Articles | Volume 23, issue 19
https://doi.org/10.5194/bg-23-6817-2026
© Author(s) 2026. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-23-6817-2026
© Author(s) 2026. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Modeling microbial regulatory feedback in organic matter decomposition identifies copiotrophic traits as key drivers of positive priming
Firnaaz Ahamed
Department of Biological Systems Engineering, University of Nebraska–Lincoln, Lincoln, NE, United States
School of Engineering, Faculty of Innovation and Technology, Taylor's University, 47500 Subang Jaya, Malaysia
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
School of the Environment, Washington State University, Pullman, WA, United States
Emily B. Graham
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
School of Biological Sciences, Washington State University, Pullman, WA, United States
Timothy D. Scheibe
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
Hyun-Seob Song
CORRESPONDING AUTHOR
Department of Biological Systems Engineering, University of Nebraska–Lincoln, Lincoln, NE, United States
Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska–Lincoln, Lincoln, NE, United States
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EGUsphere, https://doi.org/10.5194/egusphere-2026-3537, https://doi.org/10.5194/egusphere-2026-3537, 2026
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Distributed data generation, or data collected from multiple sources and locations using standardized approaches and coordination among researchers, is powerful for scalable environmental knowledge. This paper helps readers understand options for distributed data generation, offers practical guidance for outreach, operations, and sharing outcomes, and explores how artificial intelligence can help address longstanding challenges.
James C. Stegen, Morgan Barnes, Dillman Delgado, Brieanne Forbes, Vanessa A. Garayburu-Caruso, Amy E. Goldman, Maggi Laan, Sophia McKever, Peter Regier, Lupita Renteria, and Scott D. Tiegs
Biogeosciences, 23, 3981–3993, https://doi.org/10.5194/bg-23-3981-2026, https://doi.org/10.5194/bg-23-3981-2026, 2026
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Streams move and break down organic material, but it is unclear how small-scale decomposition relates to larger scale respiration. We used cotton strips at 48 sites in the Yakima River Basin, Washington, to measure decomposition and different components of river respiration. Decomposition tracked whole-river respiration more than local sediment activity, showing that spatial variation in decomposition results from integrated watershed features.
Maggi M. Laan, Stephanie G. Fulton, Vanessa A. Garayburu-Caruso, Morgan E. Barnes, Mikayla A. Borton, Xingyuan Chen, Yuliya Farris, Brieanne Forbes, Amy E. Goldman, Samantha Grieger, Robert O. Hall Jr., Matthew H. Kaufman, Xinming Lin, Erin L. M. Zionce, Sophia A. McKever, Allison Myers-Pigg, Opal Otenburg, Aaron C. Pelly, Huiying Ren, Lupita Renteria, Timothy D. Scheibe, Kyongho Son, Jerry Tagestad, Joshua M. Torgeson, and James C. Stegen
Biogeosciences, 22, 6137–6152, https://doi.org/10.5194/bg-22-6137-2025, https://doi.org/10.5194/bg-22-6137-2025, 2025
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Respiration is a process that combines carbon and oxygen to generate energy for living organisms. Within a river, respiration in sediments and water makes variable contributions to the respiration of the whole river system. Contrary to conventional wisdom, we found that water column respiration did not increase strongly when moving from small streams to big rivers. Instead, it was locally influenced by temperature, nutrients, and suspended solids.
Morgan E. Barnes, J. Alan Roebuck Jr., Samantha Grieger, Paul J. Aronstein, Vanessa A. Garayburu-Caruso, Kathleen Munson, Robert P. Young, Kevin D. Bladon, John D. Bailey, Emily B. Graham, Lupita Renteria, Peggy A. O'Day, Timothy D. Scheibe, and Allison N. Myers-Pigg
Biogeosciences, 22, 4491–4505, https://doi.org/10.5194/bg-22-4491-2025, https://doi.org/10.5194/bg-22-4491-2025, 2025
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Wildfires impact nutrient cycles on land and in water. We used burning experiments to understand the types of phosphorous (P), an essential nutrient, that might be released to the environment after different types of fires. We found the amount of P moving through the environment post-fire is dependent on the type of vegetation and degree of burning, which may influence when and where this material is processed or stored.
James Stegen, Amy J. Burgin, Michelle H. Busch, Joshua B. Fisher, Joshua Ladau, Jenna Abrahamson, Lauren Kinsman-Costello, Li Li, Xingyuan Chen, Thibault Datry, Nate McDowell, Corianne Tatariw, Anna Braswell, Jillian M. Deines, Julia A. Guimond, Peter Regier, Kenton Rod, Edward K. P. Bam, Etienne Fluet-Chouinard, Inke Forbrich, Kristin L. Jaeger, Teri O'Meara, Tim Scheibe, Erin Seybold, Jon N. Sweetman, Jianqiu Zheng, Daniel C. Allen, Elizabeth Herndon, Beth A. Middleton, Scott Painter, Kevin Roche, Julianne Scamardo, Ross Vander Vorste, Kristin Boye, Ellen Wohl, Margaret Zimmer, Kelly Hondula, Maggi Laan, Anna Marshall, and Kaizad F. Patel
Biogeosciences, 22, 995–1034, https://doi.org/10.5194/bg-22-995-2025, https://doi.org/10.5194/bg-22-995-2025, 2025
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The loss and gain of surface water (variable inundation) are common processes across Earth. Global change shifts variable inundation dynamics, highlighting a need for unified understanding that transcends individual variably inundated ecosystems (VIEs). We review the literature, highlight challenges, and emphasize opportunities to generate transferable knowledge by viewing VIEs through a common lens. We aim to inspire the emergence of a cross-VIE community based on a proposed continuum approach.
Robert E. Danczak, Amy E. Goldman, Mikayla A. Borton, Rosalie K. Chu, Jason G. Toyoda, Vanessa A. Garayburu-Caruso, Emily B. Graham, Joseph W. Morad, Lupita Renteria, Jacqueline R. Hager, Shai Arnon, Scott Brooks, Edo Bar-Zeev, Michael Jones, Nikki Jones, Jorg Lewandowski, Christof Meile, Birgit M. Muller, John Schalles, Hanna Schulz, Adam Ward, and James C. Stegen
EGUsphere, https://doi.org/10.1101/2024.01.10.575030, https://doi.org/10.1101/2024.01.10.575030, 2025
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Katherine A. Muller, Peishi Jiang, Glenn Hammond, Tasneem Ahmadullah, Hyun-Seob Song, Ravi Kukkadapu, Nicholas Ward, Madison Bowe, Rosalie K. Chu, Qian Zhao, Vanessa A. Garayburu-Caruso, Alan Roebuck, and Xingyuan Chen
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The new Lambda-PFLOTRAN workflow incorporates organic matter chemistry into reaction networks to simulate aerobic respiration and biogeochemistry. Lambda-PFLOTRAN is a Python-based workflow in a Jupyter notebook interface that digests raw organic matter chemistry data via Fourier transform ion cyclotron resonance mass spectrometry, develops a representative reaction network, and completes a biogeochemical simulation with the open-source, parallel-reactive-flow, and transport code PFLOTRAN.
Anna B. Turetcaia, Nicole G. Dix, Hannah Ramage, Matthew C. Ferner, and Emily B. Graham
EGUsphere, https://doi.org/10.31223/X50Q3S, https://doi.org/10.31223/X50Q3S, 2024
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William Kew, Allison Myers-Pigg, Christine H. Chang, Sean M. Colby, Josie Eder, Malak M. Tfaily, Jeffrey Hawkes, Rosalie K. Chu, and James C. Stegen
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Natural organic matter (NOM) is often studied via Fourier transform mass spectrometry (FTMS), which identifies organic molecules as mass spectra peaks. The intensity of peaks is data that is often discarded due to technical concerns. We review the theory behind these concerns and show they are supported empirically. However, simulations show that ecological analyses of NOM data that include FTMS peak intensities are often valid. This opens a path for robust use of FTMS peak intensities for NOM.
Stephanie G. Fulton, Morgan Barnes, Mikayla A. Borton, Xingyuan Chen, Yuliya Farris, Brieanne Forbes, Vanessa A. Garayburu-Caruso, Amy E. Goldman, Samantha Grieger, Robert Hall Jr., Matthew H. Kaufman, Xinming Lin, Erin McCann, Sophia A. McKever, Allison Myers-Pigg, Opal C. Otenburg, Aaron C. Pelly, Huiying Ren, Lupita Renteria, Timothy D. Scheibe, Kyongho Son, Jerry Tagestad, Joshua M. Torgeson, and James C. Stegen
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This research examines oxygen use in rivers, which is central to the carbon cycle and water quality. The study focused on an environmentally diverse river basin in the western United States and found that oxygen use in river water was very slow and influenced by factors like water temperature and concentrations of nutrients and carbon in the water. Results suggest that in the study system, most of the oxygen use occurs via mechanisms directly or indirectly associated with riverbed sediments.
Emily B. Graham, Hyun-Seob Song, Samantha Grieger, Vanessa A. Garayburu-Caruso, James C. Stegen, Kevin D. Bladon, and Allison N. Myers-Pigg
Biogeosciences, 20, 3449–3457, https://doi.org/10.5194/bg-20-3449-2023, https://doi.org/10.5194/bg-20-3449-2023, 2023
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Intensifying wildfires are increasing pyrogenic organic matter (PyOM) production and its impact on water quality. Recent work indicates that PyOM may have a greater impact on aquatic biogeochemistry than previously assumed, driven by higher bioavailability. We provide a full assessment of the potential bioavailability of PyOM across its chemical spectrum. We indicate that PyOM can be actively transformed within the river corridor and, therefore, may be a growing source of riverine C emissions.
James C. Stegen, Vanessa A. Garayburu-Caruso, Robert E. Danczak, Amy E. Goldman, Lupita Renteria, Joshua M. Torgeson, and Jacqueline Hager
Biogeosciences, 20, 2857–2867, https://doi.org/10.5194/bg-20-2857-2023, https://doi.org/10.5194/bg-20-2857-2023, 2023
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Chemical reactions in river sediments influence how clean the water is and how much greenhouse gas comes out of a river. Our study investigates why some sediments have higher rates of chemical reactions than others. We find that to achieve high rates, sediments need to have two things: only a few different kinds of molecules, but a lot of them. This result spans about 80 rivers such that it could be a general rule, helpful for predicting the future of rivers and our planet.
Heewon Jung, Hyun-Seob Song, and Christof Meile
Geosci. Model Dev., 16, 1683–1696, https://doi.org/10.5194/gmd-16-1683-2023, https://doi.org/10.5194/gmd-16-1683-2023, 2023
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Microbial activity responsible for many chemical transformations depends on environmental conditions. These can vary locally, e.g., between poorly connected pores in porous media. We present a modeling framework that resolves such small spatial scales explicitly, accounts for feedback between transport and biogeochemical conditions, and can integrate state-of-the-art representations of microbes in a computationally efficient way, making it broadly applicable in science and engineering use cases.
James C. Stegen, Sarah J. Fansler, Malak M. Tfaily, Vanessa A. Garayburu-Caruso, Amy E. Goldman, Robert E. Danczak, Rosalie K. Chu, Lupita Renteria, Jerry Tagestad, and Jason Toyoda
Biogeosciences, 19, 3099–3110, https://doi.org/10.5194/bg-19-3099-2022, https://doi.org/10.5194/bg-19-3099-2022, 2022
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Rivers are vital to Earth, and in rivers, organic matter (OM) is an energy source for microbes that make greenhouse gas and remove contaminants. Predicting Earth’s future requires understanding how and why river OM is transformed. Our results help meet this need. We found that the processes influencing OM transformations diverge between river water and riverbed sediments. This can be used to build new models for predicting the future of rivers and, in turn, the Earth system.
Yunxiang Chen, Jie Bao, Yilin Fang, William A. Perkins, Huiying Ren, Xuehang Song, Zhuoran Duan, Zhangshuan Hou, Xiaoliang He, and Timothy D. Scheibe
Geosci. Model Dev., 15, 2917–2947, https://doi.org/10.5194/gmd-15-2917-2022, https://doi.org/10.5194/gmd-15-2917-2022, 2022
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Climate change affects river discharge variations that alter streamflow. By integrating multi-type survey data with a computational fluid dynamics tool, OpenFOAM, we show a workflow that enables accurate and efficient streamflow modeling at 30 km and 5-year scales. The model accuracy for water stage and depth average velocity is −16–9 cm and 0.71–0.83 in terms of mean error and correlation coefficients. This accuracy indicates the model's reliability for evaluating climate impact on rivers.
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Short summary
This research examines how labile organic matter influences the breakdown of complex organic matter (termed priming). Using a new modeling method, the study shows how microbial growth traits and interactions determine whether priming effects are positive or negative. By identifying microbial strategies as critical drivers of decomposition, this work provides a unified framework to improve predictions of nutrient cycling and carbon sequestration across diverse ecosystems.
This research examines how labile organic matter influences the breakdown of complex organic...
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