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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Other accepted projects include:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Research provides new theory on cause of ice age 2.6 million years ago

New research published today (Friday 27th June 2014) in the journal Nature Scientific Reports has provided a major new theory on the cause of the ice age that covered large parts of the Northern Hemisphere 2.6 million years ago.

The study, co-authored by Dr Thomas Stevens, from the Department of Geography at Royal Holloway, University of London, found a previously unknown mechanism by which the joining of North and South America changed the salinity of the Pacific Ocean and caused major ice sheet growth across the Northern Hemisphere.

The change in salinity encouraged sea ice to form which in turn created a change in wind patterns, leading to intensified monsoons. These provided moisture that caused an increase in snowfall and the growth of major ice sheets, some of which reached 3km thick.

The team of researchers analysed deposits of wind-blown dust called red clay that accumulated between six million and two and a half million years ago in north central China, adjacent to the Tibetan plateau, and used them to reconstruct changing monsoon precipitation and temperature.

“Until now, the cause of the Quaternary ice age had been a hotly debated topic”, said Dr Stevens. “Our findings suggest a significant link between ice sheet growth, the monsoon and the closing of the Panama Seaway, as North and South America drifted closer together. This provides us with a major new theory on the origins of the ice age, and ultimately our current climate system.”

Surprisingly, the researchers found there was a strengthening of the monsoon during global cooling, instead of the intense rainfall normally associated with warmer climates.

Dr Stevens added: “This led us to discover a previously unknown interaction between plate tectonic movements in the Americas and dramatic changes in global temperature. The intensified monsoons created a positive feedback cycle, promoting more global cooling, more sea ice and even stronger precipitation, culminating in the spread of huge glaciers across the Northern Hemisphere.”

Acid mine drainage reduces radioactivity in fracking waste

Much of the naturally occurring radioactivity in fracking wastewater might be removed by blending it with another wastewater from acid mine drainage, according to a Duke University-led study.

“Fracking wastewater and acid mine drainage each pose well-documented environmental and public health risks. But in laboratory tests, we found that by blending them in the right proportions we can bind some of the fracking contaminants into solids that can be removed before the water is discharged back into streams and rivers,” said Avner Vengosh, professor of geochemistry and water quality at Duke’s Nicholas School of the Environment.

“This could be an effective way to treat Marcellus Shale hydraulic fracturing wastewater, while providing a beneficial use for acid mine drainage that currently is contaminating waterways in much of the northeastern United States,” Vengosh said. “It’s a win-win for the industry and the environment.”

Blending fracking wastewater with acid mine drainage also could help reduce the depletion of local freshwater resources by giving drillers a source of usable recycled water for the hydraulic fracturing process, he added.

“Scarcity of fresh water in dry regions or during periods of drought can severely limit shale gas development in many areas of the United States and in other regions of the world where fracking is about to begin,” Vengosh said. “Using acid mine drainage or other sources of recycled or marginal water may help solve this problem and prevent freshwater depletion.”

The peer-reviewed study was published in late December 2013 in the journal Environmental Science & Technology.

In hydraulic fracturing – or fracking, as it is sometimes called – millions of tons of water are injected at high pressure down wells to crack open shale deposits buried deep underground and extract natural gas trapped within the rock. Some of the water flows back up through the well, along with natural brines and the natural gas. This “flowback fluid” typically contains high levels of salts, naturally occurring radioactive materials such as radium, and metals such as barium and strontium.

A study last year by the Duke team showed that standard treatment processes only partially remove these potentially harmful contaminants from Marcellus Shale wastewater before it is discharged back into streams and waterways, causing radioactivity to accumulate in stream sediments near the disposal site.

Acid mine drainage flows out of abandoned coal mines into many streams in the Appalachian Basin. It can be highly toxic to animals, plants and humans, and affects the quality of hundreds of waterways in Pennsylvania and West Virginia.

Because much of the current Marcellus shale gas development is taking place in regions where large amounts of historic coal mining occurred, some experts have suggested that acid mine drainage could be used to frack shale gas wells in place of fresh water.

To test that hypothesis, Vengosh and his team blended different mixtures of Marcellus Shale fracking wastewater and acid mine drainage, all of which were collected from sites in western Pennsylvania and provided to the scientists by the industry.

After 48 hours, the scientists examined the chemical and radiological contents of 26 different mixtures. Geochemical modeling was used to simulate the chemical and physical reactions that had occurred after the blending; the results of the modeling were then verified using x-ray diffraction and by measuring the radioactivity of the newly formed solids.

“Our analysis suggested that several ions, including sulfate, iron, barium and strontium, as well as between 60 and 100 percent of the radium, had precipitated within the first 10 hours into newly formed solids composed mainly of strontium barite,” Vengosh said. These radioactive solids could be removed from the mixtures and safely disposed of at licensed hazardous-waste facilities, he said. The overall salinity of the blended fluids was also reduced, making the treated water suitable for re-use at fracking sites.

“The next step is to test this in the field. While our laboratory tests show that is it technically possible to generate recycled, treated water suitable for hydraulic fracturing, field-scale tests are still necessary to confirm its feasibility under operational conditions,” Vengosh said.

Reading ancient climate from plankton shells

This is a CT reconstruction of a foram measured at the Diamond Light Source. -  Oscar Branson, University of Cambridge
This is a CT reconstruction of a foram measured at the Diamond Light Source. – Oscar Branson, University of Cambridge

Climate changes from millions of years ago are recorded at daily rate in ancient sea shells, new research shows.

A huge X-ray microscope has revealed growth bands in plankton shells that show how shell chemistry records the sea temperature.

The results could allow scientists to chart short timescale changes in ocean temperatures hundreds of millions of years ago.

Plankton shells show features like tree rings, recording historical climate.

It’s important to understand current climate change in the light of how climate has varied in the geological past. One way to do this, for the last few thousand years, is to analyse ice from the poles. The planet’s temperature and atmosphere are recorded by bubbles of ancient air trapped in polar ice cores. The oldest Antarctic ice core records date back to around 800,000 years ago.

Results just published in the journal Earth and Planetary Sciences Letters reveal how ancient climate change, pushing back hundreds of millions of years ago into deep time, is recorded by the shells of oceanic plankton.

As microbial plankton grow in ocean waters, their shells, made of the mineral calcite, trap trace amounts of chemical impurities, maybe only a few atoms in a million getting replaced by impurity atoms. Scientists have noticed that plankton growing in warmer waters contain more impurities, but it has not been clear how and why this “proxy” for temperature works.

When the plankton die, they fall to the muddy ocean floor, and can be recovered today from that muddy ocean floor sediments, which preserve the shells as they are buried. The amount of impurity, measured in fossil plankton shells, provides a record of past ocean temperature, dating back more than 100 million years ago.

Now, researchers from the Department of Earth Sciences at the University of Cambridge have measured traces of magnesium in the shells of plankton using an X-ray microscope in Berkeley, California, at the “Advanced Light Source” synchrotron – a huge particle accelerator that generates X-rays to study matter in minuscule detail.

The powerful X-ray microscope has revealed narrow nanoscale bands in the plankton shell where the amount of magnesium is very slightly higher, at length scales as small as one hundredth that of a human hair. They are growth bands, rather like tree rings, but in plankton the bands occur daily or so, rather than yearly.

“These growth bands in plankton show the day by day variations in magnesium in the shell at a 30 nanometre length scale. For slow-growing plankton it opens the way to seeing seasonal variations in ocean temperatures or plankton growth in samples dating back tens to hundreds of millions of years”, says Professor Simon Redfern, one of the experimenters on the project.

“Our X-ray data show that the trace magnesium sits inside the crystalline mineral structure of the plankton shell. That’s important because it validates previous assumptions about using magnesium contents as a measure of past ocean temperature.”

The chemical environment of the trace elements in the plankton shell, revealed in the new measurements, shows that the magnesium sits in calcite crystal replacing calcium, rather than in microbial membranes in their impurities in the shell. This helps explain why temperature affects the chemistry of plankton shells – warmer waters favour increased magnesium in calcite.

The group are now using the UK’s “Diamond” synchrotron X-ray facility to measure how plankton shells grow and whether they change at all in the ocean floor sediments. Their latest results could allow scientists to establish climate variability in Earth’s far distant past, as well as providing new routes to measure ocean acidification and salinity in past oceans.

Radioactive shale gas contaminants found at wastewater discharge site

Elevated levels of radioactivity, salts and metals have been found in river water and sediments at a site where treated water from oil and gas operations is discharged into a western Pennsylvania creek.

“Radium levels were about 200 times greater in sediment samples collected where the Josephine Brine Treatment Facility discharges its treated wastewater into Blacklick Creek than in sediment samples collected just upstream of the plant,” said Avner Vengosh, professor of geochemistry and water quality at Duke University’s Nicholas School of the Environment.

The new Duke study examined the quality of shale gas wastewater from hydraulic fracturing and the stream water above and below the disposal site. The study found that some of the discharged effluent is derived from the Marcellus shale gas flowback water, which is naturally high in salinity and radioactivity.

High concentrations of some salts and metals were also observed in the stream water. “The treatment removes a substantial portion of the radioactivity, but it does not remove many of the other salts, including bromide,” Vengosh said. “When the high-bromide effluents are discharged to the stream, it increases the concentrations of bromide above the original background levels. This is significant because bromide increases the risks for formation of highly toxic disinfection byproducts in drinking water treatment facilities that are located downstream.”

“The radioactivity levels we found in sediments near the outflow are above management regulations in the U.S. and would only be accepted at a licensed radioactive disposal facility,” said Robert B. Jackson, professor of environmental science at Duke. “The facility is quite effective in removing metals such as barium from the water but concentrates sulfates, chlorides and bromides. In fact this single facility contributes four-fifths of the total downstream chloride flow at this point.”

The Duke team also analyzed stream-bottom sediments for radium isotopes that are typically found in Marcellus wastewater. “Although the facility’s treatment process significantly reduced radium and barium levels in the wastewater, the amount of radioactivity that has accumulated in the river sediments still exceeds thresholds for safe disposal of radioactive materials,” Vengosh said. “Years of disposal of oil and gas wastewater with high radioactivity has created potential environmental risks for thousands of years to come.”

“While water contamination can be mitigated by treatment to a certain degree, our findings indicate that disposal of wastewater from both conventional and unconventional oil and gas operations has degraded the surface water and sediments,” said Nathaniel R. Warner, a recent Ph.D. graduate of Duke who is now a postdoctoral researcher at Dartmouth College. “This could be a long-term legacy of radioactivity.”

Industry has made efforts to reuse or to transport shale gas wastewater to deep injection wells, but wastewater is still discharged to the environment in some states. “It is clear that this practice of releasing wastewater without adequate treatment should be stopped in order to protect freshwater resources in areas of oil and gas development,” Vengosh said.

The Duke team published their findings Oct. 2 in the peer-reviewed journal Environmental Science & Technology.

Sea level influenced tropical climate during the last ice age

The exposed Sunda Shelf during glacial times greatly affected the atmospheric circulation. The shelf is shown on the left for present-day as the light-blue submerged areas between Java, Sumatra, Borneo, and Thailand, and on the right for the last ice age as the green exposed area. -  Pedro DiNezio
The exposed Sunda Shelf during glacial times greatly affected the atmospheric circulation. The shelf is shown on the left for present-day as the light-blue submerged areas between Java, Sumatra, Borneo, and Thailand, and on the right for the last ice age as the green exposed area. – Pedro DiNezio

Scientists look at past climates to learn about climate change and the ability to simulate it with computer models. One region that has received a great deal of attention is the Indo-Pacific warm pool, the vast pool of warm water stretching along the equator from Africa to the western Pacific Ocean.

In a new study, Pedro DiNezio of the International Pacific Research Center, University of Hawaii at Manoa, and Jessica Tierney of Woods Hole Oceanographic Institution investigated preserved geological clues (called “proxies”) of rainfall patterns during the last ice age when the planet was dramatically colder than today. They compared these patterns with computer model simulations in order to find a physical explanation for the patterns inferred from the proxies.

Their study, which appears in the May 19, online edition of Nature Geoscience, not only reveals unique patterns of rainfall change over the Indo-Pacific warm pool, but also shows that they were caused by the effect of lowered sea level on the configuration of the Indonesian archipelago.

“For our research,” explains lead-author Pedro DiNezio at the International Pacific Research Center, “we compared the climate of the ice age with our recent warmer climate. We analyzed about 100 proxy records of rainfall and salinity stretching from the tropical western Pacific to the western Indian Ocean and eastern Africa. Rainfall and salinity signals recorded in geological sediments can tell us much about past changes in atmospheric circulation over land and the ocean respectively.”

“Our comparisons show that, as many scientists expected, much of the Indo-Pacific warm pool was drier during this glacial period compared with today. But, counter to some theories, several regions, such as the western Pacific and the western Indian Ocean, especially eastern Africa, were wetter,” adds co-author Jessica Tierney from Woods Hole Oceanographic Institute.

In the second step, the scientists matched these rainfall and salinity patterns with simulations from 12 state-of-the-art climate models that are used to also predict future climate change. For this matching they applied a method of categorical data comparison called the ‘Cohen’s kappa’ statistic. Though widely used in the medical field, this method has not yet been used to match geological climate signals with climate model simulations.

“We were taken aback that only one model out of the 12 showed statistical agreement with the proxy-inferred patterns of the rainfall changes. This model, though, agrees well with both the rainfall and salinity indicators – two entirely independent sets of proxy data covering distinct areas of the tropics,” says DiNezio.

The model reveals that the dry climate during the glacial period was driven by reduced convection over a region of the warm pool called the Sunda Shelf. Today the shelf is submerged beneath the Gulf of Thailand, but was above sea level during the glacial period, when sea level was about 120 m lower.

“The exposure of the Sunda Shelf greatly weakened convection over the warm pool, with far-reaching impacts on the large-scale circulation and on rainfall patterns from Africa to the western Pacific and northern Australia,” explains DiNezio.

The main weakness of the other models, according to the authors, is their limited ability to simulate convection, the vertical air motions that lift humid air into the atmosphere. Differences in the way each model simulates convection may explain why the results for the glacial period are so different.

“Our research resolves a decades-old question of what the response of tropical climate was to glaciation,” concludes DiNezio. “The study, moreover, presents a fine benchmark for assessing the ability of climate models to simulate the response of tropical convection to altered land masses and global temperatures.

Why Is The Ocean Salty?





Pacific Ocean at dawn. Today's ocean salt has ancient origins. As the earth formed, gases spewing from its interior released salt ions that reached the ocean via rainfall or land runoff. (Credit: Michele Hogan)
Pacific Ocean at dawn. Today’s ocean salt has ancient origins. As the earth formed, gases spewing from its interior released salt ions that reached the ocean via rainfall or land runoff. (Credit: Michele Hogan)

The saltiness of the sea comes from dissolved minerals, especially sodium, chlorine, sulfur, calcium, magnesium, and potassium, says Galen McKinley, a UW-Madison professor of atmospheric and oceanic sciences.



Today’s ocean salt has ancient origins. As the earth formed, gases spewing from its interior released salt ions that reached the ocean via rainfall or land runoff.


Now, the ocean’s salinity is basically constant. “Ions aren’t being removed or supplied in an appreciable amount,” McKinley says. “The removal and sources that do exist are so small and the reservoir is so large that those ions just stay in the water.” For example, she says, “Each year, runoff from the land adds only 0.00005 percent of total ocean salts.”



In lakes, relatively rapid turnover of water and its dissolved salts keeps the water fresh – a water droplet and its ions will stay in Lake Superior for about 200 years, compared to roughly 100 to 200 million years in the ocean. “Even if you did have any accumulation of an ion in a lake, it would be washed out quickly,” McKinley explains.



Ocean salts, however, have no place to go. “The ions that were put there long ago have managed to stick around,” McKinley says. “There is geologic evidence that the saltiness of the water has been the way that it is for at least a billion years.”