The breathing sand

An Eddy Correlation Lander analyzes the strength of the oxygen fluxes at the bottom of the North Sea. -  Photo: ROV-Team, GEOMAR
An Eddy Correlation Lander analyzes the strength of the oxygen fluxes at the bottom of the North Sea. – Photo: ROV-Team, GEOMAR

A desert at the bottom of the sea? Although the waters of the North Sea exchange about every two to three years, there is evidence of decreasing oxygen content. If lower amounts of this gas are dissolved in seawater, organisms on and in the seabed produce less energy – with implications for larger creatures and the biogeochemical cycling in the marine ecosystem. Since nutrients, carbon and oxygen circulate very well and are processed quickly in the permeable, sandy sediments that make up two-thirds of the North Sea, measurements of metabolic rates are especially difficult here. Using the new Aquatic Eddy Correlation technique, scientists from GEOMAR Helmholtz Centre for Ocean Research Kiel, Leibniz Institute of Freshwater Ecology and Inland Fisheries, the University of Southern Denmark, the University of Koblenz-Landau, the Scottish Marine Institute and Aarhus University were able to demonstrate how oxygen flows at the ground of the North Sea. Their methods and results are presented in the Journal of Geophysical Research: Oceans.

“The so-called ‘Eddy Correlation’ technique detects the flow of oxygen through these small turbulences over an area of several square meters. It considers both the mixing of sediments by organisms living in it and the hydrodynamics of the water above the rough sea floor”, Dr. Peter Linke, a marine biologist at GEOMAR, explains. “Previous methods overlooked only short periods or disregarded important parameters. Now we can create a more realistic picture.” The new method also takes into account the fact that even small objects such as shells or ripples shaped by wave action or currents are able to impact the oxygen exchange in permeable sediments.

On the expedition CE0913 with the Irish research vessel CELTIC EXPLORER, scientists used the underwater robot ROV KIEL 6000 to place three different instruments within the “Tommeliten” area belonging to Norway: Two “Eddy Correlation Landers” recorded the strength of oxygen fluxes over three tidal cycles. Information about the distribution of oxygen in the sediment was collected with a “Profiler Lander”, a seafloor observatory with oxygen sensors and flow meters. A “Benthic chamber” isolated 314 square centimetres of sediment and took samples from the overlying water over a period of 24 hours to determine the oxygen consumption of the sediment.

“The combination of traditional tools with the ‘Eddy Correlation’ technique has given us new insights into the dynamics of the exchange of substances between the sea water and the underlying sediment. A variety of factors determine the timing and amount of oxygen available. Currents that provide the sandy sediment with oxygen, but also the small-scale morphology of the seafloor, ensure that small benthic organisms are able to process carbon or other nutrients. The dependencies are so complex that they can be decrypted only by using special methods”, Dr. Linke summarizes. Therefore, detailed measurements in the water column and at the boundary to the seafloor as well as model calculations are absolutely necessary to understand basic functions and better estimate future changes in the cycle of materials. “With conventional methods, for example, we would never have been able to find that the loose sandy sediment stores oxygen brought in by the currents for periods of less water movement and less oxygen introduction.”

Original publication:
McGinnis, D. F., S. Sommer, A. Lorke, R. N. Glud, P. Linke (2014): Quantifying tidally driven benthic oxygen exchange across permeable sediments: An aquatic eddy correlation study. Journal of Geophysical Research: Oceans, doi:10.1002/2014JC010303.


GEOMAR Helmholtz Centre for Ocean Research Kiel

Eddy correlation information page

Leibniz Institute of Freshwater Ecology and Inland Fisheries, IGB

University of Southern Denmark

University of Koblenz-Landau

Scottish Marine Institute

Aarhus University

High resolution images can be downloaded at

Video footage is available on request.

Dr. Peter Linke (GEOMAR FB2-MG), Tel. 0431 600-2115,

Maike Nicolai (GEOMAR, Kommunikation & Medien), Tel. 0431 600-2807,

Researchers resolve the Karakoram glacier anomaly, a cold case of climate science

The researchers found that low-resolution models and a lack of reliable observational data obscured the Karakoram's dramatic shifts in elevation over a small area and heavy winter snowfall. They created a higher-resolution model that showed the elevation and snow water equivalent for (inlaid boxes, from left to right) the Karakoram range and northwest Himalayas, the central Himalayas that include Mount Everest, and the southeast Himalayas and the Tibetan Plateau. For elevation (left), the high-resolution model showed the sharp variations between roughly 2,500 and 5,000 meters above sea level (yellow to brown) for the Karakoram, while other areas of the map have comparatively more consistent elevations. The model also showed that the Karakoram receive much more annual snowfall (right) than other Himalayan ranges (right), an average of 100 centimeters (brown). The researchers found that the main precipitation season in the Karakoram occurs during the winter and is influenced by cold winds coming from Central Asian countries, as opposed to the heavy summer monsoons that provide the majority of precipitation to the other Himalayan ranges. -  Image by Sarah Kapnick, Program in Atmospheric and Oceanic Sciences
The researchers found that low-resolution models and a lack of reliable observational data obscured the Karakoram’s dramatic shifts in elevation over a small area and heavy winter snowfall. They created a higher-resolution model that showed the elevation and snow water equivalent for (inlaid boxes, from left to right) the Karakoram range and northwest Himalayas, the central Himalayas that include Mount Everest, and the southeast Himalayas and the Tibetan Plateau. For elevation (left), the high-resolution model showed the sharp variations between roughly 2,500 and 5,000 meters above sea level (yellow to brown) for the Karakoram, while other areas of the map have comparatively more consistent elevations. The model also showed that the Karakoram receive much more annual snowfall (right) than other Himalayan ranges (right), an average of 100 centimeters (brown). The researchers found that the main precipitation season in the Karakoram occurs during the winter and is influenced by cold winds coming from Central Asian countries, as opposed to the heavy summer monsoons that provide the majority of precipitation to the other Himalayan ranges. – Image by Sarah Kapnick, Program in Atmospheric and Oceanic Sciences

Researchers from Princeton University and other institutions may have hit upon an answer to a climate-change puzzle that has eluded scientists for years, and that could help understand the future availability of water for hundreds of millions of people.

In a phenomenon known as the “Karakoram anomaly,” glaciers in the Karakoram mountains, a range within the Himalayas, have remained stable and even increased in mass while many glaciers nearby — and worldwide — have receded during the past 150 years, particularly in recent decades. Himalayan glaciers provide freshwater to a densely populated area that includes China, Pakistan and India, and are the source of the Ganges and Indus rivers, two of the world’s major waterways.

While there have been many attempts to explain the stability of the Karakoram glaciers, the researchers report in the journal Nature Geoscience that the ice is sustained by a unique and localized seasonal pattern that keeps the mountain range relatively cold and dry during the summer. Other Himalayan ranges and the Tibetan Plateau — where glaciers have increasingly receded as Earth’s climate has warmed — receive most of their precipitation from heavy summer monsoons out of hot South and Southeast Asian nations such as India. The main precipitation season in the Karakoram, however, occurs during the winter and is influenced by cold winds coming from Central Asian countries such as Afghanistan to the west, while the main Himalayan range blocks the warmer air from the southeast throughout the year.

The researchers determined that snowfall, which is critical to maintaining glacier mass, will remain stable and even increase in magnitude at elevations above 4,500 meters (14,764 feet) in the Karakoram through at least 2100. On the other hand, snowfall over much of the Himalayas and Tibet is projected to decline even as the Indian and Southeast Asian monsoons increase in intensity under climate change.

First author Sarah Kapnick, a postdoctoral research fellow in Princeton’s Program in Atmospheric and Oceanic Sciences, said that a shortage of reliable observational data and the use of low-resolution computer models had obscured the subtleties of the Karakoram seasonal cycle and prevented scientists from unraveling the causes of the anomaly.

For models, the complication is that the Karakoram features dramatic shifts in elevation over a small area, Kapnick said. The range boasts four mountains that are more than 8,000 meters (26,246 feet) high — including K2, the world’s second highest peak — and numerous summits that exceed 7,000 meters, all of which are packed into a length of about 500 kilometers (300 miles).

Kapnick and her co-authors overcame this obstacle with a high-resolution computer model that broke the Karakoram into 50-kilometer pieces, meaning that those sharp fluctuations in altitude were better represented.

In their study, the researchers compared their model with climate models from the United Nations’ Intergovernmental Panel on Climate Change (IPCC), which averages a resolution of 210-kilometer squares, Kapnick said. At that scale, the Karakoram is reduced to an average height that is too low and results in temperatures that are too warm to sustain sufficient levels of snowfall throughout the year, and too sensitive to future temperature increases.

Thus, by the IPCC’s models, it would appear that the Karakoram’s glaciers are imperiled by climate change due to reduced snowfall, Kapnick said. This region has been a great source of controversy ever since the IPCC’s last major report, in 2007, when the panel misreported that Himalayan glaciers would likely succumb to climate change by 2035. More recent papers using current IPCC models have similarly reported snowfall losses in this region because the models do not accurately portray the topography of the Karakoram, Kapnick said.

“The higher resolution allowed us to explore what happens at these higher elevations in a way that hasn’t been able to be done,” Kapnick said. “Something that climate scientists always have to keep in mind is that models are useful for certain types of questions and not necessarily for other types of questions. While the IPCC models can be particularly useful for other parts of the world, you need a higher resolution for this area.”

Jeff Dozier, a professor of snow hydrology, earth system science and remote sensing at the University of California-Santa Barbara, said that the research addresses existing shortcomings in how mountain climates are modeled and predicted, particularly in especially steep and compact ranges. Dozier, who was not involved in the research, conducts some of his research in the Hindu Kush mountains west of the Karakoram.

Crucial information regarding water availability is often lost in computer models, observational data and other tools that typically do not represent ranges such as Karakoram accurately enough, Dozier said. For instance, a severe 2011 drought in Northern Afghanistan was a surprise partly due to erroneous runoff forecasts based on insufficient models and surface data, he said. The high-resolution model Kapnick and her co-authors developed for Karakoram potentially resolves many of the modeling issues related to mountain ranges with similar terrain, he said.

“The Karakoram Anomaly has been a puzzle, and this paper gives a credible explanation,” Dozier said. “Climate in the mountains is obviously affected strongly by the elevation, but most global climate models don’t resolve the topography well enough. So, the higher-resolution model is appropriate. About a billion people worldwide get their water resources from melting snow and many of these billion get their water from High Mountain Asia.”

The researchers used the high-resolution global-climate model GFDL-CM2.5 at the Geophysical Fluid Dynamics Laboratory (GFDL), which is on Princeton’s Forrestal Campus and administered by the National Oceanic and Atmospheric Administration (NOAA). The researchers simulated the global climate — with a focus on the Karakoram — based on observational data from 1861 to 2005, and on the IPCC’s greenhouse-gas projections for 2006-2100, which will be included in its Fifth Assessment Report scheduled for release in November.

The 50-kilometer resolution revealed conditions in Karakoram on a monthly basis, Kapnick said. It was then that she and her colleagues could observe that the monsoon months in Karakoram are not only not characterized by heavy rainfall, but also include frigid westerly winds that keep conditions in the mountain range cold enough for nearly year-round snowfall.

“There is precipitation during the summer, it just doesn’t dominate the seasonal cycle. This region, even at the same elevation as the rest of the Himalayas, is just colder,” Kapnick said.

“The high-resolution model shows us that things don’t happen perfectly across seasons. You can have statistical variations in one month but not another,” she continued. “This allows us to piece out those significant changes from one month to the next.”

Kapnick, who received her bachelor’s degree in mathematics from Princeton in 2004, worked with Thomas Delworth, a NOAA scientist and Princeton lecturer of geosciences and atmospheric and oceanic sciences; Moestasim Ashfaq, a scientist at the Oak Ridge National Laboratory Climate Change Science Institute; Sergey Malyshev, a climate modeler in Princeton’s Department of Ecology and Evolutionary Biology based at GFDL; and P.C.D. “Chris” Milly, a research hydrologist for the U.S. Geological Survey based at GFDL who received his bachelor’s degree in civil engineering from Princeton in 1978.

While the researchers show that the Karakoram will receive consistent — and perhaps increased — snowfall through 2100, more modeling work is needed to understand how the existing glaciers may change over time as a result of melt, avalanches and other factors, Kapnick said.

“Our work is an important piece to understanding the Karakoram anomaly,” Kapnick said. “But that balance of what’s coming off the glacier versus what’s coming in also matters for understanding how the glacier will change in the future.”

The paper, “Snowfall less sensitive to warming in Karakoram than in Himalayas due to a unique seasonal cycle,” was published online in-advance-of-print Oct. 12 by Nature Geoscience.

Researchers solve riddle of the rock pools

The rock goby can change both its color and brightness to match its background in just one minute. -  Alice Lown
The rock goby can change both its color and brightness to match its background in just one minute. – Alice Lown

Research from the University of Exeter has revealed that the rock goby (Gobius paganellus), an unassuming little fish commonly found in rock pools around Britain, southern Europe, and North Africa, is a master of camouflage and can rapidly change colour to conceal itself against its background.

Whether hiding from predators or from families hunting in rock pools, the rock goby can change both its colour and brightness to match its background in just one minute.

Dr Martin Stevens from the Centre for Ecology and Conservation at the University of Exeter’s Penryn Campus in Cornwall said: “Anyone who’s been rock pooling will probably have encountered rock gobies, and may even have thought they could see them change colour in buckets. Our research shows that this is the case and that rock gobies can rapidly tune their appearance to match their background.”

The researchers found that when gobies were photographed on a bright white or dark background, they could change their brightness accordingly. When photographed on coloured backgrounds they altered their colour, becoming either more red or blue.

Undertaking this rapid visual change should be a major advantage for the fish when trying to avoid predators. Gobies find themselves under intense predation pressure at low tide from birds and at high tide from larger fish. To remain concealed they must rapidly respond as they are pushed over many different backgrounds by tides and waves.

The researchers collected the gobies from Gyllyngvase beach in Falmouth, Cornwall then photographed them against different backgrounds over time to quantify the speed and extent of the colour change. The results show that the fish were capable of rapid visual change for concealment.

The colour change is driven by special cells in the fishes’ bodies called ‘chromatophores’. These are found in many animals and work to condense or spread pigments of different colour over the body, changing the appearance of the fish. This process is guided by the visual system of the goby when it moves onto a new background.

Studies of colour change for camouflage have previously been undertaken in animals including chameleons, cuttlefish, flatfish, and crabs, but rarely have studies directly quantified the changes in colour and brightness that occur, how fast this happens, and how they affect camouflage matching.

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.

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.

Meteorite that doomed the dinosaurs helped the forests bloom

<IMG SRC="/Images/537934362.jpg" WIDTH="350" HEIGHT="233" BORDER="0" ALT="Seen here is a Late Cretaceous specimen from the Hell Creek Formation, morphotype HC62, taxon
''Rhamnus” cleburni. Specimens are housed at the Denver Museum of Nature and Science in
Denver, Colorado. – Image credit: Benjamin Blonder.”>
Seen here is a Late Cretaceous specimen from the Hell Creek Formation, morphotype HC62, taxon
Rhamnus” cleburni. Specimens are housed at the Denver Museum of Nature and Science in
Denver, Colorado. – Image credit: Benjamin Blonder.

66 million years ago, a 10-km diameter chunk of rock hit the Yukatan peninsula near the site of the small town of Chicxulub with the force of 100 teratons of TNT. It left a crater more than 150 km across, and the resulting megatsunami, wildfires, global earthquakes and volcanism are widely accepted to have wiped out the dinosaurs and made way for the rise of the mammals. But what happened to the plants on which the dinosaurs fed?

A new study led by researchers from the University of Arizona reveals that the meteorite impact that spelled doom for the dinosaurs also decimated the evergreen flowering plants to a much greater extent than their deciduous peers. They hypothesize that the properties of deciduous plants made them better able to respond rapidly to chaotically varying post-apocalyptic climate conditions. The results are publishing on September 16 in the open access journal PLOS Biology.

Applying biomechanical formulae to a treasure trove of thousands of fossilized leaves of angiosperms – flowering plants excluding conifers – the team was able to reconstruct the ecology of a diverse plant community thriving during a 2.2 million-year period spanning the cataclysmic impact event, believed to have wiped out more than half of plant species living at the time. The fossilized leaf samples span the last 1,400,000 years of the Cretaceous and the first 800,000 of the Paleogene.

The researchers found evidence that after the impact, fast-growing, deciduous angiosperms had replaced their slow-growing, evergreen peers to a large extent. Living examples of evergreen angiosperms, such as holly and ivy, tend to prefer shade, don’t grow very fast and sport dark-colored leaves.

“When you look at forests around the world today, you don’t see many forests dominated by evergreen flowering plants,” said the study’s lead author, Benjamin Blonder. “Instead, they are dominated by deciduous species, plants that lose their leaves at some point during the year.”

Blonder and his colleagues studied a total of about 1,000 fossilized plant leaves collected from a location in southern North Dakota, embedded in rock layers known as the Hell Creek Formation, which at the end of the Cretaceous was a lowland floodplain crisscrossed by river channels. The collection consists of more than 10,000 identified plant fossils and is housed primarily at the Denver Museum of Nature and Science. “When you hold one of those leaves that is so exquisitely preserved in your hand knowing it’s 66 million years old, it’s a humbling feeling,” said Blonder.

“If you think about a mass extinction caused by catastrophic event such as a meteorite impacting Earth, you might imagine all species are equally likely to die,” Blonder said. “Survival of the fittest doesn’t apply – the impact is like a reset button. The alternative hypothesis, however, is that some species had properties that enabled them to survive.

“Our study provides evidence of a dramatic shift from slow-growing plants to fast-growing species,” he said. “This tells us that the extinction was not random, and the way in which a plant acquires resources predicts how it can respond to a major disturbance. And potentially this also tells us why we find that modern forests are generally deciduous and not evergreen.”

Previously, other scientists found evidence of a dramatic drop in temperature caused by dust from the impact. “The hypothesis is that the impact winter introduced a very variable climate,” Blonder said. “That would have favored plants that grew quickly and could take advantage of changing conditions, such as deciduous plants.”

“We measured the mass of a given leaf in relation to its area, which tells us whether the leaf was a chunky, expensive one to make for the plant, or whether it was a more flimsy, cheap one,” Blonder explained. “In other words, how much carbon the plant had invested in the leaf.” In addition the researchers measured the density of the leaves’ vein networks, a measure of the amount of water a plant can transpire and the rate at which it can acquire carbon.

“There is a spectrum between fast- and slow-growing species,” said Blonder. “There is the ‘live fast, die young’ strategy and there is the ‘slow but steady’ strategy. You could compare it to financial strategies investing in stocks versus bonds.” The analyses revealed that while slow-growing evergreens dominated the plant assemblages before the extinction event, fast-growing flowering species had taken their places afterward.

Scientists warn time to stop drilling in the dark

In areas where shale-drilling/hydraulic fracturing is heavy, a dense web of roads, pipelines and well pads turn continuous forests and grasslands into fragmented islands. -  Simon Fraser University PAMR
In areas where shale-drilling/hydraulic fracturing is heavy, a dense web of roads, pipelines and well pads turn continuous forests and grasslands into fragmented islands. – Simon Fraser University PAMR

The co-authors of a new study, including two Simon Fraser University research associates, cite new reasons why scientists, industry representatives and policymakers must collaborate closely on minimizing damage to the natural world from shale gas development. Viorel Popescu and Maureen Ryan, David H. Smith Conservation Research Fellows in SFU’s Biological Sciences department, are among eight international co-authors of the newly published research in Frontiers in Ecology and the Environment.

Shale gas development is the extraction of natural gas from shale formations via deep injection of high-pressure aqueous chemicals to create fractures (i.e., hydraulic fracturing), which releases trapped gas. With shale gas production projected to increase exponentially internationally during the next 30 years, the scientists say their key findings are cause for significant concern and decisive mitigation measures.

“Our findings are highly relevant to British Columbians given the impetus for developing shale resources in northeastern B.C. and the massive LNG facilities and pipeline infrastructure under development throughout the province,” notes Popescu. The SFU Earth2Ocean Group member is also a research associate in the Centre for Environmental Research at the University of Bucharest in Romania.

Key study findings:

  • One of the greatest threats to animal and plant-life is the cumulative impact of rapid, widespread shale development, with each individual well contributing collectively to air, water, noise and light pollution.

    “Think about the landscape and its habitats as a canvas,” explains Popescu. “At first, the few well pads, roads and pipelines from shale development seem like tiny holes and cuts, and the canvas still holds. But if you look at a heavily developed landscape down the road, you see more holes and cuts than natural habitats. Forests or grasslands that were once continuous are now islands fragmented by a dense web of roads, pipelines and well pads. At what point does the canvas fall apart? And what are the ecological implications for wide-ranging, sensitive species such as caribou or grizzly bears?”

  • Determining the environmental impact of chemical contamination from spills, well-casing failure and other accidents associated with shale gas production must become a top priority.

    Shale-drilling operations for oil and natural gas have increased by more than 700 per cent in the United States since 2007 and Western Canada is undergoing a similar shale gas production boom. But the industry’s effects on nature and wildlife are not well understood. Accurate data on the release of fracturing chemicals into the environment needs to be gathered before understanding can improve.

  • The lack of accessible and reliable information on spills, wastewater disposal and fracturing fluids is greatly impeding improved understanding. This study identifies that only five of 24 American states with active shale gas reservoirs maintain public records of spills and accidents.

The authors reviewed chemical disclosure statements for 150 wells in three top-gas producing American states and found that, on average, two out of three wells were fractured with at least one undisclosed chemical. Some of the wells in the chemical disclosure registry were fractured with fluid containing 20 or more undisclosed chemicals.

The authors call this an arbitrary and inconsistent standard of chemical disclosure. This is particularly worrisome given the chemical makeup of fracturing fluid and wastewater, which can include carcinogens and radioactive substances, is often unknown.

“Past lessons from large scale resource extraction and energy development -large dams, intensive forestry, or biofuel plantations – have shown us that development that outpaces our understanding of ecological impacts can have dire unintended consequences,” notes Ryan. She is a research fellow in the University of Washington’s School of Environmental and Forest Sciences.

“It’s our responsibility to look forward. For example, here in Canada, moving natural gas from northeastern B.C. to the 16 proposed LNG plants would require hundreds of kilometers of new pipeline and road infrastructure, and large port terminals on top of the effects of drilling. We must not just consider the impact of these projects individually, but also try to evaluate the ecological impacts holistically.”

‘Fracking’ in the dark: Biological fallout of shale-gas production still largely unknown

Eight conservation biologists from various organizations and institutions, including Princeton University, found that shale-gas extraction in the United States has vastly outpaced scientists' understanding of the industry's environmental impact. With shale-gas production projected to surge during the next 30 years, determining and minimizing the industry's effects on nature and wildlife must become a top priority for scientists, industry and policymakers, the researchers said. The photo above shows extensive natural-gas operations at Jonah Field in Wyoming. -  Photo courtesy of EcoFlight.
Eight conservation biologists from various organizations and institutions, including Princeton University, found that shale-gas extraction in the United States has vastly outpaced scientists’ understanding of the industry’s environmental impact. With shale-gas production projected to surge during the next 30 years, determining and minimizing the industry’s effects on nature and wildlife must become a top priority for scientists, industry and policymakers, the researchers said. The photo above shows extensive natural-gas operations at Jonah Field in Wyoming. – Photo courtesy of EcoFlight.

In the United States, natural-gas production from shale rock has increased by more than 700 percent since 2007. Yet scientists still do not fully understand the industry’s effects on nature and wildlife, according to a report in the journal Frontiers in Ecology and the Environment.

As gas extraction continues to vastly outpace scientific examination, a team of eight conservation biologists from various organizations and institutions, including Princeton University, concluded that determining the environmental impact of gas-drilling sites – such as chemical contamination from spills, well-casing failures and other accidents – must be a top research priority.

With shale-gas production projected to surge during the next 30 years, the authors call on scientists, industry representatives and policymakers to cooperate on determining – and minimizing – the damage inflicted on the natural world by gas operations such as hydraulic fracturing, or “fracking.” A major environmental concern, hydraulic fracturing releases natural gas from shale by breaking the rock up with a high-pressure blend of water, sand and other chemicals, which can include carcinogens and radioactive substances.

“We can’t let shale development outpace our understanding of its environmental impacts,” said co-author Morgan Tingley, a postdoctoral research associate in the Program in Science, Technology and Environmental Policy in Princeton’s Woodrow Wilson School of Public and International Affairs.

“The past has taught us that environmental impacts of large-scale development and resource extraction, whether coal plants, large dams or biofuel monocultures, are more than the sum of their parts,” Tingley said.

The researchers found that there are significant “knowledge gaps” when it comes to direct and quantifiable evidence of how the natural world responds to shale-gas operations. A major impediment to research has been the lack of accessible and reliable information on spills, wastewater disposal and the composition of fracturing fluids. Of the 24 American states with active shale-gas reservoirs, only five – Pennsylvania, Colorado, New Mexico, Wyoming and Texas – maintain public records of spills and accidents, the researchers report.

“The Pennsylvania Department of Environmental Protection’s website is one of the best sources of publicly available information on shale-gas spills and accidents in the nation. Even so, gas companies failed to report more than one-third of spills in the last year,” said first author Sara Souther, a postdoctoral research associate at the University of Wisconsin-Madison.

“How many more unreported spills occurred, but were not detected during well inspections?” Souther asked. “We need accurate data on the release of fracturing chemicals into the environment before we can understand impacts to plants and animals.”

One of the greatest threats to animal and plant life identified in the study is the impact of rapid and widespread shale development, which has disproportionately affected rural and natural areas. A single gas well results in the clearance of 3.7 to 7.6 acres (1.5 to 3.1 hectares) of vegetation, and each well contributes to a collective mass of air, water, noise and light pollution that has or can interfere with wild animal health, habitats and reproduction, the researchers report.

“If you look down on a heavily ‘fracked’ landscape, you see a web of well pads, access roads and pipelines that create islands out of what was, in some cases, contiguous habitat,” Souther said. “What are the combined effects of numerous wells and their supporting infrastructure on wide-ranging or sensitive species, like the pronghorn antelope or the hellbender salamander?”

The chemical makeup of fracturing fluid and wastewater is often unknown. The authors reviewed chemical-disclosure statements for 150 wells in three of the top gas-producing states and found that an average of two out of every three wells were fractured with at least one undisclosed chemical. The exact effect of fracturing fluid on natural water systems as well as drinking water supplies remains unclear even though improper wastewater disposal and pollution-prevention measures are among the top state-recorded violations at drilling sites, the researchers found.

“Some of the wells in the chemical disclosure registry were fractured with fluid containing 20 or more undisclosed chemicals,” said senior author Kimberly Terrell, a researcher at the Smithsonian Conservation Biology Institute. “This is an arbitrary and inconsistent standard of chemical disclosure.”

Geologists confirm oxygen levels of ancient oceans

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

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

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

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

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

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

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

Researchers quantify toxic ocean conditions during major extinction 93.9 million years ago

Oxygen in the atmosphere and ocean rose dramatically about 600 million years ago, coinciding with the first proliferation of animal life.Since then, numerous short lived biotic events – typically marked by significant climatic perturbations – took place when oxygen concentrations in the ocean dipped episodically.

The most studied and extensive of these events occurred 93.9 million years ago. By looking at the chemistry of rocks deposited during that time period, specifically coupled carbon and sulfur isotope data, a research team led by University of California, Riverside biogeochemists reports that oxygen-free and hydrogen sulfide-rich waters extended across roughly five percent of the global ocean during this major climatic perturbation – far more than the modern ocean’s 0.1 percent but much less than previous estimates for this event.

The research suggests that previous estimates of oxygen-free and hydrogen sulfide-rich conditions, or “euxinia,” were too high. Nevertheless, the limited and localized euxinia were still sufficiently widespread to have dramatic effect on the entire ocean’s chemistry and thus biological activity.

“These conditions must have impacted nutrient availability in the ocean and ultimately the spatial and temporal distribution of marine life,” said team member Jeremy D. Owens, a former UC Riverside graduate student, who is now a postdoctoral scientist at the Woods Hole Oceanographic Institution. “Under low-oxygen environments, many biologically important metals and other nutrients are removed from seawater and deposited in the sediments on the seafloor, making them less available for life to flourish.”

“What makes this discovery particularly noteworthy is that we mapped out a landscape of bioessential elements in the ocean that was far more perturbed than we expected, and the impacts on life were big,” said Timothy W. Lyons, a professor of biogeochemistry at UCR, Owens’s former advisor and the principal investigator on the research project.

Study results appear online this week in the Proceedings of the National Academy of Sciences.

Across the event 93.9 million years ago, a major biological extinction in the marine realm has already been documented. Also associated with this event are high levels of carbon dioxide in the atmosphere, which are linked to elevated ocean and atmospheric temperatures. Associated consequences include likely enhanced global rainfall and weathering of the continents, which further shifted the chemistry of the ocean.

“Our work shows that even though only a small portion of the ocean contained toxic and metal-scavenging hydrogen sulfide, it was sufficiently large so that changes to the ocean’s chemistry and biology were likely profound,” Owens said. “What this says is that only portions of the ocean need to contain sulfide to greatly impact biota.”

For their analysis, the researchers collected seafloor mud samples, now rock, from multiple localities in England and Italy. They then performed chemical extraction on the samples to analyze the sulfur isotope compositions in order to estimate the chemistry of the global ocean.

According to the researchers, the importance of their study is elevated by the large amount of previous work on the same interval and thus the extensive availability of supporting data and samples. Yet despite all this past research, the team was able to make a fundamental discovery about the global conditions in the ancient ocean and their impacts on life.

“Today, we are facing rising carbon dioxide contents in the atmosphere through human activities, and the amount of oxygen in the ocean may drop correspondingly in the face of rising seawater temperatures,” Lyons said. “Oxygen is less soluble in warmer water, and there are already suggestions of such decreases. In the face of these concerns, our findings from the warm, oxygen-poor ancient ocean may be a warning shot about yet another possible perturbation to marine ecology in the future.”