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Article: Accurate Simulation of Both Sensitivity and Variability for Amazonian Photosynthesis: Is It Too Much to Ask?

Gallup, Sarah M / Baker, Ian T / Gallup, John L / Restrepo-Coupe, Natalia / Haynes, Katherine D / Geyer, Nicholas M / Denning, A Scott

Journal of advances in modeling earth systems

2021 Volume 13, Issue 8, Page(s) e2021MS002555

Abstract: Estimates of Amazon rainforest gross primary productivity (GPP) differ by a factor of 2 across a suite of three statistical and 18 process models. This wide spread contributes uncertainty to predictions of future climate. We compare the mean and variance ...

Abstract	Estimates of Amazon rainforest gross primary productivity (GPP) differ by a factor of 2 across a suite of three statistical and 18 process models. This wide spread contributes uncertainty to predictions of future climate. We compare the mean and variance of GPP from these models to that of GPP at six eddy covariance (EC) towers. Only one model's mean GPP across all sites falls within a 99% confidence interval for EC GPP, and only one model matches EC variance. The strength of model response to climate drivers is related to model ability to match the seasonal pattern of the EC GPP. Models with stronger seasonal swings in GPP have stronger responses to rain, light, and temperature than does EC GPP. The model to data comparison illustrates a trade-off inherent to deterministic models between accurate simulation of a mean (average) and accurate responsiveness to drivers. The trade-off exists because all deterministic models simplify processes and lack at least some consequential driver or interaction. If a model's sensitivities to included drivers and their interactions are accurate, then deterministically predicted outcomes have less variability than is realistic. If a GPP model has stronger responses to climate drivers than found in data, model predictions may match the observed variance and seasonal pattern but are likely to overpredict GPP response to climate change. High or realistic variability of model estimates relative to reference data indicate that the model is hypersensitive to one or more drivers.
Language	English
Publishing date	2021-08-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2462132-8
ISSN	1942-2466
ISSN	1942-2466
DOI	10.1029/2021MS002555
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Surface-Atmosphere Coupling Scale, the Fate of Water, and Ecophysiological Function in a Brazilian Forest.

Baker, Ian T / Denning, A Scott / Dazlich, Don A / Harper, Anna B / Branson, Mark D / Randall, David A / Phillips, Morgan C / Haynes, Katherine D / Gallup, Sarah M

Journal of advances in modeling earth systems

2019 Volume 11, Issue 8, Page(s) 2523–2546

Abstract: Tropical South America plays a central role in global climate. Bowen ratio teleconnects to circulation and precipitation processes far afield, and the global ... ...

Abstract	Tropical South America plays a central role in global climate. Bowen ratio teleconnects to circulation and precipitation processes far afield, and the global CO
Language	English
Publishing date	2019-08-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2462132-8
ISSN	1942-2466
ISSN	1942-2466
DOI	10.1029/2019MS001650
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Article ; Online: Spring enhancement and summer reduction in carbon uptake during the 2018 drought in northwestern Europe.

Smith, Naomi E / Kooijmans, Linda M J / Koren, Gerbrand / van Schaik, Erik / van der Woude, Auke M / Wanders, Niko / Ramonet, Michel / Xueref-Remy, Irène / Siebicke, Lukas / Manca, Giovanni / Brümmer, Christian / Baker, Ian T / Haynes, Katherine D / Luijkx, Ingrid T / Peters, Wouter

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2020 Volume 375, Issue 1810, Page(s) 20190509

Abstract: We analysed gross primary productivity (GPP), total ecosystem respiration (TER) and the resulting net ecosystem exchange (NEE) of carbon dioxide ( ... ...

Abstract	We analysed gross primary productivity (GPP), total ecosystem respiration (TER) and the resulting net ecosystem exchange (NEE) of carbon dioxide (CO
MeSH term(s)	Carbon/analysis ; Carbon Cycle ; Carbon Dioxide/analysis ; Climate Change ; Droughts ; Europe ; Seasons
Chemical Substances	Carbon Dioxide (142M471B3J) ; Carbon (7440-44-0)
Language	English
Publishing date	2020-09-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2019.0509
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Article: Beyond ecosystem modeling: A roadmap to community cyberinfrastructure for ecological data‐model integration

Fer, Istem / Gardella, Anthony K / Shiklomanov, Alexey N / Campbell, Eleanor E / Cowdery, Elizabeth M / De Kauwe, Martin G / Desai, Ankur / Duveneck, Matthew J / Fisher, Joshua B / Haynes, Katherine D / Hoffman, Forrest M / Johnston, Miriam R / Kooper, Rob / LeBauer, David S / Mantooth, Joshua / Parton, William J / Poulter, Benjamin / Quaife, Tristan / Raiho, Ann /

Schaefer, Kevin / Serbin, Shawn P / Simkins, James / Wilcox, Kevin R / Viskari, Toni / Dietze, Michael C

Global change biology. 2021 Jan., v. 27, no. 1

2021

Abstract: In an era of rapid global change, our ability to understand and predict Earth's natural systems is lagging behind our ability to monitor and measure changes in the biosphere. Bottlenecks to informing models with observations have reduced our capacity to ... ...

Abstract	In an era of rapid global change, our ability to understand and predict Earth's natural systems is lagging behind our ability to monitor and measure changes in the biosphere. Bottlenecks to informing models with observations have reduced our capacity to fully exploit the growing volume and variety of available data. Here, we take a critical look at the information infrastructure that connects ecosystem modeling and measurement efforts, and propose a roadmap to community cyberinfrastructure development that can reduce the divisions between empirical research and modeling and accelerate the pace of discovery. A new era of data‐model integration requires investment in accessible, scalable, and transparent tools that integrate the expertise of the whole community, including both modelers and empiricists. This roadmap focuses on five key opportunities for community tools: the underlying foundations of community cyberinfrastructure; data ingest; calibration of models to data; model‐data benchmarking; and data assimilation and ecological forecasting. This community‐driven approach is a key to meeting the pressing needs of science and society in the 21st century.
Keywords	Biological Sciences ; biosphere ; ecosystems ; empirical research ; global change ; infrastructure
Language	English
Dates of publication	2021-01
Size	p. 13-26.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	1281439-8
ISSN	1365-2486 ; 1354-1013
ISSN (online)	1365-2486
ISSN	1354-1013
DOI	10.1111/gcb.15409
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Representing grasslands using dynamic prognostic phenology based on biological growth stages

Haynes, Katherine D. / Baker, Ian T. / Denning, A. Scott / Wolf, Sebastian / id_orcid:0 000-0001-7717-6993 / Wohlfahrt, Georg / Kiely, Gerard / Minaya, Renee C. / Haynes, John M.

Journal of Advances in Modeling Earth Systems, 11 (12)

Part 2. Carbon cycling

2019

Abstract: Grasslands are one of the most widely distributed and abundant vegetation types globally, and land surface models struggle to accurately simulate grassland carbon dioxide, energy, and water fluxes. Here we hypothesize that this is due to land surface ... ...

Abstract	Grasslands are one of the most widely distributed and abundant vegetation types globally, and land surface models struggle to accurately simulate grassland carbon dioxide, energy, and water fluxes. Here we hypothesize that this is due to land surface models having difficulties in reproducing grassland phenology, in particular in response to the seasonal and interannual variability of precipitation. Using leaf area index (LAI), net primary productivity, and flux data at 55 sites spanning climate zones, the aim of this study is to evaluate a novel prognostic phenology model (Simple Biosphere Model, SiB4) while simultaneously illustrating grassland relationships across precipitation gradients. Evaluating from 2000 to 2014, SiB4 predicts daily LAI, carbon, and energy fluxes with root‐mean‐square errors < 15% and individual biases <10%; however, not including management likely reduces its performance. Grassland mean annual LAI increases linearly with mean annual precipitation, with both SiB4 and the Moderate Resolution Imaging Spectroradiometer (MODIS) showing a 0.13 increase in LAI per 100‐mm increase in precipitation. Both gross primary production and ecosystem respiration increase with growing season length by ∼8.5 g C m−2 per day, with SiB4 and Fluxnet estimates within 18%. Despite differences in mean annual precipitation and growing season length, all grassland sites shift to seasonal carbon sinks one month prior to peak uptake. During a U.S. drought, MODIS and SiB4 had nearly identical LAI responses, and the LAI change due to drought was less than the LAI change across the precipitation gradient, indicating that grassland drought response is not as strong as the overlying climate response. ISSN:1942-2466
Keywords	Grassland ecology ; Terrestrial carbon cycle ; Prognostic phenology ; Land surface model
Subject code	550
Language	English
Publisher	American Geophysical Union
Publishing country	ch
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Spring enhancement and summer reduction in carbon uptake during the 2018 drought in northwestern Europe

Smith, Naomi E. / Kooijmans, Linda M. J. / Koren, Gerbrand / Schaik, Erik van / Woude, Auke van der / Wanders, Niko / Ramonet, Michel / Xueref-Remy, Irène / Siebicke, Lukas / Manca, Giovanni / Brümmer, Christian / Baker, Ian T. / Haynes, Katherine D. / Luijkx, Ingrid T. / Peters, Wouter

2020

Abstract: We analysed gross primary productivity (GPP), total ecosystem respiration (TER) and the resulting net ecosystem exchange (NEE) of carbon dioxide (CO2) by the terrestrial biosphere during the summer of 2018 through observed changes across the Integrated ... ...

Abstract	We analysed gross primary productivity (GPP), total ecosystem respiration (TER) and the resulting net ecosystem exchange (NEE) of carbon dioxide (CO2) by the terrestrial biosphere during the summer of 2018 through observed changes across the Integrated Carbon Observation System (ICOS) network, through biosphere and inverse modelling, and through remote sensing. Highly correlated yet independently-derived reductions in productivity from sun-induced fluorescence, vegetative near-infrared reflectance, and GPP simulated by the Simple Biosphere model version 4 (SiB4) suggest a 130–340 TgC GPP reduction in July–August–September (JAS) of 2018. This occurs over an area of 1.6 × 106 km2 with anomalously low precipitation in northwestern and central Europe. In this drought-affected area, reduced GPP, TER, NEE and soil moisture at ICOS ecosystem sites are reproduced satisfactorily by the SiB4 model. We found that, in contrast to the preceding 5 years, low soil moisture is the main stress factor across the affected area. SiB4’s NEE reduction by 57 TgC for JAS coincides with anomalously high atmospheric CO2 observations in 2018, and this is closely matched by the NEE anomaly derived by CarbonTracker Europe (52 to 83 TgC). Increased NEE during the spring (May–June) of 2018 (SiB4 −52 TgC; CTE −46 to −55 TgC) largely offset this loss, as ecosystems took advantage of favourable growth conditions. This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale’.
Keywords	Text ; ddc:630 ; European carbon balance -- CO2 -- drought -- data assimilation -- remote sensing
Subject code	550
Language	English
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Spring enhancement and summer reduction in carbon uptake during the 2018 drought in northwestern Europe

Smith, Naomi E. / Kooijmans, Linda M.J. / Koren, Gerbrand / van Schaik, Erik / van der Woude, Auke M. / Wanders, Niko / Ramonet, Michel / Xueref-Remy, Irène / Siebicke, Lukas / Manca, Giovanni / Brümmer, Christian / Baker, Ian T. / Haynes, Katherine D. / Luijkx, Ingrid T. / Peters, Wouter

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2020 Volume 375, Issue 1810

Abstract	We analysed gross primary productivity (GPP), total ecosystem respiration (TER) and the resulting net ecosystem exchange (NEE) of carbon dioxide (CO2) by the terrestrial biosphere during the summer of 2018 through observed changes across the Integrated Carbon Observation System (ICOS) network, through biosphere and inverse modelling, and through remote sensing. Highly correlated yet independently-derived reductions in productivity from sun-induced fluorescence, vegetative near-infrared reflectance, and GPP simulated by the Simple Biosphere model version 4 (SiB4) suggest a 130-340 TgC GPP reduction in July-August-September (JAS) of 2018. This occurs over an area of 1.6 × 106 km2 with anomalously low precipitation in northwestern and central Europe. In this drought-affected area, reduced GPP, TER, NEE and soil moisture at ICOS ecosystem sites are reproduced satisfactorily by the SiB4 model. We found that, in contrast to the preceding 5 years, low soil moisture is the main stress factor across the affected area. SiB4's NEE reduction by 57 TgC for JAS coincides with anomalously high atmospheric CO2 observations in 2018, and this is closely matched by the NEE anomaly derived by CarbonTracker Europe (52 to 83 TgC). Increased NEE during the spring (May-June) of 2018 (SiB4 -52 TgC; CTE -46 to -55 TgC) largely offset this loss, as ecosystems took advantage of favourable growth conditions. This article is part of the theme issue 'Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.
Keywords	CO2 ; European carbon balance ; data assimilation ; drought ; remote sensing
Subject code	550
Language	English
Publishing country	nl
Document type	Article ; Online
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Beyond ecosystem modeling: A roadmap to community cyberinfrastructure for ecological data-model integration.

Schaefer, Kevin / Serbin, Shawn P / Simkins, James / Wilcox, Kevin R / Viskari, Toni / Dietze, Michael C

Global change biology

2020 Volume 27, Issue 1, Page(s) 13–26

Abstract	In an era of rapid global change, our ability to understand and predict Earth's natural systems is lagging behind our ability to monitor and measure changes in the biosphere. Bottlenecks to informing models with observations have reduced our capacity to fully exploit the growing volume and variety of available data. Here, we take a critical look at the information infrastructure that connects ecosystem modeling and measurement efforts, and propose a roadmap to community cyberinfrastructure development that can reduce the divisions between empirical research and modeling and accelerate the pace of discovery. A new era of data-model integration requires investment in accessible, scalable, and transparent tools that integrate the expertise of the whole community, including both modelers and empiricists. This roadmap focuses on five key opportunities for community tools: the underlying foundations of community cyberinfrastructure; data ingest; calibration of models to data; model-data benchmarking; and data assimilation and ecological forecasting. This community-driven approach is a key to meeting the pressing needs of science and society in the 21st century.
MeSH term(s)	Ecosystem ; Forecasting ; Models, Theoretical
Language	English
Publishing date	2020-11-06
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.15409
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: Evaluation of carbonyl sulfide biosphere exchange in the Simple Biosphere Model (SiB4)

Kooijmans, Linda M. J. / Cho, Ara / Ma, Jin / Kaushik, Aleya / Haynes, Katherine D. / Baker, Ian / Luijkx, Ingrid T. / Groenink, Mathijs / Peters, Wouter / Miller, John B. / Berry, Joseph A. / Ogée, Jérôme / Meredith, Laura K. / Sun, Wu / Kohonen, Kukka-Maaria / Vesala, Timo / Mammarella, Ivan / Chen, Huilin / Spielmann, Felix M. /

Wohlfahrt, Georg / Berkelhammer, Max / Whelan, Mary E. / Maseyk, Kadmiel / Seibt, Ulli / Commane, Roisin / Wehr, Richard / Krol, Maarten

eISSN: 1726-4189

2021

Abstract: The uptake of carbonyl sulfide (COS) by terrestrial plants is linked to photosynthetic uptake of CO 2 by a shared diffusion pathway. Applying COS as a photosynthesis tracer in models requires an accurate representation of biosphere COS fluxes, but these ... ...

Abstract	The uptake of carbonyl sulfide (COS) by terrestrial plants is linked to photosynthetic uptake of CO 2 by a shared diffusion pathway. Applying COS as a photosynthesis tracer in models requires an accurate representation of biosphere COS fluxes, but these models have not been extensively evaluated against field observations of COS fluxes. In this paper, the COS flux as simulated by the Simple Biosphere Model, version 4 (SiB4) is updated with the latest mechanistic insights and evaluated with site observations from different biomes: one evergreen needleleaf forest, two deciduous broadleaf forests, three grasslands, and two crop fields spread over Europe and North America. To account for the effect of atmospheric COS mole fractions on COS biosphere uptake, we replaced the fixed COS mole fraction originally used in SiB4 with spatially and temporally varying COS mole fraction fields. The lower COS mole fractions in the late growing season reduces COS uptake rates in agreement with observations. We also replaced the empirical soil COS uptake model in SiB4 with a mechanistic model that represents both uptake and production of COS in soils, which improves the match with observations over agricultural fields and fertilized grassland soils. SiB4 was capable of simulating the diurnal and seasonal variation of COS fluxes in the boreal, temperate and Mediterranean region. The daytime vegetation COS flux is on average 8 ± 27 % underestimated, albeit with large variability across sites. On a global scale, our model modifications caused a drop in the COS biosphere sink from 922 Gg S yr −1 in the original SiB4 model to 753 Gg S yr −1 in the updated version. The largest drop in fluxes was driven by lower atmospheric COS mole fractions over regions with high productivity, which highlights the importance of accounting for variations in atmospheric COS mole fractions. The change to a different soil model, on the other hand, had a relatively small effect on the global biosphere COS sink. The small role of the modeled soil component in the COS budget supports the use of COS as a global photosynthesis tracer.
Subject code	551
Language	English
Publishing date	2021-07-26
Publishing country	de
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Evaluation of carbonyl sulfide biosphere exchange in the Simple Biosphere Model (SiB4)

Kooijmans, Linda M.J. / Cho, Ara / Ma, Jin / Kaushik, Aleya / Haynes, Katherine D. / Baker, Ian / Luijkx, Ingrid T. / Groenink, Mathijs / Peters, Wouter / Miller, John B. / Berry, Joseph A. / Ogée, Jerome / Meredith, Laura K. / Sun, Wu / Kohonen, Kukka Maaria / Vesala, Timo / Mammarella, Ivan / Chen, Huilin / Spielmann, Felix M. /

Wohlfahrt, Georg / Berkelhammer, Max / Whelan, Mary E. / Maseyk, Kadmiel / Seibt, Ulli / Commane, Roisin / Wehr, Richard / Krol, Maarten

Biogeosciences

2021 Volume 18, Issue 24

Abstract: The uptake of carbonyl sulfide (COS) by terrestrial plants is linked to photosynthetic uptake of CO2 as these gases partly share the same uptake pathway. Applying COS as a photosynthesis tracer in models requires an accurate representation of biosphere ... ...

Abstract	The uptake of carbonyl sulfide (COS) by terrestrial plants is linked to photosynthetic uptake of CO2 as these gases partly share the same uptake pathway. Applying COS as a photosynthesis tracer in models requires an accurate representation of biosphere COS fluxes, but these models have not been extensively evaluated against field observations of COS fluxes. In this paper, the COS flux as simulated by the Simple Biosphere Model, version 4 (SiB4), is updated with the latest mechanistic insights and evaluated with site observations from different biomes: one evergreen needleleaf forest, two deciduous broadleaf forests, three grasslands, and two crop fields spread over Europe and North America. We improved SiB4 in several ways to improve its representation of COS. To account for the effect of atmospheric COS mole fractions on COS biosphere uptake, we replaced the fixed atmospheric COS mole fraction boundary condition originally used in SiB4 with spatially and temporally varying COS mole fraction fields. Seasonal amplitudes of COS mole fractions are ∼50-200 ppt at the investigated sites with a minimum mole fraction in the late growing season. Incorporating seasonal variability into the model reduces COS uptake rates in the late growing season, allowing better agreement with observations. We also replaced the empirical soil COS uptake model in SiB4 with a mechanistic model that represents both uptake and production of COS in soils, which improves the match with observations over agricultural fields and fertilized grassland soils. The improved version of SiB4 was capable of simulating the diurnal and seasonal variation in COS fluxes in the boreal, temperate, and Mediterranean region. Nonetheless, the daytime vegetation COS flux is underestimated on average by 8±27 %, albeit with large variability across sites. On a global scale, our model modifications decreased the modeled COS terrestrial biosphere sink from 922 GgSyr-1 in the original SiB4 to 753 GgSyr-1 in the updated version. The largest decrease in fluxes was ...
Keywords	Life Science
Subject code	551
Language	English
Publishing country	nl
Document type	Article ; Online
ZDB-ID	2158181-2
ISSN	1726-4189 ; 1726-4170
ISSN (online)	1726-4189
ISSN	1726-4170
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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