCCE specialist, he said, he is trying to get students more involved in outreach and sees the International Year of Soils as an ideal rallying point for 2015. The graduate students kicked off the Year of Soils in December by sponsoring a “PED Talk” competition.  (Ped is a scientific term for an aggregate of soil. It was selected in a nod to the world-famous TED Talks.)

Graduate student Katy Dynarski won first prize and $250 for her five- minute talk titled “I ♥ soil.”

“We're continuously taught throughout our lives that soil is something bad,” said Dynarski in her presentation. “You ‘soil' your reputation. You keep ‘dirty' secrets.… In this way, we create a fundamental disconnect between ourselves and soil and we are able to banish it to the realm of things that just don't matter.”

Another student, Jessica Chiartas, invoked the world's celestial connections in her presentation.

Conservation agriculture practices, such as reduced tillage and cover cropping, have proven soil building benefits. (Photo: NRCS)
“The elements and compounds that make up every cell of every single living thing on earth may have originated on some distant star, but also at one time were present in soil,” Chiartas said in her video-taped presentation titled “Microbes.” “So, much like the planet is made up of the stuff of stardust, we are made up of the stuff of soil.”

Messages about the significance of soil conservation will be shared with California state legislators at Ag Day at the Capitol in Sacramento on March 18. An annual celebration of the state's diverse agricultural industry, the event draws farmers, 4-H members, commodity groups and agencies who work with the state's agriculture industry – including the UC Division of Agriculture and Natural Resources – to the state capitol's front steps. Elected officials, their staff, California state workers and the public visit and learn about California agriculture.

Other UC activities marking the International Year of the Soils are aimed at extending to farmers ways they can preserve and protect the soil on their California farms. The Conservation Agriculture Systems Innovation Center (CASI) – a collaborative project coordinated by UC that involves farmers, researchers and representatives of public and private agencies and environmental groups  – is a leader in promoting soil health. The group conducts research and extension activities aimed at helping landowners  maintain and improve their farms' productivity with soil management systems like cover crops, reduced tillage and no-till, and crop rotations. These systems are intended to cut sediment loss from farms and ranches, reduce dust emissions, conserve water and sequester carbon.

CASI has outlined three soil-health initiatives to accomplish during the International Year of Soils. The group will hold a series of demonstration evaluations and information-sharing field events throughout the year. The soil health outcomes from the long-term conservation agriculture and cover cropping research project at the UC West Side Research and Extension Center will be presented to 100 different audiences. A 10-segment soil health video series will be developed along with the USDA's Natural Resources Conservation Service.

The videos will present the underlying theory and principles of soil health with particular emphasis on conditions in the Central Valley. It will include vignettes about local farmers who have successfully improved soil function on their land while lowering production costs.

“Too often it seems that a big part of the information we get on soil health comes from far away in regions not at all like what we have in California,” said Dennis Chessman, NCRS state agronomist headquartered in Davis. “What we really need are examples of what works right here in the Central Valley and that's what we're trying to now develop.”

Mitchell, who has devoted his 20-year career to researching and promoting practices to improve soil health, said the International Year of Soils is adding momentum to ongoing complimentary soil health efforts in the U.S. and worldwide that have been building slowly for years.

“We need healthy soils now and in the future to provide a secure food supply to the world population,” Mitchell said. “The International Year of the Soil will help us reach the public with this fundamental work.”

An initiative to maintain and enhance sustainable natural ecosystems is part of UC Agriculture and Natural Resources Strategic Vision 2025.

Posted on Friday, February 13, 2015 at 7:57 AM

A day in the life of a 100-year agricultural experiment

Two women examine a soil sample in the background photo of the 'Soil Matters' field day flyer..
It's not every day that you can take a guided tour of a 100-year-long scientific experiment, but that's what is happening May 28 as UC Davis hosts a field day at the Russell Ranch Sustainable Agriculture Facility.

The 72-acre “Century Experiment” at Russell Ranch is exploring the long-term impacts of crop rotation, farming systems, and inputs of water, nitrogen, carbon, and other elements on agricultural sustainability. Researchers document trends affecting crop yields, soil quality, profitability, environmental impacts, and efficiency in use of limited resources.

“We look at both organic and conventional systems,” says Russell Ranch director Kate Scow, a professor in the Department of Land, Air and Water Resources at UC Davis. “We're continuing to learn how to better manage both systems in the long term, but it's also important to identify new farming systems that incorporate the best parts of both.”

The theme for the May 28 event is “Soil Matters: Underground at the Century Experiment.” Presentations will be made by faculty, farmers, graduate students, postdoctoral researchers, and visiting scholars. Topic areas include:

  • Nitrate leaching, drought and irrigation management in agriculture
  • Soil biology — microbial communities and impact on farming systems
  • Biochar — carbon sequestration and nutrient impacts
  • Soil nutrient budgets and management

The program gets underway at 8:00 a.m. with welcoming remarks, followed by a tour of research sites from the comfort of hay-bale wagons. Presentations move indoors to the barn at 10:30 a.m. A growers' panel discussion follows lunch. The program wraps up at 1:30 p.m.

Registration is $10 ($5 for students, free for farmers) and can be made online through May 26. Russell Ranch is located approximately six miles west of the main UC Davis campus.

Russell Ranch, part of the Agricultural Sustainability Institute in the College of Agricultural and Environmental Sciences, is a unique 1,500-acre facility with more than 300-acres dedicated to the study of dry-land agriculture in a Mediterranean climate. The crops grown there — tomatoes, corn and wheat — are the same crops grown in the region. Researchers have monitored changes in crop and soil properties, greenhouse gas emissions, weed ecology, and economic indicators there since 1993.

Among research highlights, scientists have shown that cover-cropped systems can be managed to store water in the soil, tomatoes grown with subsurface drip irrigation use less water and less nitrous oxide emissions, and the concentration of antioxidant compounds are higher in organic than conventional tomatoes.

“We may need to make some hard choices about water and nutrient inputs that could change the face of what we currently know as California agriculture,” Scow says. “So we need resilient systems that can endure and be productive in a changing and unpredictable climate.”

For additional information about the field day, contact Emma Torbert at eetorbert@ucdavis.edu or (530) 752-5208.

Posted on Wednesday, May 21, 2014 at 9:24 AM
Tags: Kate Scow (1), soil (8)

SoilWeb reveals what's hidden underneath the ground's surface

Anthony O'Geen in the Mojave Desert.
Beneath your home, below lawns, under asphalt streets, farms and natural areas there is a complex blend of minerals and organic matter that varies widely in texture, color and structure. Producing food, maintaining landscapes and building structures all depend on this little understood, but critical outermost layer of the Earth’s crust - the soil.

Anyone can learn about the United States’ diversity of soils using SoilWeb, a nationwide database of soil variability first developed in 2004. SoilWeb reached a new milestone this year when it was integrated with Google Maps and designed to scale across any Web-enabled device – desktop computer, tablet or smart phone.

SoilWeb has dozens of uses. The information can inform insurers about flooding frequency and builders about locations suitable for roads, basements or septic tanks. The agricultural real estate industry, farmland owners and farmers interested in renting or purchasing land commonly need information about soil productivity and land capability. Knowledge of soil is also important to home gardeners and landscapers.

“SoilWeb’s a great way to understand the landscape you live in,” said Anthony O'Geen, UC Cooperative Extension specialist in the Department of Land, Air and Water Resources at UC Davis. O’Geen developed SoilWeb with Dylan Beaudette, now a Natural Resources Conservation Service soil scientist, when Beaudette was a Ph.D. student at Davis.

The SoilWeb allows users to find information about the soil at a location by standing at the site with a GPS-enabled smart phone or tablet or by entering an address, landmark or latitude and longitude coordinates for anywhere in the United States. The location’s satellite image opens overlaid with yellow polygons marking soil-type boundaries. For each of the polygons SoilWeb provides information about soil profiles, soil taxonomy, land classification, hydraulic and erosion ratings and soil suitability ratings.

For example, the soil under Disneyland in Anaheim is 80 percent Metz loamy sand, characterized as very deep, somewhat excessively drained soil that formed in alluvial material from mixed, but dominantly sedimentary rocks. This is likely of great interest to the Imagineers who are responsible for maintaining the theme park’s extensive landscaping.

All the soil information in SoilWeb was collected from the National Cooperative Soil Survey, organized by the Natural Resources Conservation Service. NRCS began collecting the information in the 1930s.

“The surveyors create a conceptual model of the distribution of soils and soil properties by digging holes, conducting field tests and characterizing representative soils in the laboratory,” O’Geen said. “Not all soil survey areas are the same. Areas such as agricultural regions have more detailed information compared to cities. Because they started so early, they never dreamt of the intended uses of the land and demands required of soil surveys. Today, our methods of collecting data have become much more rigorous and new surveys of urban landscapes are much improved.”

The soil survey reaches about five feet below the surface or to bedrock, O’Geen said. One shortcoming of the database is in some urban areas the soil is classified simply as “urban land.” Where the California State Capitol is situated in Sacramento, for example, the locale is considered 100 percent urban land. No other information is given.

“That’s unfortunate,” O’Geen said. “They are changing that. Surveyors are remapping critical areas, but it’s tough. You can’t dig holes easily in cities.”

In addition, on some rugged terrain in the West, surveys haven’t yet been completed, including parts of the Mojave Desert, Calaveras and Tuolumne counties.

“Soil survey is one of the most detailed and expansive spatial data sets in the world,” he said. “It’s a tremendous resource that has helped our nation conserve and carefully manage soil and water resources.”

Find SoilWeb at http://ucanr.edu/SoilWeb.

Posted on Thursday, May 16, 2013 at 8:29 AM
Tags: Anthony O''Geen (2), soil (8), SoilWeb (1)

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