2015 DOE JGI’s science portfolio delves deeper into the Earth’s data mine

The U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, has announced that 32 new projects have been selected for the 2015 Community Science Program (CSP). From sampling Antarctic lakes to Caribbean waters, and from plant root micro-ecosystems, to the subsurface underneath the water table in forested watersheds, the CSP 2015 projects portfolio highlights diverse environments where DOE mission-relevant science can be extracted.

“These projects catalyze JGI’s strategic shift in emphasis from solving an organism’s genome sequence to enabling an understanding of what this information enables organisms to do,” said Jim Bristow, DOE JGI Science Deputy who oversees the CSP. “To accomplish this, the projects selected combine DNA sequencing with large-scale experimental and computational capabilities, and in some cases include JGI’s new capability to write DNA in addition to reading it. These projects will expand research communities, and help to meet the DOE JGI imperative to translate sequence to function and ultimately into solutions for major energy and environmental problems.”

The CSP 2015 projects were selected by an external review panel from 76 full proposals received that resulted from 85 letters of intent submitted. The total allocation for the CSP 2015 portfolio is expected to exceed 60 trillion bases (terabases or Tb)-or the equivalent of 20,000 human genomes of plant, fungal and microbial genome sequences. The full list of projects may be found at http://jgi.doe.gov/our-projects/csp-plans/fy-2015-csp-plans/. The DOE JGI Community Science Program also accepts proposals for smaller-scale microbial, resequencing and DNA synthesis projects and reviews them twice a year. The CSP advances projects that harness DOE JGI’s capability in massive-scale DNA sequencing, analysis and synthesis in support of the DOE missions in alternative energy, global carbon cycling, and biogeochemistry.

Among the CSP 2015 projects selected is one from Regina Lamendella of Juniata College, who will investigate how microbial communities in Marcellus shale, the country’s largest shale gas field, respond to hydraulic fracturing and natural gas extraction. For example, as fracking uses chemicals, researchers are interested in how the microbial communities can break down environmental contaminants, and how they respond to the release of methane during oil extraction operations.

Some 1,500 miles south from those gas extraction sites, Monica Medina-Munoz of Penn State University will study the effect of thermal stress on the Caribbean coral Orbicella faveolata and the metabolic contribution of its coral host Symbiodinium. The calcium carbonate in coral reefs acts as carbon sinks, but reef health depends on microbial communities. If the photosynthetic symbionts are removed from the coral host, for example, the corals can die and calcification rates decrease. Understanding how to maintain stability in the coral-microbiome community can provide information on the coral’s contribution to the global ocean carbon cycle.

Longtime DOE JGI collaborator Jill Banfield of the University of California (UC), Berkeley is profiling the diversity of microbial communities found in the subsurface from the Rifle aquifer adjacent to the Colorado River. The subsurface is a massive, yet poorly understood, repository of organic carbon as well as greenhouse gases. Another research question, based on having the microbial populations close to both the water table and the river, is how they impact carbon, nitrogen and sulfur cycles. Her project is part of the first coordinated attempt to quantify the metabolic potential of an entire subsurface ecosystem under the aegis of the Lawrence Berkeley National Laboratory’s Subsurface Biogeochemistry Scientific Focus Area.

Banfield also successfully competed for a second CSP project to characterize the tree-root microbial interactions that occur below the soil mantle in the unsaturated zone or vadose zone, which extends into unweathered bedrock. The project’s goal is to understand how microbial communities this deep underground influence tree-based carbon fixation in forested watersheds by the Eel River in northwestern California.

Several fungal projects were selected for the 2015 CSP portfolio, including one led by Kabir Peay of Stanford University. He and his colleagues will study how fungal communities in animal feces decompose organic matter. His project has a stated end goal of developing a model system that emulates the ecosystem at Point Reyes National Seashore, where Tule elk are the largest native herbivores.

Another selected fungal project comes from Timothy James of University of Michigan, who will explore the so-called “dark matter fungi” – those not represented in culture collections. By sequencing several dozen species of unculturable zoosporic fungi from freshwater, soils and animal feces, he and his colleagues hope to develop a kingdom-wide fungal phylogenetic framework.

Christian Wurzbacher of Germany’s the Leibniz Institute of Freshwater Ecology and Inland Fisheries, IGB, will characterize fungi from the deep sea to peatlands to freshwater streams to understand the potentially novel adaptations that are necessary to thrive in their aquatic environments. The genomic information would provide information on their metabolic capabilities for breaking down cellulose, lignin and other plant cell wall components, and animal polymers such as keratin and chitin.

Many of the selected projects focus on DOE JGI Flagship Plant Genomes, with most centered on the poplar (Populus trichocarpa.) For example, longtime DOE JGI collaborator Steve DiFazio of West Virginia University is interested in poplar but will study its reproductive development with the help of a close relative, the willow (Salix purpurea). With its shorter generation time, the plant is a good model system and comparator for understanding sex determination, which can help bioenergy crop breeders by, for example, either accelerating or preventing flowering.

Another project comes from Posy Busby of the University of Washington, who will study the interactions between the poplar tree and its fungal, non-pathogenic symbionts or endophytes. As disease-causing pathogens interact with endophytes in leaves, he noted in his proposal, understanding the roles and functions of endophytes could prove useful to meeting future fuel and food requirements.

Along the lines of poplar endophytes, Carolin Frank at UC Merced will investigate the nitrogen-fixing endophytes in poplar, willow, and pine, with the aim of improving growth in grasses and agricultural crops under nutrient-poor conditions.

Rotem Sorek from the Weizmann Institute of Science in Israel takes a different approach starting from the hypothesis that poplar trees have an adaptive immunity system rooted in genome-encoded immune memory. Through deep sequencing of tissues from single poplar trees (some over a century old, others younger) his team hopes to gain insights into the tree genome’s short-term evolution and how its gene expression profiles change over time, as well as to predict how trees might respond under various climate change scenarios.

Tackling a different DOE JGI Flagship Plant Genome, Debbie Laudencia-Chingcuangco of the USDA-ARS will develop a genome-wide collection of several thousand mutants of the model grass Brachypodium distachyon to help domesticate the grasses that are being considered as candidate bioenergy feedstocks. This work is being done in collaboration with researchers at the Great Lakes Bioenergy Research Center, as the team there considers Brachypodium “critical to achieving its mission of developing productive energy crops that can be easily processed into fuels.”

Continuing the theme of candidate bioenergy grasses, Kankshita Swaminathan from the University of Illinois will study gene expression in polyploidy grasses Miscanthus and sugarcane, comparing them against the closely related diploid grass sorghum to understand how these plants recycle nutrients.

Baohong Zhang of East Carolina University also focused on a bioenergy grass, and his project will look at the microRNAs in switchgrass. These regulatory molecules are each just a couple dozen nucleotides in length and can downregulate (decrease the quantity of) a cellular component. With a library of these small transcripts, he and his team hope to identify the gene expression variation associated with desirable biofuel traits in switchgrass such as increased biomass and responses to drought and salinity stressors.

Nitin Baliga of the Institute of Systems Biology will use DOE JGI genome sequences to build a working model of the networks that regulate lipid accumulation in Chlamydomonas reinhardtii, still another DOE JGI Plant Flagship Genome and a model for characterizing biofuel production by algae.

Other accepted projects include:

The study of the genomes of 32 fungi of the Agaricales order, including 16 fungi to be sequenced for the first time, will be carried out by Jose Maria Barrasa of Spain’s University of Alcala. While many of the basidiomycete fungi involved in wood degradation that have been sequenced are from the Polyporales, he noted in his proposal, many of the fungi involved in breaking down leaf litter and buried wood are from the order Agaricales.

Now at the University of Connecticut, Jonathan Klassen conducted postdoctoral studies at GLBRC researcher Cameron Currie’s lab at University of Wisconsin-Madison. His project will study interactions in ant-microbial community fungus gardens in three states to learn more about how the associated bacterial metagenomes contribute to carbon and nitrogen cycling.

Hinsby Cadillo-Quiroz, at Arizona State University, will conduct a study of the microbial communities in the Amazon peatlands to understand their roles in both emitting greenhouse gases and in storing and cycling carbon. The peatlands are hotspots of soil organic carbon accumulation, and in the tropical regions, they are estimated to hold between 11 percent and 14 percent, or nearly 90 gigatons, of the global carbon stored in soils.

Barbara Campbell, Clemson University will study carbon cycling mechanisms of active bacteria and associated viruses in the freshwater to marine transition zone of the Delaware Bay. Understanding the microbes’ metabolism would help researchers understand they capabilities with regard to dealing with contaminants, and their roles in the nitrogen, sulfur and carbon cycles.

Jim Fredrickson of Pacific Northwest National Laboratory will characterize functional profiles of microbial mats in California, Washington and Yellowstone National Park to understand various functions such as how they produce hydrogen and methane, and break down cellulose.

Joyce Loper of USDA-ARS will carry out a comparative analysis of all Pseudomonas bacteria getting from DOE JGI the sequences of just over 100 type strains to infer a evolutionary history of the this genus — a phylogeny — to characterize the genomic diversity, and determine the distribution of genes linked to key observable traits in this non-uniform group of bacteria.

Holly Simon of Oregon Health & Science University is studying microbial populations in the Columbia River estuary, in part to learn how they enhance greenhouse gas CO2 methane and nitrous oxide production.

Michael Thon from Spain’s University of Salamanca will explore sequences of strains of the Colletotrichum species complex, which include fungal pathogens that infect many crops. One of the questions he and his team will ask is how these fungal strains have adapted to break down the range of plant cell wall compositions.

Kathleen Treseder of UC Irvine will study genes involved in sensitivity to higher temperatures in fungi from a warming experiment in an Alaskan boreal forest. The team’s plan is to fold the genomic information gained into a trait-based ecosystem model called DEMENT to predict carbon dioxide emissions under global warming.

Mary Wildermuth of UC Berkeley will study nearly a dozen genomes of powdery mildew fungi, including three that infect designated bioenergy crops. The project will identify the mechanisms by which the fungi successfully infect plants, information that could lead to the development of crops with improved resistance to fungal infection and limiting fungicide use to allow more sustainable agricultural practices.

Several researchers who have previously collaborated with the DOE JGI have new projects:

Ludmila Chistoserdova from the University of Washington had a pioneering collaboration with the DOE JGI to study microbial communities in Lake Washington. In her new project, she and her team will look at the microbes in the Lake Washington sediment to understand their role in metabolizing the potent greenhouse gas methane.

Rick Cavicchioli of Australia’s University of New South Wales will track how microbial communities change throughout a complete annual cycle in three millennia-old Antarctic lakes and a near-shore marine site. By establishing what the microbes do in different seasons, he noted in his proposal, he and his colleagues hope to learn which microbial processes change and about the factors that control the evolution and speciation of marine-derived communities in cold environments.

With samples collected from surface waters down to the deep ocean, Steve Hallam from Canada’s University of British Columbia will explore metabolic pathways and compounds involved in marine carbon cycling processes to understand how carbon is regulated in the oceans.

The project of Hans-Peter Klenk, of DSMZ in Germany, will generate sequences of 1,000 strains of Actinobacteria, which represent the third most populated bacterial phylum and look for genes that encode cellulose-degrading enzymes or enzymes involved in synthesizing novel, natural products.

Han Wosten of the Netherlands’ Utrecht University will carry out a functional genomics approach to wood degradation by looking at Agaricomycetes, in particular the model white rot fungus Schizophyllum commune and the more potent wood-degrading white rots Phanaerochaete chrysosporium and Pleurotus ostreatus that the DOE JGI has previously sequenced.

Wen-Tso Liu of the University of Illinois and his colleagues want to understand the microbial ecology in anaerobic digesters, key components of the wastewater treatment process. They will study microbial communities in anaerobic digesters from the United States, East Asia and Europe to understand the composition and function of the microbes as they are harnessed for this low-cost municipal wastewater strategy efficiently removes waster and produces methane as a sustainable energy source.

Another project that involves wastewater, albeit indirectly, comes from Erica Young of the University of Wisconsin. She has been studying algae grown in wastewater to track how they use nitrogen and phosphorus, and how cellulose and lipids are produced. Her CSP project will characterize the relationship between the algae and the bacteria that help stabilize these algal communities, particularly the diversity of the bacterial community and the pathways and interactions involved in nutrient uptake and carbon sequestration.

Previous CSP projects and other DOE JGI collaborations are highlighted in some of the DOE JGI Annual User Meeting talks that can be seen here: http://usermeeting.jgi.doe.gov/past-speakers/. The 10th Annual Genomics of Energy and Environment Meeting will be held March 24-26, 2015 in Walnut Creek, Calif. A preliminary speakers list is posted here (http://usermeeting.jgi.doe.gov/) and registration will be opened in the first week of November.

Birth of a mineral

<IMG SRC="/Images/904289364.jpg" WIDTH="350" HEIGHT="233" BORDER="0" ALT="An aragonite crystal — with its characteristic 'sheaf of wheat' look — consumed a particle of amorphous calcium carbonate as it formed. – Nielsen et al. 2014/Science“>
An aragonite crystal — with its characteristic ‘sheaf of wheat’ look — consumed a particle of amorphous calcium carbonate as it formed. – Nielsen et al. 2014/Science

One of the most important molecules on earth, calcium carbonate crystallizes into chalk, shells and minerals the world over. In a study led by the Department of Energy’s Pacific Northwest National Laboratory, researchers used a powerful microscope that allows them to see the birth of crystals in real time, giving them a peek at how different calcium carbonate crystals form, they report in September 5 issue of Science.

The results might help scientists understand how to lock carbon dioxide out of the atmosphere as well as how to better reconstruct ancient climates.

“Carbonates are most important for what they represent, interactions between biology and Earth,” said lead researcher James De Yoreo, a materials scientist at PNNL. “For a decade, we’ve been studying the formation pathways of carbonates using high-powered microscopes, but we hadn’t had the tools to watch the crystals form in real time. Now we know the pathways are far more complicated than envisioned in the models established in the twentieth century.”

Earth’s Reserve


Calcium carbonate is the largest reservoir of carbon on the planet. It is found in rocks the world over, shells of both land- and water-dwelling creatures, and pearls, coral, marble and limestone. When carbon resides within calcium carbonate, it is not hanging out in the atmosphere as carbon dioxide, warming the world. Understanding how calcium carbonate turns into various minerals could help scientists control its formation to keep carbon dioxide from getting into the atmosphere.

Calcium carbonate deposits also contain a record of Earth’s history. Researchers reconstructing ancient climates delve into the mineral for a record of temperature and atmospheric composition, environmental conditions and the state of the ocean at the time those minerals formed. A better understanding of its formation pathways will likely provide insights into those events.

To get a handle on mineral formation, researchers at PNNL, the University of California, Berkeley, and Lawrence Berkeley National Laboratory examined the earliest step to becoming a mineral, called nucleation. In nucleation, molecules assemble into a tiny crystal that then grows with great speed. Nucleation has been difficult to study because it happens suddenly and unpredictably, so the scientists needed a microscope that could watch the process in real time.

Come to Order


In the 20th century, researchers established a theory that crystals formed in an orderly fashion. Once the ordered nucleus formed, more molecules added to the crystal, growing the mineral but not changing its structure. Recently, however, scientists have wondered if the process might be more complicated, with other things contributing to mineral formation. For example, in previous experiments they’ve seen forms of calcium carbonate that appear to be dense liquids that could be sources for minerals.

Researchers have also wondered if calcite forms from less stable varieties or directly from calcium and carbonate dissolved in the liquid. Aragonite and vaterite are calcium carbonate minerals with slightly different crystal architectures than calcite and could represent a step in calcite’s formation. The fourth form called amorphous calcium carbonate – or ACC, which could be liquid or solid, might also be a reservoir for sprouting minerals.

To find out, the team created a miniature lab under a transmission electron microscope at the Molecular Foundry, a DOE Office of Science User Facility at LBNL. In this miniature lab, they mixed sodium bicarbonate (used to make club soda) and calcium chloride (similar to table salt) in water. At high enough concentrations, crystals grew. Videos of nucleating and growing crystals recorded what happened [URLs to come].

Morphing Minerals


The videos revealed that mineral growth took many pathways. Some crystals formed through a two-step process. For example, droplet-like particles of ACC formed, then crystals of aragonite or vaterite appeared on the surface of the droplets. As the new crystals formed, they consumed the calcium carbonate within the drop on which they nucleated.

Other crystals formed directly from the solution, appearing by themselves far away from any ACC particles. Multiple forms often nucleated in a single experiment — at least one calcite crystal formed on top of an aragonite crystal while vaterite crystals grew nearby.

What the team didn’t see in and among the many options, however, was calcite forming from ACC even though researchers widely expect it to happen. Whether that means it never does, De Yoreo can’t say for certain. But after looking at hundreds of nucleation events, he said it is a very unlikely event.

“This is the first time we have directly visualized the formation process,” said De Yoreo. “We observed many pathways happening simultaneously. And they happened randomly. We were never able to predict what was going to come up next. In order to control the process, we’d need to introduce some kind of template that can direct which crystal forms and where.”

In future work, De Yoreo and colleagues plan to investigate how living organisms control the nucleation process to build their shells and pearls. Biological organisms keep a store of mineral components in their cells and have evolved ways to make nucleation happen when and where needed. The team is curious to know how they use cellular molecules to achieve this control.




Video
Click on this image to view the .mp4 video
Diamond-shaped crystals of calcite form directly from solution. A round particle that could be either amorphous calcium carbonate or vaterite forms nearby. – Nielsen et al. 2014/Science

Geologists confirm oxygen levels of ancient oceans

Assistant Professor Zunli Lu co-authored the study. -  Syracuse University News Services
Assistant Professor Zunli Lu co-authored the study. – Syracuse University News Services

Geologists in the College of Arts and Sciences have discovered a new way to study oxygen levels in the Earth’s oldest oceans.

Zunli Lu and Xiaoli Zhou, an assistant professor and Ph.D. student, respectively, in the Department of Earth Sciences, are part of an international team of researchers whose findings have been published by the journal Geology (Geological Society of America, 2014). Their research approach may have important implications for the study of marine ecology and global warming.

“More than 2.5 billion years ago, there was little to no oxygen in the oceans, as methane shrouded the Earth in a haze,” says Lu, a member of Syracuse University’s Low-Temperature Geochemistry Research Group. “Organisms practicing photosynthesis eventually started to overpower reducing chemical compounds [i.e., electron donors], and oxygen began building up in the atmosphere. This period has been called the Great Oxidation Event.”

Using a novel approach called iodine geochemistry, Lu, Zhou and their colleagues have confirmed the earliest appearance of dissolved oxygen in the ocean’s surface waters.

Central to their approach is iodate, a form of iodine that exists only in oxygenated waters. When iodate is detected in carbonate rocks in a marine setting, Lu and company are able to measure the elemental ratio of iodine to calcium. This measurement, known as a proxy for ocean chemistry, helps them figure out how much oxygen has dissolved in the water.

“Iodine geochemistry enables us to constrain oxygen levels in oceans that have produced calcium carbonate minerals and fossils,” says Lu, who developed the proxy. “What we’ve found in ancient rock reinforces the proxy’s reliability. Already, we’re using the proxy to better understand the consequences of ocean deoxygenation, due to rapid global warming.”

Warm US West, cold East: A 4,000-year pattern

<IMG SRC="/Images/485889256.jpg" WIDTH="350" HEIGHT="262" BORDER="0" ALT="University of Utah geochemist Gabe Bowen led a new study, published in Nature Communications, showing that the curvy jet stream pattern that brought mild weather to western North America and intense cold to the eastern states this past winter has become more dominant during the past 4,000 years than it was from 8,000 to 4,000 years ago. The study suggests global warming may aggravate the pattern, meaning such severe winter weather extremes may be worse in the future. – Lee J. Siegel, University of Utah.”>
University of Utah geochemist Gabe Bowen led a new study, published in Nature Communications, showing that the curvy jet stream pattern that brought mild weather to western North America and intense cold to the eastern states this past winter has become more dominant during the past 4,000 years than it was from 8,000 to 4,000 years ago. The study suggests global warming may aggravate the pattern, meaning such severe winter weather extremes may be worse in the future. – Lee J. Siegel, University of Utah.

Last winter’s curvy jet stream pattern brought mild temperatures to western North America and harsh cold to the East. A University of Utah-led study shows that pattern became more pronounced 4,000 years ago, and suggests it may worsen as Earth’s climate warms.

“If this trend continues, it could contribute to more extreme winter weather events in North America, as experienced this year with warm conditions in California and Alaska and intrusion of cold Arctic air across the eastern USA,” says geochemist Gabe Bowen, senior author of the study.

The study was published online April 16 by the journal Nature Communications.

“A sinuous or curvy winter jet stream means unusual warmth in the West, drought conditions in part of the West, and abnormally cold winters in the East and Southeast,” adds Bowen, an associate professor of geology and geophysics at the University of Utah. “We saw a good example of extreme wintertime climate that largely fit that pattern this past winter,” although in the typical pattern California often is wetter.

It is not new for scientists to forecast that the current warming of Earth’s climate due to carbon dioxide, methane and other “greenhouse” gases already has led to increased weather extremes and will continue to do so.

The new study shows the jet stream pattern that brings North American wintertime weather extremes is millennia old – “a longstanding and persistent pattern of climate variability,” Bowen says. Yet it also suggests global warming may enhance the pattern so there will be more frequent or more severe winter weather extremes or both.

“This is one more reason why we may have more winter extremes in North America, as well as something of a model for what those extremes may look like,” Bowen says. Human-caused climate change is reducing equator-to-pole temperature differences; the atmosphere is warming more at the poles than at the equator. Based on what happened in past millennia, that could make a curvy jet stream even more frequent and-or intense than it is now, he says.

Bowen and his co-authors analyzed previously published data on oxygen isotope ratios in lake sediment cores and cave deposits from sites in the eastern and western United States and Canada. Those isotopes were deposited in ancient rainfall and incorporated into calcium carbonate. They reveal jet stream directions during the past 8,000 years, a geological time known as middle and late stages of the Holocene Epoch.

Next, the researchers did computer modeling or simulations of jet stream patterns – both curvy and more direct west to east – to show how changes in those patterns can explain changes in the isotope ratios left by rainfall in the old lake and cave deposits.

They found that the jet stream pattern – known technically as the Pacific North American teleconnection – shifted to a generally more “positive phase” – meaning a curvy jet stream – over a 500-year period starting about 4,000 years ago. In addition to this millennial-scale change in jet stream patterns, they also noted a cycle in which increases in the sun’s intensity every 200 years make the jet stream flatter.

Bowen conducted the study with Zhongfang Liu of Tianjin Normal University in China, Kei Yoshimura of the University of Tokyo, Nikolaus Buenning of the University of Southern California, Camille Risi of the French National Center for Scientific Research, Jeffrey Welker of the University of Alaska at Anchorage, and Fasong Yuan of Cleveland State University.

The study was funded by the National Science Foundation, National Natural Science Foundation of China, Japan Society for the Promotion of Science and a joint program by the society and Japan’s Ministry of Education, Culture, Sports, Science and Technology: the Program for Risk Information on Climate Change.

Sinuous Jet Stream Brings Winter Weather Extremes

The Pacific North American teleconnection, or PNA, “is a pattern of climate variability” with positive and negative phases, Bowen says.

“In periods of positive PNA, the jet stream is very sinuous. As it comes in from Hawaii and the Pacific, it tends to rocket up past British Columbia to the Yukon and Alaska, and then it plunges down over the Canadian plains and into the eastern United States. The main effect in terms of weather is that we tend to have cold winter weather throughout most of the eastern U.S. You have a freight car of arctic air that pushes down there.”

Bowen says that when the jet stream is curvy, “the West tends to have mild, relatively warm winters, and Pacific storms tend to occur farther north. So in Northern California, the Pacific Northwest and parts of western interior, it tends to be relatively dry, but tends to be quite wet and unusually warm in northwest Canada and Alaska.”

This past winter, there were times of a strongly curving jet stream, and times when the Pacific North American teleconnection was in its negative phase, which means “the jet stream is flat, mostly west-to-east oriented,” and sometimes split, Bowen says. In years when the jet stream pattern is more flat than curvy, “we tend to have strong storms in Northern California and Oregon. That moisture makes it into the western interior. The eastern U.S. is not affected by arctic air, so it tends to have milder winter temperatures.”

The jet stream pattern – whether curvy or flat – has its greatest effects in winter and less impact on summer weather, Bowen says. The curvy pattern is enhanced by another climate phenomenon, the El Nino-Southern Oscillation, which sends a pool of warm water eastward to the eastern Pacific and affects climate worldwide.

Traces of Ancient Rains Reveal Which Way the Wind Blew

Over the millennia, oxygen in ancient rain water was incorporated into calcium carbonate deposited in cave and lake sediments. The ratio of rare, heavy oxygen-18 to the common isotope oxygen-16 in the calcium carbonate tells geochemists whether clouds that carried the rain were moving generally north or south during a given time.

Previous research determined the dates and oxygen isotope ratios for sediments in the new study, allowing Bowen and colleagues to use the ratios to tell if the jet stream was curvy or flat at various times during the past 8,000 years.

Bowen says air flowing over the Pacific picks up water from the ocean. As a curvy jet stream carries clouds north toward Alaska, the air cools and some of the water falls out as rain, with greater proportions of heavier oxygen-18 falling, thus raising the oxygen-18-to-16 ratio in rain and certain sediments in western North America. Then the jet stream curves south over the middle of the continent, and the water vapor, already depleted in oxygen-18, falls in the East as rain with lower oxygen-18-to-16 ratios.

When the jet stream is flat and moving east-to-west, oxygen-18 in rain is still elevated in the West and depleted in the East, but the difference is much less than when the jet stream is curvy.

By examining oxygen isotope ratios in lake and cave sediments in the West and East, Bowen and colleagues showed that a flatter jet stream pattern prevailed from about 8,000 to 4,000 years ago in North America, but then, over only 500 years, the pattern shifted so that curvy jet streams became more frequent or severe or both. The method can’t distinguish frequency from severity.

The new study is based mainly on isotope ratios at Buckeye Creek Cave, W. Va.; Lake Grinell, N.J.; Oregon Caves National Monument; and Lake Jellybean, Yukon.

Additional data supporting increasing curviness of the jet stream over recent millennia came from seven other sites: Crawford Lake, Ontario; Castor Lake, Wash.; Little Salt Spring, Fla.; Estancia Lake, N.M.; Crevice Lake, Mont.; and Dog and Felker lakes, British Columbia. Some sites provided oxygen isotope data; others showed changes in weather patterns based on tree ring growth or spring deposits.

Simulating the Jet Stream

As a test of what the cave and lake sediments revealed, Bowen’s team did computer simulations of climate using software that takes isotopes into account.

Simulations of climate and oxygen isotope changes in the Middle Holocene and today resemble, respectively, today’s flat and curvy jet stream patterns, supporting the switch toward increasing jet stream sinuosity 4,000 years ago.

Why did the trend start then?

“It was a when seasonality becomes weaker,” Bowen says. The Northern Hemisphere was closer to the sun during the summer 8,000 years ago than it was 4,000 years ago or is now due to a 20,000-year cycle in Earth’s orbit. He envisions a tipping point 4,000 years ago when weakening summer sunlight reduced the equator-to-pole temperature difference and, along with an intensifying El Nino climate pattern, pushed the jet stream toward greater curviness.

Earthworms could help scientists ‘dig’ into past climates

A team of UK researchers believe earthworms could provide a window into past climates, allowing scientists to piece together the prevailing weather conditions thousands of years ago.

A laboratory study by researchers from the Universities of Reading and York has demonstrated that balls of calcium carbonate (small lumps of chalk-like material) excreted by the earthworm Lumbricus terrestris – commonly known as lobworms or nightcrawlers – maintain a memory of the temperature at which they were formed.

This, say the researchers, in an article in the journal Geochimica et Cosmochimica Acta, means that calcite granules, commonly recorded at sites of archaeological interest, have the potential to reveal important information about past climates which could be used to enhance and benchmark climate change models.

The study, which also involved English Heritage’s Centre for Archaeology, was funded by the Natural Environment Research Council (NERC).
Lead author Dr Emma Versteegh from the Department of Geography and Environmental Science at the University of Reading, said: “These chalk balls will allow us to reconstruct temperatures for specific time intervals in which they were formed. Reconstructions like this are interesting for archaeologists, because they give a climatic context to their finds. More importantly, climate proxies are the only means we have to study climate beyond the instrumental record, which only goes back about 150 year

“This knowledge about past climates is of vital importance for developing and benchmarking climate models that make predictions for the future. Many different proxies already exist, but no proxy is perfect, or is available in every location, so it is good to have many different ones.”

The proof of concept study involved keeping modern-day Lumbricus terrestris at different temperatures, then carrying out isotopic testing on the calcite granules excreted. This successfully demonstrated that the granules remembered the temperature at which they were formed.

Principal Investigator Professor Mark Hodson from the University of York’s Environment Department, and formerly of the University of Reading, said: “There are many conflicting theories about why earthworms produce calcite granules, but until now, the small lumps of chalk-like material found in earthworm poo have been seen as little more than a biological curiosity. However, our research shows they may well have an important role to play, offering a window into past climates.”

The researchers are now gathering samples from archaeological sites dating back thousands of years in preparation for isotopic testing.
Dr Stuart Black, from the University of Reading’s Department of Archaeology, added: “We believe this new method of delving into past climates has distinct advantages over other biological proxies. For example, we believe it will work for the full seasonal range of temperatures, whereas methods such as tree rings, do not “record” during winter. In addition, because the chalk balls are found in direct context with archaeological finds, they will reveal temperatures at the same location. At present, links are often attempted with climate proxies many hundreds or even thousands of miles away.”

Borneo stalagmites provide new view of abrupt climate events over 100,000 years

Georgia Tech researchers Stacy Carolin (Ph.D. candidate), Jessica Moerman (Ph.D. candidate), Eleanor Middlemas (undergraduate), Danja Mewes (undergraduate) and two caving guides (Syria Lejau, Jenny Malang) climb out from Cobweb Cave in Gunung Mulu National Park after a day of rock and water sample collection during the Fall 2012 field trip. -  Credit: Kim Cobb
Georgia Tech researchers Stacy Carolin (Ph.D. candidate), Jessica Moerman (Ph.D. candidate), Eleanor Middlemas (undergraduate), Danja Mewes (undergraduate) and two caving guides (Syria Lejau, Jenny Malang) climb out from Cobweb Cave in Gunung Mulu National Park after a day of rock and water sample collection during the Fall 2012 field trip. – Credit: Kim Cobb

A new set of long-term climate records based on cave stalagmites collected from tropical Borneo shows that the western tropical Pacific responded very differently than other regions of the globe to abrupt climate change events. The 100,000-year climate record adds to data on past climate events, and may help scientists assess models designed to predict how the Earth’s climate will respond in the future.

The new record resulted from oxygen isotope analysis of more than 1,700 calcium carbonate samples taken from four stalagmites found in three different northern Borneo caves. The results suggest that climate feedbacks within the tropical regions may amplify and prolong abrupt climate change events that were first discovered in the North Atlantic.

The results were scheduled to be published June 6 in Science Express, the electronic advance online publication of the journal Science, and will appear later in an issue of printed publication. The research was supported by the National Science Foundation.

Today, relatively subtle changes in the tropical Pacific’s ocean and atmosphere have profound effects on global climate. However, there are few records of past climate changes in this key region that have the length, resolution and age controls needed to reveal the area’s response to abrupt climate change events.

“This is a new record from a very important area of the world,” said Kim Cobb, an associate professor in the School of Earth and Atmospheric Sciences at the Georgia Institute of Technology. “This record will provide a new piece of the puzzle from the tropical Pacific showing us how that climate system has responded to forcing events over the past 100,000 years.”

Among the findings were some surprises that show just how complicated the Earth’s climate system can be. While the stalagmite record reflected responses to abrupt changes known as Heinrich events, another major type of event – known as Dansgaard-Oeschger excursions – left no evidence in the Borneo stalagmites. Both types of abrupt climate change events are prominently featured in a previously-published stalagmite climate record from China – which is only slightly north of Borneo.

“To my knowledge, this is the first record that so clearly shows sensitivity to one set of major abrupt climate change events and not another,” said Cobb. “These two types of abrupt change events appear to have different degrees of tropical Pacific involvement, and because the tropical Pacific speaks with such a loud voice when it does speak, we think this is extremely important for understanding the mechanisms underlying these events.”

The researchers were also surprised to discover a very large and abrupt signal in their stalagmite climate records precisely when super-volcano Toba erupted nearby, roughly 74,000 years ago.

The team recovered the stalagmites from caves in Gunung Mulu and Gunung Buda National Parks, in northern Borneo, which is located a few degrees north of the Equator in the western Pacific. Back at their Georgia Tech lab, they analyzed the stalagmites for the ratio of oxygen isotopes contained in samples of calcium carbonate, the material from which the stalagmites were formed. That ratio is set by the oxygen isotopes in rainfall at the site, as the water that seeped into the ground dissolved limestone rock and dripped into the caves to form the stalagmites. The stalagmites accumulate at a rate of roughly one centimeter every thousand years.

“Stalagmites are time capsules of climate signals from thousands of years in the past,” said Stacy Carolin, a Georgia Tech Ph.D. candidate who gathered and analyzed the stalagmites. “We have instrumental records of climate only for the past 100 years or so, and if we want to look deeper into the past, we have to find records like these that locked in climate signals we can extract today.”

In the laboratory, Carolin sawed each stalagmite in half, opening it like a hot dog bun. She then used a tiny drill bit to take samples of the calcium carbonate down the center at one-millimeter steps. Because the stalagmites grew at varying rates, each sample represented as little as 60 years of time, or as much as 200 years. The precise ages of the samples were determined by measuring uranium and thorium isotope ratios, an analysis done with the help of Jess F. Adkins, a professor at the California Institute of Technology and a co-author of the study.

Rainfall oxygen isotopic ratios are good indicators of the amount of rainfall occurring throughout the region, as determined by a modern-day calibration study recently published by another graduate student in Cobb’s lab.

Merging data from the four different stalagmites provided a record of precipitation trends in the western Pacific over the past 100,000 years. That information can be compared to stalagmite and ice core climate records obtained elsewhere in the world.

“This record, which spans the entire last glacial period, adds significantly to the understanding of how various climate forcings are felt by the western tropical Pacific,” Carolin added.

Climate scientists are interested in learning more about abrupt climate changes because they indicate that the climate system may have “tipping points.” So far, the climate system has responded to rising carbon dioxide levels at a fairly steady rate, but many scientists worry about possible nonlinear effects.

“As a society, we haven’t really thought enough about the fact that we are moving Earth’s climate system toward a new state very quickly,” said Cobb. “It’s important to remember that the climate system has important nonlinearities that are most evident in these abrupt climate events. Ultimately, we’d like to be able to reproduce the global signatures of these abrupt climate events with numerical models of the climate system, and investigate the physics that drive such events.”

For Carolin, studying the half-meter-long stalagmites brought an awareness that the Earth has not always been as we know it today.

“You have to be impressed with the scope of what you are studying, and recognize that the state our climate is in today is incredibly different from Earth’s climate during the last Ice Age,” she said. “As we consider how humans may be affecting climate, dissecting what was going on tens of thousands of years ago in all regions of the globe can help scientists better predict how the Earth will respond to modern climate forcings.”

Hot springs microbes hold key to dating sedimentary rocks, researchers say





Mammoth Hotsprings in Yellowstone National Park
Mammoth Hotsprings in Yellowstone National Park

Scientists studying microbial communities and the growth of sedimentary rock at Mammoth Hot Springs in Yellowstone National Park have made a surprising discovery about the geological record of life and the environment.



Their discovery could affect how certain sequences of sedimentary rock are dated, and how scientists might search for evidence of life on other planets.



“We found microbes change the rate at which calcium carbonate precipitates, and that rate controls the chemistry and shape of calcium carbonate crystals,” said Bruce Fouke, a professor of geology and of molecular and cellular biology at the University of Illinois.



In fact, the precipitation rate can more than double when microbes are present, Fouke and his colleagues report in a paper accepted for publication in the Geological Society of America Bulletin.



The researchers’ findings imply changes in calcium carbonate mineralization rates in the rock record may have resulted from changes in local microbial biomass concentrations throughout geologic history.



A form of sedimentary rock, calcium carbonate is the most abundant mineral precipitated on the surface of Earth, and a great recorder of life.


“As calcium carbonate is deposited, it leaves a chemical fingerprint of the animals and environment, the plants and bacteria that were there,” said Fouke, who also is affiliated with the university’s Institute for Genomic Biology.



The extent to which microorganisms influence calcium carbonate precipitation has been one of the most controversial issues in the field of carbonate sedimentology and geochemistry. Separating biologically precipitated calcium carbonate from non-biologically precipitated calcium carbonate is difficult.



Fouke’s research team has spent 10 years quantifying the physical, chemical and biological aspects of the hot springs environment. The last step in deciphering the calcium carbonate record was performing an elaborate field experiment, which drew water from a hot springs vent and compared deposition rates with and without microbes being present.



“Angel Terrace at Mammoth Hot Springs in Yellowstone National Park is an ideal, natural laboratory because of the high precipitation rates and the abundance of microbes,” Fouke said. “Calcium carbonate grows so fast – millimeters per day – we can examine the interaction between microorganisms and the calcium-carbonate precipitation process.”



The researchers found that the rate of precipitation drops drastically – sometimes by more than half – when microbes are not present.



“So one of the fingerprints of calcium carbonate deposition that will tell us for sure if there were microbes present at the time it formed is the rate at which it formed,” Fouke said. “And, within the environmental and ecological context of the rock being studied, we can now use chemistry to fingerprint the precipitation rate.”



In a second paper, to appear in the Journal of Sedimentary Research, Fouke and colleagues show how the calcium carbonate record in a spring’s primary flow path can be used to reconstruct the pH, temperature and flux of ancient hot springs environments. The researchers also show how patterns in calcium carbonate crystallization can be used to differentiate signatures of life from those caused by environmental change.



“This means we can go into the rock record, on Earth or other planets, and determine if calcium carbonate deposits were associated with microbial life,” Fouke said.