New study measures methane emissions from natural gas production and offers insights into 2 large sources

A team of researchers from the Cockrell School of Engineering at The University of Texas at Austin and environmental testing firm URS reports that a small subset of natural gas wells are responsible for the majority of methane emissions from two major sources — liquid unloadings and pneumatic controller equipment — at natural gas production sites.

With natural gas production in the United States expected to continue to increase during the next few decades, there is a need for a better understanding of methane emissions during natural gas production. The study team believes this research, published Dec. 9 in Environmental Science & Technology, will help to provide a clearer picture of methane emissions from natural gas production sites.

The UT Austin-led field study closely examined two major sources of methane emissions — liquid unloadings and pneumatic controller equipment — at well pad sites across the United States. Researchers found that 19 percent of the pneumatic devices accounted for 95 percent of the emissions from pneumatic devices, and 20 percent of the wells with unloading emissions that vent to the atmosphere accounted for 65 percent to 83 percent of those emissions.

“To put this in perspective, over the past several decades, 10 percent of the cars on the road have been responsible for the majority of automotive exhaust pollution,” said David Allen, chemical engineering professor at the Cockrell School and principal investigator for the study. “Similarly, a small group of sources within these two categories are responsible for the vast majority of pneumatic and unloading emissions at natural gas production sites.”

Additionally, for pneumatic devices, the study confirmed regional differences in methane emissions first reported by the study team in 2013. The researchers found that methane emissions from pneumatic devices were highest in the Gulf Coast and lowest in the Rocky Mountains.

The study is the second phase of the team’s 2013 study, which included some of the first measurements for methane emissions taken directly at hydraulically fractured well sites. Both phases of the study involved a partnership between the Environmental Defense Fund, participating energy companies, an independent Scientific Advisory Panel and the UT Austin study team.

The unprecedented access to natural gas production facilities and equipment allowed researchers to acquire direct measurements of methane emissions.

Study and Findings on Pneumatic Devices

Pneumatic devices, which use gas pressure to control the opening and closing of valves, emit gas as they operate. These emissions are estimated to be among the larger sources of methane emissions from the natural gas supply chain. The Environmental Protection Agency reports that 477,606 pneumatic (gas actuated) devices are in use at natural gas production sites throughout the U.S.

“Our team’s previous work established that pneumatics are a major contributor to emissions,” Allen said. “Our goal here was to measure a more diverse population of wells to characterize the features of high-emitting pneumatic controllers.”

The research team measured emissions from 377 gas actuated (pneumatic) controllers at natural gas production sites and a small number of oil production sites throughout the U.S.

The researchers sampled all identifiable pneumatic controller devices at each well site, a more comprehensive approach than the random sampling previously conducted. The average methane emissions per pneumatic controller reported in this study are 17 percent higher than the average emissions per pneumatic controller in the 2012 EPA greenhouse gas national emission inventory (released in 2014), but the average from the study is dominated by a small subpopulation of the controllers. Specifically, 19 percent of controllers, with measured emission rates in excess of 6 standard cubic feet per hour (scf/h), accounted for 95 percent of emissions.

The high-emitting pneumatic devices are a combination of devices that are not operating as designed, are used in applications that cause them to release gas frequently or are designed to emit continuously at a high rate.

The researchers also observed regional differences in methane emission levels, with the lowest emissions per device measured in the Rocky Mountains and the highest emissions in the Gulf Coast, similar to the earlier 2013 study. At least some of the regional differences in emission rates can be attributed to the difference in controller type (continuous vent vs. intermittent vent) among regions.

Study and Findings on Liquid Unloadings

After observing variable emissions for liquid unloadings for a limited group of well types in the 2013 study, the research team made more extensive measurements and confirmed that a majority of emissions come from a small fraction of wells that vent frequently. Although it is not surprising to see some correlation between frequency of unloadings and higher annual emissions, the study’s findings indicate that wells with a high frequency of unloadings have annual emissions that are 10 or more times as great as wells that unload less frequently.

The team’s field study, which measured emissions from unloadings from wells at 107 natural gas production wells throughout the U.S., represents the most extensive measurement of emissions associated with liquid unloadings in scientific literature thus far.

A liquid unloading is one method used to clear wells of accumulated liquids to increase production. Because older wells typically produce less gas as they near the end of their life cycle, liquid unloadings happen more often in those wells than in newer wells. The team found a statistical correlation between the age of wells and the frequency of liquid unloadings. The researchers found that the key identifier for high-emitting wells is how many times the well unloads in a given year.

Because liquid unloadings can employ a variety of liquid lifting mechanisms, the study results also reflect differences in liquid unloadings emissions between wells that use two different mechanisms (wells with plunger lifts and wells without plunger lifts). Emissions for unloading events for wells without plunger lifts averaged 21,000 scf (standard cubic feet) to 35,000 scf. For wells with plunger lifts that vent to the atmosphere, emissions averaged 1,000 scf to 10,000 scf of methane per event. Although the emissions per event were higher for wells without plunger lifts, these wells had, on average, fewer events than wells with plunger lifts. Wells without plunger lifts averaged fewer than 10 unloading events per year, and wells with plunger lifts averaged more than 200 events per year.Overall, wells with plunger lifts were estimated to account for 70 percent of emissions from unloadings nationally.

Additionally, researchers found that the Rocky Mountain region, with its large number of wells with a high frequency of unloadings that vent to the atmosphere, accounts for about half of overall emissions from liquid unloadings.

The study team hopes its measurements of liquid unloadings and pneumatic devices will provide a clearer picture of methane emissions from natural gas well sites and about the relationship between well characteristics and emissions.

The study was a cooperative effort involving experts from the Environmental Defense Fund, Anadarko Petroleum Corporation, BG Group PLC, Chevron, ConocoPhillips, Encana Oil & Gas (USA) Inc., Pioneer Natural Resources Company, SWEPI LP (Shell), Statoil, Southwestern Energy and XTO Energy, a subsidiary of ExxonMobil.

The University of Texas at Austin is committed to transparency and disclosure of all potential conflicts of interest of its researchers. Lead researcher David Allen serves as chair of the Environmental Protection Agency’s Science Advisory Board and in this role is a paid Special Governmental Employee. He is also a journal editor for the American Chemical Society and has served as a consultant for multiple companies, including Eastern Research Group, ExxonMobil and the Research Triangle Institute. He has worked on other research projects funded by a variety of governmental, nonprofit and private sector sources including the National Science Foundation, the Environmental Protection Agency, the Texas Commission on Environmental Quality, the American Petroleum Institute and an air monitoring and surveillance project that was ordered by the U.S. District Court for the Southern District of Texas. Adam Pacsi and Daniel Zavala-Araiza, who were graduate students at The University of Texas at the time this work was done, have accepted positions at Chevron Energy Technology Company and the Environmental Defense Fund, respectively.

Financial support for this work was provided by the Environmental Defense Fund (EDF), Anadarko Petroleum Corporation, BG Group PLC, Chevron, ConocoPhillips, Encana Oil & Gas (USA) Inc., Pioneer Natural Resources Company, SWEPI LP (Shell), Statoil, Southwestern Energy and XTO Energy, a subsidiary of ExxonMobil.

Major funding for the EDF’s 30-month methane research series, including their portion of the University of Texas study, is provided for by the following individuals and foundations: Fiona and Stan Druckenmiller, the Heising-Simons Foundation, Bill and Susan Oberndorf, Betsy and Sam Reeves, the Robertson Foundation, TomKat Charitable Trust and the Walton Family Foundation.

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.

Rare 2.5-billion-year-old rocks reveal hot spot of sulfur-breathing bacteria

Gold miners prospecting in a mountainous region of Brazil drilled this 590-foot cylinder of bedrock from the Neoarchaean Eon, which provides rare evidence of conditions on Earth 2.5 billion years ago. -  Alan J. Kaufman
Gold miners prospecting in a mountainous region of Brazil drilled this 590-foot cylinder of bedrock from the Neoarchaean Eon, which provides rare evidence of conditions on Earth 2.5 billion years ago. – Alan J. Kaufman

Wriggle your toes in a marsh’s mucky bottom sediment and you’ll probably inhale a rotten egg smell, the distinctive odor of hydrogen sulfide gas. That’s the biochemical signature of sulfur-using bacteria, one of Earth’s most ancient and widespread life forms.

Among scientists who study the early history of our 4.5 billion-year-old planet, there is a vigorous debate about the evolution of sulfur-dependent bacteria. These simple organisms arose at a time when oxygen levels in the atmosphere were less than one-thousandth of what they are now. Living in ocean waters, they respired (or breathed in) sulfate, a form of sulfur, instead of oxygen. But how did that sulfate reach the ocean, and when did it become abundant enough for living things to use it?

New research by University of Maryland geology doctoral student Iadviga Zhelezinskaia offers a surprising answer. Zhelezinskaia is the first researcher to analyze the biochemical signals of sulfur compounds found in 2.5 billion-year-old carbonate rocks from Brazil. The rocks were formed on the ocean floor in a geologic time known as the Neoarchaean Eon. They surfaced when prospectors drilling for gold in Brazil punched a hole into bedrock and pulled out a 590-foot-long core of ancient rocks.

In research published Nov. 7, 2014 in the journal Science, Zhelezinskaia and three co-authors–physicist John Cliff of the University of Western Australia and geologists Alan Kaufman and James Farquhar of UMD–show that bacteria dependent on sulfate were plentiful in some parts of the Neoarchaean ocean, even though sea water typically contained about 1,000 times less sulfate than it does today.

“The samples Iadviga measured carry a very strong signal that sulfur compounds were consumed and altered by living organisms, which was surprising,” says Farquhar. “She also used basic geochemical models to give an idea of how much sulfate was in the oceans, and finds the sulfate concentrations are very low, much lower than previously thought.”

Geologists study sulfur because it is abundant and combines readily with other elements, forming compounds stable enough to be preserved in the geologic record. Sulfur has four naturally occurring stable isotopes–atomic signatures left in the rock record that scientists can use to identify the elements’ different forms. Researchers measuring sulfur isotope ratios in a rock sample can learn whether the sulfur came from the atmosphere, weathering rocks or biological processes. From that information about the sulfur sources, they can deduce important information about the state of the atmosphere, oceans, continents and biosphere when those rocks formed.

Farquhar and other researchers have used sulfur isotope ratios in Neoarchaean rocks to show that soon after this period, Earth’s atmosphere changed. Oxygen levels soared from just a few parts per million to almost their current level, which is around 21 percent of all the gases in the atmosphere. The Brazilian rocks Zhelezinskaia sampled show only trace amounts of oxygen, a sign they were formed before this atmospheric change.

With very little oxygen, the Neoarchaean Earth was a forbidding place for most modern life forms. The continents were probably much drier and dominated by volcanoes that released sulfur dioxide, carbon dioxide, methane and other greenhouse gases. Temperatures probably ranged between 0 and 100 degrees Celsius (32 to 212 degrees Fahrenheit), warm enough for liquid oceans to form and microbes to grow in them.

Rocks 2.5 billion years old or older are extremely rare, so geologists’ understanding of the Neoarchaean are based on a handful of samples from a few small areas, such as Western Australia, South Africa and Brazil. Geologists theorize that Western Australia and South Africa were once part of an ancient supercontinent called Vaalbara. The Brazilian rock samples are comparable in age, but they may not be from the same supercontinent, Zhelezinskaia says.

Most of the Neoarchaean rocks studied are from Western Australia and South Africa and are black shale, which forms when fine dust settles on the sea floor. The Brazilian prospector’s core contains plenty of black shale and a band of carbonate rock, formed below the surface of shallow seas, in a setting that probably resembled today’s Bahama Islands. Black shale usually contains sulfur-bearing pyrite, but carbonate rock typically does not, so geologists have not focused on sulfur signals in Neoarchaean carbonate rocks until now.

Zhelezinskaia “chose to look at a type of rock that others generally avoided, and what she saw was spectacularly different,” said Kaufman. “It really opened our eyes to the implications of this study.”

The Brazilian carbonate rocks’ isotopic ratios showed they formed in ancient seabed containing sulfate from atmospheric sources, not continental rock. And the isotopic ratios also showed that Neoarchaean bacteria were plentiful in the sediment, respiring sulfate and emitted hydrogen sulfide–the same process that goes on today as bacteria recycle decaying organic matter into minerals and gases.

How could the sulfur-dependent bacteria have thrived during a geologic time when sulfur levels were so low? “It seems that they were in shallow water, where evaporation may have been high enough to concentrate the sulfate, and that would make it abundant enough to support the bacteria,” says Zhelezinskaia.

Zhelezinskaia is now analyzing carbonate rocks of the same age from Western Australia and South Africa, to see if the pattern holds true for rocks formed in other shallow water environments. If it does, the results may change scientists’ understanding of one of Earth’s earliest biological processes.

“There is an ongoing debate about when sulfate-reducing bacteria arose and how that fits into the evolution of life on our planet,” says Farquhar. “These rocks are telling us the bacteria were there 2.5 billion years ago, and they were doing something significant enough that we can see them today.”


This research was supported by the Fulbright Program (Grantee ID 15110620), the NASA Astrobiology Institute (Grant No. NNA09DA81A) and the National Science Foundation Frontiers in Earth-System Dynamics program (Grant No. 432129). The content of this article does not necessarily reflect the views of these organizations.

“Large sulfur isotope fractionations associated with Neoarchaean microbial sulfate reductions,” Iadviga Zhelezinskaia, Alan J. Kaufman, James Farquhar and John Cliff, was published Nov. 7, 2014 in Science. Download the abstract after 2 p.m. U.S. Eastern time, Nov. 6, 2014:

James Farquhar home page

Alan J. Kaufman home page

Iadviga Zhelezinskaia home page

Media Relations Contact: Abby Robinson, 301-405-5845,

Writer: Heather Dewar

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.”

Scientists discover carbonate rocks are unrecognized methane sink

Since the first undersea methane seep was discovered 30 years ago, scientists have meticulously analyzed and measured how microbes in the seafloor sediments consume the greenhouse gas methane as part of understanding how the Earth works.

The sediment-based microbes form an important methane “sink,” preventing much of the chemical from reaching the atmosphere and contributing to greenhouse gas accumulation. As a byproduct of this process, the microbes create a type of rock known as authigenic carbonate, which while interesting to scientists was not thought to be involved in the processing of methane.

That is no longer the case. A team of scientists has discovered that these authigenic carbonate rocks also contain vast amounts of active microbes that take up methane. The results of their study, which was funded by the National Science Foundation, were reported today in the journal Nature Communications.

“No one had really examined these rocks as living habitats before,” noted Andrew Thurber, an Oregon State University marine ecologist and co-author on the paper. “It was just assumed that they were inactive. In previous studies, we had seen remnants of microbes in the rocks – DNA and lipids – but we thought they were relics of past activity. We didn’t know they were active.

“This goes to show how the global methane process is still rather poorly understood,” Thurber added.

Lead author Jeffrey Marlow of the California Institute of Technology and his colleagues studied samples from authigenic compounds off the coasts of the Pacific Northwest (Hydrate Ridge), northern California (Eel River Basin) and central America (the Costa Rica margin). The rocks range in size and distribution from small pebbles to carbonate “pavement” stretching dozens of square miles.

“Methane-derived carbonates represent a large volume within many seep systems and finding active methane-consuming archaea and bacteria in the interior of these carbonate rocks extends the known habitat for methane-consuming microorganisms beyond the relatively thin layer of sediment that may overlay a carbonate mound,” said Marlow, a geobiology graduate student in the lab of Victoria Orphan of Caltech.

These assemblages are also found in the Gulf of Mexico as well as off Chile, New Zealand, Africa, Europe – “and pretty much every ocean basin in the world,” noted Thurber, an assistant professor (senior research) in Oregon State’s College of Earth, Ocean, and Atmospheric Sciences.

The study is important, scientists say, because the rock-based microbes potentially may consume a huge amount of methane. The microbes were less active than those found in the sediment, but were more abundant – and the areas they inhabit are extensive, making their importance potential enormous. Studies have found that approximately 3-6 percent of the methane in the atmosphere is from marine sources – and this number is so low due to microbes in the ocean sediments consuming some 60-90 percent of the methane that would otherwise escape.

Now those ratios will have to be re-examined to determine how much of the methane sink can be attributed to microbes in rocks versus those in sediments. The distinction is important, the researchers say, because it is an unrecognized sink for a potentially very important greenhouse gas.

“We found that these carbonate rocks located in areas of active methane seeps are themselves more active,” Thurber said. “Rocks located in comparatively inactive regions had little microbial activity. However, they can quickly activate when methane becomes available.

“In some ways, these rocks are like armies waiting in the wings to be called upon when needed to absorb methane.”

The ocean contains vast amounts of methane, which has long been a concern to scientists. Marine reservoirs of methane are estimated to total more than 455 gigatons and may be as much as 10,000 gigatons carbon in methane. A gigaton is approximate 1.1 billion tons.

By contrast, all of the planet’s gas and oil deposits are thought to total about 200-300 gigatons of carbon.

A unique approach to monitoring groundwater supplies near Ohio fracking sites

This image shows a drilling rig in Carroll County, Ohio. -  Amy Townsend-Small
This image shows a drilling rig in Carroll County, Ohio. – Amy Townsend-Small

A University of Cincinnati research project is taking a groundbreaking approach to monitoring groundwater resources near fracking sites in Ohio. Claire Botner, a UC graduate student in geology, will outline the project at The Geological Society of America’s Annual Meeting & Exposition. The meeting takes place Oct. 19-22, in Vancouver.

Botner’s research is part of UC Groundwater Research of Ohio (GRO), a collaborative research project out of UC to examine the effects of fracking (hydraulic fracturing) on groundwater in the Utica Shale region of eastern Ohio. First launched in Carroll County in 2012, the GRO team of researchers is examining methane levels and origins of methane in private wells and springs before, during and after the onset of fracking. The team travels to the region to take water samples four times a year.

Amy Townsend-Small, the lead researcher for GRO and a UC assistant professor of geology, says the UC study is unique in comparison with studies on water wells in other shale-rich areas of the U.S. where fracking is taking place – such as the Marcellus Shale region of Pennsylvania.

Townsend-Small says water samples finding natural gas-derived methane in wells near Pennsylvania fracking sites were taken only after fracking had occurred, so methane levels in those wells were not documented prior to or during fracking in Pennsylvania.

Hydraulic fracturing, or fracking, involves using millions of gallons of water mixed with sand and chemicals to break up organic-rich shale to release natural gas resources.

Proponents say the practice promises a future in lower energy prices, an increase in domestic jobs and less dependence on foreign oil from unstable overseas governments.

Opponents raise concerns about increasing methane gas levels (a powerful greenhouse gas) and other contamination involving the spillover of fracking wastewater in the groundwater of shale-rich regions.

“The only way people with private groundwater will know whether or not their water is affected by fracking is through regular monitoring,” says Townsend-Small.

The Ohio samples are being analyzed by UC researchers for concentrations of methane as well as other hydrocarbons and salt, which is pulled up in the fracking water mixture from the shales. The shales are ancient ocean sediments.

Botner’s study involves testing on 22 private wells in Carroll County between November 2012 and last May. The first fracking permits were issued in the region in 2011. So far, results indicate that any methane readings in groundwater wells came from organic matter. In less than a handful of cases, the natural methane levels were relatively high, above 10 milligrams per liter. However, most of the wells carried low levels of methane.

The UC sampling has now been expanded into Columbiana, Harrison, Stark and Belmont counties in Ohio. Researchers then review data on private drinking water wells with the homeowners. “We’re working on interacting with these communities and educating them about fracking as well as gathering scientific data, which is lacking on a very sensitive issue,” says Botner. “It can also be reassuring to receive data on their water supplies from an objective, university resource.”

The team also is seeking additional funding to begin monitoring groundwater wells near wastewater injection wells, where fracking brine is deposited after the wells are drilled.


Funding for Botner’s research to be presented at the GSA meeting is supported by a grant from the Missouri-based Deer Creek Foundation.

Botner is among UC graduate students and faculty who are presenting more than two dozen research papers, PowerPoint presentations or poster exhibitions at the GSA meeting. The meeting draws geoscientists from around the world representing more than 40 different disciplines.

UC’s nationally ranked Department of Geology conducts field research around the world in areas spanning paleontology, Quaternary geology, geomorphology, sedimentology, stratigraphy, tectonics, environmental geology and biogeochemistry.

The Geological Society of America, founded in 1888, is a scientific society with more than 26,500 members from academia, government and industry in more than 100 countries. Through its meetings, publications and programs, GSA enhances the professional growth of its members and promotes the geosciences in the service of humankind.

Geologists dig into science around the globe, on land and at sea

University of Cincinnati geologists will be well represented among geoscientists from around the world at The Geological Society of America’s Annual Meeting and Exposition. The meeting takes place Oct. 19-22, in Vancouver, Canada, and will feature geoscientists representing more than 40 different disciplines. The meeting will feature highlights of UC’s geological research that is taking place globally, from Chile to Costa Rica, Belize, Bulgaria, Scotland, Trinidad and a new project under development in the Canary Islands.

UC faculty and graduate students are lead or supporting authors on more than two dozen Earth Sciences-related research papers and/or PowerPoint and poster exhibitions at the GSA meeting.

The presentations also cover UC’s longtime and extensive exploration and findings in the Cincinnati Arch of the Ohio Valley, world-renowned for its treasure trove of paleontology – plant and animal fossils that were preserved when a shallow sea covered the region 450 million years ago during the Paleozoic Era.

Furthermore, in an effort to diversify the field of researchers in the Earth Sciences, a UC assistant professor of science education and geology, Christopher Atchison, was awarded funding from the National Science Foundation and the Society of Exploration Geophysics to lead a research field trip in Vancouver for students with disabilities. Graduate and undergraduate student participants will conduct the research on Oct. 18 and then join events at the GSA meeting. They’ll be guided by geoscience researchers representing the United Kingdom, New Zealand, Canada and the U.S. Those guides include Atchison and Julie Hendricks, a UC special education major from Batavia, Ohio, who will be using her expertise in American Sign Language (ASL) to assist student researchers representing Deaf and Hard of Hearing communities.

The meeting will also formally introduce Arnold Miller, UC professor of geology, as the new president-elect of the national Paleontological Society Thomas Lowell, professor of geology, is a recently elected Fellow of the Geological Society of America – a recognition for producing a substantial body of research. Lowell joins colleagues Warren Huff, professor of geology, and Lewis Owen, professor and head of the Department of Geology, as GSA Fellows.

Here are highlights of the UC research to be presented at the GSA meeting Oct. 19-22:

Staying Put or Moving On? Researchers Develop Model to Identify Migrating Patterns of Different Species

Are plant and animal species what you might call lifelong residents – they never budge from the same place? That’s a relatively common belief in ecology and paleoecology – that classes of organisms tend to stay put over millions of years and either evolve or go extinct as the environment changes. UC researchers developed a series of numerical models simulating shifting habitats in fossil regions to compare whether species changed environments when factoring geological and other changes in the fossil record. They found that geologically driven changes in the quality of the fossil record did not distort the real ecological signal, and that most species maintained their particular habitat preferences through time. They did not evolve to adapt to changing environments, but rather, they migrated, following their preferred environments. That is to say, they did not stay in place geographically but by moving, they were able to track their favored habitats. Field research for the project was conducted in New York state as well as the paleontological-rich region of Cincinnati; Dayton, Ohio, Lexington, Ky.; and Indiana. Funding for the project was supported by The Paleontological Society; The Geological Society of America; The American Museum of Natural History and the UC Geology Department’s Kenneth E. Caster Memorial Fund.

Presenter: Andrew Zaffos, UC geology doctoral student

Co-authors: Arnold Miller, Carlton Brett

Pioneering Study Provides a Better Understanding of What Southern Ohio and Central Kentucky Looked Like Hundreds of Millions of Years Ago

The end of the Ordovician period resulted in one of the largest mass extinction events in the Earth’s history. T.J. Malgieri, a UC master’s student in geology, led this study examining the limestone and shales of the Upper Ordovician Period – the geologic Grant Lake Formation covering southern Ohio and central Kentucky – to recreate how the shoreline looked some 445 million years ago. In this pioneering study of mud cracks and deposits in the rocks, the researchers discovered that the shoreline existed to the south and that the water became deeper toward the north. By determining these ecological parameters, the ramp study provides a better understanding of environments during a time of significant ecological change. Malgieri says the approach can be applied to other basins throughout the world to create depth indicators in paeloenvironments.

Presenter: T.J. Malgieri, UC geology master’s student

Co-authors: Carlton Brett, Cameron Schalbach, Christopher Aucoin, UC; James Thomka (UC, University of Akron); Benjamin Dattilo, Indiana University Purdue University Ft. Wayne

UC Researchers Take a Unique Approach to Monitoring Groundwater Supplies Near Ohio Fracking Sites

A collaborative research project out of UC is examining effects of fracking on groundwater in the Utica Shale region of eastern Ohio. First launched in Carroll County in 2012, the team of researchers is examining methane levels and origins of methane in private wells and springs before, during and after the onset of fracking. The team travels to the region to take water samples four times a year.

Presenter: Claire Botner, a UC geology master’s student

Co-author: Amy Townsend-Small, UC assistant professor of geology

Sawing Through Seagrass to Reveal Clues to the Past

Kelsy Feser, a UC doctoral student in geology, is working at several sites around St. Croix in the Virgin Islands to see if human developments impact marine life. The research focuses on shells of snails and clams that have piled up on the sea floor for thousands of years. Digging through layers of thick seagrass beds on the ocean floor, Feser can examine deeper shells that were abundant thousands of years ago and compare them to shallower layers that include living clams and snails. Early analysis indicates a greater population of potentially pollution-tolerant mussels in an area near a landfill on the island, compared with shells from much earlier time periods. Feser is doing this sea grass analysis around additional sites including tourist resorts, an oil refinery, a power plant and a marina. Funding for the research is provided by the Paleontological Society, the GSA, the American Museum of Natural History and the UC Geology Department.

Presenter: Kelsy Feser, UC geology doctoral student

Co-authors: Arnold Miller

Turning to the Present to Understand the Past

In order to properly interpret changes in climate, vegetation, or animal populations over time, it is necessary to establish a comparative baseline. Stella Mosher, a UC geology master’s student, is studying stable carbon, nitrogen, sulfur and strontium isotopes in modern vegetation from the Canary Islands in order to quantify modern climatic and environmental patterns. Her findings will provide a crucial foundation for future UC research on regional paleoclimatic and paleoenvironmental shifts.

Presenter: Stella Mosher, graduate student in geology

Co-authors: Brooke Crowley, assistant professor of geology; Yurena Yanes, research assistant professor of geology

A Study on the Impact of Sea Spray

Sulfur is an element of interest in both geology and archaeology, because it can reveal information about the diets of ancient cultures. This study takes a novel approach to studying how sea spray can affect the sulfur isotope values in plants on a small island, focusing on the island of Trinidad. Researchers collected leaves from different plant species to get their sulfur isotope value, exploring whether wind direction played a role in how plants were influenced by the marine water from sea spray. Vegetation was collected from the edges of the island to the deeply forested areas. The study found that sulfur isotope values deeper inland and on the calmer west coast were dramatically lower in indicating marine water than vegetation along the edges and the east coast. The findings can help indicate the foraging activities of humans and animals. Funding for the study was supported by the Geological Society of America, the UC Graduate Student Association and the UC Department of Geology.

Presenter: Janine Sparks, UC geology doctoral student

Co-authors: Brooke Crowley, UC assistant professor, geology/anthropology; William Gilhooly III, assistant professor, Earth Sciences, Indiana University-Purdue University Indianapolis

Proxy Wars – The Paleobiology Data Debate

For the past several decades, paleobiologists have built large databases containing information on fossil plants and animals of all geological ages to investigate the timing and extent of major changes in biodiversity – changes such as mass extinctions that have taken place throughout the history of life. Biodiversity researcher Arnold Miller says that in building these databases, it can be a challenge to accurately identify species in the geological record, so it has been common for researchers to instead study biodiversity trends using data compiled at broader levels of biological classification, including the genus level, under the assumption that these patterns are effective proxies for what would be observed among species if the data were available. Miller has been involved in construction of The Paleobiology Database, an extensive public online resource that contains global genus- and species-level data, now permitting a direct, novel look at the similarities and differences between patterns at these two levels. Miller’s discussion aims to set the record straight as to when researchers can effectively use a genus as a proxy for a species and also when it’s inappropriate. This research is funded by the NASA Astrobiology Program.

Presenter: Arnold Miller, UC professor of geology

A Novel New Method for Examining the Distribution of Pores in Rocks

Oil and gas companies take an interest in the porosity of sedimentary rocks because those open spaces can be filled with fuel resources. Companies involved with hydraulic fracturing (“fracking”) are also interested in porosity because it could be a source for storing wastewater as a result of fracking. In this unique study, UC researchers made pore-size measurements similar to those used in crystal size distribution (CSD) theory to determine distribution of pores as a function of their sizes, using thin sections of rock. In addition to providing accurate porosity distribution at a given depth, their approach can be extended to evaluate variation of pore spaces as a function of depth in a drill core, percent of pores in each size range, and pore types and pore geometry. The Texas Bureau of Economic Geology provided the rock samples used in the study. Funding for the study was supported by the Turkish Petroleum Corporation.

Presenter: Ugurlu Ibrahim, master’s student in geology

Co-author: Attila Kilinc, professor of geology

Researchers Turn to 3-D Technology to Examine the Formation of Cliffband Landscapes

A blend of photos and technology takes a new twist on studying cliff landscapes and how they were formed. The method called Structure-From-Motion Photogrammetry – computational photo image processing techniques – is used to study the formation of cliff landscapes in Colorado and Utah and to understand how the layered rock formations in the cliffs are affected by erosion.

Presenter: Dylan Ward, UC assistant professor of geology

Testing the Links Between Climate and Sedimentation in the Atacama Desert, Northern Chile

The Atacama Desert is used as an analog for understanding the surface of Mars. In some localities, there has been no activity for millions of years. UC researchers have been working along the flank of the Andes Mountains in northern Chile, and this particular examination focuses on the large deposits of sediment that are transported down the plateau and gather at the base. The researchers are finding that their samples are not reflecting the million-year-old relics previously found on such expeditions, but may indicate more youthful activity possibly resulting from climatic events. The research is supported by a $273,634 grant from the National Science Foundation to explore glacio-geomorphic constraints on the climate history of subtropical northern Chile.

Presenter: Jason Cesta, UC geology master’s student

Co-author: Dylan Ward, UC assistant professor of geology

Uncovering the Explosive Mysteries Surrounding the Manganese of Northeast Bulgaria

UC’s geology collections hold minerals from field expeditions around the world, including manganese from the Obrochishte mines of northeastern Bulgaria. Found in the region’s sedimentary rock, manganese can be added to metals such as steel to improve strength. It’s widely believed that these manganese formations were the result of ocean water composition at the time the sediments were deposited in the ocean. In this presentation, UC researchers present new information on why they believe the manganese formations resulted from volcanic eruptions, perhaps during the Rupelian stage of the geologic time scale, when bentonite clay minerals were formed. The presentation evolved from an advance class project last spring under the direction of Warren Huff, a UC professor of geology.

Presenter: Jason Cesta, UC geology master’s student

Co-authors: Warren Huff, UC professor of geology; Christopher Aucoin; Michael Harrell; Thomas Malgieri; Barry Maynard; Cameron Schwalbach; Ibrahim Ugurlu; Antony Winrod

Two UC researchers will chair sessions at the GSA meeting: Doctoral student Gary Motz will chair the session, “Topics in Paleoecology: Modern Analogues and Ancient Systems,” on Oct. 19. Matt Vrazo, also a doctoral student in geology, is chairing “Paleontology: Trace Fossils, Taphonomy and Exceptional Preservation” on Oct. 21, and will present, “Taphonomic and Ecological Controls on Eurypterid Lagerstäten: A Model for Preservation in the Mid-Paleozoic.”


UC’s nationally ranked Department of Geology conducts field research around the world in areas spanning paleontology, quaternary geology, geomorphology, sedimentology, stratigraphy, tectonics, environmental geology and biogeochemistry.

The Geological Society of America, founded in 1888, is a scientific society with more than 26,500 members from academia, government, and industry in more than 100 countries. Through its meetings, publications, and programs, GSA enhances the professional growth of its members and promotes the geosciences in the service of humankind.

Space-based methane maps find largest US signal in Southwest

An unexpectedly high amount of the climate-changing gas methane, the main component of natural gas, is escaping from the Four Corners region in the U.S. Southwest, according to a new study by the University of Michigan and NASA.

The researchers mapped satellite data to uncover the nation’s largest methane signal seen from space. They measured levels of the gas emitted from all sources, and found more than half a teragram per year coming from the area where Arizona, New Mexico, Colorado and Utah meet. That’s about as much methane as the entire coal, oil, and gas industries of the United Kingdom give off each year.

Four Corners sits on North America’s most productive coalbed methane basin. Coalbed methane is a variety of the gas that’s stuck to the surface of coal. It is dangerous to miners (not to mention canaries), but in recent decades, it’s been tapped as a resource.

“There’s so much coalbed methane in the Four Corners area, it doesn’t need to be that crazy of a leak rate to produce the emissions that we see. A lot of the infrastructure is likely contributing,” said Eric Kort, assistant professor of atmospheric, oceanic and space sciences at the U-M College of Engineering.

Kort, first author of a paper on the findings published in Geophysical Research Letters, says the controversial natural gas extraction technique of hydraulic fracturing is not the main culprit.

“We see this large signal and it’s persistent since 2003,” Kort said. “That’s a pre- fracking timeframe in this region. While fracking has become a focal point in conversations about methane emissions, it certainly appears from this and other studies that in the U.S., fossil fuel extraction activities across the board likely emit higher than inventory estimates.”

While the signal represents the highest concentration of methane seen from space, the researchers caution that Four Corners isn’t necessarily the highest emitting region.

“One has to be somewhat careful in equating abundances with emissions,” said study contributor Christian Frankenberg at Jet Propulsion Laboratory. “The Four Corners methane source is in a relatively isolated area with little other methane emissions, hence causing a well distinguishable hot-spot in methane abundances. Local or more diffuse emissions in other areas, such as the eastern U.S., may be convoluted with other nearby sources

Natural gas is often touted as more sustainable than coal and oil because it releases fewer pollutants when it burns. But when it leaks into the air before it gets to the pilot light, methane has 30 times the short-term heat-trapping effects of carbon dioxide. Policymakers, energy companies and environmentalists alike are aiming to reduce methane emissions as a way to curb climate change. But pinpointing plumes—a first step to stopping them—has been a difficult task with today’s tools.

The research team demonstrated a new approach to finding leaks. They used a satellite instrument—the European Space Agency’s SCIAMACHY—to get regional methane measurements over the entire United States. They ran the data through a mathematical model to account for mountains and valleys, which can trap methane. That’s how they identified the anomaly at Four Corners. Then they zoomed in on that region and ran another mathematical model to control for wind, to make sure that didn’t negate the original signal. It didn’t.

“We didn’t know this was a region we should look at. We found it from space,” Kort said. “We’ve demonstrated that satellite measurements can help identify, locate and quantify anomalous methane emissions in regions that are unexpected.”

Methane gets into the atmosphere from both natural and human-made sources. Wetlands and landfills release it, as do certain bacteria. Agriculture is a big contributor. So are gas and oil drilling and distribution. Inventories such as those the EPA compiles make estimates based on measurements from a sampling of these sources. In previous work, air measurements from planes and a sparse network of monitoring towers have revealed that the inventory-based numbers are coming in low—roughly 50 percent low. But towers and planes can’t see everywhere to figure out exactly where all the methane is coming from. With limited observations there can be blind spots, the researchers say.

This study used satellite data from 2003 to 2009. In later years, they were able to validate the satellite measurements with a year of ground-based data.

SCIAMACHY is no longer operating, so there aren’t equivalent satellites to provide this information for other parts of the world. For the Four Corners region, Kort will be taking readings from an airplane next year, to get even closer to identifying the leaks.


The study is titled “Four Corners: the largest US methane anomaly viewed from space.” The research was funded by NASA and Los Alamos National Lab.

Eric Kort:


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.