Research links soil mineral surfaces to key atmospheric processes

Pictured are, from left, are David Bish, Melissa Donaldson and Jonathan Raff. -  Indiana University
Pictured are, from left, are David Bish, Melissa Donaldson and Jonathan Raff. – Indiana University

Research by Indiana University scientists finds that soil may be a significant and underappreciated source of nitrous acid, a chemical that plays a pivotal role in atmospheric processes such as the formation of smog and determining the lifetime of greenhouse gases.

The study shows for the first time that the surface acidity of common minerals found in soil determines whether the gas nitrous acid will be released into the atmosphere. The finding could contribute to improved models for understanding and controlling air pollution, a significant public health concern.

“We find that the surfaces of minerals in the soil can be much more acidic than the overall pH of the soil would suggest,” said Jonathan Raff, assistant professor in the School of Public and Environmental Affairs and Department of Chemistry. “It’s the acidity of the soil minerals that acts as a knob or a control lever, and that determines whether nitrous acid outgasses from soil or remains as nitrite.”

The article, “Soil surface acidity plays a determining role in the atmospheric-terrestrial exchange of nitrous acid,” will be published this week in the journal Proceedings of the National Academy of Sciences. Melissa A. Donaldson, a Ph.D. student in the School of Public and Environmental Affairs, is the lead author. Co-authors are Raff and David L. Bish, the Haydn Murray Chair of Applied Clay Mineralogy in the Department of Geological Sciences.

Nitrous acid, or HONO, plays a key role in regulating atmospheric processes. Sunlight causes it to break down into nitric oxide and the hydroxyl radical, OH. The latter controls the atmospheric lifetime of gases important to air quality and climate change and initiates the chemistry leading to the formation of ground-level ozone, a primary component of smog.

Scientists have known about the nitrous acid’s role in air pollution for 40 years, but they haven’t fully understood how it is produced and destroyed or how it interacts with other substances, because HONO is unstable and difficult to measure.

“Only in the last 10 years have we had the technology to study nitrous acid under environmentally relevant conditions,” Raff said.

Recent studies have shown nitrous acid to be emitted from soil in many locations. But this was unexpected because, according to basic chemistry, the reactions that release nitrous acid should take place only in extremely acidic soils, typically found in rain forests or the taiga of North America and Eurasia.

The standard method to determine the acidity of soil is to mix bulk soil with water and measure the overall pH. But the IU researchers show that the crucial factor is not overall pH but the acidity at the surface of soil minerals, especially iron oxides and aluminum oxides. At the molecular level, the water adsorbed directly to these minerals is unusually acidic and facilitates the conversion of nitrite in the soil to nitrous acid, which then volatilizes.

“With the traditional approach of calculating soil pH, we were severely underestimating nitrous acid emissions from soil,” Raff said. “I think the source is going to turn out to be more important than was previously imagined.”

The research was carried out using soil from a farm field near Columbus, Ind. But aluminum and iron oxides are ubiquitous in soil, and the researchers say the results suggest that about 70 percent of Earth’s soils could be sources of nitrous acid.

Ultimately, the research will contribute to a better understanding of how nitrous acid is produced and how it affects atmospheric processes. That in turn will improve the computer models used by the U.S. Environmental Protection Agency and other regulatory agencies to control air pollution, which the World Health Organization estimates contributes to 7 million premature deaths annually.

“With improved models, policymakers can make better judgments about the costs and benefits of regulations,” Raff said. “If we don’t get the chemistry right, we’re not going to get the right answers to our policy questions regarding air pollution.”

Research links soil mineral surfaces to key atmospheric processes

Pictured are, from left, are David Bish, Melissa Donaldson and Jonathan Raff. -  Indiana University
Pictured are, from left, are David Bish, Melissa Donaldson and Jonathan Raff. – Indiana University

Research by Indiana University scientists finds that soil may be a significant and underappreciated source of nitrous acid, a chemical that plays a pivotal role in atmospheric processes such as the formation of smog and determining the lifetime of greenhouse gases.

The study shows for the first time that the surface acidity of common minerals found in soil determines whether the gas nitrous acid will be released into the atmosphere. The finding could contribute to improved models for understanding and controlling air pollution, a significant public health concern.

“We find that the surfaces of minerals in the soil can be much more acidic than the overall pH of the soil would suggest,” said Jonathan Raff, assistant professor in the School of Public and Environmental Affairs and Department of Chemistry. “It’s the acidity of the soil minerals that acts as a knob or a control lever, and that determines whether nitrous acid outgasses from soil or remains as nitrite.”

The article, “Soil surface acidity plays a determining role in the atmospheric-terrestrial exchange of nitrous acid,” will be published this week in the journal Proceedings of the National Academy of Sciences. Melissa A. Donaldson, a Ph.D. student in the School of Public and Environmental Affairs, is the lead author. Co-authors are Raff and David L. Bish, the Haydn Murray Chair of Applied Clay Mineralogy in the Department of Geological Sciences.

Nitrous acid, or HONO, plays a key role in regulating atmospheric processes. Sunlight causes it to break down into nitric oxide and the hydroxyl radical, OH. The latter controls the atmospheric lifetime of gases important to air quality and climate change and initiates the chemistry leading to the formation of ground-level ozone, a primary component of smog.

Scientists have known about the nitrous acid’s role in air pollution for 40 years, but they haven’t fully understood how it is produced and destroyed or how it interacts with other substances, because HONO is unstable and difficult to measure.

“Only in the last 10 years have we had the technology to study nitrous acid under environmentally relevant conditions,” Raff said.

Recent studies have shown nitrous acid to be emitted from soil in many locations. But this was unexpected because, according to basic chemistry, the reactions that release nitrous acid should take place only in extremely acidic soils, typically found in rain forests or the taiga of North America and Eurasia.

The standard method to determine the acidity of soil is to mix bulk soil with water and measure the overall pH. But the IU researchers show that the crucial factor is not overall pH but the acidity at the surface of soil minerals, especially iron oxides and aluminum oxides. At the molecular level, the water adsorbed directly to these minerals is unusually acidic and facilitates the conversion of nitrite in the soil to nitrous acid, which then volatilizes.

“With the traditional approach of calculating soil pH, we were severely underestimating nitrous acid emissions from soil,” Raff said. “I think the source is going to turn out to be more important than was previously imagined.”

The research was carried out using soil from a farm field near Columbus, Ind. But aluminum and iron oxides are ubiquitous in soil, and the researchers say the results suggest that about 70 percent of Earth’s soils could be sources of nitrous acid.

Ultimately, the research will contribute to a better understanding of how nitrous acid is produced and how it affects atmospheric processes. That in turn will improve the computer models used by the U.S. Environmental Protection Agency and other regulatory agencies to control air pollution, which the World Health Organization estimates contributes to 7 million premature deaths annually.

“With improved models, policymakers can make better judgments about the costs and benefits of regulations,” Raff said. “If we don’t get the chemistry right, we’re not going to get the right answers to our policy questions regarding air pollution.”

Predicting landslides with light

Optical fiber sensors are used around the world to monitor the condition of difficult-to-access segments of infrastructure-such as the underbellies of bridges, the exterior walls of tunnels, the feet of dams, long pipelines and railways in remote rural areas.

Now, a team of researchers in Italy are expanding the reach of optical fiber sensors “to the hills” by embedding them in shallow trenches within slopes to detect and monitor both large landslides and slow slope movements. The team will present their research at The Optical Society’s (OSA) 98th Annual Meeting, Frontiers in Optics, being held Oct. 19-23 in Tucson, Arizona, USA.

As major disasters around the world this year have shown, landslides can be stark examples of nature at her most unforgiving. Within seconds, a major landslide can completely erase houses and structures that have stood for years, and the catastrophic toll they inflict on communities is felt not just in that destructive loss of property but in the devastating loss of life. The 1999 Vargus tragedy in Venezuela, for instance, killed tens of thousands of people and erased whole towns from the map without warning.

The motivation for an early warning technology, like the one the Italian team has devised, is to find a way to mitigate such losses -just as hurricane tracking can prompt coastal evacuations and save lives.

Predicting Landslides by Detecting Land Strains


Landslides are failures of a rock or soil mass, and are always preceded by various types of “pre-failure” strains-known technically as elastic, plastic and viscous volumetric and shear strains. While the magnitude of these pre-failure strains depends on the rock or soil involved-ranging from fractured rock debris and pyroclastic flows to fine-grained soils-they are measurable. This new technology can detect small shifts in soil slopes, and thus can detect the onset of landslides. Usually, electrical sensors have been used for monitoring landslides, but these sensors are easily damaged. Optical fiber sensors are more robust, economical and sensitive. This is where the new technology could make a difference.

“Distributed optical fiber sensors can act as a ‘nervous system’ of slopes by measuring the tensile strain of the soil they’re embedded within,” explained Professor Luigi Zeni, who is in the Department of Industrial & Information Engineering at the Second University of Naples.

Taking it a step further, Zeni and his colleagues worked out a way of combining several types of optical fiber sensors into a plastic tube that twists and moves under the forces of pre-failure strains. Researchers are then able to monitor the movement and bending of the optical fiber remotely to determine if a landslide is imminent.

The use of novel fiber optic sensors “allows us to overcome some limitations of traditional inclinometers, because fiber-based ones have no moving parts and can withstand larger soil deformations,” Zeni said. “These sensors can be used to cover very large areas-several square kilometers-and interrogated in a time-continuous way to pinpoint any critical zones.”

The findings clearly demonstrate the potential of distributed optical fiber sensors as an entirely new tool to monitor areas subject to landslide risk, Zeni said, and to develop early warning systems based on geo-indicators-early deformations-of slope failures.

Predicting landslides with light

Optical fiber sensors are used around the world to monitor the condition of difficult-to-access segments of infrastructure-such as the underbellies of bridges, the exterior walls of tunnels, the feet of dams, long pipelines and railways in remote rural areas.

Now, a team of researchers in Italy are expanding the reach of optical fiber sensors “to the hills” by embedding them in shallow trenches within slopes to detect and monitor both large landslides and slow slope movements. The team will present their research at The Optical Society’s (OSA) 98th Annual Meeting, Frontiers in Optics, being held Oct. 19-23 in Tucson, Arizona, USA.

As major disasters around the world this year have shown, landslides can be stark examples of nature at her most unforgiving. Within seconds, a major landslide can completely erase houses and structures that have stood for years, and the catastrophic toll they inflict on communities is felt not just in that destructive loss of property but in the devastating loss of life. The 1999 Vargus tragedy in Venezuela, for instance, killed tens of thousands of people and erased whole towns from the map without warning.

The motivation for an early warning technology, like the one the Italian team has devised, is to find a way to mitigate such losses -just as hurricane tracking can prompt coastal evacuations and save lives.

Predicting Landslides by Detecting Land Strains


Landslides are failures of a rock or soil mass, and are always preceded by various types of “pre-failure” strains-known technically as elastic, plastic and viscous volumetric and shear strains. While the magnitude of these pre-failure strains depends on the rock or soil involved-ranging from fractured rock debris and pyroclastic flows to fine-grained soils-they are measurable. This new technology can detect small shifts in soil slopes, and thus can detect the onset of landslides. Usually, electrical sensors have been used for monitoring landslides, but these sensors are easily damaged. Optical fiber sensors are more robust, economical and sensitive. This is where the new technology could make a difference.

“Distributed optical fiber sensors can act as a ‘nervous system’ of slopes by measuring the tensile strain of the soil they’re embedded within,” explained Professor Luigi Zeni, who is in the Department of Industrial & Information Engineering at the Second University of Naples.

Taking it a step further, Zeni and his colleagues worked out a way of combining several types of optical fiber sensors into a plastic tube that twists and moves under the forces of pre-failure strains. Researchers are then able to monitor the movement and bending of the optical fiber remotely to determine if a landslide is imminent.

The use of novel fiber optic sensors “allows us to overcome some limitations of traditional inclinometers, because fiber-based ones have no moving parts and can withstand larger soil deformations,” Zeni said. “These sensors can be used to cover very large areas-several square kilometers-and interrogated in a time-continuous way to pinpoint any critical zones.”

The findings clearly demonstrate the potential of distributed optical fiber sensors as an entirely new tool to monitor areas subject to landslide risk, Zeni said, and to develop early warning systems based on geo-indicators-early deformations-of slope failures.

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.

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.

Trinity geologists re-write Earth’s evolutionary history books

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

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

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

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

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

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

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

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

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

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

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

Trinity geologists re-write Earth’s evolutionary history books

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

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

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

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

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

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

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

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

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

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

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

New Oso report, rockfall in Yosemite, and earthquake models

From AGU’s blogs: Oso disaster had its roots in earlier landslides

A research team tasked with being some of the first scientists and engineers to evaluate extreme events has issued its findings on disastrous Oso, Washington, landslide. The report studies the conditions and causes related to the March 22 mudslide that killed 43 people and destroyed the Steelhead Haven neighborhood in Oso, Washington. The team from the Geotechnical Extreme Events Reconnaissance (GEER) Association, funded by the National Science Foundation, determined that intense rainfall in the three weeks before the slide likely was a major issue, but factors such as altered groundwater migration, weakened soil consistency because of previous landslides and changes in hillside stresses played key roles.

From this week’s Eos: Reducing Rockfall Risk in Yosemite National Park

The glacially sculpted granite walls of Yosemite Valley attract 4 million visitors a year, but rockfalls from these cliffs pose substantial hazards. Responding to new studies, the National Park Service recently took actions to reduce the human risk posed by rockfalls in Yosemite National Park.

From AGU’s journals: A new earthquake model may explain discrepancies in San Andreas fault slip

Investigating the earthquake hazards of the San Andreas Fault System requires an accurate understanding of accumulating stresses and the history of past earthquakes. Faults tend to go through an “earthquake cycle”-locking and accumulating stress, rupturing in an earthquake, and locking again in a well-accepted process known as “elastic rebound.” One of the key factors in preparing for California’s next “Big One” is estimating the fault slip rate, the speed at which one side of the San Andreas Fault is moving past the other.

Broadly speaking, there are two ways geoscientists study fault slip. Geologists formulate estimates by studying geologic features at key locations to study slip rates through time. Geodesists, scientists who measure the size and shape of the planet, use technologies like GPS and satellite radar interferometry to estimate the slip rate, estimates which often differ from the geologists’ estimations.

In a recent study by Tong et al., the authors develop a new three-dimensional viscoelastic earthquake cycle model that represents 41 major fault segments of the San Andreas Fault System. While previous research has suggested that there are discrepancies between the fault slip rates along the San Andreas as measured by geologic and geodetic means, the authors find that there are no significant differences between the two measures if the thickness of the tectonic plate and viscoelasticity are taken into account. The authors find that the geodetic slip rate depends on the plate thickness over the San Andreas, a variable lacking in previous research.

The team notes that of the 41 studied faults within the San Andreas Fault system, a small number do in fact have disagreements between the geologic and geodetic slip rates. These differences could be attributed to inadequate data coverage or to incomplete knowledge of the fault structures or the chronological sequence of past events.

New Oso report, rockfall in Yosemite, and earthquake models

From AGU’s blogs: Oso disaster had its roots in earlier landslides

A research team tasked with being some of the first scientists and engineers to evaluate extreme events has issued its findings on disastrous Oso, Washington, landslide. The report studies the conditions and causes related to the March 22 mudslide that killed 43 people and destroyed the Steelhead Haven neighborhood in Oso, Washington. The team from the Geotechnical Extreme Events Reconnaissance (GEER) Association, funded by the National Science Foundation, determined that intense rainfall in the three weeks before the slide likely was a major issue, but factors such as altered groundwater migration, weakened soil consistency because of previous landslides and changes in hillside stresses played key roles.

From this week’s Eos: Reducing Rockfall Risk in Yosemite National Park

The glacially sculpted granite walls of Yosemite Valley attract 4 million visitors a year, but rockfalls from these cliffs pose substantial hazards. Responding to new studies, the National Park Service recently took actions to reduce the human risk posed by rockfalls in Yosemite National Park.

From AGU’s journals: A new earthquake model may explain discrepancies in San Andreas fault slip

Investigating the earthquake hazards of the San Andreas Fault System requires an accurate understanding of accumulating stresses and the history of past earthquakes. Faults tend to go through an “earthquake cycle”-locking and accumulating stress, rupturing in an earthquake, and locking again in a well-accepted process known as “elastic rebound.” One of the key factors in preparing for California’s next “Big One” is estimating the fault slip rate, the speed at which one side of the San Andreas Fault is moving past the other.

Broadly speaking, there are two ways geoscientists study fault slip. Geologists formulate estimates by studying geologic features at key locations to study slip rates through time. Geodesists, scientists who measure the size and shape of the planet, use technologies like GPS and satellite radar interferometry to estimate the slip rate, estimates which often differ from the geologists’ estimations.

In a recent study by Tong et al., the authors develop a new three-dimensional viscoelastic earthquake cycle model that represents 41 major fault segments of the San Andreas Fault System. While previous research has suggested that there are discrepancies between the fault slip rates along the San Andreas as measured by geologic and geodetic means, the authors find that there are no significant differences between the two measures if the thickness of the tectonic plate and viscoelasticity are taken into account. The authors find that the geodetic slip rate depends on the plate thickness over the San Andreas, a variable lacking in previous research.

The team notes that of the 41 studied faults within the San Andreas Fault system, a small number do in fact have disagreements between the geologic and geodetic slip rates. These differences could be attributed to inadequate data coverage or to incomplete knowledge of the fault structures or the chronological sequence of past events.