COSORE: A community database for continuous soil respiration and other soil-atmosphere greenhouse gas flux data

Ben Bond-Lamberty¹, Danielle S Christianson², Avni Malhotra³, Stephanie C Pennington¹, Debjani Sihi⁴, Amir AghaKouchak⁵, Hassan Anjileli⁵, M Altaf Arain⁶, Juan J Armesto^{7

8}, Samaneh Ashraf⁹, Mioko Ataka¹⁰, Dennis Baldocchi¹¹, Thomas Andrew Black¹², Nina Buchmann¹³, Mariah S Carbone¹⁴, Shih-Chieh Chang¹⁵, Patrick Crill¹⁶, Peter S Curtis¹⁷, Eric A Davidson¹⁸, Ankur R Desai¹⁹, John E Drake²⁰, Tarek S El-Madany²¹, Michael Gavazzi²², Carolyn-Monika Görres²³, Christopher M Gough²⁴, Michael Goulden²⁵, Jillian Gregg²⁶, Omar Gutiérrez Del Arroyo¹¹, Jin-Sheng He²⁷, Takashi Hirano²⁸, Anya Hopple^{29

30}, Holly Hughes³¹, Järvi Järveoja³², Rachhpal Jassal¹², Jinshi Jian¹, Haiming Kan³³, Jason Kaye³⁴, Yuji Kominami³⁵, Naishen Liang³⁶, David Lipson³⁷, Catriona A Macdonald³⁸, Kadmiel Maseyk³⁹, Kayla Mathes⁴⁰, Marguerite Mauritz⁴¹, Melanie A Mayes⁴, Steve McNulty²², Guofang Miao⁴², Mirco Migliavacca²¹, Scott Miller⁴³, Chelcy F Miniat⁴⁴, Jennifer G Nietz¹⁷, Mats B Nilsson³², Asko Noormets⁴⁵, Hamidreza Norouzi⁴⁶, Christine S O'Connell^{11

47}, Bruce Osborne⁴⁸, Cecilio Oyonarte⁴⁹, Zhuo Pang³³, Matthias Peichl³², Elise Pendall³⁸, Jorge F Perez-Quezada^{50

51}, Claire L Phillips⁵², Richard P Phillips⁵³, James W Raich⁵⁴, Alexandre A Renchon³⁸, Nadine K Ruehr⁵⁵, Enrique P Sánchez-Cañete⁵⁶, Matthew Saunders⁵⁷, Kathleen E Savage⁵⁸, Marion Schrumpf²¹, Russell L Scott⁵⁹, Ulli Seibt⁶⁰, Whendee L Silver¹¹, Wu Sun⁶¹, Daphne Szutu¹¹, Kentaro Takagi⁶², Masahiro Takagi⁶³, Munemasa Teramoto³⁶, Mark G Tjoelker³⁸, Susan Trumbore²¹, Masahito Ueyama⁶⁴, Rodrigo Vargas⁶⁵, Ruth K Varner⁶⁶, Joseph Verfaillie¹¹, Christoph Vogel⁶⁷, Jinsong Wang⁶⁸, Greg Winston⁶⁹, Tana E Wood⁷⁰, Juying Wu³³, Thomas Wutzler²¹, Jiye Zeng³⁶, Tianshan Zha⁷¹, Quan Zhang⁷², Junliang Zou³³

Affiliations

¹ Pacific Northwest National Laboratory, Joint Global Change Research Institute at the University of Maryland-College Park, College Park, MD, USA.
² Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
³ Department of Earth System Science, Stanford University, Stanford, CA, USA.
⁴ Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
⁵ Department of Civil and Environmental Engineering, University of California Irvine, Irvine, CA, USA.
⁶ School of Geography and Earth Sciences, McMaster University, Hamilton, Ontario, Canada.
⁷ Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile.
⁸ Instituto de Ecología y Biodiversidad, Santiago, Chile.
⁹ Department of Building, Civil and Environmental Engineering, Concordia University, Montreal, QC, Canada.
¹⁰ Research Institute for Sustainable Humanosphere, Kyoto University, Uji City, Kyoto, Japan.
¹¹ Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
¹² Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada.
¹³ Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.
¹⁴ Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
¹⁵ Department of Natural Resources and Environmental Studies, Center for Interdisciplinary Research on Ecology and Sustainability, National Dong Hwa University, Hualien, Taiwan.
¹⁶ Department of Geological Sciences and Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden.
¹⁷ Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH, USA.
¹⁸ Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, USA.
¹⁹ Department of Atmospheric and Oceanic Sciences, University of Wisconsin-Madison, Madison, WI, USA.
²⁰ Sustainable Resources Management, SUNY-ESF, Syracuse, NY, USA.
²¹ Max Planck Institute for Biogeochemistry, Jena, Germany.
²² Eastern Forest Environmental Threat Assessment Center, USDA Forest Service, Research Triangle Park, NC, USA.
²³ Plants and Ecosystems, Department of Biology, University of Antwerp, Wilrijk, Belgium.
²⁴ Department of Biology, Virginia Commonwealth University, Richmond, VA, USA.
²⁵ University of California at Irvine, Irvine, CA, USA.
²⁶ Sustainability Double Degree Program, Oregon State University, Corvallis, OR, USA.
²⁷ Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.
²⁸ Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.
²⁹ Pacific Northwest National Laboratory, Richland, WA, USA.
³⁰ Smithsonian Environmental Research Center, Edgewater, MD, USA.
³¹ School of Forest Resources, University of Maine, Orono, ME, USA.
³² Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden.
³³ Beijing Research & Development Centre for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
³⁴ The Pennsylvania State University, University Park, PA, USA.
³⁵ Forestry and Forest Products Research Institute, Tsukuba-city, Japan.
³⁶ Center for Global Environmental Research, National Institute for Environmental Studies, Tsukuba, Japan.
³⁷ Biology Department, San Diego State University, San Diego, CA, USA.
³⁸ Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
³⁹ School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UK.
⁴⁰ Integrated Life Sciences, Virginia Commonwealth University, Richmond, VA, USA.
⁴¹ Biological Sciences, University of Texas at El Paso, El Paso, TX, USA.
⁴² School of Geographical Sciences, Fujian Normal University, Fuzhou, P.R. China.
⁴³ University at Albany, State University of New York, New York, NY, USA.
⁴⁴ USDA Forest Service, Southern Research Station, Coweeta Hydrologic Lab, Otto, NC, USA.
⁴⁵ Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA.
⁴⁶ New York City College of Technology and the Graduate Center, The City University of New York, New York, NY, USA.
⁴⁷ Department of Environmental Studies, Macalester College, St Paul, MN, USA.
⁴⁸ UCD School of Biology and Environmental Science and UCD Earth Institute, University College Dublin, Dublin, Ireland.
⁴⁹ Department of Agronomy, University of Almería, Almería, Spain.
⁵⁰ Department of Environmental Science and Renewable Natural Resources, University of Chile, Santiago, Chile.
⁵¹ Institute of Ecology and Biodiversity, Santiago, Chile.
⁵² USDA Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR, USA.
⁵³ Department of Biology, Indiana University, Bloomington, IN, USA.
⁵⁴ Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, USA.
⁵⁵ Institute of Meteorology and Climate Research-Atmospheric Environmental Research, KIT-Campus Alpin, Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany.
⁵⁶ Department of Applied Physics, University of Granada, Granada, Spain.
⁵⁷ School of Natural Sciences, Botany Department, Trinity College Dublin, Dublin, Ireland.
⁵⁸ Woods Hole Research Center, Falmouth, MA, USA.
⁵⁹ Southwest Watershed Research Center, USDA-ARS, Tucson, AZ, USA.
⁶⁰ Department of Atmospheric and Oceanic Sciences, University of California Los Angeles, Los Angeles, CA, USA.
⁶¹ Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA.
⁶² Field Science Center for Northern Biosphere, Hokkaido University, Horonobe, Japan.
⁶³ Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
⁶⁴ Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan.
⁶⁵ Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
⁶⁶ Department of Earth Sciences and Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, NH, USA.
⁶⁷ University of Michigan Biological Station, Pellston, MI, USA.
⁶⁸ Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.
⁶⁹ Department of Science, Engineering and Mathematics, Cypress College, Cypress, CA, USA.
⁷⁰ USDA Forest Service International Institute of Tropical Forestry, Río Piedras, Puerto Rico.
⁷¹ School of Soil and Water Conservation, Beijing Forestry University, Beijing, P.R. China.
⁷² State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, P.R. China.

PMID: 33026137
PMCID: PMC7756728
DOI: 10.1111/gcb.15353

COSORE: A community database for continuous soil respiration and other soil-atmosphere greenhouse gas flux data

Ben Bond-Lamberty et al. Glob Chang Biol. 2020 Dec.

. 2020 Dec;26(12):7268-7283.

doi: 10.1111/gcb.15353. Epub 2020 Oct 7.

Authors

Affiliations

¹ Pacific Northwest National Laboratory, Joint Global Change Research Institute at the University of Maryland-College Park, College Park, MD, USA.
² Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
³ Department of Earth System Science, Stanford University, Stanford, CA, USA.
⁴ Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
⁵ Department of Civil and Environmental Engineering, University of California Irvine, Irvine, CA, USA.
⁶ School of Geography and Earth Sciences, McMaster University, Hamilton, Ontario, Canada.
⁷ Departamento de Ecología, Pontificia Universidad Católica de Chile, Santiago, Chile.
⁸ Instituto de Ecología y Biodiversidad, Santiago, Chile.
⁹ Department of Building, Civil and Environmental Engineering, Concordia University, Montreal, QC, Canada.
¹⁰ Research Institute for Sustainable Humanosphere, Kyoto University, Uji City, Kyoto, Japan.
¹¹ Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
¹² Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, Canada.
¹³ Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland.
¹⁴ Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
¹⁵ Department of Natural Resources and Environmental Studies, Center for Interdisciplinary Research on Ecology and Sustainability, National Dong Hwa University, Hualien, Taiwan.
¹⁶ Department of Geological Sciences and Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden.
¹⁷ Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH, USA.
¹⁸ Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, USA.
¹⁹ Department of Atmospheric and Oceanic Sciences, University of Wisconsin-Madison, Madison, WI, USA.
²⁰ Sustainable Resources Management, SUNY-ESF, Syracuse, NY, USA.
²¹ Max Planck Institute for Biogeochemistry, Jena, Germany.
²² Eastern Forest Environmental Threat Assessment Center, USDA Forest Service, Research Triangle Park, NC, USA.
²³ Plants and Ecosystems, Department of Biology, University of Antwerp, Wilrijk, Belgium.
²⁴ Department of Biology, Virginia Commonwealth University, Richmond, VA, USA.
²⁵ University of California at Irvine, Irvine, CA, USA.
²⁶ Sustainability Double Degree Program, Oregon State University, Corvallis, OR, USA.
²⁷ Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, China.
²⁸ Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.
²⁹ Pacific Northwest National Laboratory, Richland, WA, USA.
³⁰ Smithsonian Environmental Research Center, Edgewater, MD, USA.
³¹ School of Forest Resources, University of Maine, Orono, ME, USA.
³² Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Umeå, Sweden.
³³ Beijing Research & Development Centre for Grass and Environment, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
³⁴ The Pennsylvania State University, University Park, PA, USA.
³⁵ Forestry and Forest Products Research Institute, Tsukuba-city, Japan.
³⁶ Center for Global Environmental Research, National Institute for Environmental Studies, Tsukuba, Japan.
³⁷ Biology Department, San Diego State University, San Diego, CA, USA.
³⁸ Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.
³⁹ School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UK.
⁴⁰ Integrated Life Sciences, Virginia Commonwealth University, Richmond, VA, USA.
⁴¹ Biological Sciences, University of Texas at El Paso, El Paso, TX, USA.
⁴² School of Geographical Sciences, Fujian Normal University, Fuzhou, P.R. China.
⁴³ University at Albany, State University of New York, New York, NY, USA.
⁴⁴ USDA Forest Service, Southern Research Station, Coweeta Hydrologic Lab, Otto, NC, USA.
⁴⁵ Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA.
⁴⁶ New York City College of Technology and the Graduate Center, The City University of New York, New York, NY, USA.
⁴⁷ Department of Environmental Studies, Macalester College, St Paul, MN, USA.
⁴⁸ UCD School of Biology and Environmental Science and UCD Earth Institute, University College Dublin, Dublin, Ireland.
⁴⁹ Department of Agronomy, University of Almería, Almería, Spain.
⁵⁰ Department of Environmental Science and Renewable Natural Resources, University of Chile, Santiago, Chile.
⁵¹ Institute of Ecology and Biodiversity, Santiago, Chile.
⁵² USDA Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR, USA.
⁵³ Department of Biology, Indiana University, Bloomington, IN, USA.
⁵⁴ Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, USA.
⁵⁵ Institute of Meteorology and Climate Research-Atmospheric Environmental Research, KIT-Campus Alpin, Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany.
⁵⁶ Department of Applied Physics, University of Granada, Granada, Spain.
⁵⁷ School of Natural Sciences, Botany Department, Trinity College Dublin, Dublin, Ireland.
⁵⁸ Woods Hole Research Center, Falmouth, MA, USA.
⁵⁹ Southwest Watershed Research Center, USDA-ARS, Tucson, AZ, USA.
⁶⁰ Department of Atmospheric and Oceanic Sciences, University of California Los Angeles, Los Angeles, CA, USA.
⁶¹ Department of Global Ecology, Carnegie Institution for Science, Stanford, CA, USA.
⁶² Field Science Center for Northern Biosphere, Hokkaido University, Horonobe, Japan.
⁶³ Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
⁶⁴ Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan.
⁶⁵ Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.
⁶⁶ Department of Earth Sciences and Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, NH, USA.
⁶⁷ University of Michigan Biological Station, Pellston, MI, USA.
⁶⁸ Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China.
⁶⁹ Department of Science, Engineering and Mathematics, Cypress College, Cypress, CA, USA.
⁷⁰ USDA Forest Service International Institute of Tropical Forestry, Río Piedras, Puerto Rico.
⁷¹ School of Soil and Water Conservation, Beijing Forestry University, Beijing, P.R. China.
⁷² State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, P.R. China.

PMID: 33026137
PMCID: PMC7756728
DOI: 10.1111/gcb.15353

Abstract

Globally, soils store two to three times as much carbon as currently resides in the atmosphere, and it is critical to understand how soil greenhouse gas (GHG) emissions and uptake will respond to ongoing climate change. In particular, the soil-to-atmosphere CO₂ flux, commonly though imprecisely termed soil respiration (R_S ), is one of the largest carbon fluxes in the Earth system. An increasing number of high-frequency R_S measurements (typically, from an automated system with hourly sampling) have been made over the last two decades; an increasing number of methane measurements are being made with such systems as well. Such high frequency data are an invaluable resource for understanding GHG fluxes, but lack a central database or repository. Here we describe the lightweight, open-source COSORE (COntinuous SOil REspiration) database and software, that focuses on automated, continuous and long-term GHG flux datasets, and is intended to serve as a community resource for earth sciences, climate change syntheses and model evaluation. Contributed datasets are mapped to a single, consistent standard, with metadata on contributors, geographic location, measurement conditions and ancillary data. The design emphasizes the importance of reproducibility, scientific transparency and open access to data. While being oriented towards continuously measured R_S , the database design accommodates other soil-atmosphere measurements (e.g. ecosystem respiration, chamber-measured net ecosystem exchange, methane fluxes) as well as experimental treatments (heterotrophic only, etc.). We give brief examples of the types of analyses possible using this new community resource and describe its accompanying R software package.

Keywords: carbon dioxide; greenhouse gases; methane; open data; open science; soil respiration.

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Figures

**FIGURE 1**
Summary of COSORE structure (multiple datasets, each with six tables; Tables 2, 3, 4, 5) and primary accessor R functions, as described in the text (see Section 2.1 in text). For example, R users can join specific tables across all datasets using the *csr_table()* function, and can access individual datasets with *csr_dataset()*. Non‐R users access flat‐file versions of the same data, with essentially the same structure as the R internal structure shown here

**FIGURE 2**
Geographic distribution of COSORE datasets (N = 89), with point sizes corresponding to the number of records in each dataset. Map tiles show USGS land cover and national elevation data and are by Stamen Design, under CC BY 3.0; data by OpenStreetMap, under ODbL; figure rendered using R’s *ggmap* (Kahle & Wickham, 2013)

**FIGURE 3**
Distribution of COSORE datasets (black markers) in global climate space (WorldClim 2, Fick & Hijmans, 2017) of mean annual temperature (MAT) versus mean annual precipitation (MAP). Background colours indicate the number of half‐degree grid cells with each particular MAT–MAP combination. Inset plot shows the same points in Whittaker biome space (Ricklefs, 2008)

**FIGURE 4**
Flux observations, by IGBP (defined in Table 1), over time. Each square represents 5,000 observations, with categories of <5,000 observations rounded up so that they occupy a single square

**FIGURE 5**
Temporal density of COSORE datasets, by latitude of the observational site

**FIGURE 6**
Number of observations by day of year, for northern and southern hemisphere and by gas (CO₂ or CH₄), in the current COSORE datasets; the database currently has no CH₄ data from the Southern hemisphere (bottom left)

**FIGURE 7**
Temporal resolution (time interval between successive measurements, minutes; note logarithmic scale of x‐axis) of COSORE data

**FIGURE 8**
Distribution of CO₂ fluxes in COSORE datasets, by IGBP classification (cf. Table 1). For visual clarity this figure excludes fluxes <−1 and >10 µmol m⁻² s⁻¹ (210,752 observations, 2.6% of the data). Number of datasets (sites) making up data is given in parentheses after IGBP abbreviations in each panel

**FIGURE 9**
Distribution of CH₄ fluxes in COSORE datasets, by IGBP classification (cf. Table 1). For visual clarity this figure excludes some extreme values (18,719 observations or 4.5% of the data). Number of datasets (sites) making up data is given in parentheses after IGBP abbreviations in each panel. Positive values are emissions to the atmosphere, and negative values uptake by the soil

See this image and copyright information in PMC

References

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COSORE: A community database for continuous soil respiration and other soil-atmosphere greenhouse gas flux data

Affiliations

COSORE: A community database for continuous soil respiration and other soil-atmosphere greenhouse gas flux data

Authors

Affiliations

Abstract

Figures

References

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources