New tracers can identify frack fluids in the environment

Scientists have developed new geochemical tracers that can identify hydraulic fracturing flowback fluids that have been spilled or released into the environment.

The tracers, which were created by a team of U.S. and French researchers, have been field-tested at a spill site in West Virginia and downstream from an oil and gas brine wastewater treatment plant in Pennsylvania.

“This gives us new forensic tools to detect if ‘frac fluids’ are escaping into our water supply and what risks, if any, they might pose,” said Duke University geochemist Avner Vengosh, who co-led the research.

“By characterizing the isotopic and geochemical fingerprints of enriched boron and lithium in flowback water from hydraulic fracturing, we can now track the presence of frac fluids in the environment and distinguish them from wastewater coming from other sources, including conventional oil and gas wells,” Vengosh said.

Using the tracers, scientists can determine where fracturing fluids have or haven’t been released to the environment and, ultimately, help identify ways to improve how shale gas wastewater is treated and disposed of.

Vengosh and his colleagues published their peer-reviewed findings October 20 in the journal Environmental Science & Technology. Their study, which was funded in part by the National Science Foundation, is the first to report on the development of the boron and lithium tracers.

Nathaniel R. Warner, Obering Postdoctoral Fellow at Dartmouth College, was lead author of the study. “This new technology can be combined with other methods to identify specific instances of accidental releases to surface waters in areas of unconventional drilling,” he said. “It could benefit industry as well as federal and state agencies charged with monitoring water quality and protecting the environment.”

Hydraulic fracturing fluids, or frac fluids, typically contain mixes of water, proprietary chemicals and sand. Mixtures can vary from site to site. Drillers inject large volumes of the fluids down gas wells at high pressure to crack open shale formations deep underground and allow natural gas trapped within the shale to flow out and be extracted. After the shale has been fractured, the frac fluids flow back up the well to the surface along with the gas and highly saline brines from the shale formation.

Some people fear that toxic frac fluid chemicals in this flowback could contaminate nearby water supplies if flowback were accidentally spilled or insufficiently treated before being disposed of.

“The flowback fluid that returns to the surface becomes a waste that needs to be managed,” Vengosh explained. “Deep-well injection is the preferable disposal method, but injecting large volumes of wastewater into deep wells can cause earthquakes in sensitive areas and is not geologically available in some states. In Pennsylvania, much of the flowback is now recycled and reused, but a significant amount of it is still discharged into local streams or rivers.”

Vengosh said it’s possible to identify the presence of frac fluid in spilled or discharged flowback by tracing synthetic organic compounds that are added to the fluid before it’s injected down a well. But the proprietary nature of these chemicals, combined with their instability in the environment, limits the usefulness of such tracers.

By contrast, the new boron and lithium tracers remain stable in the environment. “The difference is that we are using tracers based on elements that occur naturally in shale formations,” Vengosh said.

When drillers inject frac fluids into a shale formation, they not only release hydrocarbon but also boron and lithium that are attached to clay minerals within the formation, he explained. As the fluids react and mix at depth, they become enriched in boron and lithium. As they are brought back to the surface, they have distinctive isotopic fingerprints that are different from other types of wastewater, including wastewater from a conventional gas or oil well, as well as from naturally occurring background water.

“This type of forensic research allows us to clearly delineate between the possible sources of wastewater contamination,” Vengosh said.

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.

Hydraulic fracturing linked to earthquakes in Ohio

Hydraulic fracturing triggered a series of small earthquakes in 2013 on a previously unmapped fault in Harrison County, Ohio, according to a study published in the journal Seismological Research Letters (SRL).

Nearly 400 small earthquakes occurred between Oct. 1 and Dec. 13, 2013, including 10 “positive” magnitude earthquake, none of which were reported felt by the public. The 10 positive magnitude earthquakes, which ranged from magnitude 1.7 to 2.2, occurred between Oct. 2 and 19, coinciding with hydraulic fracturing operations at nearby wells.

This series of earthquakes is the first known instance of seismicity in the area.

Hydraulic fracturing, or fracking, is a method for extracting gas and oil from shale rock by injecting a high-pressure water mixture directed at the rock to release the gas inside. The process of hydraulic fracturing involves injecting water, sand and chemicals into the rock under high pressure to create cracks. The process of cracking rocks results in micro-earthquakes. Hydraulic fracturing usually creates only small earthquakes, ones that have magnitude in the range of negative 3 (−3) to negative 1 (-1).

“Hydraulic fracturing has the potential to trigger earthquakes, and in this case, small ones that could not be felt, however the earthquakes were three orders of magnitude larger than normally expected,” said Paul Friberg, a seismologist with Instrumental Software Technologies, Inc. (ISTI) and a co-author of the study.

The earthquakes revealed an east-west trending fault that lies in the basement formation at approximately two miles deep and directly below the three horizontal gas wells. The EarthScope Transportable Array Network Facility identified the first earthquakes on Oct. 2, 2013, locating them south of Clendening Lake near the town of Uhrichsville, Ohio. A subsequent analysis identified 190 earthquakes during a 39-hour period on Oct. 1 and 2, just hours after hydraulic fracturing began on one of the wells.

The micro-seismicity varied, corresponding with the fracturing activity at the wells. The timing of the earthquakes, along with their tight linear clustering and similar waveform signals, suggest a unique source for the cause of the earthquakes — the hydraulic fracturing operation. The fracturing likely triggered slip on a pre-existing fault, though one that is located below the formation expected to confine the fracturing, according to the authors.

“As hydraulic fracturing operations explore new regions, more seismic monitoring will be needed since many faults remain unmapped.” Friberg co-authored the paper with Ilya Dricker, also with ISTI, and Glenda Besana-Ostman originally with Ohio Department of Natural Resources, and now with the Bureau of Reclamation at the U.S. Department of Interior.

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.

Fracking’s environmental impacts scrutinized

Greenhouse gas emissions from the production and use of shale gas would be comparable to conventional natural gas, but the controversial energy source actually faired better than renewables on some environmental impacts, according to new research.

The UK holds enough shale gas to supply its entire gas demand for 470 years, promising to solve the country’s energy crisis and end its reliance on fossil-fuel imports from unstable markets. But for many, including climate scientists and environmental groups, shale gas exploitation is viewed as environmentally dangerous and would result in the UK reneging on its greenhouse gas reduction obligations under the Climate Change Act.

University of Manchester scientists have now conducted one of the most thorough examinations of the likely environmental impacts of shale gas exploitation in the UK in a bid to inform the debate. Their research has just been published in the leading academic journal Applied Energy and study lead author, Professor Adisa Azapagic, will outline the findings at the Labour Party Conference in Manchester, England, today (Monday, 22 September).

“While exploration is currently ongoing in the UK, commercial extraction of shale gas has not yet begun, yet its potential has stirred controversy over its environmental impacts, its safety and the difficulty of justifying its use to a nation conscious of climate change,” said Professor Azapagic.

“There are many unknowns in the debate surrounding shale gas, so we have attempted to address some of these unknowns by estimating its life cycle environmental impacts from ‘cradle to grave’. We looked at 11 different impacts from the extraction of shale gas using hydraulic fracturing – known as ‘fracking’- as well as from its processing and use to generate electricity.”

The researchers compared shale gas to other fossil-fuel alternatives, such as conventional natural gas and coal, as well as low-carbon options, including nuclear, offshore wind and solar power (solar photovoltaics).

The results of the research suggest that the average emissions of greenhouse gases from shale gas over its entire life cycle are about 460 grams of carbon dioxide-equivalent per kilowatt-hour of electricity generated. This, the authors say, is comparable to the emissions from conventional natural gas. For most of the other life-cycle environmental impacts considered by the team, shale gas was also comparable to conventional natural gas.

But the study also found that shale gas was better than offshore wind and solar for four out of 11 impacts: depletion of natural resources, toxicity to humans, as well as the impact on freshwater and marine organisms. Additionally, shale gas was better than solar (but not wind) for ozone layer depletion and eutrophication (the effect of nutrients such as phosphates, on natural ecosystems).

On the other hand, shale gas was worse than coal for three impacts: ozone layer depletion, summer smog and terrestrial eco-toxicity.

Professor Azapagic said: “Some of the impacts of solar power are actually relatively high, so it is not a complete surprise that shale gas is better in a few cases. This is mainly because manufacturing solar panels is very energy and resource-intensive, while their electrical output is quite low in a country like the UK, as we don’t have as much sunshine. However, our research shows that the environmental impacts of shale gas can vary widely, depending on the assumptions for various parameters, including the composition and volume of the fracking fluid used, disposal routes for the drilling waste and the amount of shale gas that can be recovered from a well.

“Assuming the worst case conditions, several of the environmental impacts from shale gas could be worse than from any other options considered in the research, including coal. But, under the best-case conditions, shale gas may be preferable to imported liquefied natural gas.”

The authors say their results highlight the need for tight regulation of shale gas exploration – weak regulation, they claim, may result in shale gas having higher impacts than coal power, resulting in a failure to meet climate change and sustainability imperatives and undermining the deployment of low-carbon technologies.

Professor Azapagic added: “Whether shale gas is an environmentally sound option depends on the perceived importance of different environmental impacts and the regulatory structure under which shale gas operates.

“From the government policy perspective – focusing mainly on economic growth and energy security – it appears likely that shale gas represents a good option for the UK energy sector, assuming that it can be extracted at reasonable cost.

“However, a wider view must also consider other aspects of widespread use of shale gas, including the impact on climate change, as well as many other environmental considerations addressed in our study. Ultimately, the environmental impacts from shale gas will depend on which options it is displacing and how tight the regulation is.”

Study co-author Dr Laurence Stamford, from Manchester’s School of Chemical Engineering and Analytical Science, said: “Appropriate regulation should introduce stringent controls on the emissions from shale gas extraction and disposal of drilling waste. It should also discourage extraction from sites where there is little shale gas in order to avoid the high emissions associated with a low-output well.

He continued: “If shale gas is extracted under tight regulations and is reasonably cheap, there is no obvious reason, as yet, why it should not make some contribution to our energy mix. However, regulation should also ensure that investment in sustainable technologies is not reduced at the expense of shale gas.”

Wastewater injection is culprit for most quakes in southern Colorado and northern New Mexico

The deep injection of wastewater underground is responsible for the dramatic rise in the number of earthquakes in Colorado and New Mexico since 2001, according to a study to be published in the Bulletin of the Seismological Society of America (BSSA).

The Raton Basin, which stretches from southern Colorado into northern New Mexico, was seismically quiet until shortly after major fluid injection began in 1999. Since 2001, there have been 16 magnitude > 3.8 earthquakes (including M 5.0 and 5.3), compared to only one (M 4.0) the previous 30 years. The increase in earthquakes is limited to the area of industrial activity and within 5 kilometers (3.1 miles) of wastewater injection wells.

In 1994, energy companies began producing coal-bed methane in Colorado and expanded production to New Mexico in 1999. Along with the production of methane, there is the production of wastewater, which is injected underground in disposal wells and can raise the pore pressure in the surrounding area, inducing earthquakes. Several lines of evidence suggest the earthquakes in the area are directly related to the disposal of wastewater, a by-product of extracting methane, and not to hydraulic fracturing occurring in the area.

Beginning in 2001, the production of methane expanded, with the number of high-volume wastewater disposal wells increasing (21 presently in Colorado and 7 in New Mexico) along with the injection rate. Since mid-2000, the total injection rate across the basin has ranged from 1.5 to 3.6 million barrels per month.

The authors, all scientists with the U.S. Geological Survey, detail several lines of evidence directly linking the injection wells to the seismicity. The timing and location of seismicity correspond to the documented pattern of injected wastewater. Detailed investigations of two seismic sequences (2001 and 2011) places them in proximity to high-volume, high-injection-rate wells, and both sequences occurred after a nearby increase in the rate of injection. A comparison between seismicity and wastewater injection in Colorado and New Mexico reveals similar patterns, suggesting seismicity is initiated shortly after an increase in injection rates.

Contaminated water in 2 states linked to faulty shale gas wells

Faulty well integrity, not hydraulic fracturing deep underground, is the primary cause of drinking water contamination from shale gas extraction in parts of Pennsylvania and Texas, according to a new study by researchers from five universities.

The scientists from Duke, Ohio State, Stanford, Dartmouth and the University of Rochester
published their peer-reviewed study Sept. 15 in the Proceedings of the National Academy of Sciences. Using noble gas and hydrocarbon tracers, they analyzed the gas content of more than 130 drinking water wells in the two states.

“We found eight clusters of wells — seven in Pennsylvania and one in Texas — with contamination, including increased levels of natural gas from the Marcellus shale in Pennsylvania and from shallower, intermediate layers in both states,” said Thomas H. Darrah, assistant professor of earth science at Ohio State, who led the study while he was a research scientist at Duke.

“Our data clearly show that the contamination in these clusters stems from well-integrity problems such as poor casing and cementing,” Darrah said.

“These results appear to rule out the possibility that methane has migrated up into drinking water aquifers because of horizontal drilling or hydraulic fracturing, as some people feared,” said Avner Vengosh, professor of geochemistry and water quality at Duke.

In four of the affected clusters, the team’s noble gas analysis shows that methane from drill sites escaped into drinking water wells from shallower depths through faulty or insufficient rings of cement surrounding a gas well’s shaft. In three clusters, the tests suggest the methane leaked through faulty well casings. In one cluster, it was linked to an underground well failure.

“People’s water has been harmed by drilling,” said Robert B. Jackson, professor of environmental and earth sciences at Stanford and Duke. “In Texas, we even saw two homes go from clean to contaminated after our sampling began.”

“The good news is that most of the issues we have identified can potentially be avoided by future improvements in well integrity,” Darrah stressed.

Using both noble gas and hydrocarbon tracers — a novel combination that enabled the researchers to identify and distinguish between the signatures of naturally occurring methane and stray gas contamination from shale gas drill sites — the team analyzed gas content in 113 drinking-water wells and one natural methane seep overlying the Marcellus shale in Pennsylvania, and in 20 wells overlying the Barnett shale in Texas. Sampling was conducted in 2012 and 2013. Sampling sites included wells where contamination had been debated previously; wells known to have naturally high level of methane and salts, which tend to co-occur in areas overlying shale gas deposits; and wells located both within and beyond a one-kilometer distance from drill sites.

Noble gases such as helium, neon or argon are useful for tracing fugitive methane because although they mix with natural gas and can be transported with it, they are inert and are not altered by microbial activity or oxidation. By measuring changes in ratios in these tag-along noble gases, researchers can determine the source of fugitive methane and the mechanism by which it was transported into drinking water aquifers — whether it migrated there as a free gas or was dissolved in water.

“This is the first study to provide a comprehensive analysis of noble gases and their isotopes in groundwater near shale gas wells,” said Darrah, who is continuing the analysis in his lab at Ohio State. “Using these tracers, combined with the isotopic and chemical fingerprints of hydrocarbons in the water and its salt content, we can pinpoint the sources and pathways of methane contamination, and determine if it is natural or not.”

Gas leaks from faulty wells linked to contamination in some groundwater

A study has pinpointed the likely source of most natural gas contamination in drinking-water wells associated with hydraulic fracturing, and it’s not the source many people may have feared.

What’s more, the problem may be fixable: improved construction standards for cement well linings and casings at hydraulic fracturing sites.

A team led by a researcher at The Ohio State University and composed of researchers at Duke, Stanford, Dartmouth, and the University of Rochester devised a new method of geochemical forensics to trace how methane migrates under the earth. The study identified eight clusters of contaminated drinking-water wells in Pennsylvania and Texas.

Most important among their findings, published this week in the Proceedings of the National Academy of Sciences, is that neither horizontal drilling nor hydraulic fracturing of shale deposits seems to have caused any of the natural gas contamination.

“There is no question that in many instances elevated levels of natural gas are naturally occurring, but in a subset of cases, there is also clear evidence that there were human causes for the contamination,” said study leader Thomas Darrah, assistant professor of earth sciences at Ohio State. “However our data suggests that where contamination occurs, it was caused by poor casing and cementing in the wells,” Darrah said.

In hydraulic fracturing, water is pumped underground to break up shale at a depth far below the water table, he explained. The long vertical pipes that carry the resulting gas upward are encircled in cement to keep the natural gas from leaking out along the well. The study suggests that natural gas that has leaked into aquifers is the result of failures in the cement used in the well.

“Many of the leaks probably occur when natural gas travels up the outside of the borehole, potentially even thousands of feet, and is released directly into drinking-water aquifers” said Robert Poreda, professor of geochemistry at the University of Rochester.

“These results appear to rule out the migration of methane up into drinking water aquifers from depth because of horizontal drilling or hydraulic fracturing, as some people feared,” said Avner Vengosh, professor of geochemistry and water quality at Duke.

“This is relatively good news because it means that most of the issues we have identified can potentially be avoided by future improvements in well integrity,” Darrah said.

“In some cases homeowner’s water has been harmed by drilling,” said Robert B. Jackson, professor of environmental and earth sciences at Stanford and Duke. “In Texas, we even saw two homes go from clean to contaminated after our sampling began.”

The method that the researchers used to track the source of methane contamination relies on the basic physics of the noble gases (which happen to leak out along with the methane). Noble gases such as helium and neon are so called because they don’t react much with other chemicals, although they mix with natural gas and can be transported with it.

That means that when they are released underground, they can flow long distances without getting waylaid by microbial activity or chemical reactions along the way. The only important variable is the atomic mass, which determines how the ratios of noble gases change as they tag along with migrating natural gas. These properties allow the researchers to determine the source of fugitive methane and the mechanism by which it was transported into drinking water aquifers.

The researchers were able to distinguish between the signatures of naturally occurring methane and stray gas contamination from shale gas drill sites overlying the Marcellus shale in Pennsylvania and the Barnett shale in Texas.

The researchers sampled water from the sites in 2012 and 2013. Sampling sites included wells where contamination had been debated previously; wells known to have naturally high level of methane and salts, which tend to co-occur in areas overlying shale gas deposits; and wells located both within and beyond a one-kilometer distance from drill sites.

As hydraulic fracturing starts to develop around the globe, including countries South Africa, Argentina, China, Poland, Scotland, and Ireland, Darrah and his colleagues are continuing their work in the United States and internationally. And, since the method that the researchers employed relies on the basic physics of the noble gases, it can be employed anywhere. Their hope is that their findings can help highlight the necessity to improve well integrity.

A new look at what’s in ‘fracking’ fluids raises red flags

Scientists are getting to the bottom of what's in fracking fluids — with some troubling results. -  Doug Duncan/U.S. Geological Survey
Scientists are getting to the bottom of what’s in fracking fluids — with some troubling results. – Doug Duncan/U.S. Geological Survey

As the oil and gas drilling technique called hydraulic fracturing (or “fracking”) proliferates, a new study on the contents of the fluids involved in the process raises concerns about several ingredients. The scientists presenting the work today at the 248th National Meeting & Exposition of the American Chemical Society (ACS) say that out of nearly 200 commonly used compounds, there’s very little known about the potential health risks of about one-third, and eight are toxic to mammals.

The meeting features nearly 12,000 presentations on a wide range of science topics and is being held here through Thursday by ACS, the world’s largest scientific society.

William Stringfellow, Ph.D., says he conducted the review of fracking contents to help resolve the public debate over the controversial drilling practice. Fracking involves injecting water with a mix of chemical additives into rock formations deep underground to promote the release of oil and gas. It has led to a natural gas boom in the U.S., but it has also stimulated major opposition and troubling reports of contaminated well water, as well as increased air pollution near drill sites.

“The industrial side was saying, ‘We’re just using food additives, basically making ice cream here,'” Stringfellow says. “On the other side, there’s talk about the injection of thousands of toxic chemicals. As scientists, we looked at the debate and asked, ‘What’s the real story?'”

To find out, Stringfellow’s team at Lawrence Berkeley National Laboratory and University of the Pacific scoured databases and reports to compile a list of substances commonly used in fracking. They include gelling agents to thicken the fluids, biocides to keep microbes from growing, sand to prop open tiny cracks in the rocks and compounds to prevent pipe corrosion.

What their analysis revealed was a little truth to both sides’ stories – with big caveats. Fracking fluids do contain many nontoxic and food-grade materials, as the industry asserts. But if something is edible or biodegradable, it doesn’t automatically mean it can be easily disposed of, Stringfellow notes.

“You can’t take a truckload of ice cream and dump it down the storm drain,” he says, building on the industry’s analogy. “Even ice cream manufacturers have to treat dairy wastes, which are natural and biodegradable. They must break them down rather than releasing them directly into the environment.”

His team found that most fracking compounds will require treatment before being released. And, although not in the thousands as some critics suggest, the scientists identified eight substances, including biocides, that raised red flags. These eight compounds were identified as being particularly toxic to mammals.

“There are a number of chemicals, like corrosion inhibitors and biocides in particular, that are being used in reasonably high concentrations that potentially could have adverse effects,” Stringfellow says. “Biocides, for example, are designed to kill bacteria – it’s not a benign material.”

They’re also looking at the environmental impact of the fracking fluids, and they are finding that some have toxic effects on aquatic life.

In addition, for about one-third of the approximately 190 compounds the scientists identified as ingredients in various fracking formulas, the scientists found very little information about toxicity and physical and chemical properties.

“It should be a priority to try to close that data gap,” Stringfellow says.