Articles | Volume 16, issue 19
https://doi.org/10.5194/bg-16-3911-2019
© Author(s) 2019. 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-16-3911-2019
© Author(s) 2019. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
10 Oct 2019
Research article |
| 10 Oct 2019
| 10 Oct 2019
Spatial gradients in the characteristics of soil-carbon fractions are associated with abiotic features but not microbial communities
Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box
999 MSIN: J4-18, Richland, WA 99352, USA
Julia Indivero
Marine Sciences Laboratory, Pacific Northwest National Laboratory, 1529 West
Sequim Bay Road, Sequim, WA 98382, USA
Cailene Gunn
Marine Sciences Laboratory, Pacific Northwest National Laboratory, 1529 West
Sequim Bay Road, Sequim, WA 98382, USA
Malak M. Tfaily
Department of Soil, Water and Environmental Sciences, University of
Arizona, Tucson, AZ 85719, USA
Environmental Molecular Sciences Laboratory, Pacific Northwest National
Laboratory, Richland, WA 99352, USA
Rosalie K. Chu
Environmental Molecular Sciences Laboratory, Pacific Northwest National
Laboratory, Richland, WA 99352, USA
Jason Toyoda
Environmental Molecular Sciences Laboratory, Pacific Northwest National
Laboratory, Richland, WA 99352, USA
Vanessa L. Bailey
Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box
999 MSIN: J4-18, Richland, WA 99352, USA
Nicholas D. Ward
Marine Sciences Laboratory, Pacific Northwest National Laboratory, 1529 West
Sequim Bay Road, Sequim, WA 98382, USA
School of Oceanography, University of Washington, Seattle, WA 98195, USA
James C. Stegen
Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box
999 MSIN: J4-18, Richland, WA 99352, USA
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Conceptual models link microbes with the environment but are untested. We test a recent model using riverbed sediments. We exposed sediments to disturbances, going dry and becoming wet again. As the length of dry conditions got longer, there was a sudden shift in the ecology of microbes, chemistry of organic matter, and rates of microbial metabolism. We propose a new model based on feedbacks initiated by disturbance that cascade across biological, chemical, and functional aspects of the system.
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.
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James Stegen, Amy Burgin, Michelle Busch, Joshua Fisher, Joshua Ladau, Jenna Abrahamson, Lauren Kinsman-Costello, Li Li, Xingyuan Chen, Thibault Datry, Nate McDowell, Corianne Tatariw, Anna Braswell, Jillian Deines, Julia Guimond, Peter Regier, Kenton Rod, Edward Bam, Etienne Fluet-Chouinard, Inke Forbrich, Kristin Jaeger, Teri O'Meara, Tim Scheibe, Erin Seybold, Jon Sweetman, Jianqiu Zheng, Daniel Allen, Elizabeth Herndon, Beth Middleton, Scott Painter, Kevin Roche, Julianne Scamardo, Ross Vander Vorste, Kristin Boye, Ellen Wohl, Margaret Zimmer, Kelly Hondula, Maggi Laan, Anna Marshall, and Kaizad Patel
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Christian Lønborg, Cátia Carreira, Gwenaël Abril, Susana Agustí, Valentina Amaral, Agneta Andersson, Javier Arístegui, Punyasloke Bhadury, Mariana B. Bif, Alberto V. Borges, Steven Bouillon, Maria Ll. Calleja, Luiz C. Cotovicz Jr., Stefano Cozzi, Maryló Doval, Carlos M. Duarte, Bradley Eyre, Cédric G. Fichot, E. Elena García-Martín, Alexandra Garzon-Garcia, Michele Giani, Rafael Gonçalves-Araujo, Renee Gruber, Dennis A. Hansell, Fuminori Hashihama, Ding He, Johnna M. Holding, William R. Hunter, J. Severino P. Ibánhez, Valeria Ibello, Shan Jiang, Guebuem Kim, Katja Klun, Piotr Kowalczuk, Atsushi Kubo, Choon-Weng Lee, Cláudia B. Lopes, Federica Maggioni, Paolo Magni, Celia Marrase, Patrick Martin, S. Leigh McCallister, Roisin McCallum, Patricia M. Medeiros, Xosé Anxelu G. Morán, Frank E. Muller-Karger, Allison Myers-Pigg, Marit Norli, Joanne M. Oakes, Helena Osterholz, Hyekyung Park, Maria Lund Paulsen, Judith A. Rosentreter, Jeff D. Ross, Digna Rueda-Roa, Chiara Santinelli, Yuan Shen, Eva Teira, Tinkara Tinta, Guenther Uher, Masahide Wakita, Nicholas Ward, Kenta Watanabe, Yu Xin, Youhei Yamashita, Liyang Yang, Jacob Yeo, Huamao Yuan, Qiang Zheng, and Xosé Antón Álvarez-Salgado
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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
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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
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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
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Aditi Sengupta, Sarah J. Fansler, Rosalie K. Chu, Robert E. Danczak, Vanessa A. Garayburu-Caruso, Lupita Renteria, Hyun-Seob Song, Jason Toyoda, Jacqueline Hager, and James C. Stegen
Biogeosciences, 18, 4773–4789, https://doi.org/10.5194/bg-18-4773-2021, https://doi.org/10.5194/bg-18-4773-2021, 2021
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Conceptual models link microbes with the environment but are untested. We test a recent model using riverbed sediments. We exposed sediments to disturbances, going dry and becoming wet again. As the length of dry conditions got longer, there was a sudden shift in the ecology of microbes, chemistry of organic matter, and rates of microbial metabolism. We propose a new model based on feedbacks initiated by disturbance that cascade across biological, chemical, and functional aspects of the system.
Yang Lin, Ashley N. Campbell, Amrita Bhattacharyya, Nicole DiDonato, Allison M. Thompson, Malak M. Tfaily, Peter S. Nico, Whendee L. Silver, and Jennifer Pett-Ridge
Biogeosciences Discuss., https://doi.org/10.5194/bg-2020-59, https://doi.org/10.5194/bg-2020-59, 2020
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Soils in tropical forests play an important role of breaking down dead plant tissue and returning carbon to the atmosphere. This process is previously thought to be regulated soil oxygen level. However, we found that the break-down of new plant carbon by soils did not depend on oxygen. Even without oxygen, some soil microbes can use plant carbons in the forms like sugar and protein. Once these compounds were exhausted, oxygen limitation became to influence organic matter break-down.
Stephanie C. Pennington, Nate G. McDowell, J. Patrick Megonigal, James C. Stegen, and Ben Bond-Lamberty
Biogeosciences, 17, 771–780, https://doi.org/10.5194/bg-17-771-2020, https://doi.org/10.5194/bg-17-771-2020, 2020
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Soil respiration (Rs) is the flow of CO2 from the soil surface to the atmosphere and is one of the largest carbon fluxes on land. This study examined the effect of local basal area (tree area) on Rs in a coastal forest in eastern Maryland, USA. Rs measurements were taken as well as distance from soil collar, diameter, and species of each tree within a 15 m radius. We found that trees within 5 m of our sampling points had a positive effect on how sensitive soil respiration was to temperature.
Adam S. Ward, Steven M. Wondzell, Noah M. Schmadel, Skuyler Herzog, Jay P. Zarnetske, Viktor Baranov, Phillip J. Blaen, Nicolai Brekenfeld, Rosalie Chu, Romain Derelle, Jennifer Drummond, Jan H. Fleckenstein, Vanessa Garayburu-Caruso, Emily Graham, David Hannah, Ciaran J. Harman, Jase Hixson, Julia L. A. Knapp, Stefan Krause, Marie J. Kurz, Jörg Lewandowski, Angang Li, Eugènia Martí, Melinda Miller, Alexander M. Milner, Kerry Neil, Luisa Orsini, Aaron I. Packman, Stephen Plont, Lupita Renteria, Kevin Roche, Todd Royer, Catalina Segura, James Stegen, Jason Toyoda, Jacqueline Hager, and Nathan I. Wisnoski
Hydrol. Earth Syst. Sci., 23, 5199–5225, https://doi.org/10.5194/hess-23-5199-2019, https://doi.org/10.5194/hess-23-5199-2019, 2019
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The movement of water and solutes between streams and their shallow, connected subsurface is important to many ecosystem functions. These exchanges are widely expected to vary with stream flow across space and time, but these assumptions are seldom tested across basin scales. We completed more than 60 experiments across a 5th-order river basin to document these changes, finding patterns in space but not time. We conclude space-for-time and time-for-space substitutions are not good assumptions.
Adam S. Ward, Jay P. Zarnetske, Viktor Baranov, Phillip J. Blaen, Nicolai Brekenfeld, Rosalie Chu, Romain Derelle, Jennifer Drummond, Jan H. Fleckenstein, Vanessa Garayburu-Caruso, Emily Graham, David Hannah, Ciaran J. Harman, Skuyler Herzog, Jase Hixson, Julia L. A. Knapp, Stefan Krause, Marie J. Kurz, Jörg Lewandowski, Angang Li, Eugènia Martí, Melinda Miller, Alexander M. Milner, Kerry Neil, Luisa Orsini, Aaron I. Packman, Stephen Plont, Lupita Renteria, Kevin Roche, Todd Royer, Noah M. Schmadel, Catalina Segura, James Stegen, Jason Toyoda, Jacqueline Hager, Nathan I. Wisnoski, and Steven M. Wondzell
Earth Syst. Sci. Data, 11, 1567–1581, https://doi.org/10.5194/essd-11-1567-2019, https://doi.org/10.5194/essd-11-1567-2019, 2019
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Studies of river corridor exchange commonly focus on characterization of the physical, chemical, or biological system. As a result, complimentary systems and context are often lacking, which may limit interpretation. Here, we present a characterization of all three systems at 62 sites in a 5th-order river basin, including samples of surface water, hyporheic water, and sediment. These data will allow assessment of interacting processes in the river corridor.
Ryan D. Cook, Ying-Hsuan Lin, Zhuoyu Peng, Eric Boone, Rosalie K. Chu, James E. Dukett, Matthew J. Gunsch, Wuliang Zhang, Nikola Tolic, Alexander Laskin, and Kerri A. Pratt
Atmos. Chem. Phys., 17, 15167–15180, https://doi.org/10.5194/acp-17-15167-2017, https://doi.org/10.5194/acp-17-15167-2017, 2017
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Reactions occur within water in both atmospheric particles and cloud droplets, yet little is known about the organic compounds in cloud water. In this work, cloud water samples were collected at Whiteface Mountain, New York, and analyzed using ultra-high-resolution mass spectrometry to investigate the molecular composition of the dissolved organic compounds. The results focus on changes in cloud water composition with air mass origin – influences of forest, urban, and wildfire emissions.
James C. Stegen, Carolyn G. Anderson, Ben Bond-Lamberty, Alex R. Crump, Xingyuan Chen, and Nancy Hess
Biogeosciences, 14, 4341–4354, https://doi.org/10.5194/bg-14-4341-2017, https://doi.org/10.5194/bg-14-4341-2017, 2017
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CO2 loss from soil to the atmosphere (
soil respiration) is a key ecosystem function, especially in systems with permafrost. We find that soil respiration shows a non-linear threshold at permafrost depths > 140 cm and that the number of large trees governs soil respiration. This suggests that remote sensing could be used to estimate spatial variation in soil respiration and (with knowledge of key thresholds) empirically constrain models that predict ecosystem responses to permafrost thaw.
Amy E. Goldman, Emily B. Graham, Alex R. Crump, David W. Kennedy, Elvira B. Romero, Carolyn G. Anderson, Karl L. Dana, Charles T. Resch, Jim K. Fredrickson, and James C. Stegen
Biogeosciences, 14, 4229–4241, https://doi.org/10.5194/bg-14-4229-2017, https://doi.org/10.5194/bg-14-4229-2017, 2017
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The history of river inundation influences shoreline sediment biogeochemical cycling and microbial dynamics. Sediment exhibited a binary respiration response to rewetting, in which respiration from less recently saturated sediment was suppressed relative to more recently saturated sediment, likely due to inhibition of fungal metabolic activity. River shorelines should likely be integrated as a distinct environment into hydrobiogeochemical models to predict watershed biogeochemical function.
Ben Bond-Lamberty, A. Peyton Smith, and Vanessa Bailey
Biogeosciences, 13, 6669–6681, https://doi.org/10.5194/bg-13-6669-2016, https://doi.org/10.5194/bg-13-6669-2016, 2016
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We used a laboratory experiment to examine how climate change and permafrost melting might alter soils in high-latitude regions. Soils were subjected to two temperatures and drought, and gas emissions were monitored. Carbon dioxide fluxes were influenced by temperature, water, and soil nitrogen, while methane emissions were much smaller and linked only with nitrogen. This suggests that such soils may be very sensitive to changes in moisture as discontinuous permafrost thaws in interior Alaska.
B. Bond-Lamberty, J. P. Fisk, J. A. Holm, V. Bailey, G. Bohrer, and C. M. Gough
Biogeosciences, 12, 513–526, https://doi.org/10.5194/bg-12-513-2015, https://doi.org/10.5194/bg-12-513-2015, 2015
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How will aging forests behave as they undergo ecological transitions? Can our models, which support scientific, policy, and management analyses, accurately simulate these transitions? We tested whether three forest ecosystem models could reproduce dynamics observed in an experimentally manipulated forest in northern Michigan, USA. None of the models fully captured the post-disturbance C fluxes observed, raising doubts about their ability to simulate tree death after moderate disturbances.
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Soils store organic carbon composed of multiple compounds from plants and microbes for different lengths of time. To understand how soils store these different carbon types, we measure the time each carbon fraction is in a grassland soil profile. Our results show that the length of time each individual soil fraction is in our soil changes. Our approach allows a detailed look at the different components in soils. This study can help improve our understanding of soil dynamics.
Peter Levy, Laura Bentley, Peter Danks, Bridget Emmett, Angus Garbutt, Stephen Heming, Peter Henrys, Aidan Keith, Inma Lebron, Niall McNamara, Richard Pywell, John Redhead, David Robinson, and Alexander Wickenden
Biogeosciences, 21, 4301–4315, https://doi.org/10.5194/bg-21-4301-2024, https://doi.org/10.5194/bg-21-4301-2024, 2024
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We collated a large data set (15 790 soil cores) on soil carbon stock in different land uses. Soil carbon stocks were highest in woodlands and lowest in croplands. The variability in the effects was large. This has important implications for agri-environment schemes seeking to sequester carbon in the soil by altering land use because the effect of a given intervention is very hard to verify.
Marija Stojanova, Pierre Arbelet, François Baudin, Nicolas Bouton, Giovanni Caria, Lorenza Pacini, Nicolas Proix, Edouard Quibel, Achille Thin, and Pierre Barré
Biogeosciences, 21, 4229–4237, https://doi.org/10.5194/bg-21-4229-2024, https://doi.org/10.5194/bg-21-4229-2024, 2024
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Because of its importance for climate regulation and soil health, many studies focus on carbon dynamics in soils. However, quantifying organic and inorganic carbon remains an issue in carbonated soils. In this technical note, we propose a validated correction method to quantify organic and inorganic carbon in soils using Rock-Eval® thermal analysis. With this correction, the Rock-Eval® method has the potential to become the standard method for quantifying carbon in carbonate soils.
Armando Molina, Veerle Vanacker, Oliver Chadwick, Santiago Zhiminaicela, Marife Corre, and Edzo Veldkamp
Biogeosciences, 21, 3075–3091, https://doi.org/10.5194/bg-21-3075-2024, https://doi.org/10.5194/bg-21-3075-2024, 2024
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EGUsphere, https://doi.org/10.5194/egusphere-2024-1757, https://doi.org/10.5194/egusphere-2024-1757, 2024
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When microbes consume carbon within soils, it is important to know how much carbon is respired and lost as carbon dioxide versus how much is used to make new biomass. We used a new approach of monitoring carbon dioxide and oxygen to track the fate of consumed carbon during a series of laboratory experiments where sugar was added to moistened soil. Our approach allowed us to estimate how much sugar was converted to dead microbial biomass, which is more likely to be preserved in soils.
Sahiti Bulusu, Cristina Prieto García, Helen E. Dahlke, and Elad Levintal
Biogeosciences, 21, 3007–3013, https://doi.org/10.5194/bg-21-3007-2024, https://doi.org/10.5194/bg-21-3007-2024, 2024
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Do-it-yourself hardware is a new way to improve measurement resolution. We present a low-cost, automated system for field measurements of low nitrate concentrations in soil porewater and open water bodies. All data hardware components cost USD 1100, which is much cheaper than other available commercial solutions. We provide the complete building guide to reduce technical barriers, which we hope will allow easier reproducibility and set up new soil and environmental monitoring applications.
Violeta Mendoza-Martinez, Scott L. Collins, and Jennie R. McLaren
Biogeosciences, 21, 2655–2667, https://doi.org/10.5194/bg-21-2655-2024, https://doi.org/10.5194/bg-21-2655-2024, 2024
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We examine the impacts of multi-decadal nitrogen additions on a dryland ecosystem N budget, including the soil, microbial, and plant N pools. After 26 years, there appears to be little impact on the soil microbial or plant community and only minimal increases in N pools within the soil. While perhaps encouraging from a conservation standpoint, we calculate that greater than 95 % of the nitrogen added to the system is not retained and is instead either lost deeper in the soil or emitted as gas.
Sean Fettrow, Andrew Wozniak, Holly A. Michael, and Angelia L. Seyfferth
Biogeosciences, 21, 2367–2384, https://doi.org/10.5194/bg-21-2367-2024, https://doi.org/10.5194/bg-21-2367-2024, 2024
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Salt marshes play a big role in global carbon (C) storage, and C stock estimates are used to predict future changes. However, spatial and temporal gradients in C burial rates over the landscape exist due to variations in water inundation, dominant plant species and stage of growth, and tidal action. We quantified soil C concentrations in soil cores across time and space beside several porewater biogeochemical variables and discussed the controls on variability in soil C in salt marsh ecosystems.
Shanshan Bai, Yifei Ge, Dongtan Yao, Yifan Wang, Jinfang Tan, Shuai Zhang, Yutao Peng, and Xiaoqian Jiang
EGUsphere, https://doi.org/10.5194/egusphere-2024-983, https://doi.org/10.5194/egusphere-2024-983, 2024
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Mineral fertilization led to increases in total P, available P, high-activity inorganic P fractions and organic P, but decreased the abundances of P cycling genes by decreasing soil pH and increasing P in bulk soil. Straw retention brought increases for organic C, total P, available P concentrations in water-extractable colloids (WECs). Abundances of phoD gene and phoD-harbouring Proteobacteria in WECs increased under straw retention, suggesting that the P mineralizing capacity increased.
Andrés Tangarife-Escobar, Georg Guggenberger, Xiaojuan Feng, Guohua Dai, Carolina Urbina-Malo, Mina Azizi-Rad, and Carlos A. Sierra
Biogeosciences, 21, 1277–1299, https://doi.org/10.5194/bg-21-1277-2024, https://doi.org/10.5194/bg-21-1277-2024, 2024
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Soil organic matter stability depends on future temperature and precipitation scenarios. We used radiocarbon (14C) data and model predictions to understand how the transit time of carbon varies under environmental change in grasslands and peatlands. Soil moisture affected the Δ14C of peatlands, while temperature did not have any influence. Our models show the correspondence between Δ14C and transit time and could allow understanding future interactions between terrestrial and atmospheric carbon
Emiko K. Stuart, Laura Castañeda-Gómez, Wolfram Buss, Jeff R. Powell, and Yolima Carrillo
Biogeosciences, 21, 1037–1059, https://doi.org/10.5194/bg-21-1037-2024, https://doi.org/10.5194/bg-21-1037-2024, 2024
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We inoculated wheat plants with various types of fungi whose impacts on soil carbon are poorly understood. After several months of growth, we examined both their impacts on soil carbon and the underlying mechanisms using multiple methods. Overall the fungi benefitted the storage of carbon in soil, mainly by improving the stability of pre-existing carbon, but several pathways were involved. This study demonstrates their importance for soil carbon storage and, therefore, climate change mitigation.
Huimin Sun, Michael W. I. Schmidt, Jintao Li, Jinquan Li, Xiang Liu, Nicholas O. E. Ofiti, Shurong Zhou, and Ming Nie
Biogeosciences, 21, 575–589, https://doi.org/10.5194/bg-21-575-2024, https://doi.org/10.5194/bg-21-575-2024, 2024
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A soil organic carbon (SOC) molecular structure suggested that the easily decomposable and stabilized SOC is similarly affected after 9-year warming and N treatments despite large changes in SOC stocks. Given the long residence time of some SOC, the similar loss of all measurable chemical forms of SOC under global change treatments could have important climate consequences.
Haoli Zhang, Doudou Chang, Zhifeng Zhu, Chunmei Meng, and Kaiyong Wang
Biogeosciences, 21, 1–11, https://doi.org/10.5194/bg-21-1-2024, https://doi.org/10.5194/bg-21-1-2024, 2024
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Soil salinity mediates microorganisms and soil processes like soil organic carbon (SOC) cycling. We observed that negative priming effects at the early stages might be due to the preferential utilization of cottonseed meal. The positive priming that followed decreased with the increase in salinity.
Joséphine Hazera, David Sebag, Isabelle Kowalewski, Eric Verrecchia, Herman Ravelojaona, and Tiphaine Chevallier
Biogeosciences, 20, 5229–5242, https://doi.org/10.5194/bg-20-5229-2023, https://doi.org/10.5194/bg-20-5229-2023, 2023
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This study adapts the Rock-Eval® protocol to quantify soil organic carbon (SOC) and soil inorganic carbon (SIC) on a non-pretreated soil aliquot. The standard protocol properly estimates SOC contents once the TOC parameter is corrected. However, it cannot complete the thermal breakdown of SIC amounts > 4 mg, leading to an underestimation of high SIC contents by the MinC parameter, even after correcting for this. Thus, the final oxidation isotherm is extended to 7 min to quantify any SIC amount.
Bo Zhao, Amin Dou, Zhiwei Zhang, Zhenyu Chen, Wenbo Sun, Yanli Feng, Xiaojuan Wang, and Qiang Wang
Biogeosciences, 20, 4761–4774, https://doi.org/10.5194/bg-20-4761-2023, https://doi.org/10.5194/bg-20-4761-2023, 2023
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This study provided a comprehensive analysis of the spatial variability and determinants of Fe-bound organic carbon (Fe-OC) among terrestrial, wetland, and marine ecosystems and its governing factors globally. We illustrated that reactive Fe was not only an important sequestration mechanism for OC in terrestrial ecosystems but also an effective “rusty sink” of OC preservation in wetland and marine ecosystems, i.e., a key factor for long-term OC storage in global ecosystems.
Han Sun, Tomoyasu Nishizawa, Hiroyuki Ohta, and Kazuhiko Narisawa
Biogeosciences, 20, 4737–4749, https://doi.org/10.5194/bg-20-4737-2023, https://doi.org/10.5194/bg-20-4737-2023, 2023
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In this research, we assessed the diversity and function of the dark septate endophytic (DSE) fungi community associated with Miscanthus condensatus root in volcanic ecosystems. Both metabarcoding and isolation were adopted in this study. We further validated effects on plant growth by inoculation of some core DSE isolates. This study helps improve our understanding of the role of Miscanthus condensatus-associated DSE fungi during the restoration of post-volcanic ecosystems.
Xianjin He, Laurent Augusto, Daniel S. Goll, Bruno Ringeval, Ying-Ping Wang, Julian Helfenstein, Yuanyuan Huang, and Enqing Hou
Biogeosciences, 20, 4147–4163, https://doi.org/10.5194/bg-20-4147-2023, https://doi.org/10.5194/bg-20-4147-2023, 2023
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We identified total soil P concentration as the most important predictor of all soil P pool concentrations, except for primary mineral P concentration, which is primarily controlled by soil pH and only secondarily by total soil P concentration. We predicted soil P pools’ distributions in natural systems, which can inform assessments of the role of natural P availability for ecosystem productivity, climate change mitigation, and the functioning of the Earth system.
Imane Slimani, Xia Zhu-Barker, Patricia Lazicki, and William Horwath
Biogeosciences, 20, 3873–3894, https://doi.org/10.5194/bg-20-3873-2023, https://doi.org/10.5194/bg-20-3873-2023, 2023
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There is a strong link between nitrogen availability and iron minerals in soils. These minerals have multiple outcomes for nitrogen availability depending on soil conditions and properties. For example, iron can limit microbial degradation of nitrogen in aerated soils but has opposing outcomes in non-aerated soils. This paper focuses on the multiple ways iron can affect nitrogen bioavailability in soils.
Shane W. Stoner, Marion Schrumpf, Alison Hoyt, Carlos A. Sierra, Sebastian Doetterl, Valier Galy, and Susan Trumbore
Biogeosciences, 20, 3151–3163, https://doi.org/10.5194/bg-20-3151-2023, https://doi.org/10.5194/bg-20-3151-2023, 2023
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Soils store more carbon (C) than any other terrestrial C reservoir, but the processes that control how much C stays in soil, and for how long, are very complex. Here, we used a recent method that involves heating soil in the lab to measure the range of C ages in soil. We found that most C in soil is decades to centuries old, while some stays for much shorter times (days to months), and some is thousands of years old. Such detail helps us to estimate how soil C may react to changing climate.
Adetunji Alex Adekanmbi, Laurence Dale, Liz Shaw, and Tom Sizmur
Biogeosciences, 20, 2207–2219, https://doi.org/10.5194/bg-20-2207-2023, https://doi.org/10.5194/bg-20-2207-2023, 2023
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The decomposition of soil organic matter and flux of carbon dioxide are expected to increase as temperatures rise. However, soil organic matter decomposition is a two-step process whereby large molecules are first broken down outside microbial cells and then respired within microbial cells. We show here that these two steps are not equally sensitive to increases in soil temperature and that global warming may cause a shift in the rate-limiting step from outside to inside the microbial cell.
Mercedes Román Dobarco, Alexandre M. J-C. Wadoux, Brendan Malone, Budiman Minasny, Alex B. McBratney, and Ross Searle
Biogeosciences, 20, 1559–1586, https://doi.org/10.5194/bg-20-1559-2023, https://doi.org/10.5194/bg-20-1559-2023, 2023
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Soil organic carbon (SOC) is of a heterogeneous nature and varies in chemistry, stabilisation mechanisms, and persistence in soil. In this study we mapped the stocks of SOC fractions with different characteristics and turnover rates (presumably PyOC >= MAOC > POC) across Australia, combining spectroscopy and digital soil mapping. The SOC stocks (0–30 cm) were estimated as 13 Pg MAOC, 2 Pg POC, and 5 Pg PyOC.
Frederick Büks
Biogeosciences, 20, 1529–1535, https://doi.org/10.5194/bg-20-1529-2023, https://doi.org/10.5194/bg-20-1529-2023, 2023
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Ultrasonication with density fractionation of soils is a commonly used method to separate soil organic matter pools, which is, e.g., important to calculate carbon turnover in landscapes. It is shown that the approach that merges soil and dense solution without mixing has a low recovery rate and causes co-extraction of parts of the retained labile pool along with the intermediate pool. An alternative method with high recovery rates and no cross-contamination was recommended.
Tino Peplau, Christopher Poeplau, Edward Gregorich, and Julia Schroeder
Biogeosciences, 20, 1063–1074, https://doi.org/10.5194/bg-20-1063-2023, https://doi.org/10.5194/bg-20-1063-2023, 2023
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We buried tea bags and temperature loggers in a paired-plot design in soils under forest and agricultural land and retrieved them after 2 years to quantify the effect of land-use change on soil temperature and litter decomposition in subarctic agricultural systems. We could show that agricultural soils were on average 2 °C warmer than forests and that litter decomposition was enhanced. The results imply that deforestation amplifies effects of climate change on soil organic matter dynamics.
Joseph Okello, Marijn Bauters, Hans Verbeeck, Samuel Bodé, John Kasenene, Astrid Françoys, Till Engelhardt, Klaus Butterbach-Bahl, Ralf Kiese, and Pascal Boeckx
Biogeosciences, 20, 719–735, https://doi.org/10.5194/bg-20-719-2023, https://doi.org/10.5194/bg-20-719-2023, 2023
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The increase in global and regional temperatures has the potential to drive accelerated soil organic carbon losses in tropical forests. We simulated climate warming by translocating intact soil cores from higher to lower elevations. The results revealed increasing temperature sensitivity and decreasing losses of soil organic carbon with increasing elevation. Our results suggest that climate warming may trigger enhanced losses of soil organic carbon from tropical montane forests.
Johanna Pihlblad, Louise C. Andresen, Catriona A. Macdonald, David S. Ellsworth, and Yolima Carrillo
Biogeosciences, 20, 505–521, https://doi.org/10.5194/bg-20-505-2023, https://doi.org/10.5194/bg-20-505-2023, 2023
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Elevated CO2 in the atmosphere increases forest biomass productivity when growth is not limited by soil nutrients. This study explores how mature trees stimulate soil availability of nitrogen and phosphorus with free-air carbon dioxide enrichment after 5 years of fumigation. We found that both nutrient availability and processes feeding available pools increased in the rhizosphere, and phosphorus increased at depth. This appears to not be by decomposition but by faster recycling of nutrients.
Rodrigo Vargas and Van Huong Le
Biogeosciences, 20, 15–26, https://doi.org/10.5194/bg-20-15-2023, https://doi.org/10.5194/bg-20-15-2023, 2023
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Quantifying the role of soils in nature-based solutions requires accurate estimates of soil greenhouse gas (GHG) fluxes. We suggest that multiple GHG fluxes should not be simultaneously measured at a few fixed time intervals, but an optimized sampling approach can reduce bias and uncertainty. Our results have implications for assessing GHG fluxes from soils and a better understanding of the role of soils in nature-based solutions.
Kristine Karstens, Benjamin Leon Bodirsky, Jan Philipp Dietrich, Marta Dondini, Jens Heinke, Matthias Kuhnert, Christoph Müller, Susanne Rolinski, Pete Smith, Isabelle Weindl, Hermann Lotze-Campen, and Alexander Popp
Biogeosciences, 19, 5125–5149, https://doi.org/10.5194/bg-19-5125-2022, https://doi.org/10.5194/bg-19-5125-2022, 2022
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Soil organic carbon (SOC) has been depleted by anthropogenic land cover change and agricultural management. While SOC models often simulate detailed biochemical processes, the management decisions are still little investigated at the global scale. We estimate that soils have lost around 26 GtC relative to a counterfactual natural state in 1975. Yet, since 1975, SOC has been increasing again by 4 GtC due to a higher productivity, recycling of crop residues and manure, and no-tillage practices.
Petri Kiuru, Marjo Palviainen, Arianna Marchionne, Tiia Grönholm, Maarit Raivonen, Lukas Kohl, and Annamari Laurén
Biogeosciences, 19, 5041–5058, https://doi.org/10.5194/bg-19-5041-2022, https://doi.org/10.5194/bg-19-5041-2022, 2022
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Peatlands are large carbon stocks. Emissions of carbon dioxide and methane from peatlands may increase due to changes in management and climate. We studied the variation in the gas diffusivity of peat with depth using pore network simulations and laboratory experiments. Gas diffusivity was found to be lower in deeper peat with smaller pores and lower pore connectivity. However, gas diffusivity was not extremely low in wet conditions, which may reflect the distinctive structure of peat.
Rachael Akinyede, Martin Taubert, Marion Schrumpf, Susan Trumbore, and Kirsten Küsel
Biogeosciences, 19, 4011–4028, https://doi.org/10.5194/bg-19-4011-2022, https://doi.org/10.5194/bg-19-4011-2022, 2022
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Soils will likely become warmer in the future, and this can increase the release of carbon dioxide (CO2) into the atmosphere. As microbes can take up soil CO2 and prevent further escape into the atmosphere, this study compares the rate of uptake and release of CO2 at two different temperatures. With warming, the rate of CO2 uptake increases less than the rate of release, indicating that the capacity to modulate soil CO2 release into the atmosphere will decrease under future warming.
Giuseppe Cipolla, Salvatore Calabrese, Amilcare Porporato, and Leonardo V. Noto
Biogeosciences, 19, 3877–3896, https://doi.org/10.5194/bg-19-3877-2022, https://doi.org/10.5194/bg-19-3877-2022, 2022
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Enhanced weathering (EW) is a promising strategy for carbon sequestration. Since models may help to characterize field EW, the present work applies a hydro-biogeochemical model to four case studies characterized by different rainfall seasonality, vegetation and soil type. Rainfall seasonality strongly affects EW dynamics, but low carbon sequestration suggests that an in-depth analysis at the global scale is required to see if EW may be effective to mitigate climate change.
Vao Fenotiana Razanamahandry, Marjolein Dewaele, Gerard Govers, Liesa Brosens, Benjamin Campforts, Liesbet Jacobs, Tantely Razafimbelo, Tovonarivo Rafolisy, and Steven Bouillon
Biogeosciences, 19, 3825–3841, https://doi.org/10.5194/bg-19-3825-2022, https://doi.org/10.5194/bg-19-3825-2022, 2022
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In order to shed light on possible past vegetation shifts in the Central Highlands of Madagascar, we measured stable isotope ratios of organic carbon in soil profiles along both forested and grassland hillslope transects in the Lake Alaotra region. Our results show that the landscape of this region was more forested in the past: soils in the C4-dominated grasslands contained a substantial fraction of C3-derived carbon, increasing with depth.
Katherine E. O. Todd-Brown, Rose Z. Abramoff, Jeffrey Beem-Miller, Hava K. Blair, Stevan Earl, Kristen J. Frederick, Daniel R. Fuka, Mario Guevara Santamaria, Jennifer W. Harden, Katherine Heckman, Lillian J. Heran, James R. Holmquist, Alison M. Hoyt, David H. Klinges, David S. LeBauer, Avni Malhotra, Shelby C. McClelland, Lucas E. Nave, Katherine S. Rocci, Sean M. Schaeffer, Shane Stoner, Natasja van Gestel, Sophie F. von Fromm, and Marisa L. Younger
Biogeosciences, 19, 3505–3522, https://doi.org/10.5194/bg-19-3505-2022, https://doi.org/10.5194/bg-19-3505-2022, 2022
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Research data are becoming increasingly available online with tantalizing possibilities for reanalysis. However harmonizing data from different sources remains challenging. Using the soils community as an example, we walked through the various strategies that researchers currently use to integrate datasets for reanalysis. We find that manual data transcription is still extremely common and that there is a critical need for community-supported informatics tools like vocabularies and ontologies.
Alessandro Montemagno, Christophe Hissler, Victor Bense, Adriaan J. Teuling, Johanna Ziebel, and Laurent Pfister
Biogeosciences, 19, 3111–3129, https://doi.org/10.5194/bg-19-3111-2022, https://doi.org/10.5194/bg-19-3111-2022, 2022
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We investigated the biogeochemical processes that dominate the release and retention of elements (nutrients and potentially toxic elements) during litter degradation. Our results show that toxic elements are retained in the litter, while nutrients are released in solution during the first stages of degradation. This seems linked to the capability of trees to distribute the elements between degradation-resistant and non-degradation-resistant compounds of leaves according to their chemical nature.
Laura Sereni, Bertrand Guenet, Charlotte Blasi, Olivier Crouzet, Jean-Christophe Lata, and Isabelle Lamy
Biogeosciences, 19, 2953–2968, https://doi.org/10.5194/bg-19-2953-2022, https://doi.org/10.5194/bg-19-2953-2022, 2022
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This study focused on the modellisation of two important drivers of soil greenhouse gas emissions: soil contamination and soil moisture change. The aim was to include a Cu function in the soil biogeochemical model DNDC for different soil moisture conditions and then to estimate variation in N2O, NO2 or NOx emissions. Our results show a larger effect of Cu on N2 and N2O emissions than on the other nitrogen species and a higher effect for the soils incubated under constant constant moisture.
Marie Spohn and Johan Stendahl
Biogeosciences, 19, 2171–2186, https://doi.org/10.5194/bg-19-2171-2022, https://doi.org/10.5194/bg-19-2171-2022, 2022
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We explored the ratios of carbon (C), nitrogen (N), and phosphorus (P) of organic matter in Swedish forest soils. The N : P ratio of the organic layer was most strongly related to the mean annual temperature, while the C : N ratios of the organic layer and mineral soil were strongly related to tree species even in the subsoil. The organic P concentration in the mineral soil was strongly affected by soil texture, which diminished the effect of tree species on the C to organic P (C : OP) ratio.
Moritz Mainka, Laura Summerauer, Daniel Wasner, Gina Garland, Marco Griepentrog, Asmeret Asefaw Berhe, and Sebastian Doetterl
Biogeosciences, 19, 1675–1689, https://doi.org/10.5194/bg-19-1675-2022, https://doi.org/10.5194/bg-19-1675-2022, 2022
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The largest share of terrestrial carbon is stored in soils, making them highly relevant as regards global change. Yet, the mechanisms governing soil carbon stabilization are not well understood. The present study contributes to a better understanding of these processes. We show that qualitative changes in soil organic matter (SOM) co-vary with alterations of the soil matrix following soil weathering. Hence, the type of SOM that is stabilized in soils might change as soils develop.
Jasmin Fetzer, Emmanuel Frossard, Klaus Kaiser, and Frank Hagedorn
Biogeosciences, 19, 1527–1546, https://doi.org/10.5194/bg-19-1527-2022, https://doi.org/10.5194/bg-19-1527-2022, 2022
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As leaching is a major pathway of nitrogen and phosphorus loss in forest soils, we investigated several potential drivers in two contrasting beech forests. The composition of leachates, obtained by zero-tension lysimeters, varied by season, and climatic extremes influenced the magnitude of leaching. Effects of nitrogen and phosphorus fertilization varied with soil nutrient status and sorption properties, and leaching from the low-nutrient soil was more sensitive to environmental factors.
Karis J. McFarlane, Heather M. Throckmorton, Jeffrey M. Heikoop, Brent D. Newman, Alexandra L. Hedgpeth, Marisa N. Repasch, Thomas P. Guilderson, and Cathy J. Wilson
Biogeosciences, 19, 1211–1223, https://doi.org/10.5194/bg-19-1211-2022, https://doi.org/10.5194/bg-19-1211-2022, 2022
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Planetary warming is increasing seasonal thaw of permafrost, making this extensive old carbon stock vulnerable. In northern Alaska, we found more and older dissolved organic carbon in small drainages later in summer as more permafrost was exposed by deepening thaw. Younger and older carbon did not differ in chemical indicators related to biological lability suggesting this carbon can cycle through aquatic systems and contribute to greenhouse gas emissions as warming increases permafrost thaw.
Pengzhi Zhao, Daniel Joseph Fallu, Sara Cucchiaro, Paolo Tarolli, Clive Waddington, David Cockcroft, Lisa Snape, Andreas Lang, Sebastian Doetterl, Antony G. Brown, and Kristof Van Oost
Biogeosciences, 18, 6301–6312, https://doi.org/10.5194/bg-18-6301-2021, https://doi.org/10.5194/bg-18-6301-2021, 2021
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We investigate the factors controlling the soil organic carbon (SOC) stability and temperature sensitivity of abandoned prehistoric agricultural terrace soils. Results suggest that the burial of former topsoil due to terracing provided an SOC stabilization mechanism. Both the soil C : N ratio and SOC mineral protection regulate soil SOC temperature sensitivity. However, which mechanism predominantly controls SOC temperature sensitivity depends on the age of the buried terrace soils.
Heleen Deroo, Masuda Akter, Samuel Bodé, Orly Mendoza, Haichao Li, Pascal Boeckx, and Steven Sleutel
Biogeosciences, 18, 5035–5051, https://doi.org/10.5194/bg-18-5035-2021, https://doi.org/10.5194/bg-18-5035-2021, 2021
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We assessed if and how incorporation of exogenous organic carbon (OC) such as straw could affect decomposition of native soil organic carbon (SOC) under different irrigation regimes. Addition of exogenous OC promoted dissolution of native SOC, partly because of increased Fe reduction, leading to more net release of Fe-bound SOC. Yet, there was no proportionate priming of SOC-derived DOC mineralisation. Water-saving irrigation can retard both priming of SOC dissolution and mineralisation.
Frances A. Podrebarac, Sharon A. Billings, Kate A. Edwards, Jérôme Laganière, Matthew J. Norwood, and Susan E. Ziegler
Biogeosciences, 18, 4755–4772, https://doi.org/10.5194/bg-18-4755-2021, https://doi.org/10.5194/bg-18-4755-2021, 2021
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Soil respiration is a large and temperature-responsive flux in the global carbon cycle. We found increases in microbial use of easy to degrade substrates enhanced the temperature response of respiration in soils layered as they are in situ. This enhanced response is consistent with soil composition differences in warm relative to cold climate forests. These results highlight the importance of the intact nature of soils rarely studied in regulating responses of CO2 fluxes to changing temperature.
Elisa Bruni, Bertrand Guenet, Yuanyuan Huang, Hugues Clivot, Iñigo Virto, Roberta Farina, Thomas Kätterer, Philippe Ciais, Manuel Martin, and Claire Chenu
Biogeosciences, 18, 3981–4004, https://doi.org/10.5194/bg-18-3981-2021, https://doi.org/10.5194/bg-18-3981-2021, 2021
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Increasing soil organic carbon (SOC) stocks is beneficial for climate change mitigation and food security. One way to enhance SOC stocks is to increase carbon input to the soil. We estimate the amount of carbon input required to reach a 4 % annual increase in SOC stocks in 14 long-term agricultural experiments around Europe. We found that annual carbon input should increase by 43 % under current temperature conditions, by 54 % for a 1 °C warming scenario and by 120 % for a 5 °C warming scenario.
Rainer Brumme, Bernd Ahrends, Joachim Block, Christoph Schulz, Henning Meesenburg, Uwe Klinck, Markus Wagner, and Partap K. Khanna
Biogeosciences, 18, 3763–3779, https://doi.org/10.5194/bg-18-3763-2021, https://doi.org/10.5194/bg-18-3763-2021, 2021
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In order to study the fate of litter nitrogen in forest soils, we combined a leaf litterfall exchange experiment using 15N-labeled leaf litter with long-term element budgets at seven European beech sites in Germany. It appears that fructification intensity, which has increased in recent decades, has a distinct impact on N retention in forest soils. Despite reduced nitrogen deposition, about 6 and 10 kg ha−1 of nitrogen were retained annually in the soils and in the forest stands, respectively.
Lorenz Gfeller, Andrea Weber, Isabelle Worms, Vera I. Slaveykova, and Adrien Mestrot
Biogeosciences, 18, 3445–3465, https://doi.org/10.5194/bg-18-3445-2021, https://doi.org/10.5194/bg-18-3445-2021, 2021
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Our incubation experiment shows that flooding of polluted floodplain soils may induce pulses of both mercury (Hg) and methylmercury to the soil solution and threaten downstream ecosystems. We demonstrate that mobilization of Hg bound to manganese oxides is a relevant process in organic-matter-poor soils. Addition of organic amendments accelerates this mobilization but also facilitates the formation of nanoparticulate Hg and the subsequent fixation of Hg from soil solution to the soil.
Yao Zhang, Jocelyn M. Lavallee, Andy D. Robertson, Rebecca Even, Stephen M. Ogle, Keith Paustian, and M. Francesca Cotrufo
Biogeosciences, 18, 3147–3171, https://doi.org/10.5194/bg-18-3147-2021, https://doi.org/10.5194/bg-18-3147-2021, 2021
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Soil organic matter (SOM) is essential for the health of soils, and the accumulation of SOM helps removal of CO2 from the atmosphere. Here we present the result of the continued development of a mathematical model that simulates SOM and its measurable fractions. In this study, we simulated several grassland sites in the US, and the model generally captured the carbon and nitrogen amounts in SOM and their distribution between the measurable fractions throughout the entire soil profile.
Zhongkui Luo, Raphael A. Viscarra-Rossel, and Tian Qian
Biogeosciences, 18, 2063–2073, https://doi.org/10.5194/bg-18-2063-2021, https://doi.org/10.5194/bg-18-2063-2021, 2021
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Using the data from 141 584 whole-soil profiles across the globe, we disentangled the relative importance of biotic, climatic and edaphic variables in controlling global SOC stocks. The results suggested that soil properties and climate contributed similarly to the explained global variance of SOC in four sequential soil layers down to 2 m. However, the most important individual controls are consistently soil-related, challenging current climate-driven framework of SOC dynamics.
Debjani Sihi, Xiaofeng Xu, Mónica Salazar Ortiz, Christine S. O'Connell, Whendee L. Silver, Carla López-Lloreda, Julia M. Brenner, Ryan K. Quinn, Jana R. Phillips, Brent D. Newman, and Melanie A. Mayes
Biogeosciences, 18, 1769–1786, https://doi.org/10.5194/bg-18-1769-2021, https://doi.org/10.5194/bg-18-1769-2021, 2021
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Humid tropical soils are important sources and sinks of methane. We used model simulation to understand how different kinds of microbes and observed soil moisture and oxygen dynamics contribute to production and consumption of methane along a wet tropical hillslope during normal and drought conditions. Drought alters the diffusion of oxygen and microbial substrates into and out of soil microsites, resulting in enhanced methane release from the entire hillslope during drought recovery.
Mathieu Chassé, Suzanne Lutfalla, Lauric Cécillon, François Baudin, Samuel Abiven, Claire Chenu, and Pierre Barré
Biogeosciences, 18, 1703–1718, https://doi.org/10.5194/bg-18-1703-2021, https://doi.org/10.5194/bg-18-1703-2021, 2021
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Evolution of organic carbon content in soils could be a major driver of atmospheric greenhouse gas concentrations over the next century. Understanding factors controlling carbon persistence in soil is a challenge. Our study of unique long-term bare-fallow samples, depleted in labile organic carbon, helps improve the separation, evaluation and characterization of carbon pools with distinct residence time in soils and gives insight into the mechanisms explaining soil organic carbon persistence.
Melisa A. Diaz, Christopher B. Gardner, Susan A. Welch, W. Andrew Jackson, Byron J. Adams, Diana H. Wall, Ian D. Hogg, Noah Fierer, and W. Berry Lyons
Biogeosciences, 18, 1629–1644, https://doi.org/10.5194/bg-18-1629-2021, https://doi.org/10.5194/bg-18-1629-2021, 2021
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Water-soluble salt and nutrient concentrations of soils collected along the Shackleton Glacier, Antarctica, show distinct geochemical gradients related to latitude, longitude, elevation, soil moisture, and distance from coast and glacier. Machine learning algorithms were used to estimate geochemical gradients for the region given the relationship with geography. Geography and surface exposure age drive salt and nutrient abundances, influencing invertebrate habitat suitability and biogeography.
Marion Schrumpf, Klaus Kaiser, Allegra Mayer, Günter Hempel, and Susan Trumbore
Biogeosciences, 18, 1241–1257, https://doi.org/10.5194/bg-18-1241-2021, https://doi.org/10.5194/bg-18-1241-2021, 2021
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A large amount of organic carbon (OC) in soil is protected against decay by bonding to minerals. We studied the release of mineral-bonded OC by NaF–NaOH extraction and H2O2 oxidation. Unexpectedly, extraction and oxidation removed mineral-bonded OC at roughly constant portions and of similar age distributions, irrespective of mineral composition, land use, and soil depth. The results suggest uniform modes of interactions between OC and minerals across soils in quasi-steady state with inputs.
Cited articles
Ardón, M., Helton, A. M., and Bernhardt, E. S.: Drought and saltwater
incursion synergistically reduce dissolved organic carbon export from
coastal freshwater wetlands, Biogeochemistry, 127, 411–426,
https://doi.org/10.1007/s10533-016-0189-5, 2016.
Ardón, M., Helton, A. M., and Bernhardt, E. S.: Salinity effects on
greenhouse gas emissions from wetland soils are contingent upon hydrologic
setting: a microcosm experiment, Biogeochemistry, 140, 217–232,
https://doi.org/10.1007/s10533-018-0486-2, 2018.
Aronesty, E.: Comparison of sequencing utility programs, Open Bioinformatics Journal, 7, 1–8, 2013.
Bailey, V. L., Smith, A. P., Tfaily, M., Fansler, S. J., and Bond-Lamberty,
B.: Differences in soluble organic carbon chemistry in pore waters sampled
from different pore size domains, Soil Biol. Biochem., 107, 133–143,
https://doi.org/10.1016/J.SOILBIO.2016.11.025, 2017.
Barry, S. C., Bianchi, T. S., Shields, M. R., Hutchings, J. A., Jacoby, C.
A., and Frazer, T. K.: Characterizing blue carbon stocks in Thalassia testudinum meadows
subjected to different phosphorus supplies: A lignin biomarker approach,
Limnol. Oceanogr., 63, 2630–2646, https://doi.org/10.1002/lno.10965, 2018.
Bond-Lamberty, B., Bolton, H., Fansler, S., Heredia-Langner, A., Liu, C.,
McCue, L. A., Smith, J., and Bailey, V.: Soil Respiration and Bacterial
Structure and Function after 17 Years of a Reciprocal Soil Transplant
Experiment, edited by: Treseder, K., PLoS One, 11, e0150599,
https://doi.org/10.1371/journal.pone.0150599, 2016.
Bottos, E. M., Kennedy, D. W., Romero, E. B., Fansler, S. J., Brown, J. M.,
Bramer, L. M., Chu, R. K., Tfaily, M. M., Jansson, J. K., and Stegen, J. C.:
Dispersal limitation and thermodynamic constraints govern spatial structure
of permafrost microbial communities, FEMS Microbiol. Ecol., 94,
https://doi.org/10.1093/femsec/fiy110, 2018.
Boye, K., Noël, V., Tfaily, M. M., Bone, S. E., Williams, K. H., Bargar,
J. R., and Fendorf, S.: Thermodynamically controlled preservation of organic
carbon in floodplains, Nat. Geosci., 10, 415–419, https://doi.org/10.1038/NGEO2940, 2017.
Bramucci, A., Han, S., Beckers, J., Haas, C., Lanoil, B., Bramucci, A., Han,
S., Beckers, J., Haas, C., and Lanoil, B.: Composition, Diversity, and
Stability of Microbial Assemblages in Seasonal Lake Ice, Miquelon Lake,
Central Alberta, Biology (Basel), 2, 514–532,
https://doi.org/10.3390/biology2020514, 2013.
Breitling, R., Ritchie, S., Goodenowe, D., Stewart, M. L., and Barrett, M.
P.: Ab initio prediction of metabolic networks using Fourier transform mass
spectrometry data, Metabolomics, 2, 155–164,
https://doi.org/10.1007/s11306-006-0029-z, 2006.
Brown, J., Zavoshy, N., Brislawn, C. J., and McCue, L. A.: Hundo: a Snakemake
workflow for microbial community sequence data, PeerJ Preprints, 6, e27272v1,
https://doi.org/10.7287/peerj.preprints.27272v1, 2018.
Burke, C., Steinberg, P., Rusch, D., Kjelleberg, S., and Thomas, T.:
Bacterial community assembly based on functional genes rather than species,
P. Natl. Acad. Sci. USA, 108, 14288–14293,
https://doi.org/10.1073/pnas.1101591108, 2011.
Bushnell, B.: BBMap, available at: https://sourceforge.net/projects/bbmap/ (last access: 7 October 2019), 2018.
Caruso, T., Chan, Y., Lacap, D. C., Lau, M. C. Y., McKay, C. P., and
Pointing, S. B.: Stochastic and deterministic processes interact in the
assembly of desert microbial communities on a global scale, ISME J., 5,
1406–13, https://doi.org/10.1038/ismej.2011.21, 2011.
Chambers, L. G., Reddy, K. R., and Osborne, T. Z.: Short-Term Response of
Carbon Cycling to Salinity Pulses in a Freshwater Wetland, Soil Sci. Soc.
Am. J., 75, 2000, https://doi.org/10.2136/sssaj2011.0026, 2011.
Chambers, L. G., Osborne, T. Z., and Reddy, K. R.: Effect of
salinity-altering pulsing events on soil organic carbon loss along an
intertidal wetland gradient: a laboratory experiment, Biogeochemistry,
115, 363–383, https://doi.org/10.1007/s10533-013-9841-5, 2013.
Chambers, L. G., Davis, S. E., Troxler, T., Boyer, J. N., Downey-Wall, A.,
and Scinto, L. J.: Biogeochemical effects of simulated sea level rise on
carbon loss in an Everglades mangrove peat soil, Hydrobiologia, 726,
195–211, https://doi.org/10.1007/s10750-013-1764-6, 2014.
Conant, R. T., Ogle, S. M., Paul, E. A., and Paustian, K.: Measuring and
monitoring soil organic carbon stocks in agricultural lands for climate
mitigation, Front. Ecol. Environ., 9, 169–173, https://doi.org/10.1890/090153, 2011.
Conrads, P. A. and Darby, L. S.: Development of a coastal drought index
using salinity data, B. Am. Meteorol. Soc., 98, 753–766,
https://doi.org/10.1175/BAMS-D-15-00171.1, 2017.
Dang, C., Morrissey, E. M., Neubauer, S. C., and Franklin, R. B.: Novel
microbial community composition and carbon biogeochemistry emerge over time
following saltwater intrusion in wetlands, Glob. Change Biol., 25, 549–561, https://doi.org/10.1111/gcb.14486, 2019.
Dini-Andreote, F., Stegen, J. C., van Elsas, J. D., and Salles, J. F.:
Disentangling mechanisms that mediate the balance between stochastic and
deterministic processes in microbial succession, P. Natl. Acad. Sci. USA, 112, E1326–1332, https://doi.org/10.1073/pnas.1414261112, 2015.
Dittmar, T., Koch, B., Hertkorn, N., and Kattner, G.: A simple and efficient
method for the solid-phase extraction of dissolved organic matter (SPE-DOM)
from seawater, Limnol. Oceanogr.-Meth., 6, 230–235, 2008.
Dungait, J. A. J., Hopkins, D. W., Gregory, A. S., and Whitmore, A. P.: Soil
organic matter turnover is governed by accessibility not recalcitrance,
Glob. Change Biol., 18, 1781–1796, https://doi.org/10.1111/j.1365-2486.2012.02665.x,
2012.
Edgar, R. C.: Search and clustering orders of magnitude faster than BLAST,
Bioinformatics,
26, 2460–2461, 2010.
Ensign, S. H. and Noe, G. B.: Tidal extension and sea-level rise:
recommendations for a research agenda, Front. Ecol. Environ., 16, 37–43,
https://doi.org/10.1002/fee.1745, 2018.
ESRI: ArcGIS Desktop: Release 10.5 Redlands, Environmental Systems Research Institute, CA, 2017.
Fernández, A., Huang, S., Seston, S., Xing, J., Hickey, R., Criddle, C.,
and Tiedje, J.: How stable is stable? Function versus community
composition, Appl. Environ. Microb., 65, 3697–704,
1999.
Fierer, N.: Embracing the unknown: disentangling the complexities of the
soil microbiome, Nat. Publ. Gr., 15, 579–590, https://doi.org/10.1038/nrmicro.2017.87, 2017.
Fierer, N. and Jackson, R. B.: The diversity and biogeography of soil
bacterial communities, P. Natl. Acad. Sci. USA, 103, 626–631, https://doi.org/10.1073/pnas.0507535103, 2006.
Garbeva, P., van Veen, J. A., and van Elsas, J. D.: Microbial diversity in
soil: selection microbial populations by plant and soil type and
implications for disease suppressiveness, Annu. Rev. Phytopathol., 42,
243–270, https://doi.org/10.1146/annurev.phyto.42.012604.135455, 2004.
Goldman, A. E., Graham, E. B., Crump, A. R., Kennedy, D. W., Romero, E. B., Anderson, C. G., Dana, K. L., Resch, C. T., Fredrickson, J. K., and Stegen, J. C.: Biogeochemical cycling at the aquatic–terrestrial interface is linked to parafluvial hyporheic zone inundation history, Biogeosciences, 14, 4229–4241, https://doi.org/10.5194/bg-14-4229-2017, 2017.
Gouffi, K., Pica, N., Pichereau, V., and Blanco, C.: Disaccharides as a new
class of nonaccumulated osmoprotectants for Sinorhizobium meliloti, Appl.
Environ. Microb., 65, 1491–1500, https://doi.org/10.1186/1746-1448-1-5, 1999.
Graham, E. B. and Stegen, J. C.: Stochastic microbial community assembly decreases biogeochemical function, bioRxiv, 183897, https://doi.org/10.1101/183897, 2017.
Graham, E. B., Knelman, J. E., Schindlbacher, A., Siciliano, S., Breulmann,
M., Yannarell, A., Beman, J. M., Abell, G., Philippot, L., Prosser, J.,
Foulquier, A., Yuste, J. C., Glanville, H. C., Jones, D. L., Angel, R.,
Salminen, J., Newton, R. J., Bürgmann, H., Ingram, L. J., Hamer, U.,
Siljanen, H. M. P., Peltoniemi, K., Potthast, K., Bañeras, L., Hartmann,
M., Banerjee, S., Yu, R.-Q., Nogaro, G., Richter, A., Koranda, M., Castle,
S. C., Goberna, M., Song, B., Chatterjee, A., Nunes, O. C., Lopes, A. R.,
Cao, Y., Kaisermann, A., Hallin, S., Strickland, M. S., Garcia-Pausas, J.,
Barba, J., Kang, H., Isobe, K., Papaspyrou, S., Pastorelli, R., Lagomarsino,
A., Lindström, E. S., Basiliko, N. and Nemergut, D. R.: Microbes as
Engines of Ecosystem Function: When Does Community Structure Enhance
Predictions of Ecosystem Processes?, Front. Microbiol., 7, 214,
https://doi.org/10.3389/fmicb.2016.00214, 2016.
Graham, E. B., Tfaily, M. M., Crump, A. R., Goldman, A. E., Bramer, L. M.,
Arntzen, E., Romero, E., Resch, C. T., Kennedy, D. W., and Stegen, J. C.:
Carbon Inputs From Riparian Vegetation Limit Oxidation of Physically Bound
Organic Carbon Via Biochemical and Thermodynamic Processes, J. Geophys. Res.-Biogeo, 122, 3188–3205, https://doi.org/10.1002/2017JG003967, 2017a.
Graham, E. B., Crump, A. R., Resch, C. T., Fansler, S., Arntzen, E.,
Kennedy, D. W., Fredrickson, J. K., and Stegen, J. C.: Deterministic
influences exceed dispersal effects on hydrologically-connected microbiomes,
Environ. Microbiol., 19, 1552–1567, https://doi.org/10.1111/1462-2920.13720, 2017b.
Graham, E. B., Crump, A. R., Kennedy, D. W., Arntzen, E., Fansler, S.,
Purvine, S. O., Nicora, C. D., Nelson, W., Tfaily, M. M., and Stegen, J. C.:
Multi'omics comparison reveals metabolome biochemistry, not microbiome
composition or gene expression, corresponds to elevated biogeochemical
function in the hyporheic zone, Sci. Total Environ., 642, 742–753,
https://doi.org/10.1016/J.SCITOTENV.2018.05.256, 2018.
Green, J. L., Holmes, A. J., Westoby, M., Oliver, I., Briscoe, D.,
Dangerfield, M., Gillings, M., and Beattie, A. J.: Spatial scaling of
microbial eukaryote diversity, Nature, 432, 747–750,
https://doi.org/10.1038/nature03034, 2004.
Green, J. L., Bohannan, B. J. M., and Whitaker, R. J.: Microbial
Biogeography: From Taxonomy to Traits, Science, 320,
1039–1043, https://doi.org/10.1126/SCIENCE.1153475, 2008.
Guillemette, R., Kaneko, R., Blanton, J., Tan, J., Witt, M., Hamilton, S.,
Allen, E. E., Medina, M., Hamasaki, K., Koch, B. P., and Azam, F.:
Bacterioplankton drawdown of coral mass-spawned organic matter, ISME J.,
12, 2238–2251, https://doi.org/10.1038/s41396-018-0197-7, 2018.
Hawkes, C. V. and Keitt, T. H.: Resilience vs. historical contingency in
microbial responses to environmental change, edited by: Classen, A., Ecol.
Lett., 18, 612–625, https://doi.org/10.1111/ele.12451, 2015.
Hawkes, C. V., Waring, B. G., Rocca, J. D., and Kivlin, S. N.: Historical
climate controls soil respiration responses to current soil moisture, P.
Natl. Acad. Sci. USA, 114, 6322–6327, https://doi.org/10.1073/pnas.1620811114,
2017.
Hedges, J. I. and Oades, J. M.: Comparative organic geochemistries of soils
and marine sediments, Org. Geochem., 27, 319–361, 1997.
Hedges, J. I., Keil, R. G., and Benner, R.: What happens to terrestrial
organic matter in the ocean?, Org. Geochem., 27, 195–212,
https://doi.org/10.1016/S0146-6380(97)00066-1, 1997.
Herbert, E. R., Schubauer-Berigan, J., and Craft, C. B.: Differential effects
of chronic and acute simulated seawater intrusion on tidal freshwater marsh
carbon cycling, Biogeochemistry, 138, 137–154,
https://doi.org/10.1007/s10533-018-0436-z, 2018.
Hinson, A. L., Feagin, R. A., Eriksson, M., Najjar, R. G., Herrmann, M.,
Bianchi, T. S., Kemp, M., Hutchings, J. A., Crooks, S., and Boutton, T.: The
spatial distribution of soil organic carbon in tidal wetland soils of the
continental United States, Glob. Change Biol., 23, 5468–5480,
https://doi.org/10.1111/gcb.13811, 2017.
Hoitink, A. J. F. and Jay, D. A.: Tidal river dynamics: Implications for
deltas, Rev. Geophys., 54, 240–272, https://doi.org/10.1002/2015RG000507, 2016.
Hoitink, A. J. F., Buschman, F. A., and Vermeulen, B.: Continuous
measurements of discharge from a horizontal acoustic Doppler current
profiler in a tidal river, Water Resour. Res, 45, 11406,
https://doi.org/10.1029/2009WR007791, 2009.
Holmquist, J. R., Windham-Myers, L., Bliss, N., Crooks, S., Morris, J. T.,
Megonigal, J. P., Troxler, T., Weller, D., Callaway, J., Drexler, J.,
Ferner, M. C., Gonneea, M. E., Kroeger, K. D., Schile-Beers, L., Woo, I.,
Buffington, K., Breithaupt, J., Boyd, B. M., Brown, L. N., Dix, N., Hice,
L., Horton, B. P., MacDonald, G. M., Moyer, R. P., Reay, W., Shaw, T.,
Smith, E., Smoak, J. M., Sommerfield, C., Thorne, K., Velinsky, D., Watson,
E., Grimes, K. W., and Woodrey, M.: Accuracy and Precision of Tidal Wetland
Soil Carbon Mapping in the Conterminous United States, Sci. Rep.-UK, 8,
9478, https://doi.org/10.1038/s41598-018-26948-7, 2018.
Hubbell, S. P.: The Unified Neutral Theory of Biodiversity and Biogeography,
Princeton University Press, available at:
http://www.jstor.org/stable/j.ctt7rj8w (last access: 7 October 2019), 2001.
Jobbágy, E. G. and Jackson, R. B.: The vertical distribution of soil
organic carbon and its relation to climate and vegetation, Ecol. Appl.,
10, 423–436, https://doi.org/10.1890/1051-0761(2000)010[0423:TVDOSO]2.0.CO;2, 2000.
Kim, S., Kramer, R. W., and Hatcher, P. G.: Graphical Method for Analysis of
Ultrahigh-Resolution Broadband Mass Spectra of Natural Organic Matter, the
Van Krevelen Diagram, Anal. Chem., 75, 5336–5344,
https://doi.org/10.1021/ac034415p, 2003.
Koch, B. P. and Dittmar, T.: From mass to structure: an aromaticity index
for high-resolution mass data of natural organic matter, Rapid Commun. Mass
Sp., 20, 926–932, https://doi.org/10.1002/rcm.2386, 2006.
Koch, B. P. and Dittmar, T.: From mass to structure: an aromaticity index
for high-resolution mass data of natural organic matter, Rapid Commun. Mass
Sp., 30, 250–250, https://doi.org/10.1002/rcm.7433, 2016.
Koch, B. P., Kattner, G., Witt, M., and Passow, U.: Molecular insights into the microbial formation of marine dissolved organic matter: recalcitrant or labile?, Biogeosciences, 11, 4173–4190, https://doi.org/10.5194/bg-11-4173-2014, 2014.
Kramer, C. and Gleixner, G.: Variable use of plant- and soil-derived carbon
by microorganisms in agricultural soils, Soil Biol. Biochem., 38,
3267–3278, https://doi.org/10.1016/J.SOILBIO.2006.04.006, 2006.
Kramer, C. and Gleixner, G.: Soil organic matter in soil depth profiles:
Distinct carbon preferences of microbial groups during carbon
transformation, Soil Biol. Biochem., 40, 425–433,
https://doi.org/10.1016/J.SOILBIO.2007.09.016, 2008.
Krauss, K. W., Noe, G. B., Duberstein, J. A., Conner, W. H., Stagg, C. L.,
Cormier, N., Jones, M. C., Bernhardt, C. E., Graeme Lockaby, B., From, A.
S., Doyle, T. W., Day, R. H., Ensign, S. H., Pierfelice, K. N., Hupp, C. R.,
Chow, A. T., and Whitbeck, J. L.: The Role of the Upper Tidal Estuary in
Wetland Blue Carbon Storage and Flux, Global Biogeochem. Cy., 32,
817–839, https://doi.org/10.1029/2018GB005897, 2018.
Ksionzek, K. B., Lechtenfeld, O. J., McCallister, S. L., Schmitt-Kopplin,
P., Geuer, J. K., Geibert, W., and Koch, B. P.: Dissolved organic sulfur in
the ocean: Biogeochemistry of a petagram inventory, Science, 354,
456–459, https://doi.org/10.1126/science.aaf7796, 2016.
Kubartová, A., Ottosson, E., and Stenlid, J.: Linking fungal communities
to wood density loss after 12 years of log decay, FEMS Microbiol. Ecol.,
91, fiv032, https://doi.org/10.1093/femsec/fiv032, 2015.
Kujawinski, E. B. and Behn, M. D.: Automated analysis of electrospray
ionization fourier transform ion cyclotron resonance mass spectra of natural
organic matter, Anal. Chem., 78, 4363–73, https://doi.org/10.1021/ac0600306, 2006.
Langer, U. and Rinklebe, J.: Lipid biomarkers for assessment of microbial
communities in floodplain soils of the Elbe River (Germany), Wetlands,
29, 353–362, https://doi.org/10.1672/08-114.1, 2009.
Langley, J. A., Sigrist, M. V., Duls, J., Cahoon, D. R., Lynch, J. C., and
Megonigal, J. P.: Global Change and Marsh Elevation Dynamics: Experimenting
Where Land Meets Sea and Biology Meets Geology, in: Proceedings of the
Smithsonian Marine Sciences Symposium, 391–400, Smithsonian Institution
Scholarly Press, Washington, DC, available at:
https://repository.si.edu/bitstream/handle/10088/18988/serc_Langley_et_al._2009_Smithsonian_Marine_Sciences_.pdf?sequence=1&isAllowed=y (last access: 7 May
2019), 2007.
Langston, A. K., Kaplan, D. A., and Putz, F. E.: A casualty of climate
change? Loss of freshwater forest islands on Florida's Gulf Coast, Glob.
Change Biol., 23, 5383–5397, https://doi.org/10.1111/gcb.13805, 2017.
LaRowe, D. E. and Van Cappellen, P.: Degradation of natural organic matter:
A thermodynamic analysis, Geochim. Cosmochim. Ac., 75, 2030–2042,
https://doi.org/10.1016/J.GCA.2011.01.020, 2011.
Lechtenfeld, O. J., Hertkorn, N., Shen, Y., Witt, M., and Benner, R.: Marine
sequestration of carbon in bacterial metabolites., Nat. Commun., 6, 6711,
https://doi.org/10.1038/ncomms7711, 2015.
Liebold, M. A. and Chase, M. J.: Combining Taxonomic and Functional Patterns
to Disentangle Metacommunity Assembly Processes, in: Metacommunity Ecology,
Vol. 9, edited by: Liebold, M. A. and Chase, M. J., p. 504, Princeton
University Press, Princeton, New Jersey, 2017.
Lima-Mendez, G., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F.,
Chaffron, S., Ignacio-Espinosa, J. C., Roux, S., Vincent, F., Bittner, L.,
Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A. M.,
Coppola, L., Cornejo-Castillo, F. M., d'Ovidio, F., Meester, L. De, Ferrera,
I., Garet-Delmas, M.-J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M.,
Salazar, G., Sánchez, P., Sebastian, M., Souffreau, C., Dimier, C.,
Picheral, M., Searson, S., Kandels-Lewis, S., TARA Oceans coordinators, Gorsky,
G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker,
P., Acinas, S. G., Sunagawa, S., Bork, P., Sullivan, M. B., Karsenti, E.,
Bowler, C., Vargas, C. de, and Raes, J.: Determinants of community structure
in the global plankton interactome, Science, 348, 1262073,
https://doi.org/10.1126/SCIENCE.1262073, 2015.
Liu, X., Ruecker, A., Song, B., Xing, J., Conner, W. H., and Chow, A. T.:
Effects of salinity and wet–dry treatments on C and N dynamics in
coastal-forested wetland soils: Implications of sea level rise, Soil Biol.
Biochem., 112, 56–67, https://doi.org/10.1016/J.SOILBIO.2017.04.002, 2017.
Loreau, M.: Does functional redundancy exist?, Oikos, 104, 606–611,
https://doi.org/10.1111/j.0030-1299.2004.12685.x, 2004.
Louca, S., Parfrey, L. W., and Doebeli, M.: Decoupling function and taxonomy
in the global ocean microbiome, Science, 353, 1272–1277,
https://doi.org/10.1126/science.aaf4507, 2016.
Louca, S., Polz, M. F., Mazel, F., Albright, M. B. N., Huber, J. A.,
O'connor, M. I., Ackermann, M., Hahn, A. S., Srivastava, D. S., Crowe, S.
A., Doebeli, M., and Parfrey, L. W.: Disentangling function from taxonomy in
microbial systems Function and functional redundancy in microbial systems, Nature Ecology & Evolution, 2, 936–943,
https://doi.org/10.1038/s41559-018-0519-1, 2018.
Martiny, J. B. H., Bohannan, B. J. M., Brown, J. H., Colwell, R. K.,
Fuhrman, J. A., Green, J. L., Horner-Devine, M. C., Kane, M., Krumins, J.
A., Kuske, C. R., Morin, P. J., Naeem, S., Øvreås, L., Reysenbach,
A.-L., Smith, V. H., and Staley, J. T.: Microbial biogeography: putting
microorganisms on the map, Nat. Rev. Microbiol., 4, 102–112,
https://doi.org/10.1038/nrmicro1341, 2006.
Marton, J. M., Herbert, E. R., and Craft, C. B.: Effects of Salinity on
Denitrification and Greenhouse Gas Production from Laboratory-incubated
Tidal Forest Soils, Wetlands, 32, 347–357,
https://doi.org/10.1007/s13157-012-0270-3, 2012.
Mau, R. L., Liu, C. M., Aziz, M., Schwartz, E., Dijkstra, P., Marks, J. C.,
Price, L. B., Keim, P., and Hungate, B. A.: Linking soil bacterial
biodiversity and soil carbon stability, ISME J., 9, 1477–1480,
https://doi.org/10.1038/ismej.2014.205, 2015.
McCarthy, M., Dimmitt, B., Muller-Karger, F., McCarthy, M. J., Dimmitt, B.,
and Muller-Karger, F. E.: Rapid Coastal Forest Decline in Florida's Big
Bend, Remote Sens., 10, 1721, https://doi.org/10.3390/rs10111721, 2018.
McClain, C. R., Stegen, J. C., and Hurlbert, A. H.: Dispersal, environmental
niches and oceanic-scale turnover in deep-sea bivalves, P. Roy. Soc. B-Biol. Sci., 279, https://doi.org/10.1098/RSPB.2011.2166, 2012.
Medeiros, P. M., Seidel, M., Ward, N. D., Carpenter, E. J., Gomes, H. R.,
Niggemann, J., Krusche, A. V., Richey, J. E., Yager, P. L., and Dittmar, T.:
Fate of the Amazon River dissolved organic matter in the tropical Atlantic
Ocean, Global Biogeochem. Cy., 29, 677–690, https://doi.org/10.1002/2015GB005115,
2015.
Minor, E. C., Steinbring, C. J., Longnecker, K., and Kujawinski, E. B.:
Characterization of dissolved organic matter in Lake Superior and its
watershed using ultrahigh resolution mass spectrometry, Org. Geochem., 43,
1–11, https://doi.org/10.1016/J.ORGGEOCHEM.2011.11.007, 2012.
Nemergut, D. R., Schmidt, S. K., Fukami, T., O'Neill, S. P., Bilinski, T.
M., Stanish, L. F., Knelman, J. E., Darcy, J. L., Lynch, R. C., Wickey, P.,
and Ferrenberg, S.: Patterns and processes of microbial community assembly,
Microbiol. Mol. Biol. R., 77, 342–56, https://doi.org/10.1128/MMBR.00051-12,
2013.
Neubauer, S. C., Givler, K., Valentine, S., and Megonigal, J. P.: Seasonal
patterns and plant-mediated controls of subsurface wetland biogeochemistry,
Ecology, 86, 3334–3344, https://doi.org/10.1890/04-1951, 2005.
Neubauer, S. C., Franklin, R. B., and Berrier, D. J.: Saltwater intrusion into tidal freshwater marshes alters the biogeochemical processing of organic carbon, Biogeosciences, 10, 8171–8183, https://doi.org/10.5194/bg-10-8171-2013, 2013.
Nyman, J. A. and Delaune, R. D.: CO, emission and soil Eh responses to
different hydrological conditions in fresh, brackish, and saline marsh
soils, available at:
https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.4319/lo.1991.36.7.1406
(last access: 31 October 2018), 1991.
R Development Core Team: The R Project for Statistical Computing, available at: https://www.r-project.org/, last access: 9 May 2019.
Reynolds, L. L., Lajtha, K., Bowden, R. D., Tfaily, M. M., Johnson, B. R.,
and Bridgham, S. D.: The Path From Litter to Soil: Insights Into Soil C
Cycling From Long-Term Input Manipulation and High-Resolution Mass
Spectrometry, J. Geophys. Res.-Biogeo., 123, 1486–1497,
https://doi.org/10.1002/2017JG004076, 2018.
Rivas-Ubach, A., Liu, Y., Bianchi, T. S., Tolić, N., Jansson, C., and
Paša-Tolić, L.: Moving beyond the van Krevelen Diagram: A New
Stoichiometric Approach for Compound Classification in Organisms, Anal.
Chem., 90, 6152–6160, https://doi.org/10.1021/acs.analchem.8b00529, 2018.
Rocca, J. D., Hall, E. K., Lennon, J. T., Evans, S. E., Waldrop, M. P.,
Cotner, J. B., Nemergut, D. R., Graham, E. B., and Wallenstein, M. D.:
Relationships between protein-encoding gene abundance and corresponding
process are commonly assumed yet rarely observed, ISME J., 9, 1693–1699,
https://doi.org/10.1038/ismej.2014.252, 2015.
Sawakuchi, H. O., Neu, V., Ward, N. D., Barros, M. de L. C., Valerio, A. M.,
Gagne-Maynard, W., Cunha, A. C., Less, D. F. S., Diniz, J. E. M., Brito, D.
C., Krusche, A. V., and Richey, J. E.: Carbon Dioxide Emissions along the
Lower Amazon River, Front. Mar. Sci., 4, 76, https://doi.org/10.3389/fmars.2017.00076, 2017.
Schmidt, M. W. I., Torn, M. S., Abiven, S., Dittmar, T., Guggenberger, G.,
Janssens, I. A., Kleber, M., Kögel-Knabner, I., Lehmann, J., Manning, D.
A. C., Nannipieri, P., Rasse, D. P., Weiner, S., and Trumbore, S. E.:
Persistence of soil organic matter as an ecosystem property, Nature,
478, 49–56, https://doi.org/10.1038/nature10386, 2011.
Seidel, M., Dittmar, T., Ward, N. D., Krusche, A. V., Richey, J. E., Yager,
P. L., and Medeiros, P. M.: Seasonal and spatial variability of dissolved
organic matter composition in the lower Amazon River, Biogeochemistry,
131, 281–302, https://doi.org/10.1007/s10533-016-0279-4, 2016.
Sengupta, A. and Stegen, J. C.: PREMIS – Terrestrial-Aquatic Interface, DataHub, https://datahub.pnnl.gov/datahub/project/8 (last access: 8 October 2019), 2019.
Sengupta, A., Stegen, J. C., Meira Neto, A. A., Wang, Y., Neilson, J. W.,
Chorover, J., Troch, P. A., Maier, R. M., Chorover, J., Troch, P. A., and
Maier, R. M.: Assessing Microbial Community Patterns During Incipient Soil
Formation From Basalt, J. Geophys. Res.-Biogeo., 124, 941–958,
https://doi.org/10.1029/2017JG004315, 2019.
Shen, Y., Chapelle, F. H., Strom, E. W., and Benner, R.: Origins and
bioavailability of dissolved organic matter in groundwater, Biogeochemistry,
122, 61–78, https://doi.org/10.1007/s10533-014-0029-4, 2015.
Simon, C., Roth, V.-N., Dittmar, T., and Gleixner, G.: Molecular Signals of
Heterogeneous Terrestrial Environments Identified in Dissolved Organic
Matter: A Comparative Analysis of Orbitrap and Ion Cyclotron Resonance Mass
Spectrometers, Front. Earth Sci., 6, 138, https://doi.org/10.3389/feart.2018.00138,
2018.
Sleator, R. D. and Hill, C.: Bacterial osmoadaptation: The role of osmolytes
in bacterial stress and virulence, FEMS Microbiol. Rev., 26, 49–71,
https://doi.org/10.1016/S0168-6445(01)00071-7, 2002.
Smith, C. J., DeLaune, R. D., and Patrick, W. H.: Carbon dioxide emission and
carbon accumulation in coastal wetlands, Estuar. Coast. Shelf S., 17,
21–29, https://doi.org/10.1016/0272-7714(83)90042-2, 1983.
Stegen, J. C., Lin, X., Konopka, A. E., and Fredrickson, J. K.: Stochastic
and deterministic assembly processes in subsurface microbial communities,
ISME J., 6, 1653–1664, https://doi.org/10.1038/ismej.2012.22, 2012.
Stegen, J. C., Lin, X., Fredrickson, J. K., Chen, X., Kennedy, D. W.,
Murray, C. J., Rockhold, M. L., and Konopka, A.: Quantifying community
assembly processes and identifying features that impose them, ISME J.,
7, 2069–2079, https://doi.org/10.1038/ismej.2013.93, 2013.
Stegen, J. C., Lin, X., Fredrickson, J. K., and Konopka, A. E.: Estimating
and mapping ecological processes influencing microbial community assembly,
Front. Microbiol., 6, 370, https://doi.org/10.3389/fmicb.2015.00370, 2015.
Stegen, J. C., Fredrickson, J. K., Wilkins, M. J., Konopka, A. E., Nelson, W. C., Arntzen, E. V., Chrisler, W. B., Chu, R. K., Danczak, R. E., Fansler, S. J., Kennedy, D. W., Resch, C. T., and Tfaily, M.: Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover, Nat. Commun., 7, 11237, https://doi.org/10.1038/ncomms11237, 2016.
Stegen, J. C., Bottos, E. M., and Jansson, J. K.: A unified conceptual
framework for prediction and control of microbiomes, Curr. Opin. Microbiol.,
44, 20–27, https://doi.org/10.1016/J.MIB.2018.06.002, 2018a.
Stegen, J. C., Johnson, T., Fredrickson, J. K., Wilkins, M. J., Konopka, A.
E., Nelson, W. C., Arntzen, E. V., Chrisler, W. B., Chu, R. K., Fansler, S.
J., Graham, E. B., Kennedy, D. W., Resch, C. T., Tfaily, M., and Zachara, J.:
Influences of organic carbon speciation on hyporheic corridor
biogeochemistry and microbial ecology, Nat. Commun., 9, 1–11,
https://doi.org/10.1038/s41467-018-02922-9, 2018b.
Steinmuller, H. E. and Chambers, L. G.: Can Saltwater Intrusion Accelerate
Nutrient Export from Freshwater Wetland Soils? An Experimental Approach,
Soil Sci. Soc. Am. J., 82, 283, https://doi.org/10.2136/sssaj2017.05.0162, 2018.
Sumner, M. E.: Handbook of Soil Science, edited by: Sumner, M. E., CRC Press, New York, 1999.
Tank, S. E., Fellman, J. B., Hood, E., and Kritzberg, E. S.: Beyond
respiration: Controls on lateral carbon fluxes across the
terrestrial-aquatic interface, Limnol. Oceanogr. Lett., 3, 76–88,
https://doi.org/10.1002/lol2.10065, 2018.
Tfaily, M. M., Hodgkins, S., Podgorski, D. C., Chanton, J. P., and Cooper, W.
T.: Comparison of dialysis and solid-phase extraction for isolation and
concentration of dissolved organic matter prior to Fourier transform ion
cyclotron resonance mass spectrometry, Anal. Bioanal. Chem., 404,
447–457, https://doi.org/10.1007/s00216-012-6120-6, 2012.
Tfaily, M. M., Cooper, W. T., Kostka, J. E., Chanton, P. R., Schadt, C. W.,
Hanson, P. J., Iversen, C. M., and Chanton, J. P.: Organic matter
transformation in the peat column at Marcell Experimental Forest:
Humification and vertical stratification, J. Geophys. Res.-Biogeo., 119, 661–675,
https://doi.org/10.1002/2013JG002492, 2014.
Tfaily, M. M., Chu, R. K., Tolić, N., Roscioli, K. M., Anderton, C. R.,
Paša-Tolić, L., Robinson, E. W., and Hess, N. J.: Advanced Solvent
Based Methods for Molecular Characterization of Soil Organic Matter by
High-Resolution Mass Spectrometry, Anal. Chem., 87, 5206–5215,
https://doi.org/10.1021/acs.analchem.5b00116, 2015.
Tfaily, M. M., Chu, R. K., Toyoda, J., Tolić, N., Robinson, E. W.,
Paša-Tolić, L., and Hess, N. J.: Sequential extraction protocol for
organic matter from soils and sediments using high resolution mass
spectrometry, Anal. Chim. Acta, 972, 54–61, https://doi.org/10.1016/J.ACA.2017.03.031,
2017.
Tolić, N., Liu, Y., Liyu, A., Shen, Y., Tfaily, M. M., Kujawinski, E.
B., Longnecker, K., Kuo, L.-J., Robinson, E. W., Paša-Tolić, L., and
Hess, N. J.: Formularity: Software for Automated Formula Assignment of
Natural and Other Organic Matter from Ultrahigh-Resolution Mass Spectra,
Anal. Chem., 89, 12659–12665, https://doi.org/10.1021/acs.analchem.7b03318, 2017.
Trivedi, P., Delgado-Baquerizo, M., Trivedi, C., Hu, H., Anderson, I. C.,
Jeffries, T. C., Zhou, J., and Singh, B. K.: Microbial regulation of the soil
carbon cycle: evidence from gene–enzyme relationships, ISME J., 10,
2593–2604, https://doi.org/10.1038/ismej.2016.65, 2016.
Tzortziou, M., Neale, P. J., Megonigal, P., Pow, C. L., and Butterworth, M.:
Spatial gradients in dissolved carbon due to tidal marsh outwelling into a
Chesapeake Bay estuary, Mar. Ecol.-Prog. Ser., 426, 41–56,
https://doi.org/10.3354/meps09017, 2011.
U.S. DOE: Research Priorities to Incorporate Terrestrial-Aquatic Interfaces
in Earth System Models: Workshop Report, DOE/SC-0187, 2017.
van der Wal, A., Ottosson, E., and de Boer, W.: Neglected role of fungal
community composition in explaining variation in wood decay rates, Ecology,
96, 124–133, https://doi.org/10.1890/14-0242.1, 2015.
Vidon, P., Allan, C., Burns, D., Duval, T. P., Gurwick, N., Inamdar, S.,
Lowrance, R., Okay, J., Scott, D., and Sebestyen, S.: Hot Spots and Hot
Moments in Riparian Zones: Potential for Improved Water Quality Management1, J. Am. Water Resour. As., 46, 278–298,
https://doi.org/10.1111/j.1752-1688.2010.00420.x, 2010.
Wang, W., McDowell, N. G., Ward, N. D., Indivero, J., Gunn, C., and Bailey, V. L.: Constrained tree growth and gas‐exchange of seawater exposed forests in the Pacific Northwest, USA, J. Ecol., https://doi.org/10.1111/1365-2745.13225, online first, 2019.
Ward, C. P., Nalven, S. G., Crump, B. C., Kling, G. W., and Cory, R. M.:
Photochemical alteration of organic carbon draining permafrost soils shifts
microbial metabolic pathways and stimulates respiration, Nat. Commun., 8, 772,
https://doi.org/10.1038/s41467-017-00759-2, 2017.
Ward, N. D., Keil, R. G., Medeiros, P. M., Brito, D. C., Cunha, A. C.,
Dittmar, T., Yager, P. L., Krusche, A. V., and Richey, J. E.: Degradation of
terrestrially derived macromolecules in the Amazon River, Nat. Geosci.,
6, 530–533, https://doi.org/10.1038/ngeo1817, 2013.
Ward, N. D., Bianchi, T. S., Medeiros, P. M., Seidel, M., Richey, J. E.,
Keil, R. G., and Sawakuchi, H. O.: Where Carbon Goes When Water Flows: Carbon
Cycling across the Aquatic Continuum, Front. Mar. Sci., 4, 7,
https://doi.org/10.3389/fmars.2017.00007, 2017.
Ward, N. D., Indivero, J., Gunn, C., Wang, W., Bailey, V., and McDowell, N.
G.: Longitudinal gradients in tree stem greenhouse gas concentrations across
six Pacific Northwest coastal forests, J. Geophys. Res.-Biogeo., 124, 1401–1412, https://doi.org/10.1029/2019JG005064, 2019a.
Ward, N. D., Morrison, E. S., Liu, Y., Rivas-Ubach, A., Osborne, T. Z.,
Ogram, A. V., and Bianchi, T. S.: Marine microbial community responses
related to wetland carbon mobilization in the coastal zone, Limnol.
Oceanogr. Lett., 4, 25–33, https://doi.org/10.1002/lol2.10101, 2019b.
Washington Department of Fish and Wildlife: Fish Passage & Diversion
Screening Inventory, available at: https://geo.wa.gov/datasets/4477faa67e95467cb5d3db75f41e7291_0?geometry=-135.166%2C47.551%2C-107.414%2C52.487
, last access: 7 October 2019.
Weston, N. B., Dixon, R. E., and Joye, S. B.: Ramifications of increased
salinity in tidal freshwater sediments: Geochemistry and microbial pathways
of organic matter mineralization, J. Geophys. Res., 111, G01009,
https://doi.org/10.1029/2005JG000071, 2006.
Weston, N. B., Vile, M. A., Neubauer, S. C., and Velinsky, D. J.: Accelerated
microbial organic matter mineralization following salt-water intrusion into
tidal freshwater marsh soils, Biogeochemistry, 102, 135–151,
https://doi.org/10.1007/s10533-010-9427-4, 2011.
Weston, N. B., Neubauer, S. C., Velinsky, D. J., and Vile, M. A.: Net
ecosystem carbon exchange and the greenhouse gas balance of tidal marshes
along an estuarine salinity gradient, Biogeochemistry, 120, 163–189,
https://doi.org/10.1007/s10533-014-9989-7, 2014.
Yang, J., Zhan, C., Li, Y., Zhou, D., Yu, Y., and Yu, J.: Effect of salinity
on soil respiration in relation to dissolved organic carbon and microbial
characteristics of a wetland in the Liaohe River estuary, Northeast China,
Sci. Total Environ., 642, 946–953, https://doi.org/10.1016/J.SCITOTENV.2018.06.121,
2018.
Zark, M. and Dittmar, T.: Universal molecular structures in natural
dissolved organic matter, Nat. Commun., 9, 3178,
https://doi.org/10.1038/s41467-018-05665-9, 2018.
Short summary
Coastal terrestrial–aquatic interfaces represent dynamic yet poorly understood zones of biogeochemical cycles. We evaluated associations between the soil salinity gradient, molecular-level soil-C chemistry, and microbial community assembly processes in a coastal watershed on the Olympic Peninsula in Washington, USA. Results revealed salinity-driven gradients in molecular-level C chemistry, with little evidence of an association between C chemistry and microbial community assembly processes.
Coastal terrestrial–aquatic interfaces represent dynamic yet poorly understood zones of...
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