No laughing matter: Nitrous oxide rose at end of last ice age

Researchers measured increases in atmospheric nitrous oxide concentrations about 16,000 to 10,000 years ago using ice from Taylor Glacier in Antarctica. -  Adrian Schilt
Researchers measured increases in atmospheric nitrous oxide concentrations about 16,000 to 10,000 years ago using ice from Taylor Glacier in Antarctica. – Adrian Schilt

Nitrous oxide (N2O) is an important greenhouse gas that doesn’t receive as much notoriety as carbon dioxide or methane, but a new study confirms that atmospheric levels of N2O rose significantly as the Earth came out of the last ice age and addresses the cause.

An international team of scientists analyzed air extracted from bubbles enclosed in ancient polar ice from Taylor Glacier in Antarctica, allowing for the reconstruction of the past atmospheric composition. The analysis documented a 30 percent increase in atmospheric nitrous oxide concentrations from 16,000 years ago to 10,000 years ago. This rise in N2O was caused by changes in environmental conditions in the ocean and on land, scientists say, and contributed to the warming at the end of the ice age and the melting of large ice sheets that then existed.

The findings add an important new element to studies of how Earth may respond to a warming climate in the future. Results of the study, which was funded by the U.S. National Science Foundation and the Swiss National Science Foundation, are being published this week in the journal Nature.

“We found that marine and terrestrial sources contributed about equally to the overall increase of nitrous oxide concentrations and generally evolved in parallel at the end of the last ice age,” said lead author Adrian Schilt, who did much of the work as a post-doctoral researcher at Oregon State University. Schilt then continued to work on the study at the Oeschger Centre for Climate Change Research at the University of Bern in Switzerland.

“The end of the last ice age represents a partial analog to modern warming and allows us to study the response of natural nitrous oxide emissions to changing environmental conditions,” Schilt added. “This will allow us to better understand what might happen in the future.”

Nitrous oxide is perhaps best known as laughing gas, but it is also produced by microbes on land and in the ocean in processes that occur naturally, but can be enhanced by human activity. Marine nitrous oxide production is linked closely to low oxygen conditions in the upper ocean and global warming is predicted to intensify the low-oxygen zones in many of the world’s ocean basins. N2O also destroys ozone in the stratosphere.

“Warming makes terrestrial microbes produce more nitrous oxide,” noted co-author Edward Brook, an Oregon State paleoclimatologist whose research team included Schilt. “Greenhouse gases go up and down over time, and we’d like to know more about why that happens and how it affects climate.”

Nitrous oxide is among the most difficult greenhouse gases to study in attempting to reconstruct the Earth’s climate history through ice core analysis. The specific technique that the Oregon State research team used requires large samples of pristine ice that date back to the desired time of study – in this case, between about 16,000 and 10,000 years ago.

The unusual way in which Taylor Glacier is configured allowed the scientists to extract ice samples from the surface of the glacier instead of drilling deep in the polar ice cap because older ice is transported upward near the glacier margins, said Brook, a professor in Oregon State’s College of Earth, Ocean, and Atmospheric Sciences.

The scientists were able to discern the contributions of marine and terrestrial nitrous oxide through analysis of isotopic ratios, which fingerprint the different sources of N2O in the atmosphere.

“The scientific community knew roughly what the N2O concentration trends were prior to this study,” Brook said, “but these findings confirm that and provide more exact details about changes in sources. As nitrous oxide in the atmosphere continues to increase – along with carbon dioxide and methane – we now will be able to more accurately assess where those contributions are coming from and the rate of the increase.”

Atmospheric N2O was roughly 200 parts per billion at the peak of the ice age about 20,000 years ago then rose to 260 ppb by 10,000 years ago. As of 2014, atmospheric N2Owas measured at about 327 ppb, an increase attributed primarily to agricultural influences.

Although the N2O increase at the end of the last ice age was almost equally attributable to marine and terrestrial sources, the scientists say, there were some differences.

“Our data showed that terrestrial emissions changed faster than marine emissions, which was highlighted by a fast increase of emissions on land that preceded the increase in marine emissions,” Schilt pointed out. “It appears to be a direct response to a rapid temperature change between 15,000 and 14,000 years ago.”

That finding underscores the complexity of analyzing how Earth responds to changing conditions that have to account for marine and terrestrial influences; natural variability; the influence of different greenhouse gases; and a host of other factors, Brook said.

“Natural sources of N2O are predicted to increase in the future and this study will help up test predictions on how the Earth will respond,” Brook said.

Abandoned wells can be ‘super-emitters’ of greenhouse gas

One of the wells the researchers tested; this one in the Allegheny National Forest. -  Princeton University
One of the wells the researchers tested; this one in the Allegheny National Forest. – Princeton University

Princeton University researchers have uncovered a previously unknown, and possibly substantial, source of the greenhouse gas methane to the Earth’s atmosphere.

After testing a sample of abandoned oil and natural gas wells in northwestern Pennsylvania, the researchers found that many of the old wells leaked substantial quantities of methane. Because there are so many abandoned wells nationwide (a recent study from Stanford University concluded there were roughly 3 million abandoned wells in the United States) the researchers believe the overall contribution of leaking wells could be significant.

The researchers said their findings identify a need to make measurements across a wide variety of regions in Pennsylvania but also in other states with a long history of oil and gas development such as California and Texas.

“The research indicates that this is a source of methane that should not be ignored,” said Michael Celia, the Theodore Shelton Pitney Professor of Environmental Studies and professor of civil and environmental engineering at Princeton. “We need to determine how significant it is on a wider basis.”

Methane is the unprocessed form of natural gas. Scientists say that after carbon dioxide, methane is the most important contributor to the greenhouse effect, in which gases in the atmosphere trap heat that would otherwise radiate from the Earth. Pound for pound, methane has about 20 times the heat-trapping effect as carbon dioxide. Methane is produced naturally, by processes including decomposition, and by human activity such as landfills and oil and gas production.

While oil and gas companies work to minimize the amount of methane emitted by their operations, almost no attention has been paid to wells that were drilled decades ago. These wells, some of which date back to the 19th century, are typically abandoned and not recorded on official records.

Mary Kang, then a doctoral candidate at Princeton, originally began looking into methane emissions from old wells after researching techniques to store carbon dioxide by injecting it deep underground. While examining ways that carbon dioxide could escape underground storage, Kang wondered about the effect of old wells on methane emissions.

“I was looking for data, but it didn’t exist,” said Kang, now a postdoctoral researcher at Stanford.

In a paper published Dec. 8 in the Proceedings of the National Academy of Sciences, the researchers describe how they chose 19 wells in the adjacent McKean and Potter counties in northwestern Pennsylvania. The wells chosen were all abandoned, and records about the origin of the wells and their conditions did not exist. Only one of the wells was on the state’s list of abandoned wells. Some of the wells, which can look like a pipe emerging from the ground, are located in forests and others in people’s yards. Kang said the lack of documentation made it hard to tell when the wells were originally drilled or whether any attempt had been made to plug them.

“What surprised me was that every well we measured had some methane coming out,” said Celia.

To conduct the research, the team placed enclosures called flux chambers over the tops of the wells. They also placed flux chambers nearby to measure the background emissions from the terrain and make sure the methane was emitted from the wells and not the surrounding area.

Although all the wells registered some level of methane, about 15 percent emitted the gas at a markedly higher level — thousands of times greater than the lower-level wells. Denise Mauzerall, a Princeton professor and a member of the research team, said a critical task is to discover the characteristics of these super-emitting wells.

Mauzerall said the relatively low number of high-emitting wells could offer a workable solution: while trying to plug every abandoned well in the country might be too costly to be realistic, dealing with the smaller number of high emitters could be possible.

“The fact that most of the methane is coming out of a small number of wells should make it easier to address if we can identify the high-emitting wells,” said Mauzerall, who has a joint appointment as a professor of civil and environmental engineering and as a professor of public and international affairs at the Woodrow Wilson School.

The researchers have used their results to extrapolate total methane emissions from abandoned wells in Pennsylvania, although they stress that the results are preliminary because of the relatively small sample. But based on that data, they estimate that emissions from abandoned wells represents as much as 10 percent of methane from human activities in Pennsylvania — about the same amount as caused by current oil and gas production. Also, unlike working wells, which have productive lifetimes of 10 to 15 years, abandoned wells can continue to leak methane for decades.

“This may be a significant source,” Mauzerall said. “There is no single silver bullet but if it turns out that we can cap or capture the methane coming off these really big emitters, that would make a substantial difference.”

Besides Kang, who is the paper’s lead author, Celia and Mauzerall, the paper’s co-authors include: Tullis Onstott, a professor of geosciences at Princeton; Cynthia Kanno, who was a Princeton undergraduate and who is a graduate student at the Colorado School of Mines; Matthew Reid, who was a graduate student at Princeton and is a postdoctoral researcher at EPFL in Luzerne, Switzerland; Xin Zhang, a postdoctoral researcher in the Woodrow Wilson School at Princeton; and Yuheng Chen, an associate research scholar in geosciences at Princeton.

New study shows 3 abrupt pulse of CO2 during last deglaciation

A new study shows that the rise of atmospheric carbon dioxide that contributed to the end of the last ice age more than 10,000 years ago did not occur gradually, but was characterized by three “pulses” in which C02 rose abruptly.

Scientists are not sure what caused these abrupt increases, during which C02 levels rose about 10-15 parts per million – or about 5 percent per episode – over a period of 1-2 centuries. It likely was a combination of factors, they say, including ocean circulation, changing wind patterns, and terrestrial processes.

The finding is important, however, because it casts new light on the mechanisms that take the Earth in and out of ice age regimes. Results of the study, which was funded by the National Science Foundation, appear this week in the journal Nature.

“We used to think that naturally occurring changes in carbon dioxide took place relatively slowly over the 10,000 years it took to move out of the last ice age,” said Shaun Marcott, lead author on the article who conducted his study as a post-doctoral researcher at Oregon State University. “This abrupt, centennial-scale variability of CO2 appears to be a fundamental part of the global carbon cycle.”

Some previous research has hinted at the possibility that spikes in atmospheric carbon dioxide may have accelerated the last deglaciation, but that hypothesis had not been resolved, the researchers say. The key to the new finding is the analysis of an ice core from the West Antarctic that provided the scientists with an unprecedented glimpse into the past.

Scientists studying past climate have been hampered by the limitations of previous ice cores. Cores from Greenland, for example, provide unique records of rapid climate events going back 120,000 years – but high concentrations of impurities don’t allow researchers to accurately determine atmospheric carbon dioxide records. Antarctic ice cores have fewer impurities, but generally have had lower “temporal resolution,” providing less detailed information about atmospheric CO2.

However, a new core from West Antarctica, drilled to a depth of 3,405 meters in 2011 and spanning the last 68,000 years, has “extraordinary detail,” said Oregon State paleoclimatologist Edward Brook, a co-author on the Nature study and an internationally recognized ice core expert. Because the area where the core was taken gets high annual snowfall, he said, the new ice core provides one of the most detailed records of atmospheric CO2.

“It is a remarkable ice core and it clearly shows distinct pulses of carbon dioxide increase that can be very reliably dated,” Brook said. “These are some of the fastest natural changes in CO2 we have observed, and were probably big enough on their own to impact the Earth’s climate.

“The abrupt events did not end the ice age by themselves,” Brook added. “That might be jumping the gun a bit. But it is fair to say that the natural carbon cycle can change a lot faster than was previously thought – and we don’t know all of the mechanisms that caused that rapid change.”

The researchers say that the increase in atmospheric CO2 from the peak of the last ice age to complete deglaciation was about 80 parts per million, taking place over 10,000 years. Thus, the finding that 30-45 ppm of the increase happened in just a few centuries was significant.

The overall rise of atmospheric carbon dioxide during the last deglaciation was thought to have been triggered by the release of CO2 from the deep ocean – especially the Southern Ocean. However, the researchers say that no obvious ocean mechanism is known that would trigger rises of 10-15 ppm over a time span as short as one to two centuries.

“The oceans are simply not thought to respond that fast,” Brook said. “Either the cause of these pulses is at least part terrestrial, or there is some mechanism in the ocean system we don’t yet know about.”

One reason the researchers are reluctant to pin the end of the last ice age solely on CO2 increases is that other processes were taking place, according to Marcott, who recently joined the faculty of the University of Wisconsin-Madison.

“At the same time CO2 was increasing, the rate of methane in the atmosphere was also increasing at the same or a slightly higher rate,” Marcott said. “We also know that during at least two of these pulses, the Atlantic Meridional Overturning Circulation changed as well. Changes in the ocean circulation would have affected CO2 – and indirectly methane, by impacting global rainfall patterns.”

“The Earth is a big coupled system,” he added, “and there are many pieces to the puzzle. The discovery of these strong, rapid pulses of CO2 is an important piece.”

Past climate change and continental ice melt linked to varying CO2 levels

Scientists at the Universities of Southampton and Cardiff have discovered that a globally warm period in Earth’s geological past featured highly variable levels of CO2.

Previous studies have found that the Miocene climatic optimum, a period that extends from about 15 to 17 million years ago, was associated with big changes in both temperature and the amount of continental ice on the planet.

Now a new study, published in Paleoceanography, has found that these changes in temperature and ice volume were matched by equally dramatic shifts in atmospheric CO2.

Using more detailed records than has previously been available, scientists have shown that CO2 levels in this period reached around 500 ppm (parts per million), the same level that the Intergovernmental Panel on Climate Change (IPPC) projects for the end of the century.

Lead author Rosanna Greenop, from Ocean and Earth Science at the University of Southampton, says: “The drivers of short term, orbital-scale temperature and ice volume change during warm periods of the Earth’s history have never been analysed before. Here we are able to show that in the same way as the more recent ice ages are linked with cycles of CO2, it also plays an important role in cyclical climate changes during warm periods.

Researchers also showed that at low levels of CO2, ice volume varied strongly, but at higher levels, there was little or no additional change in volume. The authors of the study hypothesis that there must be a portion of the East Antarctic ice sheet that varies in volume at the lower end of the CO2 range. However, the absence of additional ice melt at higher CO2 levels suggests that there is also a portion of the ice sheet that remains stable at the maximum CO2 levels.

Evidence suggests that the northern Hemisphere and West Antarctic ice sheets did not exist during the warm Miocene climatic optimum.

“While we recognise that the Miocene climatic optimum is not a perfect analogue for our own warm future, the geological past does represent an actual reality that the Earth system experienced,” says the University of Southampton’s Dr Gavin Foster, co-author of the study. “As such the findings of this study have large implications for the stability of the continental ice sheets in the future. They indicate that portions of the East Antarctic ice sheet can act in a dynamic fashion, growing and shrinking in response to climate forcing.”

Co-author Caroline Lear, of Cardiff University, adds: “We tend to think of the Antarctic ice sheet as a sluggish ice sheet, but these records show that in past warm climates it has been surprisingly sensitive to natural variations in carbon dioxide levels.

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 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: 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 ( and registration will be opened in the first week of November.

Asian monsoon much older than previously thought

University of Arizona geoscientist Alexis Licht (bottom left) and his colleagues from the French-Burmese Paleontological Team led by Jean-Jacques Jaeger of the University of Poitiers, France (center with hiking staff) used fossils they collected in Myanmar to figure out that the Asian monsoon started at least 40 million years ago. -  French-Burmese Paleontological Team 2012
University of Arizona geoscientist Alexis Licht (bottom left) and his colleagues from the French-Burmese Paleontological Team led by Jean-Jacques Jaeger of the University of Poitiers, France (center with hiking staff) used fossils they collected in Myanmar to figure out that the Asian monsoon started at least 40 million years ago. – French-Burmese Paleontological Team 2012

The Asian monsoon already existed 40 million years ago during a period of high atmospheric carbon dioxide and warmer temperatures, reports an international research team led by a University of Arizona geoscientist.

Scientists thought the climate pattern known as the Asian monsoon began 22-25 million years ago as a result of the uplift of the Tibetan Plateau and the Himalaya Mountains.

“It is surprising,” said lead author Alexis Licht, now a research associate in the UA department of geosciences. “People thought the monsoon started much later.”

The monsoon, the largest climate system in the world, governs the climate in much of mainland Asia, bringing torrential summer rains and dry winters.

Co-author Jay Quade, a UA professor of geosciences, said, “This research compellingly shows that a strong Asian monsoon system was in place at least by 35-40 million years ago.”

The research by Licht and his colleagues shows the earlier start of the monsoon occurred at a time when atmospheric CO2 was three to four times greater than it is now. The monsoon then weakened 34 million years ago when atmospheric CO2 then decreased by 50 percent and an ice age occurred.

Licht said the study is the first to show the rise of the monsoon is as much a result of global climate as it is a result of topography. The team’s paper is scheduled for early online publication in the journal Nature on Sept. 14.

“This finding has major consequences for the ongoing global warming,” he said. “It suggests increasing the atmospheric CO2 will increase the monsoonal precipitation significantly.”

Unraveling the monsoon’s origins required contributions from three different teams of scientists that were independently studying the environment of 40 million years ago.

All three investigations showed the monsoon climate pattern occurred 15 million years earlier than previously thought. Combining different lines of evidence from different places strengthened the group’s confidence in the finding, Licht said. The climate modeling team also linked the development of the monsoon to the increased CO2 of the time.

Licht and his colleagues at Poitiers and Nancy universities in France examined snail and mammal fossils in Myanmar. The group led by G. Dupont-Nivet and colleagues at Utrecht University in the Netherlands studied lake deposits in Xining Basin in central China. J.-B. Ladant and Y. Donnadieu of the Laboratory of Sciences of the Climate and Environment (LSCE) in Gif-sur-Yvette, France, created climate simulations of the Asian climate 40 million years ago.

A complete list of authors of the group’s publication, “Asian monsoons in a late Eocene greenhouse world,” is at the bottom of this release, as is a list of funding sources.

Licht didn’t set out to study the origin of the monsoon.

He chose his study site in Myanmar because the area was rich in mammal fossils, including some of the earliest ancestors of modern monkeys and apes. The research, part of his doctoral work at the University of Poitiers, focused on understanding the environments those early primates inhabited. Scientists thought those primates had a habitat like the current evergreen tropical rain forests of Borneo, which do not have pronounced differences between wet and dry seasons.

To learn about the past environment, Licht analyzed 40-million-year-old freshwater snail shells and teeth of mammals to see what types of oxygen they contained. The ratio of two different forms of oxygen, oxygen-18 and oxygen-16, shows whether the animal lived in a relatively wet climate or an arid one.

“One of the goals of the study was to document the pre-monsoonal conditions, but what we found were monsoonal conditions,” he said.

To his surprise, the oxygen ratios told an unexpected story: The region had a seasonal pattern very much like the current monsoon – dry winters and very rainy summers.

“The early primates of Myanmar lived under intense seasonal stress – aridity and then monsoons,” he said. “That was completely unexpected.”

The team of researchers working in China found another line of evidence pointing to the existence of the monsoon about 40 million years ago. The monsoon climate pattern generates winter winds that blow dust from central Asia and deposits it in thick piles in China. The researchers found deposits of such dust dating back 41 million years ago, indicating the monsoon had occurred that long ago.

The third team’s climate simulations indicated strong Asian monsoons 40 million years ago. The simulations showed the level of atmospheric CO2 was connected to the strength of the monsoon, which was stronger 40 million years ago when CO2 levels were higher and weakened 34 million years ago when CO2 levels dropped.

Licht’s next step is to investigate how geologically short-term increases of atmospheric CO2 known as hyperthermals affected the monsoon’s behavior 40 million years ago.

“The response of the monsoon to those hyperthermals could provide interesting analogs to the ongoing global warming,” he said.

Past temperature in Greenland adjusted

The revised Greenland temperature history (black curve, grey uncertainties) for the period 18,000 to 10,000 before present. This temperature history is based on temperature interpretation from nitrogen measurements (green curve) and O18 diffusion measurements (red curve). The blue curve is from a previous study, based on nitrogen measurements. -  Niels Bohr Institute
The revised Greenland temperature history (black curve, grey uncertainties) for the period 18,000 to 10,000 before present. This temperature history is based on temperature interpretation from nitrogen measurements (green curve) and O18 diffusion measurements (red curve). The blue curve is from a previous study, based on nitrogen measurements. – Niels Bohr Institute

One of the common perceptions about the climate is that the amount of carbon dioxide in the atmosphere, solar radiation and temperature follow each other – the more solar radiation and the more carbon dioxide, the hotter the temperature. This correlation is also seen in the Greenland ice cores that are drilled through the approximately three kilometer thick ice sheet. But during a period of several thousand years up until the last ice age ended approximately 12,000 years ago, this pattern did not fit and this was a mystery to researchers. Now researchers from the Niels Bohr Institute have solved this mystery using new analytical techniques. The results are published in the prestigious scientific journal Science.

The Greenland ice sheet is an archive of knowledge about the Earth’s climate more than 125,000 years back in time. The ice was formed by the precipitation that fell as snow from the clouds and remained year after year, gradually being compressed into ice. By drilling down through the approximately three kilometer thick ice sheet, the researchers draw up ice cores, which provide detailed knowledge of the climate of the past annual layer after annual layer. By measuring the content of the special oxygen isotope O18 in the ice cores, you can get information about the temperature in the past climate, year by year.

But something didn’t fit. In Greenland, the end of the Ice Age started 15,000 years ago and the temperature rose quickly. Then it became colder again until 12,000 years ago, when there was again a rapid rise in temperature. The first rise in temperature is called the Bølling-Allerød interstadial and the second is called the Holocene interglacial.

Temperatures contrary to expectations

“We could see that the concentration of carbon dioxide and solar radiation was higher during the cold period between the two warm periods compared with the cold period before the first warming 15,000 years ago. But the temperature measurements based on the oxygen isotope O18 showed that the period between the two warm periods was colder than the cold period before the first warming 15,000 years ago. This was the exact opposite of what you would expect,” explains postdoc Vasileios Gkinis, Centre for Ice and Climate, Niels Bohr Institute, University of Copenhagen.

The researchers investigated ice cores from three different Greenland ice cores: the NEEM project, the NGRIP project and the GISP 2 project. But amount of the oxygen isotope O18 was not enough to reconstruct period temperatures in detail or their geographic distribution.

To get more detailed temperature data, the researchers used two relatively new methods of investigation, both of which examine the layer of compressed granular snow that is formed between the top layer of soft and fluffy snow and the layer deeper down in the ice sheet, where the compressed snow has been turned into ice. This process of transforming the fluffy snow into hard ice is physical and both the thickness and the movement of the water molecules are dependent on the temperature.

“With the first method, we measured the nitrogen content and by measuring the relationship between the two isotopes of nitrogen, N15 and N14, we could reconstruct the thickness of the compressed snow 19,000 years back in time,” explains Vasileios Gkinis.

The second method involved measuring the spread of air with water molecules with different isotope composition in the layers with the compressed snow. This process of smoothing the original water isotope variations from precipitation is dependent on the temperature, as the water molecules in vapour form are more mobile at warmer temperatures.

Temperatures ‘fall into place’

Data for the spread of the water molecules in the individual annual layers in the Greenland ice cores has thus made it possible to calculate the temperature in the layers with compressed snow 19,000 years back in time.

“What we discovered was that the previous temperature curve, which was only based on the measurements of the oxygen isotope O18, was inaccurate. The oxygen temperature curve said that the climate in central Greenland was colder around 12,000 years ago than around 15,000 years ago, despite the fact that two key climate drivers – carbon dioxide in the atmosphere and solar radiation – would suggest the opposite. With our new, more direct reconstruction, we have been able to show that the climate in central Greenland was actually warmer around 12,000 years ago compared to 15,000 years ago. So the temperatures actually follow the solar radiation and the amount of carbon dioxide in the atmosphere. We estimate that the temperature difference was 2-6 degrees,” says Bo Vinther, Associate Professor at the Centre for Ice and Climate at the Niels Bohr Institute, University of Copenhagen.

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.

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

Trinity geologists re-write Earth’s evolutionary history books

The study site landscape is shown with boulders of the paleosol in the foreground. -  Quentin Crowley
The study site landscape is shown with boulders of the paleosol in the foreground. – Quentin Crowley

Geologists from Trinity College Dublin have rewritten the evolutionary history books by finding that oxygen-producing life forms were present on Earth some 3 billion years ago – a full 60 million years earlier than previously thought. These life forms were responsible for adding oxygen (O2) to our atmosphere, which laid the foundations for more complex life to evolve and proliferate.

Working with Professors Joydip Mukhopadhyay and Gautam Ghosh and other colleagues from the Presidency University in Kolkata, India, the geologists found evidence for chemical weathering of rocks leading to soil formation that occurred in the presence of O2. Using the naturally occurring uranium-lead isotope decay system, which is used for age determinations on geological time-scales, the authors deduced that these events took place at least 3.02 billion years ago. The ancient soil (or paleosol) came from the Singhbhum Craton of Odisha, and was named the ‘Keonjhar Paleosol’ after the nearest local town.

The pattern of chemical weathering preserved in the paleosol is compatible with elevated atmospheric O2 levels at that time. Such substantial levels of oxygen could only have been produced by organisms converting light energy and carbon dioxide to O2 and water. This process, known as photosynthesis, is used by millions of different plant and bacteria species today. It was the proliferation of such oxygen-producing species throughout Earth’s evolutionary trajectory that changed the composition of our atmosphere – adding much more O2 – which was as important for the development of ancient multi-cellular life as it is for us today.

Quentin Crowley, Ussher Assistant Professor in Isotope Analysis and the Environment in the School of Natural Sciences at Trinity, is senior author of the journal article that describes this research which has just been published online in the world’s top-ranked Geology journal, Geology. He said: “This is a very exciting finding, which helps to fill a gap in our knowledge about the evolution of the early Earth. This paleosol from India is telling us that there was a short-lived pulse of atmospheric oxygenation and this occurred considerably earlier than previously envisaged.”

The early Earth was very different to what we see today. Our planet’s early atmosphere was rich in methane and carbon dioxide and had only very low levels of O2. The widely accepted model for evolution of the atmosphere states that O2 levels did not appreciably rise until about 2.4 billion years ago. This ‘Great Oxidation Event’ event enriched the atmosphere and oceans with O2, and heralded one of the biggest shifts in evolutionary history.

Micro-organisms were certainly present before 3.0 billion years ago but they were not likely capable of producing O2 by photosynthesis. Up until very recently however, it has been unclear if any oxygenation events occurred prior to the Great Oxidation Event and the argument for an evolutionary capability of photosynthesis has largely been based on the first signs of an oxygen build-up in the atmosphere and oceans.

“It is the rare examples from the rock record that provide glimpses of how rocks weathered,” added Professor Crowley. “The chemical changes which occur during this weathering tell us something about the composition of the atmosphere at that time. Very few of these ‘paleosols’ have been documented from a period of Earth’s history prior to 2.5 billion years ago. The one we worked on is at least 3.02 billion years old, and it shows chemical evidence that weathering took place in an atmosphere with elevated O2 levels.”

There was virtually no atmospheric O2 present 3.4 billion years ago, but recent work from South African paleosols suggested that by about 2.96 billion years ago O2 levels may have begun to increase. Professor Crowley’s finding therefore moves the goalposts back at least 60 million years, which, given humans have only been on the planet for around a tenth of that time, is not an insignificant drop in the evolutionary ocean.

Professor Crowley concluded: “Our research gives further credence to the notion of early and short-lived atmospheric oxygenation.

This particular example is the oldest known example of oxidative weathering from a terrestrial environment, occurring about 600 million years before the Great Oxidation Event that laid the foundations for the evolution of complex life.”

Antarctic ice sheet is result of CO2 decrease, not continental breakup

Climate modelers from the University of New Hampshire have shown that the most likely explanation for the initiation of Antarctic glaciation during a major climate shift 34 million years ago was decreased carbon dioxide (CO2) levels. The finding counters a 40-year-old theory suggesting massive rearrangements of Earth’s continents caused global cooling and the abrupt formation of the Antarctic ice sheet. It will provide scientists insight into the climate change implications of current rising global CO2 levels.

In a paper published today in Nature, Matthew Huber of the UNH Institute for the Study of Earth, Oceans, and Space and department of Earth sciences provides evidence that the long-held, prevailing theory known as “Southern Ocean gateway opening” is not the best explanation for the climate shift that occurred during the Eocene-Oligocene transition when Earth’s polar regions were ice-free.

“The Eocene-Oligocene transition was a major event in the history of the planet and our results really flip the whole story on its head,” says Huber. “The textbook version has been that gateway opening, in which Australia pulled away from Antarctica, isolated the polar continent from warm tropical currents, and changed temperature gradients and circulation patterns in the ocean around Antarctica, which in turn began to generate the ice sheet. We’ve shown that, instead, CO2-driven cooling initiated the ice sheet and that this altered ocean circulation.”

Huber adds that the gateway theory has been supported by a specific, unique piece of evidence-a “fingerprint” gleaned from oxygen isotope records derived from deep-sea sediments. These sedimentary records have been used to map out gradient changes associated with ocean circulation shifts that were thought to bear the imprint of changes in ocean gateways.

Although declining atmospheric levels of CO2 has been the other main hypothesis used to explain the Eocene-Oligocene transition, previous modeling efforts were unsuccessful at bearing this out because the CO2 drawdown does not by itself match the isotopic fingerprint. It occurred to Huber’s team that the fingerprint might not be so unique and that it might also have been caused indirectly from CO2 drawdown through feedbacks between the growing Antarctic ice sheet and the ocean.

Says Huber, “One of the things we were always missing with our CO2 studies, and it had been missing in everybody’s work, is if conditions are such to make an ice sheet form, perhaps the ice sheet itself is affecting ocean currents and the climate system-that once you start getting an ice sheet to form, maybe it becomes a really active part of the climate system and not just a passive player.”

For their study, Huber and colleagues used brute force to generate results: they simply modeled the Eocene-Oligocene world as if it contained an Antarctic ice sheet of near-modern size and shape and explored the results within the same kind of coupled ocean-atmosphere model used to project future climate change and across a range of CO2 values that are likely to occur in the next 100 years (560 to 1200 parts per million).

“It should be clear that resolving these two very different conceptual models for what caused this huge transformation of the Earth’s surface is really important because today as a global society we are, as I refer to it, dialing up the big red knob of carbon dioxide but we’re not moving continents around.”

Just what caused the sharp drawdown of CO2 is unknown, but Huber points out that having now resolved whether gateway opening or CO2 decline initiated glaciation, more pointed scientific inquiry can be focused on answering that question.

Huber notes that despite his team’s finding, the gateway opening theory won’t now be shelved, for that massive continental reorganization may have contributed to the CO2 drawdown by changing ocean circulation patterns that created huge upwellings of nutrient-rich waters containing plankton that, upon dying and sinking, took vast loads of carbon with them to the bottom of the sea.