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  1. Article ; Online: Machine learning for accelerating process‐based computation of land biogeochemical cycles

    Sun, Yan / Goll, Daniel S. / Huang, Yuanyuan / Ciais, Philippe / Wang, Ying‐Ping / Bastrikov, Vladislav / Wang, Yilong

    Global Change Biology. 2023 June, v. 29, no. 11 p.3221-3234

    2023  

    Abstract: Global change ecology nowadays embraces ever‐growing large observational datasets (big‐data) and complex mathematical models that track hundreds of ecological processes (big‐model). The rapid advancement of the big‐data‐big‐model has reached its ... ...

    Abstract Global change ecology nowadays embraces ever‐growing large observational datasets (big‐data) and complex mathematical models that track hundreds of ecological processes (big‐model). The rapid advancement of the big‐data‐big‐model has reached its bottleneck: high computational requirements prevent further development of models that need to be integrated over long time‐scales to simulate the distribution of ecosystems carbon and nutrient pools and fluxes. Here, we introduce a machine‐learning acceleration (MLA) tool to tackle this grand challenge. We focus on the most resource‐consuming step in terrestrial biosphere models (TBMs): the equilibration of biogeochemical cycles (spin‐up), a prerequisite that can take up to 98% of the computational time. Through three members of the ORCHIDEE TBM family part of the IPSL Earth System Model, including versions that describe the complex interactions between nitrogen, phosphorus and carbon that do not have any analytical solution for the spin‐up, we show that an unoptimized MLA reduced the computation demand by 77%–80% for global studies via interpolating the equilibrated state of biogeochemical variables for a subset of model pixels. Despite small biases in the MLA‐derived equilibrium, the resulting impact on the predicted regional carbon balance over recent decades is minor. We expect a one‐order of magnitude lower computation demand by optimizing the choices of machine learning algorithms, their settings, and balancing the trade‐off between quality of MLA predictions and need for TBM simulations for training data generation and bias reduction. Our tool is agnostic to gridded models (beyond TBMs), compatible with existing spin‐up acceleration procedures, and opens the door to a wide variety of future applications, with complex non‐linear models benefit most from the computational efficiency.
    Keywords Biological Sciences ; artificial intelligence ; biosphere ; carbon ; data collection ; ecology ; global change ; models ; nitrogen ; phosphorus
    Language English
    Dates of publication 2023-06
    Size p. 3221-3234.
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 1281439-8
    ISSN 1365-2486 ; 1354-1013
    ISSN (online) 1365-2486
    ISSN 1354-1013
    DOI 10.1111/gcb.16623
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Machine learning for accelerating process-based computation of land biogeochemical cycles.

    Sun, Yan / Goll, Daniel S / Huang, Yuanyuan / Ciais, Philippe / Wang, Ying-Ping / Bastrikov, Vladislav / Wang, Yilong

    Global change biology

    2023  Volume 29, Issue 11, Page(s) 3221–3234

    Abstract: Global change ecology nowadays embraces ever-growing large observational datasets (big-data) and complex mathematical models that track hundreds of ecological processes (big-model). The rapid advancement of the big-data-big-model has reached its ... ...

    Abstract Global change ecology nowadays embraces ever-growing large observational datasets (big-data) and complex mathematical models that track hundreds of ecological processes (big-model). The rapid advancement of the big-data-big-model has reached its bottleneck: high computational requirements prevent further development of models that need to be integrated over long time-scales to simulate the distribution of ecosystems carbon and nutrient pools and fluxes. Here, we introduce a machine-learning acceleration (MLA) tool to tackle this grand challenge. We focus on the most resource-consuming step in terrestrial biosphere models (TBMs): the equilibration of biogeochemical cycles (spin-up), a prerequisite that can take up to 98% of the computational time. Through three members of the ORCHIDEE TBM family part of the IPSL Earth System Model, including versions that describe the complex interactions between nitrogen, phosphorus and carbon that do not have any analytical solution for the spin-up, we show that an unoptimized MLA reduced the computation demand by 77%-80% for global studies via interpolating the equilibrated state of biogeochemical variables for a subset of model pixels. Despite small biases in the MLA-derived equilibrium, the resulting impact on the predicted regional carbon balance over recent decades is minor. We expect a one-order of magnitude lower computation demand by optimizing the choices of machine learning algorithms, their settings, and balancing the trade-off between quality of MLA predictions and need for TBM simulations for training data generation and bias reduction. Our tool is agnostic to gridded models (beyond TBMs), compatible with existing spin-up acceleration procedures, and opens the door to a wide variety of future applications, with complex non-linear models benefit most from the computational efficiency.
    MeSH term(s) Ecosystem ; Models, Theoretical ; Carbon ; Nitrogen ; Carbon Cycle
    Chemical Substances Carbon (7440-44-0) ; Nitrogen (N762921K75)
    Language English
    Publishing date 2023-02-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 1281439-8
    ISSN 1365-2486 ; 1354-1013
    ISSN (online) 1365-2486
    ISSN 1354-1013
    DOI 10.1111/gcb.16623
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: Constraining a land cover map with satellite-based aboveground biomass estimates over Africa

    Marie, Guillaume / Luyssaert, B. Sebastiaan / Dardel, Cecile / Toan, Thuy / Bouvet, Alexandre / Mermoz, Stéphane / Villard, Ludovic / Bastrikov, Vladislav / Peylin, Philippe

    eISSN: 1991-9603

    2022  

    Abstract: Most land surface models can, depending on the simulation experiment, calculate the vegetation distribution and dynamics internally by making use of biogeographical principles or use vegetation maps to prescribe spatial and temporal changes in vegetation ...

    Abstract Most land surface models can, depending on the simulation experiment, calculate the vegetation distribution and dynamics internally by making use of biogeographical principles or use vegetation maps to prescribe spatial and temporal changes in vegetation distribution. Irrespective of whether vegetation dynamics are simulated or prescribed, it is not practical to represent vegetation across the globe at the species level because of its daunting diversity. This issue can be circumvented by making use of 5 to 20 plant functional types (PFTs) by assuming that all species within a single functional type show identical land–atmosphere interactions irrespective of their geographical location. In this study, we hypothesize that remote-sensing-based assessments of aboveground biomass can be used to constrain the process in which real-world vegetation is discretized in PFT maps. Remotely sensed biomass estimates for Africa were used in a Bayesian framework to estimate the probability density distributions of woody, herbaceous and bare soil fractions for the 15 land cover classes, according to the United Nations Land Cover Classification System (UN-LCCS) typology, present in Africa. Subsequently, the 2.5th and 97.5th percentiles of the probability density distributions were used to create 2.5 % and 97.5 % credible interval PFT maps. Finally, the original and constrained PFT maps were used to drive biomass and albedo simulations with the Organising Carbon and Hydrology In Dynamic Ecosystems (ORCHIDEE) model. This study demonstrates that remotely sensed biomass data can be used to better constrain the share of dense forest PFTs but that additional information on bare soil fraction is required to constrain the share of herbaceous PFTs. Even though considerable uncertainties remain, using remotely sensed biomass data enhances the objectivity and reproducibility of the process by reducing the dependency on expert knowledge and allows assessing and reporting the credible interval of the PFT maps which could be used to benchmark future developments.
    Subject code 910
    Language English
    Publishing date 2022-03-30
    Publishing country de
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Book ; Online: A 29-year time series of annual 300 m resolution plant-functional-type maps for climate models

    Harper, Kandice L. / Lamarche, Céline / Hartley, Andrew / Peylin, Philippe / Ottlé, Catherine / Bastrikov, Vladislav / San Martín, Rodrigo / Bohnenstengel, Sylvia I. / Kirches, Grit / Boettcher, Martin / Shevchuk, Roman / Brockmann, Carsten / Defourny, Pierre

    eISSN: 1866-3516

    2023  

    Abstract: The existing medium-resolution land cover time series produced under the European Space Agency's Climate Change Initiative provides 29 years (1992–2020) of annual land cover maps at 300 m resolution, allowing for a detailed study of land change dynamics ... ...

    Abstract The existing medium-resolution land cover time series produced under the European Space Agency's Climate Change Initiative provides 29 years (1992–2020) of annual land cover maps at 300 m resolution, allowing for a detailed study of land change dynamics over the contemporary era. Because models need two-dimensional parameters rather than two-dimensional land cover information, the land cover classes must be converted into model-appropriate plant functional types (PFTs) to apply this time series to Earth system and land surface models. The first-generation cross-walking table that was presented with the land cover product prescribed pixel-level PFT fractional compositions that varied by land cover class but that lacked spatial variability. Here we describe a new ready-to-use data product for climate modelling: spatially explicit annual maps of PFT fractional composition at 300 m resolution for 1992–2020, created by fusing the 300 m medium-resolution land cover product with several existing high-resolution datasets using a globally consistent method. In the resulting data product, which has 14 layers for each of the 29 years, pixel values at 300 m resolution indicate the percentage cover (0 %–100 %) for each of 14 PFTs, with pixel-level PFT composition exhibiting significant intra-class spatial variability at the global scale. We additionally present an updated version of the user tool that allows users to modify the baseline product (e.g. re-mapping, re-projection, PFT conversion, and spatial sub-setting) to meet individual needs. Finally, these new PFT maps have been used in two land surface models – Organising Carbon and Hydrology in Dynamic Ecosystems (ORCHIDEE) and the Joint UK Land Environment Simulator (JULES) – to demonstrate their benefit over the conventional maps based on a generic cross-walking table. Regional changes in the fractions of trees, short vegetation, and bare-soil cover induce changes in surface properties, such as the albedo, leading to significant changes in surface turbulent fluxes, ...
    Subject code 910 ; 333
    Language English
    Publishing date 2023-03-31
    Publishing country de
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Carbon and Water Fluxes of the Boreal Evergreen Needleleaf Forest Biome Constrained by Assimilating Ecosystem Carbonyl Sulfide Flux Observations

    Abadie, Camille / Maignan, Fabienne / Remaud, Marine / Kohonen, Kukka Maaria / Sun, Wu / Kooijmans, Linda / Vesala, Timo / Seibt, Ulli / Raoult, Nina / Bastrikov, Vladislav / Belviso, Sauveur / Peylin, Philippe

    Journal of Geophysical Research: Biogeosciences

    2023  Volume 128, Issue 7

    Abstract: Gross primary production (GPP) by boreal forests is highly sensitive to environmental changes. However, GPP simulated by land surface models (LSMs) remains highly uncertain due to the lack of direct photosynthesis observations at large scales. Carbonyl ... ...

    Abstract Gross primary production (GPP) by boreal forests is highly sensitive to environmental changes. However, GPP simulated by land surface models (LSMs) remains highly uncertain due to the lack of direct photosynthesis observations at large scales. Carbonyl sulfide (COS) has emerged as a promising proxy to improve the representation of GPP in LSMs. Because COS is absorbed by vegetation following the same diffusion pathway as CO2 during photosynthesis and not emitted back to the atmosphere, incorporating a mechanistic representation of vegetation COS uptake in LSMs allows using COS observations to refine GPP representation. Here, we perform ecosystem COS flux and GPP data assimilations to constrain the COS- and GPP-related parameters in the ORCHIDEE LSM for boreal evergreen needleleaf forests (BorENF). Assimilating ecosystem COS fluxes at Hyytiälä forest increases the simulated net ecosystem COS uptake by 14%. This increase largely results from changes in the internal conductance to COS, highlighting the need to improve the representation of COS internal diffusion and consumption. Moreover, joint assimilation of ecosystem COS flux and GPP at Hyytiälä improves the simulated latent heat flux, contrary to the GPP-only data assimilation, which fails to do so. Finally, we scaled this assimilation framework up to the boreal region and find that the joint assimilation of COS at Hyytiälä and GPP fluxes at 10 BorENF sites increases the modeled vegetation COS uptake up to 18%, but not GPP. Therefore, this study encourages the use of COS flux observations to inform GPP and latent heat flux representations in LSMs.
    Keywords Life Science
    Subject code 551
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 2220777-6
    ISSN 2169-8961 ; 2169-8953
    ISSN (online) 2169-8961
    ISSN 2169-8953
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Radon measurements--discussion of error estimates for selected methods.

    Zhukovsky, Michael / Onischenko, Alexandra / Bastrikov, Vladislav

    Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine

    2010  Volume 68, Issue 4-5, Page(s) 816–820

    Abstract: The main sources of uncertainties for grab sampling, short-term (charcoal canisters) and long term (track detectors) measurements are: systematic bias of reference equipment; random Poisson and non-Poisson errors during calibration; random Poisson and ... ...

    Abstract The main sources of uncertainties for grab sampling, short-term (charcoal canisters) and long term (track detectors) measurements are: systematic bias of reference equipment; random Poisson and non-Poisson errors during calibration; random Poisson and non-Poisson errors during measurements. The origins of non-Poisson random errors during calibration are different for different kinds of instrumental measurements. The main sources of uncertainties for retrospective measurements conducted by surface traps techniques can be divided in two groups: errors of surface (210)Pb ((210)Po) activity measurements and uncertainties of transfer from (210)Pb surface activity in glass objects to average radon concentration during this object exposure. It's shown that total measurement error of surface trap retrospective technique can be decreased to 35%.
    MeSH term(s) Air Pollutants, Radioactive/analysis ; Artifacts ; Computer-Aided Design ; Equipment Design ; Equipment Failure Analysis ; Radiation Monitoring/instrumentation ; Radiation Monitoring/methods ; Radon/analysis ; Reproducibility of Results ; Sensitivity and Specificity
    Chemical Substances Air Pollutants, Radioactive ; Radon (Q74S4N8N1G)
    Language English
    Publishing date 2010-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1142596-9
    ISSN 1872-9800 ; 0883-2889 ; 0969-8043
    ISSN (online) 1872-9800
    ISSN 0883-2889 ; 0969-8043
    DOI 10.1016/j.apradiso.2009.09.049
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Reconciling the Carbon Balance of Northern Sweden Through Integration of Observations and Modelling

    Sathyanadh, Anusha / Monteil, Guillaume / Scholze, Marko / Klosterhalfen, Anne / Laudon, Hjalmar / Wu, Zhendong / Gerbig, Christoph / Peters, Wouter / Bastrikov, Vladislav / Nilsson, Mats B. / Peichl, Matthias

    Journal of Geophysical Research: Atmospheres

    2021  Volume 126, Issue 23

    Abstract: The boreal biome plays an important role in the global carbon cycle. However, current estimates of its sink-source strength and responses to changes in climate are primarily derived from models and thus remain uncertain. A major challenge is the ... ...

    Abstract The boreal biome plays an important role in the global carbon cycle. However, current estimates of its sink-source strength and responses to changes in climate are primarily derived from models and thus remain uncertain. A major challenge is the validation of these models at a regional scale since empirical flux estimates are typically confined to ecosystem or continental scales. The Integrated Carbon Observation System (ICOS)-Svartberget atmospheric station (SVB) provides observations including tall tower eddy covariance (EC) and atmospheric concentration measurements that can contribute to such validation in Northern Sweden. Thus, the overall aim of this study was to quantify the carbon balance in Northern Sweden region by integrating land-atmosphere fluxes and atmospheric carbon dioxide (CO2) concentrations. There were three specific objectives. First, to compare flux estimates from four models (VPRM, LPJ-GUESS, ORCHIDEE, and SiBCASA) to tall tower EC measurements at SVB during the years 2016–2018. Second to assess the fluxes' impact on atmospheric CO2 concentrations using a regional transport model. Third, to assess the impact of the drought in 2018. The comparison of estimated concentrations with ICOS observations helped the evaluation of the models' regional scale performance. Both the simulations and observations indicate there were similar reductions in the net CO2 uptake during drought. All the models (except for SiBCASA) and observations indicated the region was a net carbon sink during the 3-year study period. Our study highlights a need to improve vegetation models through comparisons with empirical data and demonstrate the ICOS network's potential utility for constraining CO2 fluxes in the region.
    Keywords FLEXPART ; atmospheric transport model ; boreal biome ; net ecosystem exchange ; tall tower eddy covariance ; vegetation model
    Subject code 551
    Language English
    Publishing country nl
    Document type Article ; Online
    ZDB-ID 710256-2
    ISSN 2169-8996 ; 2169-897X ; 0148-0227
    ISSN (online) 2169-8996
    ISSN 2169-897X ; 0148-0227
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Process-oriented analysis of dominant sources of uncertainty in the land carbon sink.

    O'Sullivan, Michael / Friedlingstein, Pierre / Sitch, Stephen / Anthoni, Peter / Arneth, Almut / Arora, Vivek K / Bastrikov, Vladislav / Delire, Christine / Goll, Daniel S / Jain, Atul / Kato, Etsushi / Kennedy, Daniel / Knauer, Jürgen / Lienert, Sebastian / Lombardozzi, Danica / McGuire, Patrick C / Melton, Joe R / Nabel, Julia E M S / Pongratz, Julia /
    Poulter, Benjamin / Séférian, Roland / Tian, Hanqin / Vuichard, Nicolas / Walker, Anthony P / Yuan, Wenping / Yue, Xu / Zaehle, Sönke

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 4781

    Abstract: The observed global net land carbon sink is captured by current land models. All models agree that atmospheric ... ...

    Abstract The observed global net land carbon sink is captured by current land models. All models agree that atmospheric CO
    MeSH term(s) Carbon ; Carbon Dioxide/analysis ; Carbon Sequestration ; Ecosystem ; Plants ; Soil ; Uncertainty
    Chemical Substances Soil ; Carbon Dioxide (142M471B3J) ; Carbon (7440-44-0)
    Language English
    Publishing date 2022-08-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-32416-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Online: Linking global terrestrial CO2 fluxes and environmental drivers

    Chen, Zichong / Liu, Junjie / Henze, Daven K. / Huntzinger, Deborah N. / Wells, Kelley C. / Sitch, Stephen / Friedlingstein, Pierre / Joetzjer, Emilie / Bastrikov, Vladislav / Goll, Daniel S. / Haverd, Vanessa / Jain, Atul K. / Kato, Etsushi / Lienert, Sebastian / Lombardozzi, Danica L. / McGuire, Patrick C. / Melton, Joe R. / Nabel, Julia E. M. S. / Poulter, Benjamin /
    Tian, Hanqin / Wiltshire, Andrew J. / Zaehle, Sönke / Miller, Scot M.

    eISSN: 1680-7324

    inferences from the Orbiting Carbon Observatory 2 satellite and terrestrial biospheric models

    2021  

    Abstract: Observations from the Orbiting Carbon Observatory 2 (OCO-2) satellite have been used to estimate CO 2 fluxes in many regions of the globe and provide new insight into the global carbon cycle. The objective of this study is to infer the relationships ... ...

    Abstract Observations from the Orbiting Carbon Observatory 2 (OCO-2) satellite have been used to estimate CO 2 fluxes in many regions of the globe and provide new insight into the global carbon cycle. The objective of this study is to infer the relationships between patterns in OCO-2 observations and environmental drivers (e.g., temperature, precipitation) and therefore inform a process understanding of carbon fluxes using OCO-2. We use a multiple regression and inverse model, and the regression coefficients quantify the relationships between observations from OCO-2 and environmental driver datasets within individual years for 2015–2018 and within seven global biomes. We subsequently compare these inferences to the relationships estimated from 15 terrestrial biosphere models (TBMs) that participated in the TRENDY model inter-comparison. Using OCO-2, we are able to quantify only a limited number of relationships between patterns in atmospheric CO 2 observations and patterns in environmental driver datasets (i.e., 10 out of the 42 relationships examined). We further find that the ensemble of TBMs exhibits a large spread in the relationships with these key environmental driver datasets. The largest uncertainty in the models is in the relationship with precipitation, particularly in the tropics, with smaller uncertainties for temperature and photosynthetically active radiation (PAR). Using observations from OCO-2, we find that precipitation is associated with increased CO 2 uptake in all tropical biomes, a result that agrees with half of the TBMs. By contrast, the relationships that we infer from OCO-2 for temperature and PAR are similar to the ensemble mean of the TBMs, though the results differ from many individual TBMs. These results point to the limitations of current space-based observations for inferring environmental relationships but also indicate the potential to help inform key relationships that are very uncertain in state-of-the-art TBMs.
    Subject code 333
    Language English
    Publishing date 2021-05-04
    Publishing country de
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Book ; Online: Assessing methane emissions for northern peatlands in ORCHIDEE-PEAT revision 7020

    Salmon, Elodie / Jégou, Fabrice / Guenet, Bertrand / Jourdain, Line / Qiu, Chunjing / Bastrikov, Vladislav / Guimbaud, Christophe / Zhu, Dan / Ciais, Philippe / Peylin, Philippe / Gogo, Sébastien / Laggoun-Défarge, Fatima / Aurela, Mika / Bret-Harte, M. Syndonia / Chen, Jiquan / Chojnicki, Bogdan H. / Chu, Housen / Edgar, Colin W. / Euskirchen, Eugenie S. /
    Flanagan, Lawrence B. / Fortuniak, Krzysztof / Holl, David / Klatt, Janina / Kolle, Olaf / Kowalska, Natalia / Kutzbach, Lars / Lohila, Annalea / Merbold, Lutz / Pawlak, Włodzimierz / Sachs, Torsten / Ziemblińska, Klaudia

    eISSN: 1991-9603

    2022  

    Abstract: In the global methane budget, the largest natural source is attributed to wetlands, which encompass all ecosystems composed of waterlogged or inundated ground, capable of methane production. Among them, northern peatlands that store large amounts of soil ...

    Abstract In the global methane budget, the largest natural source is attributed to wetlands, which encompass all ecosystems composed of waterlogged or inundated ground, capable of methane production. Among them, northern peatlands that store large amounts of soil organic carbon have been functioning, since the end of the last glaciation period, as long-term sources of methane (CH 4 ) and are one of the most significant methane sources among wetlands. To reduce uncertainty of quantifying methane flux in the global methane budget, it is of significance to understand the underlying processes for methane production and fluxes in northern peatlands. A methane model that features methane production and transport by plants, ebullition process and diffusion in soil, oxidation to CO 2 , and CH 4 fluxes to the atmosphere has been embedded in the ORCHIDEE-PEAT land surface model that includes an explicit representation of northern peatlands. ORCHIDEE-PCH 4 was calibrated and evaluated on 14 peatland sites distributed on both the Eurasian and American continents in the northern boreal and temperate regions. Data assimilation approaches were employed to optimized parameters at each site and at all sites simultaneously. Results show that methanogenesis is sensitive to temperature and substrate availability over the top 75 cm of soil depth. Methane emissions estimated using single site optimization (SSO) of model parameters are underestimated by 9 g CH 4 m −2 yr −1 on average (i.e., 50 % higher than the site average of yearly methane emissions). While using the multi-site optimization (MSO), methane emissions are overestimated by 5 g CH 4 m −2 yr −1 on average across all investigated sites (i.e., 37 % lower than the site average of yearly methane emissions).
    Subject code 333
    Language English
    Publishing date 2022-04-06
    Publishing country de
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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