AGU: Latest from EMSL in Earth science research, new capabilities to support advanced models

Thousands of scientists will converge in Chicago on December 12–16 to hear about the latest and greatest research in the fields of Earth and space science as part of the American Geophysical Union (AGU) Fall Meeting.

Among those featured will be a variety of scientists and users from the Environmental Molecular Sciences Laboratory (EMSL) who will present on topics ranging from techniques for unearthing details about the soil microbiome, to aerosols and atmospheric processes, to carbon cycling and stabilization. EMSL scientists will also present on new tools, capabilities, and programs that stand to advance environmental and atmospheric models, contribute efforts to better understand climate change, as well as generally provide an elevated understanding of the processes in soils and molecular ecosystems.

In addition to the latest research, a team from EMSL will present details about EMSL’s new Molecular Observation Network (MONet). As part of MONet, scientists from around the United States are invited to participate in calls for soil sample submission from key and underrepresented soil ecosystems starting in February. EMSL, in partnership with the Joint Genome Institute and other institutional partners, will catalog, analyze, and create an extensive digital network of soil samples that provide a detailed look at soils and soil processes from across the nation. This network will contribute data and metadata to help advance Earth-system models. Users will also have access to the data, which is supported and developed using EMSL’s advanced computational tools and software.

Below, read about a selection of EMSL researchers and users whose presentations will be delivered at the AGU Fall Meeting.

For more information about EMSL staff scientist and user presentations at AGU, check out the EMSL schedule on the EMSL at AGU web page.

Qian Zhao | Earth scientist  

Mineral dependent persistence of microbial necromass in soil

Monday, Dec. 12 | 10:05 a.m. CST | McCormick Place – S501bcd (South, Level 5)

Qian Zhao aims to grow understanding about the processes that lead to global climate change through his work in geochemistry. Specifically, his research focuses on mineral–organic matter interactions, studying how organic matter is stabilized in soil environments.

“Through chemical interactions with minerals, carbon can be stabilized in soil over hundreds of thousands of years,” he says. “But if carbon does not bond with the minerals in the soil, they can easily be released into the atmosphere—sometimes in the span of just hours.”

At AGU, Zhao will present a recent study regarding mineral–microbe interactions to see how minerals can be stabilized with microbial residues. His team specifically studied agricultural soils, where they used X-ray photoelectron spectroscopy (XPS) to study how carbon signatures are different between carbon that bonds with minerals vs. carbon that does not bond with minerals.

“XPS allows us to measure the bonding energy of electrons from a sample surface,” he says. “It gives us chemical information, including elemental composition and the chemical compound’s oxidation state of elements. With that, we know the chemical information about our sample surface.”

In addition to his work with XPS, Zhao will elaborate on other types of analysis that allowed his team to identify differences between mineral-bonded microbial residues and non-mineral-bonded microbial residues.

“I care about the environment, and most of us are aware of global climate change,” he says. “Soil is one of the largest carbon reservoirs, which can pump tons of carbon into the atmosphere. Our goal is to develop more quantitative information regarding how much carbon contributes to climate change, which will help to provide answers and solutions regarding this global issue.”

 

Emily Graham | EMSL Earth scientist  

The 1000 Soils Pilot: Cross-Biome Multi ‘Omics for Linking Microbial Metabolism to Soil Decomposition

Tuesday, Dec. 13 | 3:15 p.m. CST | McCormick Place – S501a (South, Level 5)

EMSL Earth scientist Emily Graham led an EMSL research pilot known as 1000 Soils that served as a stepping stone for the larger MONet initiative. At AGU, she will present on several datasets from the 1000 Soils Pilot that present a larger picture of how microbes are turning microbial food sources from soils into carbon dioxide under different environments.

As part of her presentation, Graham will discuss microbial genomic content where scientists take microorganisms out of the soil, re-sequence their DNA using advanced instrumentation, and try to understand their genetic makeup. In turn, the data helps expose what functions the microorganisms serve for the larger environment. She will be coupling that information with metabolomics data, where she and her team looked at the different microbial food sources in the soil and broke them down into various microorganism products.

“If you look at microbial genomes and metabolites together, you can get a really good idea of what the microbes are doing and how they are turning food sources into carbon dioxide under different environments,” she says.

Graham said soils hold a tremendous amount of carbon. As the environment changes, those soils become vulnerable to releasing carbon dioxide into the atmosphere, she said.

“What MONet does is provide high-resolution data on some of these very important processes that are happening, which will inform how we represent processes like soil carbon flux in larger-scale models,” she says. “They are key components of making accurate predictions for how environments respond to climate change.”

 

Yuri Corilo | EMSL computational scientist 

Molecular Observations Network Data Portal and Access Gateway: Enabling Data Analysis, Exploration, Visualization, and Seamless Data-Model Integration

Tuesday, Dec. 13 | 3:35 p.m. CST | McCormick Place – E252 (Lakeside, Level 2)

As scientific instruments continue to advance, a challenge scientists face today is how to quickly organize, segregate, and model data from those instruments so that it can be accessed and used in a meaningful way. Advanced scientific instruments deliver thousands of data points that, without proper modeling capabilities and artificial intelligence strategies, may not be used to their fullest potential. EMSL computational scientist Yuri Corilo will discuss the data portal and access gateway for MONet that turns hundreds of thousands of data points into usable and accessible information as part of his presentation at AGU.

“MONet brings together a collection of analytical techniques done for sets of environmental samples from different types of environments from across the country,” he says. “I’ll be talking about the combination of the three main characteristics of the data—data management, metadata management, and data processing and how to make that data available and accessible for the research community.”

Corilo’s research primarily focuses on the development of processing capabilities for data acquired using mass spectrometry. His work applies to metabolomics, natural organic matter, and a range of other applications.

“We are developing ways to standardize the processing, analysis, and capture of metadata,” he says. “We are also developing a way to organize that metadata and how to build a software architecture that makes MONet, itself, come to fruition.”

Corilo says the infrastructure that comprises MONet will help users search for new hypotheses and discover how they can integrate data with new modeling capabilities.

“It is a bigger, high-level view of how we put those pieces together,” he says.

 

Susannah Burrows | EMSL user 

The Agricultural Ice Nuclei at SGP (AGINSGP) experiment: Understanding sources and variability of ice-nucleating particles in the Great Plains

Thursday, Dec. 15 | 12:55 p.m. CST | McCormick Place - E350 (Lakeside, Level 3)

Susannah Burrows, an atmospheric modeler at Pacific Northwest National Laboratory and an EMSL user, will be presenting her research that used EMSL capabilities to support detailed measurements of aerosol physical and chemical properties during a recent field experiment at the Department of Energy's Atmospheric Research Measurement user facility's Southern Great Plains research site. EMSL capabilities enabled Burrows to quantify ice-nucleating particle (INP) concentrations in ambient air, and also to separate them for physical and chemical analysis.

"I’ll be sharing some of our key preliminary findings from the campaign," Burrows says. "I hope the audience will take away that we have some exciting early results from our single-particle analysis of individual INPs, and a lot of high-quality data still waiting to be fully analyzed and explored for additional scientific findings. We’re in the process of making our campaign data available to the community now through the ARM data archive."

Burrows has been an EMSL user for more than eight years. She has been awarded funding through Facilities Integrating Collaborations for User Science (FICUS) program calls with EMSL and ARM and through EMSL's Large-Scale Research call.

"EMSL’s capabilities enabled me to step into field research and pull off an ambitious experiment, comprehensively measuring the chemical and physical properties of INPs in ambient air," Burrows says. "The single particle mass spectrometer, miniSPLAT, was especially critical to enable real-time measurement of individual INPs. Few instruments have the required sensitivity to achieve this measurement, and to the best of my knowledge, the miniSPLAT is the only such instrument that is available to the community through competitively awarded resources at a user facility. By integrating the miniSPLAT with EMSL’s ice nucleation chamber, as well as collecting offline samples on substrates for scanning electron microscope with energy dispersive X-ray analysis at EMSL, we were able to chemically characterize an unprecedented number of ambient INPs in our study."

Jared Ellenbogen | EMSL user 

Methylotrophic Metabolism in the Mire: Unearthing Direct and Indirect Routes for Methane Production in a Model Permafrost Thaw Peatland

Thursday, Dec. 15 | 3:25 p.m. CST | McCormick Place – S405a (South, Level 4)

Jared Ellenbogen, a postdoctoral researcher at Colorado State University, is presenting at AGU on EMSL user science research looking at the biological methane cycle and how soil microorganisms influence atmospheric methane emissions. Ellenbogen is part of a research team led by Kelly Wrighton, who is a longtime EMSL user. Their research project, “Incorporating hydrologic perturbation and microbial processes into carbon budgets from coastal wetland soils,” was funded through an EMSL Large-Scale Research call for proposals.

“For this work, through collaboration with David Hoyt and Elizabeth Eder at EMSL, we were able to bolster our story based primarily on metagenomic and metatranscriptomic data with really exciting field metabolite data, which we’ve been able to analyze for multiple stories in the lab,” Ellenbogen explains.

Odeta Qafoku | EMSL soil and geochemist 

Macro and Molecular Insights on Preferential Association of Organic Matter Compounds with Soil Minerals

Friday, Dec. 16 | 9:40 a.m. CST | McCormick Place – S405a (south, Level 4)

Odeta Qafoku, EMSL soil and geochemist, will present on key processes of how organic carbon interacts with common soil minerals. Additionally, she will discuss how this organic carbon can be stabilized during these interactions.

“My presentation is focused primarily on using batch adsorption experiments that can be utilized in EMSL or different labs across the United States,” she says. “We then apply specialized equipment that are available in EMSL to examine organic carbon–mineral interaction. The research I conduct at EMSL uses a number of high-resolution instruments.”

Qafoku’s research interests include studying organic–mineral interactions using methods that extend from the nano- to macroscale, studying iron mineral transformations induced by reductive reactions, and studying mineral weathering as a function of biological inputs and environmental changes. She also applies electron microscopy to study reactivity and transformation at reaction boundaries.

Some of the scientific instruments she uses in her research include nuclear magnetic resonance, a new instrument called infrared scanning and scattering optical microscopy, electron microscopy, and focused ion beam.

“I would like users to know how well some of these capabilities we have available at EMSL can address research questions,” she says. “The overarching goal of this research is to understand the stabilization of organic carbon in soils. This research can further help advance knowledge in reducing emissions of carbon dioxide into the atmosphere.”

 

Jianqiu Zheng | EMSL user

“A model framework for scaling the molecular complexity of soil processes (Invited)”

Friday, Dec. 16 | 3:25 p.m. CST | McCormick Place – S405a (South, Level 4)

Jianqiu Zheng, a PNNL Earth scientist and EMSL user, is invited to speak about her user research on soil processes and biogeochemical cycling at AGU.

“I will present some distinctive approaches I have developed for soil-centered microbial explicit modeling,” Zheng says. “A key challenge in soil biogeochemistry is to be able to build predictive models that adequately capture the complexity of soil processes spanning various physical, chemical, and biological aspects. My talk is about how to use a probability distribution approach to represent such complexity in models.”

Zheng wants session attendees to understand how soil biogeochemistry modeling can improve through better integration of models and experiments across scales and through effective communications among scientists across disciplines.

As an EMSL user, Zheng has used various data types generated by EMSL capabilities, including organic matter chemistry characterization using Fourier transform ion cyclotron resonance mass spectrometry and soil structure data using micro X-ray computed tomography.

Zheng, who has been an EMSL user for two years, was recently named to the EMSL User Executive Committee.