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Coast Redwood and Giant Sequoia Mega-Genomes Sequenced: Sequencing Brings Modern Tools to Redwood Conservation Efforts

Reposted from UC Davis news 

Scientists have successfully sequenced the coast redwood and giant sequoia genomes, completing the first major milestone of a five-year project to develop the tools necessary to study these forests' genomic diversity. The research partners, composed of the University of California, Davis, Johns Hopkins University and the Save the Redwoods League, are making the data publicly available today.

The coast redwood genome is now the second-largest ever sequenced at nearly nine times the size of the human genome. The genome of the giant sequoia is roughly three times that of the human genome.

data graphic

‘23 and Tree?'

Much like sequencing the human genome opened the door to finding cures for things like sickle cell anemia, sequencing the redwood and sequoia genome could help conserve and restore those species. 

“Our patient is the redwood forest,” said David Neale, distinguished professor in the Department of Plant Sciences at UC Davis. “It's not healthy. We seek to make it healthy again, and we need that same foundational resource as a human physician or medical professional needs for their patients.”

 https://youtu.be/nCQDnBND_Fo

Over the past 150 years, 95 percent of the ancient coast redwood range and about one-third of the giant sequoia range have been logged. With this unprecedented loss of old trees and the addition of redwood clones often planted in their place, conservationists have grown concerned that the forests' genomic diversity has fundamentally changed. If diversity has declined, it could leave the redwoods vulnerable to drought, fire and other stressors related to climate change.

By sequencing these trees' genomes, the scientists are providing a tool that resource managers can use to help discern a redwood forest's genetic potential for adapting to its current or future environment. 

“We're trying to build a 23andMe for trees, where a manager sends in their samples and gets a risk evaluation of their forest populations, if not individual trees,” Neale said. “Completing the sequences of the coast redwood and giant sequoia genomes is the first step.”

David Neale
UC Davis Professor David Neale helped sequence the coast redwood and giant sequoia genomes. Here, he examines a coast redwood in the UC Davis Arboretum. (Ann Filmer/UC Davis)  

Sequencing conifer ‘mega-genomes'

These conifers have giant genomes, and full sequencing of them has only been possible in the last decade.

Man looking at redwood tree
Del Norte County's Grove of Titans features some of California's biggest coast redwood trees. (Max Forster/ Save the Redwoods League)

The coast redwood has six sets of chromosomes (hexaploid) and 27 billion base pairs of DNA. The giant sequoia has two sets of chromosomes (diploid) and over 8 billion base pairs. For comparison, the largest genome sequenced to date belongs to the axolotl, a North American salamander whose genome was completed in 2018 and has more than 28 billion base pairs. 

“We pushed the boundaries of genome-sequencing technology to take on the redwood and sequoia mega-genomes,” said Steven Salzberg, professor of Biomedical Engineering at Johns Hopkins University. “After using our specially developed algorithms to assemble these enormous and complex genome sequences, we have gained a new appreciation for how difficult it is to put together a hexaploid genome, especially one as large as the coast redwood's.”

What's next?

The redwood genome project was launched in late 2017, with a projected five-year timeline. By the end of the project, the genome sequences and screening tools developed will allow field crews to quickly assess adaptive genomic diversity in redwood forests to inform management plans that restore the health and resilience of these forests throughout their natural ranges. 

With the genomes sequenced, the League will work to inventory diversity across the landscapes and identify "hot spots" of genomic diversity for enhanced protection and areas of low diversity for restoration.

cone from giant sequoia
A cone from a giant sequoia. (Mark Bult/Save the Redwoods League)

“Every time we plant a seedling or thin a redwood stand to reduce fuel loads or accelerate growth, we potentially affect the genomic diversity of the forest,” said Emily Burns, director of science for Save the Redwoods League. “With the new genome tools we're developing now, we will soon be able to see the hidden genomic diversity in the forest for the first time and design local conservation strategies that promote natural genomic diversity. This is a gift of resilience we can give our iconic redwood forests for the future.”

The coast redwood and giant sequoia sequence data are available to the scientific community at large through the UC Davis website

During the next stage of the project, researchers will create a database capturing range-wide genomic variation within each species; develop tools that will allow resource managers to identify coast redwood and giant sequoia genetic variation while in the field; compile forest genetic inventories; and launch pilot restoration projects based on the accrued data.

“When we celebrated the League's 100th anniversary last year, we reaffirmed our commitment to restore entire landscapes of young, recovering redwood forests,” said Sam Hodder, president and CEO of Save the Redwoods League. “Sequencing the coast redwood and giant sequoia genomes for the first time opens a new scientific frontier for our restoration projects. This work will reveal the forests' genetic identity so that we can protect the diversity that's left, and in some areas, restore what was lost.”

Redwood tree
Coast redwood tree, UC Davis Arboretum. (Ann Filmer/UC Davis)

Major funding for the research came from Save the Redwoods League. A significant lead gift to the league to fund the initial sequencing of the genomes was provided by Ralph Eschenbach and Carol Joy Provan.

 

Posted on Tuesday, May 7, 2019 at 10:12 AM
  • Author: Kat Kerlin

UC Cooperative Extension ramps up its climate change response

Reposted from UCANR News

While scientific reports continue to mount confirming that global climate change is increasing temperatures, causing more frequent weather extremes and raising the sea level in California, UC Cooperative Extension is working to ensure the worst predictions are avoided and California residents and businesses will be able to adapt to the change.

Each year, a diverse group of UC Agriculture and Natural Resources academics and program implementation professionals meet to share and collect the latest climate change experiences, ideas, science and solutions. The team works with farmers across the state to improve production practices and minimize environmental impact, conduct agricultural and natural resources conservation research, and coordinate programs like California Naturalist and UC Master Gardener, which recruit and educate volunteers to reach out to communities statewide to extend research-based information.

A possible climate change outcome in California may be returning farmland to less-intensive uses, such as grazing.
 

Reaching real people

In 2019, extension practitioners explored new approaches to delivery of information and services. For example, the first speaker addressed the way climate change impacts may be viewed through the lens of African-American or First Nation experiences, influenced by poverty, historical trauma and even spirituality.

Theopia Jackson, clinical psychologist at Saybrook University in Oakland, encouraged the team to consider whether assisting Americans navigating the changing climate or suffering the consequences of extreme weather events have “the bandwidth to take in one more helping hand.” Jackson has a long history of providing therapy services, specializing in serving populations coping with chronic illness and complex trauma.

Jackson suggested helpers ask themselves, “Are we inadvertently causing more stress than good? Do I have a sense for what they are already dealing with before bringing something new into the community?”

Jackson said the conversation about climate change in many communities might be more productive focused less on whether climate change exists or not, and instead on how to “join with them around the human experience.”

“If I'm trying to ‘talk them into it,' I need to step back,” Jackson said. “The conversation could be about scarcity or lifestyle. We need to find a way to join and hope they will get it before we've done irreversible damage.”

The careful selection of terminology and approach in climate change conversations was also raised by Dan Sonke, director of sustainable agriculture for Campbell's Soup. The company's primary and best-known product is soup, but it owns other familiar brands, including Pepperidge Farms, Snyder Pretzels, Kettle Chips and Emerald Nuts.

In California, Sonke works closely with farmers producing fresh produce to be used in Campbell's products, particularly processing tomatoes. During his career, he also worked in Campbell's marketing, based on its “corporate purpose.”

“We make real food for real people,” says the Campbell's corporate purpose. “People love that our food fits their real lives, fuels their bodies, and feeds their souls. And they appreciate knowing what goes into our food, and why — so they can feel good about the choices they make, for themselves and their loved ones.”

Sonke was hired to increase the use of sustainable farming practices by the company's producers and help farmers apply for grant funding from the state to implement climate-smart irrigation practices. The company was able to track a 20 percent reduction in water use and document a significant reduction in the emission of nitrous oxide, a greenhouse gas. The program is successful, but isn't driving their farmer communications or soup sales, Sonke said.

“Farmers don't think in terms of climate change, but they respond to what they know,” Sonke said. “Consumers don't respond to climate change adaptation in terms of what products they buy. They respect sustainability, but have no understanding of ‘sustainable agriculture' and ‘carbon sequestration.'”

More extreme weather events - such as heavy rain, flooding, cold snaps and heat waves - are expected due to climate change.
 

Growing UCCE climate mitigation, adaptation and resilience programs

UC ANR is working on new ways to reach out to farmers and the public with information on climate change. Six community education specialists have been hired and four more are being recruited to work in counties around the state to help farmers access programs that will help them reduce greenhouse gas emissions on farms and dairies, build resilience to climate change and increase profit.

The Climate-Smart Farming Program is a collaborative effort with the California Department of Food and Agriculture focused on implementing on-farm solutions to improve soil health, nutrient management, irrigation management, on-farm composting and manure management.

The CDFA programs involved are:

The new community education specialists are already deployed in Mendocino, Glenn, Yolo, Santa Cruz, Ventura and San Diego counties. The four positions under recruitment will serve Imperial, San Joaquin, Fresno and Kern counties. To get information about these programs, contact:

Climate stewards

To reach a broad swath of California residents with research-based information on climate change mitigation and adaptation, UC ANR's California Naturalist program is leveraging its well-established partnerships with formal and informal science education institutions across the state to create a legion of climate stewards. At the team meeting, CalNat coordinator Greg Ira announced that the California Naturalist program has hired an academic coordinator to develop curriculum that will allow existing partners to deliver the material as part of the California Naturalist program. The graduates of this California Naturalist course focused on climate change will be encouraged to engage in volunteer service that helps build community resilience to climate change. These include participation in local adaptation planning efforts, community and citizen science projects, or addressing issues of social justice. The coordinator begins Feb. 19.

Areas where peaches and cherries have flourished in the past may no longer provide adequate winter chilling due to climate change.
 

The future

Renata Brillinger of the California Climate Action Network shared optimistic thoughts about the opportunities for climate change mitigation, adaptation and resilience. In terms of politics, she said California leadership has accepted climate change as a settled matter and are supportive of programs to address the issue. At the federal level, it is not easy to talk about climate change, but “that will change,” she assured.

Brillinger said biodiversification of California is an exciting area for climate change adaptation. Research is needed to understand how to shift crop locations for future production, and determine where, for example, water-intensive crops or orchards with chill requirements should be grown. More information is needed, she said, on how healthy soil will relate to climate resilience in agriculture.

 “We have to reinvest in extension and Resource Conservation Districts,” Brillinger said.

Other possible climate change outcomes in California may be returning farmland to less-intensive uses, such as grazing. Fallowing land was one way that the agriculture industry coped with the drought of 2011-16, and implementation of the Sustainable Groundwater Management Act – a direct result of the drought – is estimated to take 1 million acres of farmland out of production. This approach won't be a solution for all farmers and ranchers, said David Lile, UC Cooperative Extension natural resources advisor.

“Ranchers and farmers interested in long-term sustainability, keeping the farm in place, will need help to integrate competing forces,” Lile said. “Economics will not be the only driving force.”

 

Posted on Tuesday, April 23, 2019 at 8:56 AM
  • Author: jeannette warnert

Falling levels of air pollution drove decline in California’s tule fog

Reposted from the UC Berkeley News

Cranes fly through the fog over a marsh

Cranes glide through the tule fog at the Merced National Wildlife Refuge. (Photo by Steve Corey via Flickr)

The Central Valley's heavy wintertime tule fog – known for snarling traffic and closing schools — has been on the decline over the past 30 years, and falling levels of air pollution are the cause, says a new study by scientists at the University of California, Berkeley.

Tule fog, named for a sedge grass that populates California's wetlands, is a thick ground fog that periodically blankets the Central Valley during the winter months.

To find out why the fog is fading, the researchers analyzed meteorological and air pollution data from the Central Valley reaching back to 1930. They found that while yearly fluctuations in fog frequency could be explained by changes in annual weather patterns, the long-term trends matched those of pollutants in the air.

The results help explain the puzzling decades-long rise and fall in the number of “fog days” affecting the region, which increased 85 percent between 1930 to 1970 and then decreased 76 percent between 1980 to 2016. This up-and-down pattern follows trends in air pollution in the valley, which rose during the first half of the century, when the region was increasingly farmed and industrialized, and then dropped off after the enactment of air pollution regulations in the 1970s.

A satellite image of the Central Valley of California, showing thick white clouds in the valley

NASA's Terra – MODIS satellite captures a thick blanket of fog covering California's Central Valley. (NASA photo by Jeff Schmaltz)

“That increase and then decrease in fog frequency can't be explained by the rising temperatures due to climate change that we've seen in recent decades, and that's what really motivated our interest in looking at trends in air pollution,” said Ellyn Gray, a graduate student in environmental science, policy and management at UC Berkeley and first author on the paper, which appears online in The Journal of Geophysical Research: Atmospheres. “When we looked at the long-term trends, we found a strong correlation between the trend in fog frequency and the trend in air pollutant emissions.”

The link between air pollution and fog also explains why southern parts of the valley — where higher temperatures should suppress the formation of fog — actually have a higher occurrence of fog than northern parts of the valley.

“We have a lot more fog in the southern part of the valley, which is also where we have the highest air pollution concentrations,” Gray said.

And it makes sense, given what we know about how clouds and fog form, Gray says. Oxides of nitrogen (NOx) react with ammonia to form ammonium nitrate particles, which help trigger water vapor to condense into small fog droplets. Emissions of NOx have declined dramatically since the 1980s, resulting in a decrease in ammonium nitrate aerosols and fog.

“In order to get fog to form, not only do you need the temperature to go down, but there has to be some sort of seed for water to condense around, similar to how you would have a cloud seed in the atmosphere,” Gray said. “Ammonium nitrate happens to make very good fog seeds — water is very attracted to it.”

As a next step, the team plans to take a close look at the association between air pollution, tule fog and traffic safety in the valley.

“When I was growing up in California in the 1970s and early 1980s, tule fog was a major story that we would hear about on the nightly news,” said Allen Goldstein, a professor in the Department of Environmental Science, Policy, and Management, and in the Department of Civil and Environmental Engineering at UC Berkeley and senior author on the paper. “These tule fogs were associated with very damaging multi-vehicle accidents on freeways in the Central Valley resulting from the low visibility. Today, those kind of fog events and associated major accidents are comparatively rare.”

Co-authors of the paper include S. Gilardoni and Maria Cristina Facchini of the Institute of Atmospheric Sciences and Climate in Italy; Dennis Baldocchi of UC Berkeley, and Brian C. McDonald of the University of Colorado, Boulder, and the NOAA Earth System Research Laboratory in Boulder.

This research was supported by a National Science Foundation (NSF) Graduate Fellowship, the California Agricultural Experiment Station and McIntire-Stennis Cooperative Forestry Program of the U.S. Department of Agriculture, and the National Research Council of Italy.

Posted on Friday, April 12, 2019 at 5:46 PM
  • Author: Kara Manke

The worst fire in California history illuminates fire preparation needs

Reposted from the UCANR Green Blog

Four months have passed since the Camp Four months have passed since the Camp Fire, the worst wildfire in California history, ravaged bucolic communities in the Butte County foothills, including Paradise, Concow, Butte Creek Canyon, Cherokee, Yankee Hill and Magalia. Eighty-five people died, many of them elderly and unable to safely evacuate from an area where a wind-driven fire raced from home to home.

Fire resilient forests have the benefit of offering greater access for recreation. (Photo: Butte County Fire Safe Council)

The unspeakable loss of human life and the serious challenges being faced by survivors has dominated the Camp Fire conversation. Now, UC Cooperative Extension is beginning a dialog with many agencies involved to understand how such tragedies can be prevented in the future.

UC Cooperative Extension fire scientists and representatives of many California organizations conduct fire behavior research, study forest treatments – such as prescribed burns, timber harvest and mastication – and share best practices for home and community preparation. In the Butte County area where the Camp Fire took place, cooperating agencies include CalFIRE, the U.S. Forest Service, the Butte County Fire Safe Council, the Yankee Hill Fire Safe Council, Sacramento River Watershed Program, the Sierra Nevada Conservancy, the Bureau of Land Management, and others.

While the Camp Fire was devastating, it could have been far worse. Working together for decades, the partner agencies have improved community safety and resilience.

They have educated the public about defensible space, fire resistant homes, and evacuation plans. They have coordinated fuels treatments along evacuation routes and around the communities. Through their actions, they saved many lives and structures, protected the town's drinking water supply, and in some cases, provided access for hiking in areas that had been overgrown by brush.

“When you drive for miles through blackened, burned trees and then arrive in a thinning project area full of green tree tops, you know that these efforts are worth it, we are having success and we can make a difference together,” said Calli-Jane DeAnda, executive director of the Butte County Fire Safe Council

Because of the Camp Fire tragedy, the partner agencies learned many lessons that can inform future maintenance and treatments to improve fire resilience in Butte County and other wildland areas. Kate Wilkin, the UC Cooperative Extension fire advisor for Sutter, Yuba, Butte, and Nevada counties, is able to point to projects implemented in the Camp Fire zone that saved lives and structures.

For example, one family in Paradise was featured by the news media for their successful advance fire planning, which even included the installation of sprinklers on top of the house.

“When I think about what saves a house, a sprinkler is a cherry on top of the cake,” Wilkin said. “If a house is constructed with a combustible roof and siding, if unprotected vents allow embers to get into the attic, or the landscape is not maintained, a sprinkler isn't going to save the house. The sprinkler's power from the grid or a generator will likely fail. High winds may even prevent the sprinkler's mist from hitting the house.”

Rather, passive resistance to fires through better building design, materials and maintenance greatly reduce structure loss.

“Maintenance is an unsung hero of fire resilience,” Wilkin said. “Individual actions at our homes matter.”

First 5 feet around a structure

State law requires homeowners in wildfire areas to clear 100 feet of defensible space around their structures. Most towns in wildfire-prone areas also have their own defensible space codes. Wilkin said where she lives in Grass Valley, anyone with less than an acre of land must maintain their entire property as defensible space.

This guideline is a start, but there is more that people who live in wildfire-prone areas can do to make their homes resilient to fire. UC Cooperative Extension scientists recommend creating a five-foot buffer immediately surrounding the home almost completely devoid of plants and anything that can burn - including wooden fences, firewood, deck chairs and pillows, brooms and other wooden tools.

This extra precaution is important as embers from a distant wildfire can land on or adjacent to a house and ignite combustible items which in turn ignite the home. It was evident in the Camp Fire that the first five feet around homes was a critical factor in the survivability of structures.

The zone can include noncombustible materials such as rock mulch, stone pavers, cement, bare earth, gravel or sand. Low combustibility materials, such as irrigated and maintained lawn or herbaceous plants less than five inches high, are okay. All leaves, needles or other vegetation that falls in this five-foot zone must be removed during the fire season.

“The non-combustible space adjoining the house may be the difference between losing it and all the contents to a wildfire versus returning to the property with the home unscathed,” Wilkin said.

Community fire resilience

Fire survival measures can also be taken at the community level.

In Paradise, the Butte County Fire Safe Council funded CalFIRE crews to thin a number of areas in the watershed below Paradise Lake in 2013 and 2014. Taking these actions allowed an area for firefighters to start a defense and start putting out the flame front, Wilkin said.

“A CalFIRE chief told residents, ‘You provide the offense, we provide the defense.' Homeowners and communities need to get everything set up for successful firefighting,” she said.

Forest thinning has the added benefit of improving recreational opportunities. Near Magalia Pine Ridge School, an 11-acre mastication project in 2018 funded with $30,000 from the Butte County Fire Safe Council cleared overgrown vegetation around the school. This helped strengthen the area's public assembly location, which was identified on the community's evacuation map, and opened up access to a forest hiking trail that was blocked by tangled brush.

The open space dramatically slowed the raging Camp Fire when it approached the school, which is now one of the only schools open in the Paradise Ridge community.

Note the No. 9 marker in the lower left corner of each photo. (Click the photo to see a higher resolution version.) The the image on the right was taken after mastication, which opened up the forest for recreation and made the forest more resilient before the Camp Fire. (Photos: Butte County Fire Safe Council)
 

Forest thinning also protected the drinking water for the town of Paradise. A combination of projects undertaken by U.S. Forest Service, Sierra Pacific Industries and the Butte County Fire Safe Council aligned to allow fire fighters to combat the fire and ensure that the source of drinking water was protected.

Concow wildfire safety zone

In 2013 and 2014, the Butte County Fire Safe Council and Yankee Hill Fire Safe Council created a wildfire public assembly safety zone in Concow. The work was completed by inmate crews. During the Camp Fire, dozens of lives were saved when sheriff deputies, firefighters and citizens were able to shelter in the area.

“Wildfire safety zones are pretty uncommon and we may want to create more in wildfire prone areas,” Wilkin said. “But there is a hitch.”

CalFIRE is reluctant to designate temporary refuges because they don't want people to rely on them in place of evacuation. During a quick-moving firestorm, it could be an area where people can shelter if they cannot get out.

“It's a complex and dangerous puzzle,” Wilkin said. “In Australia, they had a similar idea and some places where people sheltered in a fire caused them to die.”

Wilkin is working with Paradise parks to identify areas ahead of time with enough space to meet new national firefighter standards to protect people's lungs from superheated air.

“Historically, we thought sufficient space was four times as great as the flame heights. If you have a Ponderosa pine that's torching 150 feet high, you would need 800 feet around the people,” Wilkin said. “New research has found that the safety zone calculation must also consider potential wind speed and slope. Significantly more space may be needed.”

A wildfire safety zone at Camelot Meadow. (Photo: Butte County Fire Safe Council)
 
Posted on Thursday, April 4, 2019 at 11:00 AM
  • Author: jeannette warnert

This beetle’s gut may hide clues to making better biofuels

Reposted from UC Berkeley Public Affairs

A close up of a black shiny beetle against a green background.

The passalid beetle's unique gut architecture helps it transform decaying wood into energy-rich materials. (Graham Wise photo, via Wikimedia commons)

Decaying wood doesn't make the most nutritious food, but the long-horned passalid beetle has evolved to make the best of it. The guts of this forest-dwelling insect are adapted to take tough plant materials, like lignin and cellulose, and transform them into hydrogen, ethanol, methane and other energy-rich biofuels.

In a new study, researchers at UC Berkeley and Berkeley Lab describe how the architecture of the beetle's gut — and the beneficial microbes that inhabit it — help the beetle carry out such a transformation. This knowledge could help scientists engineer more efficient systems for producing bioproducts in the lab.

“We brought together a team of experts and used advanced molecular biology tools, together with spectrometry and tiny sensors, to discover that the beetle's gut is made of up specialized compartments — each with a distinct microbiome — that work together almost like a factory production line, using unique biochemistry to turn the wood into food and fuel,” said Eoin Brodie, assistant adjunct professor of environmental science, policy and management at UC Berkeley and senior author of the paper, which appears Monday, March 11, in the journal Nature Microbiology.

“The key innovation that nature has provided here is a way to combine biochemical processes that are otherwise incompatible,” Brodie said. For example, some of the compartments are optimized to carry out reactions that require lots of oxygen, while others carry out reactions inhibited by oxygen.

“It turns out that the beetle's gut architecture, such as the length and thickness of its gut walls, has evolved to suit its microbiome so that specific metabolic processes are favored in different gut regions,” said Javier Ceja-Navarro, a Berkeley Lab research scientist and lead author of the paper.

The shape of the gut also prevents certain compounds, like hydrogen, from escaping. These compounds help propel the production of products like acetate, which is a critical energy source, not only for the beetle itself, but also for its offspring.

“This beetle and its microbes have worked out what scientists around the world are hurrying to optimize – how to efficiently turn woody plant biomass into biofuels and bioproducts,” Ceja-Navarro said.

Posted on Monday, March 11, 2019 at 1:39 PM
  • Author: UC Berkeley Public Affairs

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