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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

August 19th is National Honey Bee Day: Dr. Elina Niño reminds us to help honey bees cope with pests

National Honey Bee Day is celebrated on the third Saturday of every August. This year it falls on Saturday the 19th. If you use integrated pest management, or IPM, you are probably aware that it can solve pest problems and reduce the use of pesticides that harm beneficial insects, including honey bees. But did you know that it is also used to manage pests that live inside honey bee colonies? In this timely podcast below, Elina Niño, UC Cooperative Extension apiculture extension specialist, discusses the most serious pests of honey bees, how beekeepers manage them to keep their colonies alive, and what you can do to help bees survive these challenges.

https://soundcloud.com/ucipm/help-honey-bees-cope-with-pests

To read the full transcript of the audio, click here.

Successful IPM in honey bee colonies involves understanding honey bee pest biology, regularly monitoring for pests, and using a combination of different methods to control their damage.

Visit the following resources for more information

For beekeepers:

For all bee lovers:

Sources on the value of honey bees:

 

 

Posted on Thursday, August 17, 2017 at 9:14 AM

New dust sources resulting from a shrinking Salton Sea have negative ecological and health impacts

Salton Sea. Photo courtesy of NASA
UC Riverside study shows soils once submerged under the sea and airborne particulate matter are high in sodium and selenium

Scientists at UC Riverside investigating the composition of particulate matter (PM) and its sources at the Salton Sea have found that this shrinking lake in Southern California is exposing large areas of dry lakebed, called playa, that are acting as new dust sources with the potential to impact human health.

“Playas have a high potential to act as dust sources because playa surfaces often lack vegetation,” said Roya Bahreini, an associate professor of environmental sciences, who led the research project. “Dust emissions from playas increase airborne PM mass, which has been linked to cardiovascular disease, respiratory disease, and mortality.”

Study results appeared recently in Environmental Science and Technology.

Bahreini's team set out to test whether emissions from playas change the composition of PM10 (particulate matter with diameters up to 10 microns) near the Salton Sea. The team assessed the composition of playa soils (recently submerged underneath the Salton Sea), desert soils (located farther from the sea), and PM10 collected during August 2015 and February 2016.

They found that dust sources contributed to about 45 percent of PM10 at the Salton Sea during the sampling period while playa emissions contributed to about 10 percent. Further, they found that playa emissions significantly increased the sodium content of PM10.

Roya Bahreini is an associate professor of environmental sciences at UC Riverside.
“Increase in the sodium content of PM10 can affect the ecosystem when the sodium-rich particles deposit downwind and change the natural balance for soils and agricultural lands or when these particles form clouds,” Bahreini said. “Currently, the primary concern for PM emissions from playa is the contribution to total concentration of PM10, which regardless of composition, is an irritant and can have negative respiratory effects.”

Her team also found that playa soils and PM10 are significantly enriched in selenium relative to desert soils.

Bahreini explained that selenium can be a driver of aquatic and avian toxicity. “Additionally, higher selenium enrichments in PM10 during summertime suggest that selenium volatilization from the playa may become an important factor controlling the selenium budget in the area as more playa gets exposed,” she said.

Alexander L. Frie, a graduate student in environmental sciences and the first author of the research paper, urges that the Salton Sea be paid close attention since, although it is widely considered a large ecological disaster, with no serious monitoring and remediation efforts the sea may also create a human health crisis for the surrounding area.

Alexander L. Frie, a graduate student in environmental sciences and the first author of the research paper, at the sampling site.
“Although our results indicate playa emission may not be especially toxic when compared to other dust particles, increased emissions from a shrinking sea will reduce the quality of life of the residents within the Imperial Valley and other downwind regions,” he said.

Samantha C. Ying, an assistant professor of environmental sciences and a coauthor on the paper, stresses that monitoring the increase in dust sources over time is necessary to quantify its contribution to local health problems.

“Our study shows that the shrinking Salton Sea is contributing to dust sources in the region,” she said. “Even considering just the small area of playa that is exposed now, the contributions are significant.”

Another concern the researchers point out is that water that is currently diverted from the Colorado River and directed into the Salton Sea is scheduled to end before 2018. The resultant decrease of inflow into the sea will likely cause a decline in water level, exposing more playa, and therefore emitting more dust.

“With more playa being exposed, we expect total PM10 concentrations to increase and human exposure to these particles in downwind areas will also increase,” Bahreini said. “Therefore implementing any project, for example, creating shallow water pools over the playa, that limits formation of salt crusts on the playa will be valuable.”

Bahreini, Frie and Ying were joined in the study by Justin H. Dingle, a graduate student in Bahreini's lab.

The study was funded by UCR Regents' Faculty Development Award, USDA National Institute of Food and Agriculture, a UCR Provost Research Fellowship, the U.S. Geological Survey and ANR's California Institute for Water Resources.

Read more: 

KPBS, David Wagner New Study Traces Airborne Dust Back to Shrinking Salton Sea

The Desert Sun, Ian James Studying dust around the Salton Sea, scientists find initial answers

Palm Desert Patch The Hidden, Potentially Deadly, Dangers of The Salton Sea

 

 

Posted on Tuesday, August 8, 2017 at 10:36 AM
  • Author: Iqbal Pittalwala

How to check your citrus trees for a deadly disease and the pest that spreads it

There is no known treatment for huanglongbing, which kills citrus trees.

The incurable citrus tree disease huanglongbing, or HLB, has been detected in Los Angeles and Orange counties and most recently in Riverside. The citrus disease is spread from tree to tree by Asian citrus psyllids, the insects that move the bacteria that cause huanglongbing.

Citrus trees infected with huanglongbing develop mottled leaves and produce fruit that is misshapen, stays green and tastes bitter. There is no known treatment for the disease, which usually kills the tree within three to five years, according to UC Cooperative Extension specialist Beth Grafton-Cardwell.

Huanglongbing causes blotchy yellow mottling that is not the same on both sides of the leaf
Huanglongbing, which is also known as citrus greening, has already devastated the citrus industries in Florida, Georgia, Louisiana, South Carolina and Texas.

You can help prevent this disease from destroying California's citrus as well as your own trees.

Look for yellowed leaves on citrus trees. Nutritional deficiencies can also cause citrus trees to have yellow leaves so it is important to know the difference. Nutrient deficiency causes a similar pattern of yellowing on both sides of the leaf. HLB causes blotchy yellow mottling and is not the same on both sides of the leaf.

To identify the Asian citrus psyllid and the disease symptoms of HLB, see the fact sheets, videos in English and Spanish and other resources at http://ucanr.edu/acp.

If you see any trees that display symptoms of huanglongbing, contact your local agriculture commissioner.

To learn about the latest research, visit UC ANR's new Science for Citrus Health website at http://ucanr.edu/sites/scienceforcitrushealth.

More resources on Asian citrus psyllids and huanglongbing:

 

Posted on Friday, July 28, 2017 at 2:04 PM

UC has boots on the ground in an unrelenting search for Asian citrus psyllid

With two magnifying loops around her neck and a truck stocked with vials and tools for insect collection, Joanne O'Sullivan scouts Ventura County citrus orchards every day. She walks the perimeter, examining newly emerging leaves and tapping branches with a PVC wand to bat pests onto her clipboard.

O'Sullivan is one of four scouts hired and trained by UC Agriculture and Natural Resources scientists to carefully and continuously monitor citrus orchards for Asian citrus psyllid, an invasive pest in California that can spread the devastating huanglongbing disease.

Joanne O'Sullivan is one of the scouts hired by UC to search for and collect Asian citrus psyllids.

In Florida, where the pest was left unchecked when it first invaded citrus growing regions, the disease swept through the state. Citrus production in the Sunshine State plummeted 60 percent in 15 years.

“We don't want to let that happen here,” said Beth Grafton-Cardwell, UC Cooperative Extension entomology specialist. Grafton-Cardwell hired O'Sullivan and her colleagues who monitor citrus in San Diego, Imperial, Riverside and San Bernardino counties to scour dozens of orchards to document how treatments to control ACP are working. Next year scouts will be added in Tulare and Kern counties.

When ACP are found, they are carefully bottled and sent to the lab to determine whether they carry the bacterium that causes huanglongbing disease.

O'Sullivan taps branches with a PVC wand to knock off insects.

The expansive ACP monitoring effort is funded by a $1.45 million multi-agency coordination grant from the USDA. The project funds promising tools and long-term solutions to reduce the spread of huanglongbing. Led by Neil McRoberts, a professor of plant pathology at UC Davis, the grant also provides funds for two other activities. 

One is a collaboration with California Citrus Mutual to offer free citrus tree removal to homeowners in areas where HLB is known to occur. The second is modeling data from the CDFA HLB survey program, in which psyllids and symptomatic plant tissue are tested for the bacteria. Trees may have the disease but not show symptoms, so testing the psyllids is a more effective way to find infected trees. The modeling work will improve the ability to predict the locations of infected trees.

However, the main thrust is monitoring citrus treatments and their impacts on the ACP population with a team of scouts. A mix of conventional and organic farmers and growers who use biological integrated pest management programs to manage their orchards were recruited for the project. The farmers make ACP treatment decisions informed by research results that show the best treatments and timing.

“Most growers are coordinating their treatments to get a bigger bang for their buck,” Grafton-Cardwell said.

If she finds ACP, O'Sullivan places them in vials to be sent to a lab for testing to determine whether they are carrying the bacterium that causes huanglongbing disease.

With just six months of data, the monitoring program has already yielded important information about Asian citrus psyllid.

“We're seeing more psyllids on the borders than the centers of groves,” Grafton-Cardwell said. “And so eventually, we will make recommendations that at certain times of year or when populations are low, the grower will only need to spray the borders of the grove."

This will reduce costs and the impact of pesticides on natural enemies.

"The early data have also revealed which chemicals are the most effective for psyllid control. We've found that organic growers need to be more aggressive in the frequency of treatments, because the organic insecticides are not as effective as conventional insecticides," she said.

At 8 of the 49 Ventura County ranches in the project, yellow sticky traps were placed in trees to monitor for ACP's natural enemies, including lady bugs, green lacewings, and Tamorixia radiata, tiny wasps from Pakistan that were released in California to battle ACP.

O'Sullivan spends her days looking for ACP and rooting for natural enemies that can help control them.

When O'Sullivan sees one of the natural enemies at work in the field, she pauses to observe the process.

“Sometimes I'll see a lacewing munching on an ACP and I'll say, ‘Go man, go!'” O'Sullivan said.

Posted on Friday, July 28, 2017 at 8:19 AM

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