Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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The kinetics of cellular and humoral immune responses of common carp to presporogonic development of the myxozoan Sphaerospora molnari
Korytář, Tomáš ; Wiegertjes, Geert F. ; Zusková, Eliška ; Tomanová, Anna ; Lisnerová, Martina ; Patra, Sneha ; Sieranski, Viktor ; Šíma, Radek ; Born-Torrijos, Ana ; Wentzel, Annelieke S. ; Blasco-Monleon, Sandra ; Yanes-Roca, Carlos ; Policar, Tomáš ; Holzer, Astrid S. - \ 2019
Parasites & Vectors 12 (2019)1. - ISSN 1756-3305 - 1 p.
B cells - Cyprinus carpio - Cytokines - Host–parasite interaction - IgM - Myxozoa - Sphaerospora molnari - Teleost

BACKGROUND: Sphaerospora molnari is a myxozoan parasite causing skin and gill sphaerosporosis in common carp (Cyprinus carpio) in central Europe. For most myxozoans, little is known about the early development and the expansion of the infection in the fish host, prior to spore formation. A major reason for this lack of information is the absence of laboratory model organisms, whose life-cycle stages are available throughout the year. RESULTS: We have established a laboratory infection model for early proliferative stages of myxozoans, based on separation and intraperitoneal injection of motile and dividing S. molnari stages isolated from the blood of carp. In the present study we characterize the kinetics of the presporogonic development of S. molnari, while analyzing cellular host responses, cytokine and systemic immunoglobulin expression, over a 63-day period. Our study shows activation of innate immune responses followed by B cell-mediated immune responses. We observed rapid parasite efflux from the peritoneal cavity (< 40 hours), an initial covert infection period with a moderate proinflammatory response for about 1-2 weeks, followed by a period of parasite multiplication in the blood which peaked at 28 days post-infection (dpi) and was associated with a massive lymphocyte response. Our data further revealed a switch to a massive anti-inflammatory response (up to 1456-fold expression of il-10), a strong increase in the expression of IgM transcripts and increased number of IgM+ B lymphocytes, which produce specific antibodies for the elimination of most of the parasites from the fish at 35 dpi. However, despite the presence of these antibodies, S. molnari invades the liver 42 dpi, where an increase in parasite cell number and indistinguishable outer cell membranes are indicative of effective exploitation and disguise mechanisms. From 49 dpi onwards, the acute infection changes to a chronic one, with low parasite numbers remaining in the fish. CONCLUSIONS: To our knowledge, this is the first time myxozoan early development and immune modulation mechanisms have been analyzed along with innate and adaptive immune responses of its fish host, in a controlled laboratory system. Our study adds important information on host-parasite interaction and co-evolutionary adaptation of early metazoans (Cnidaria) with basic vertebrate (fish) immune systems and the evolution of host adaptation and parasite immune evasion strategies.

The value of manure - Manure as co-product in life cycle assessment
Leip, Adrian ; Ledgard, Stewart ; Uwizeye, Aimable ; Palhares, Julio C.P. ; Aller, M.F. ; Amon, Barbara ; Binder, Michael ; Cordovil, Claudia M.D.S. ; Camillis, Camillo De; Dong, Hongming ; Fusi, Alessandra ; Helin, Janne ; Hörtenhuber, Stefan ; Hristov, Alexander N. ; Koelsch, Richard ; Liu, Chunjiang ; Masso, Cargele ; Nkongolo, Nsalambi V. ; Patra, Amlan K. ; Redding, Matthew R. ; Rufino, Mariana C. ; Sakrabani, Ruben ; Thoma, Greg ; Vertès, Françoise ; Wang, Ying - \ 2019
Journal of Environmental Management 241 (2019). - ISSN 0301-4797 - p. 293 - 304.
Livestock production is important for food security, nutrition, and landscape maintenance, but it is associated with several environmental impacts. To assess the risk and benefits arising from livestock production, transparent and robust indicators are required, such as those offered by life cycle assessment. A central question in such approaches is how environmental burden is allocated to livestock products and to manure that is re-used for agricultural production. To incentivize sustainable use of manure, it should be considered as a co-product as long as it is not disposed of, or wasted, or applied in excess of crop nutrient needs, in which case it should be treated as a waste. This paper proposes a theoretical approach to define nutrient requirements based on nutrient response curves to economic and physical optima and a pragmatic approach based on crop nutrient yield adjusted for nutrient losses to atmosphere and water. Allocation of environmental burden to manure and other livestock products is then based on the nutrient value from manure for crop production using the price of fertilizer nutrients. We illustrate and discuss the proposed method with two case studies.
Global atmospheric CO2 inverse models converging on neutral tropical land exchange, but disagreeing on fossil fuel and atmospheric growth rate
Gaubert, Benjamin ; Stephens, Britton B. ; Basu, Sourish ; Chevallier, Frédéric ; Deng, Feng ; Kort, Eric A. ; Patra, Prabir K. ; Peters, Wouter ; Rödenbeck, Christian ; Saeki, Tazu ; Schimel, David ; Laan-Luijkx, Ingrid van der; Wofsy, Steven ; Yin, Yi - \ 2019
Biogeosciences 16 (2019)1. - ISSN 1726-4170 - p. 117 - 134.

We have compared a suite of recent global CO2 atmospheric inversion results to independent airborne observations and to each other, to assess their dependence on differences in northern extratropical (NET) vertical transport and to identify some of the drivers of model spread. We evaluate posterior CO2 concentration profiles against observations from the High-Performance Instrumented Airborne Platform for Environmental Research (HIAPER) Pole-To-Pole Observations (HIPPO) aircraft campaigns over the mid-Pacific in 2009-2011. Although the models differ in inverse approaches, assimilated observations, prior fluxes, and transport models, their broad latitudinal separation of land fluxes has converged significantly since the Atmospheric Carbon Cycle Inversion Intercomparison (TransCom 3) and the REgional Carbon Cycle Assessment and Processes (RECCAP) projects, with model spread reduced by 80% since TransCom 3 and 70% since RECCAP. Most modeled CO2 fields agree reasonably well with the HIPPO observations, specifically for the annual mean vertical gradients in the Northern Hemisphere. Northern Hemisphere vertical mixing no longer appears to be a dominant driver of northern versus tropical (T) annual flux differences. Our newer suite of models still gives northern extratropical land uptake that is modest relative to previous estimates (Gurney et al., 2002; Peylin et al., 2013) and near-neutral tropical land uptake for 2009- 2011. Given estimates of emissions from deforestation, this implies a continued uptake in intact tropical forests that is strong relative to historical estimates (Gurney et al., 2002; Peylin et al., 2013). The results from these models for other time periods (2004-2014, 2001-2004, 1992-1996) and reevaluation of the TransCom 3 Level 2 and RECCAP results confirm that tropical land carbon fluxes including deforestation have been near neutral for several decades. However, models still have large disagreements on ocean-land partitioning. The fossil fuel (FF) and the atmospheric growth rate terms have been thought to be the best-known terms in the global carbon budget, but we show that they currently limit our ability to assess regional-scale terrestrial fluxes and ocean-land partitioning from the model ensemble.

Global Carbon Budget 2018
Quéré, Corinne ; Andrew, Robbie ; Friedlingstein, Pierre ; Sitch, Stephen ; Hauck, Judith ; Pongratz, Julia ; Pickers, Penelope ; Ivar Korsbakken, Jan ; Peters, Glen ; Canadell, Josep ; Arneth, Almut ; Arora, Vivek ; Barbero, Leticia ; Bastos, Ana ; Bopp, Laurent ; Ciais, Philippe ; Chini, Louise ; Ciais, Philippe ; Doney, Scott ; Gkritzalis, Thanos ; Goll, Daniel ; Harris, Ian ; Haverd, Vanessa ; Hoffman, Forrest ; Hoppema, Mario ; Houghton, Richard ; Hurtt, George ; Ilyina, Tatiana ; Jain, Atul ; Johannessen, Truls ; Jones, Chris ; Kato, Etsushi ; Keeling, Ralph ; Klein Goldewijk, Kees ; Landschützer, Peter ; Lefèvre, Nathalie ; Lienert, Sebastian ; Liu, Zhu ; Lombardozzi, Danica ; Metzl, Nicolas ; Munro, David ; Nabel, Julia ; Nakaoka, Shin Ichiro ; Neill, Craig ; Olsen, Are ; Ono, Tsueno ; Patra, Prabir ; Peregon, Anna ; Peters, Wouter ; Laan-Luijkx, Ingrid Van Der - \ 2018
Earth System Science Data 10 (2018)4. - ISSN 1866-3508 - p. 2141 - 2194.

Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere - the "global carbon budget" - is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. Fossil CO2 emissions (EFF) are based on energy statistics and cement production data, while emissions from land use and land-use change (ELUC), mainly deforestation, are based on land use and land-use change data and bookkeeping models. Atmospheric CO2 concentration is measured directly and its growth rate (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) and terrestrial CO2 sink (SLAND) are estimated with global process models constrained by observations. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and understanding of the contemporary carbon cycle. All uncertainties are reported as ±1σ. For the last decade available (2008-2017), EFF was 9.4±0.5 GtC yrĝ'1, ELUC 1.5±0.7 GtC yrĝ'1, GATM 4.7±0.02 GtC yrĝ'1, SOCEAN 2.4±0.5 GtC yrĝ'1, and SLAND 3.2±0.8 GtC yrĝ'1, with a budget imbalance BIM of 0.5 GtC yrĝ'1 indicating overestimated emissions and/or underestimated sinks. For the year 2017 alone, the growth in EFF was about 1.6 % and emissions increased to 9.9±0.5 GtC yrĝ'1. Also for 2017, ELUC was 1.4±0.7 GtC yrĝ'1, GATM was 4.6±0.2 GtC yrĝ'1, SOCEAN was 2.5±0.5 GtC yrĝ'1, and SLAND was 3.8±0.8 GtC yrĝ'1, with a BIM of 0.3 GtC. The global atmospheric CO2 concentration reached 405.0±0.1 ppm averaged over 2017. For 2018, preliminary data for the first 6-9 months indicate a renewed growth in EFF of +2.7 % (range of 1.8 % to 3.7 %) based on national emission projections for China, the US, the EU, and India and projections of gross domestic product corrected for recent changes in the carbon intensity of the economy for the rest of the world. The analysis presented here shows that the mean and trend in the five components of the global carbon budget are consistently estimated over the period of 1959-2017, but discrepancies of up to 1 GtC yrĝ'1 persist for the representation of semi-decadal variability in CO2 fluxes. A detailed comparison among individual estimates and the introduction of a broad range of observations show (1) no consensus in the mean and trend in land-use change emissions, (2) a persistent low agreement among the different methods on the magnitude of the land CO2 flux in the northern extra-tropics, and (3) an apparent underestimation of the CO2 variability by ocean models, originating outside the tropics. This living data update documents changes in the methods and data sets used in this new global carbon budget and the progress in understanding the global carbon cycle compared with previous publications of this data set (Le Quéré et al., 2018, 2016, 2015a, b, 2014, 2013).

Age of air as a diagnostic for transport timescales in global models
Krol, Maarten ; Bruine, Marco de; Killaars, Lars ; Ouwersloot, Huug ; Pozzer, Andrea ; Yin, Yi ; Chevallier, Frederic ; Bousquet, Philippe ; Patra, Prabir ; Belikov, Dmitry ; Maksyutov, Shamil ; Dhomse, Sandip ; Feng, Wuhu ; Chipperfield, Martyn P. - \ 2018
Geoscientific Model Development 11 (2018)8. - ISSN 1991-959X - p. 3109 - 3130.

This paper presents the first results of an age-of-air (AoA) inter-comparison of six global transport models. Following a protocol, three global circulation models and three chemistry transport models simulated five tracers with boundary conditions that grow linearly in time. This allows for an evaluation of the AoA and transport times associated with inter-hemispheric transport, vertical mixing in the troposphere, transport to and in the stratosphere, and transport of air masses between land and ocean. Since AoA is not a directly measurable quantity in the atmosphere, simulations of 222Rn and SF6 were also performed. We focus this first analysis on averages over the period 2000-2010, taken from longer simulations covering the period 1988-2014. We find that two models, NIES and TOMCAT, show substantially slower vertical mixing in the troposphere compared to other models (LMDZ, TM5, EMAC, and ACTM). However, while the TOMCAT model, as used here, has slow transport between the hemispheres and between the atmosphere over land and ocean, the NIES model shows efficient horizontal mixing and a smaller latitudinal gradient in SF6 compared to the other models and observations. We find consistent differences between models concerning vertical mixing of the troposphere, expressed as AoA differences and modelled 222Rn gradients between 950 and 500 hPa. All models agree, however, on an interesting asymmetry in inter-hemispheric mixing, with faster transport from the Northern Hemisphere surface to the Southern Hemisphere than vice versa. This is attributed to a rectifier effect caused by a stronger seasonal cycle in boundary layer venting over Northern Hemispheric land masses, and possibly to a related asymmetric position of the intertropical convergence zone. The calculated AoA in the mid-upper stratosphere varies considerably among the models (4-7 years). Finally, we find that the inter-model differences are generally larger than differences in AoA that result from using the same model with a different resolution or convective parameterisation. Taken together, the AoA model inter-comparison provides a useful addition to traditional approaches to evaluate transport timescales. Results highlight that inter-model differences associated with resolved transport (advection, reanalysis data, nudging) and parameterised transport (convection, boundary layer mixing) are still large and require further analysis. For this purpose, all model output and analysis software are available.

Pulsed electric field treatment to increase intracellular trehalose in L. plantarum WCFS1
Vaessen, E.M.J. ; Besten, H.M.W. den; Mossevelde, Niels van; Patra, T. ; Boom, R.M. ; Schutyser, M.A.I. - \ 2018
Pulsed electric field for increasing intracellular trehalose content in Lactobacillus plantarum WCFS1
Vaessen, E.M.J. ; Besten, H.M.W. den; Patra, T. ; Mossevelde, Niels van; Boom, R.M. ; Schutyser, M.A.I. - \ 2018
Innovative Food Science and Emerging Technologies 47 (2018). - ISSN 1466-8564 - p. 256 - 261.
Pulsed electric field (PEF) processing has been developed and applied in food industry for several purposes. In this study we used PEF for increasing the intracellular trehalose content in Lactobacillus plantarum WCFS1. Our results indicated that it is possible to increase intracellular trehalose content in Lactobacillus plantarum WCFS1 to ~100 mM with 75% survival when applying a PEF treatment with an electric field strength of 7.5 kV/cm. Fluorescence staining of PEF-treated cells with propidium iodide (PI) and SYTO 9 showed that at 7.5 kV/cm only a small fraction (23%) of the cells had a permeated membrane by this PEF treatment, of which approximately half had an irreversible permeated membrane. Resealing of the pores in the membrane for PI uptake was very fast, in the order of seconds. These results indicate that PEF treatment is promising for increasing intracellular trehalose, but further optimization is required to increase the trehalose content in all cells.
Global inverse modeling of CH4 sources and sinks : An overview of methods
Houweling, Sander ; Bergamaschi, Peter ; Chevallier, Frederic ; Heimann, Martin ; Kaminski, Thomas ; Krol, Maarten ; Michalak, Anna M. ; Patra, Prabir - \ 2017
Atmospheric Chemistry and Physics 17 (2017)1. - ISSN 1680-7316 - p. 235 - 256.

The aim of this paper is to present an overview of inverse modeling methods that have been developed over the years for estimating the global sources and sinks of CH4. It provides insight into how techniques and estimates have evolved over time and what the remaining shortcomings are. As such, it serves a didactical purpose of introducing apprentices to the field, but it also takes stock of developments so far and reflects on promising new directions. The main focus is on methodological aspects that are particularly relevant for CH4, such as its atmospheric oxidation, the use of methane isotopologues, and specific challenges in atmospheric transport modeling of CH4. The use of satellite retrievals receives special attention as it is an active field of methodological development, with special requirements on the sampling of the model and the treatment of data uncertainty. Regional scale flux estimation and attribution is still a grand challenge, which calls for new methods capable of combining information from multiple data streams of different measured parameters. A process model representation of sources and sinks in atmospheric transport inversion schemes allows the integrated use of such data. These new developments are needed not only to improve our understanding of the main processes driving the observed global trend but also to support international efforts to reduce greenhouse gas emissions.

Designer ecosystems : A solution for the conservation-exploitation dilemma
Awasthi, Ashutosh ; Singh, Kripal ; O'Grady, Audrey ; Courtney, Ronan ; Kalra, Alok ; Singh, Rana Pratap ; Cerda Bolinches, Artemio ; Steinberger, Yosef ; Patra, D.D. - \ 2016
Ecological Engineering 93 (2016). - ISSN 0925-8574 - p. 73 - 75.
Biodiversity - Community - Conservation - Ecosystem - Exotic invasion - Restoration - Sustainability

Increase in human population is accelerating the rate of land use change, biodiversity loss and habitat degradation, triggering a serious threat to life supporting ecosystem services. Existing strategies for biological conservation remain insufficient to achieve a sustainable human-nature relationship and this situation has fueled a debate on the conservation-exploitation dilemma. We need to devise novel strategies, in a mutually inclusive way, which can support biological conservation and secure economic development of deprived populations. Here we propose the use of designer ecosystems which can ensure ecological sustainability while providing ample and some new means of livelihood to local people. Such designer ecosystems may provide a solution to the conservation-exploitation dilemma through lessening population pressure on conserved ecosystems and remediating environmental pollution and ecosystem degradation to secure a broad range of ecosystem services of economic and cultural values.

Top-down assessment of the Asian carbon budget since the mid 1990s
Thompson, R.L. ; Patra, P.K. ; Chevallier, F. ; Maksyutov, S. ; Law, R.M. ; Ziehn, T. ; Laan-Luijkx, I.T. Van Der; Peters, W. ; Ganshin, A. ; Zhuravlev, R. ; Maki, T. ; Nakamura, T. ; Shirai, T. ; Ishizawa, M. ; Saeki, T. ; Machida, T. ; Poulter, B. ; Canadell, J.G. ; Ciais, P. - \ 2016
Nature Communications 7 (2016). - ISSN 2041-1723

Increasing atmospheric carbon dioxide (CO2) is the principal driver of anthropogenic climate change. Asia is an important region for the global carbon budget, with 4 of the world's 10 largest national emitters of CO2. Using an ensemble of seven atmospheric inverse systems, we estimated land biosphere fluxes (natural, land-use change and fires) based on atmospheric observations of CO2 concentration. The Asian land biosphere was a net sink of -0.46 (-0.70-0.24) PgC per year (median and range) for 1996-2012 and was mostly located in East Asia, while in South and Southeast Asia the land biosphere was close to carbon neutral. In East Asia, the annual CO2 sink increased between 1996-2001 and 2008-2012 by 0.56 (0.30-0.81) PgC, accounting for ∼35% of the increase in the global land biosphere sink. Uncertainty in the fossil fuel emissions contributes significantly (32%) to the uncertainty in land biosphere sink change.

The seasonal variation of the CO2 flux over Tropical Asia estimated from GOSAT, CONTRAIL, and IASI
Basu, S. ; Krol, M.C. ; Butz, A. ; Clerbaux, C. ; Sawa, Y. ; Machida, T. ; Matsueda, H. ; Frankenberg, C. ; Hasekamp, O.P. ; Aben, I. - \ 2014
Geophysical Research Letters 41 (2014)5. - ISSN 0094-8276 - p. 1809 - 1815.
atmospheric co2 - carbon balance - emissions - gosat - retrievals - aerosol - fires
We estimate the CO2 flux over Tropical Asia in 2009, 2010, and 2011 using Greenhouse Gases Observing Satellite (GOSAT) total column CO2(XCO2) and in situ measurements of CO2. Compared to flux estimates from assimilating surface measurements of CO2, GOSAT XCO2 estimates a more dynamic seasonal cycle and a large source in March–May 2010. The more dynamic seasonal cycle is consistent with earlier work by Patra et al. (2011), and the enhanced 2010 source is supported by independent upper air CO2 measurements from the Comprehensive Observation Network for Trace gases by Airliner (CONTRAIL) project. Using Infrared Atmospheric Sounding Interferometer (IASI) measurements of total column CO (XCO), we show that biomass burning CO2 can explain neither the dynamic seasonal cycle nor the 2010 source. We conclude that both features must come from the terrestrial biosphere. In particular, the 2010 source points to biosphere response to above-average temperatures that year.
Observational evidence for interhemispheric hydroxyl-radical parity
Patra, P.K. ; Krol, M.C. ; Montzka, S.A. ; Arnold, T. ; Atlas, E.L. ; Lintner, B.R. ; Stephens, B.B. ; Xiang, B. - \ 2014
Nature 513 (2014)7517. - ISSN 0028-0836 - p. 219 - 223.
atmospheric hydroxyl - sulfur-hexafluoride - methyl chloroform - tropospheric oh - model - variability - transport - chemistry - climate - methane
The hydroxyl radical (OH) is a key oxidant involved in the removal of air pollutants and greenhouse gases from the atmosphere1, 2, 3. The ratio of Northern Hemispheric to Southern Hemispheric (NH/SH) OH concentration is important for our understanding of emission estimates of atmospheric species such as nitrogen oxides and methane4, 5, 6. It remains poorly constrained, however, with a range of estimates from 0.85 to 1.4 (refs 4, 7,8,9,10). Here we determine the NH/SH ratio of OH with the help of methyl chloroform data (a proxy for OH concentrations) and an atmospheric transport model that accurately describes interhemispheric transport and modelled emissions. We find that for the years 2004–2011 the model predicts an annual mean NH–SH gradient of methyl chloroform that is a tight linear function of the modelled NH/SH ratio in annual mean OH. We estimate a NH/SH OH ratio of 0.97 ± 0.12 during this time period by optimizing global total emissions and mean OH abundance to fit methyl chloroform data from two surface-measurement networks and aircraft campaigns11, 12, 13. Our findings suggest that top-down emission estimates of reactive species such as nitrogen oxides in key emitting countries in the NH that are based on a NH/SH OH ratio larger than 1 may be overestimated.
Off-line algorithm for calculation of vertical tracer transport in the troposphere due to deep convection
Belikov, D.A. ; Maksyutov, S. ; Krol, M.C. ; Fraser, A. ; Rigby, M. ; Bian, H. ; Agusti-Panareda, A. ; Bergmann, D. ; Bousquet, P. ; Cameron-Smith, P. ; Chipperfield, M.P. ; Fortems-Cheiney, A. ; Gloor, E. ; Haynes, K. ; Hess, P. ; Houweling, S. ; Kawa, S.R. ; Law, R.M. ; Loh, Z. ; Meng, L. ; Palmer, P.I. ; Patra, P.K. ; Prinn, R.G. ; Saito, R. ; Wilson, C. - \ 2013
Atmospheric Chemistry and Physics 13 (2013)3. - ISSN 1680-7316 - p. 1093 - 1114.
general-circulation model - observed radon profiles - cumulus convection - atmospheric transport - climate simulations - meteorological data - cloud ensemble - precipitation - rn-222 - parameterization
A modified cumulus convection parametrisation scheme is presented. This scheme computes the mass of air transported upward in a cumulus cell using conservation of moisture and a detailed distribution of convective precipitation provided by a reanalysis dataset. The representation of vertical transport within the scheme includes entrainment and detrainment processes in convective updrafts and downdrafts. Output from the proposed parametrisation scheme is employed in the National Institute for Environmental Studies (NIES) global chemical transport model driven by JRA-25/JCDAS reanalysis. The simulated convective precipitation rate and mass fluxes are compared with observations and reanalysis data. A simulation of the short-lived tracer Rn-222 is used to further evaluate the performance of the cumulus convection scheme. Simulated distributions of Rn-222 are evaluated against observations at the surface and in the free troposphere, and compared with output from models that participated in the TransCom-CH4 Transport Model Intercomparison. From this comparison, we demonstrate that the proposed convective scheme in general is consistent with observed and modeled results.
On the variation of regional CO2 exchange over temperate and boreal North America
Zhang, X. ; Gurney, K.R. ; Peylin, P. ; Chevallier, F. ; Law, R.M. ; Patra, P.K. ; Rayner, P.J. ; Roedenbeck, C. ; Krol, M.C. - \ 2013
Global Biogeochemical Cycles 27 (2013)4. - ISSN 0886-6236 - p. 991 - 1000.
atmospheric carbon-dioxide - terrestrial ecosystems - united-states - interannual variability - climate - forest - trends - drought - fluxes - land
Inverse-estimated net carbon exchange time series spanning two decades for six North American regions are analyzed to examine long-term trends and relationships to temperature and precipitation variations. Results reveal intensification of carbon uptake in eastern boreal North America (0.1 PgC/decade) and the Midwest United States (0.08 PgC/decade). Seasonal cross-correlation analysis shows a significant relationship between net carbon exchange and temperature/precipitation anomalies during the western United States growing season with warmer, dryer conditions leading reduced carbon uptake. This relationship is consistent with global change-type drought dynamics which drive increased vegetation mortality, increases in dry woody material, and increased wildfire occurrence. This finding supports the contention that future climate change may increase carbon loss in this region. Similarly, higher temperatures and reduced precipitation are accompanied by decreased net carbon uptake in the Midwestern United States toward the end of the growing season. Additionally, intensified net carbon uptake during the eastern boreal North America growing season is led by increased precipitation anomalies in the previous year, suggesting the influence of climate memory carried by regional snowmelt water. The two regions of boreal North America exhibit opposing seasonal carbon-temperature relationships with the eastern half experiencing a net carbon loss with near coincident increases in temperature and the western half showing increased net carbon uptake. The carbon response in the boreal west region lags the temperature anomalies by roughly 6months. This opposing carbon-temperature relationship in boreal North America may be a combination of different dominant vegetation types, the amount and timing of snowfall, and temperature anomaly differences across boreal North America.
TransCom model simulations of methane: Comparison of vertical profiles with aircraft measurements
Saito, R. ; Patra, P.K. ; Sweeney, C. ; Machida, T. ; Krol, M.C. ; Houweling, S. ; Bousquet, P. ; Agusti-Panareda, A. ; Belikov, D. ; Bergmann, D. ; Bian, H.S. ; Cameron-Smith, P. ; Chipperfield, M.P. ; Fortems-Cheiney, A. ; Fraser, A. ; Gatti, L.V. ; Gloor, E. ; Hess, P. ; Kawa, S.R. ; Law, R.M. ; Locatelli, R. ; Loh, Z. ; Maksyutov, S. ; Meng, L. ; Miller, J.B. ; Palmer, P.I. ; Prinn, R.G. ; Rigby, M. ; Wilson, C. - \ 2013
Journal of Geophysical Research: Atmospheres 118 (2013)9. - ISSN 2169-897X - p. 3891 - 3904.
chemical-transport model - atmospheric co2 - troposphere - stratosphere - variability - sensitivity - version - ozone - flux - air
To assess horizontal and vertical transports of methane (CH4) concentrations at different heights within the troposphere, we analyzed simulations by 12 chemistry transport models (CTMs) that participated in the TransCom-CH4 intercomparison experiment. Model results are compared with aircraft measurements at 13 sites in Amazon/Brazil, Mongolia, Pacific Ocean, Siberia/Russia, and United States during the period of 2001-2007. The simulations generally show good agreement with observations for seasonal cycles and vertical gradients. The correlation coefficients of the daily averaged model and observed CH4 time series for the analyzed years are generally larger than 0.5, and the observed seasonal cycle amplitudes are simulated well at most sites, considering the between-model variances. However, larger deviations show up below 2 km for the model-observation differences in vertical profiles at some locations, e.g., at Santarem, Brazil, and in the upper troposphere, e.g., at Surgut, Russia. Vertical gradients and concentrations are underestimated at Southern Great Planes, United States, and Santarem and overestimated at Surgut. Systematic overestimation and underestimation of vertical gradients are mainly attributed to inaccurate emission and only partly to the transport uncertainties. However, large differences in model simulations are found over the regions/seasons of strong convection, which is poorly represented in the models. Overall, the zonal and latitudinal variations in CH4 are controlled by surface emissions below 2.5 km and transport patterns in the middle and upper troposphere. We show that the models with larger vertical gradients, coupled with slower horizontal transport, exhibit greater CH4 interhemispheric gradients in the lower troposphere. These findings have significant implications for the future development of more accurate CTMs with the possibility of reducing biases in estimated surface fluxes by inverse modeling.
Impact of transport model errors on the global and regional methane emissions estimated by inverse modelling
Locatelli, R. ; Bousquet, P. ; Chevallier, F. ; Fortems-Cheney, A. ; Szopa, S. ; Saunois, M. ; Agusti-Panareda, A. ; Bergmann, D. ; Bian, H. ; Cameron-Smith, P. ; Chipperfield, M.P. ; Gloor, E. ; Houweling, S. ; Kawa, S.R. ; Krol, M.C. ; Patra, P.K. ; Prinn, R.G. ; Rigby, M. ; Saito, R. ; Wilson, C. - \ 2013
Atmospheric Chemistry and Physics 13 (2013)19. - ISSN 1680-7316 - p. 9917 - 9937.
general-circulation model - atmospheric transport - tracer transport - co2 inversions - boundary-layer - vertical profiles - data assimilation - climate-change - growth-rate - part i
A modelling experiment has been conceived to assess the impact of transport model errors on methane emissions estimated in an atmospheric inversion system. Synthetic methane observations, obtained from 10 different model outputs from the international TransCom-CH4 model inter-comparison exercise, are combined with a prior scenario of methane emissions and sinks, and integrated into the three-component PYVAR-LMDZ-SACS (PYthon VARiational-Laboratoire de Meteorologie Dynamique model with Zooming capability-Simplified Atmospheric Chemistry System) inversion system to produce 10 different methane emission estimates at the global scale for the year 2005. The same methane sinks, emissions and initial conditions have been applied to produce the 10 synthetic observation datasets. The same inversion set-up (statistical errors, prior emissions, inverse procedure) is then applied to derive flux estimates by inverse modelling. Consequently, only differences in the modelling of atmospheric transport may cause differences in the estimated fluxes. In our framework, we show that transport model errors lead to a discrepancy of 27 Tg yr(-1) at the global scale, representing 5% of total methane emissions. At continental and annual scales, transport model errors are proportionally larger than at the global scale, with errors ranging from 36 Tg yr(-1) in North America to 7 Tg yr(-1) in Boreal Eurasia (from 23 to 48 %, respectively). At the model grid-scale, the spread of inverse estimates can reach 150% of the prior flux. Therefore, transport model errors contribute significantly to overall uncertainties in emission estimates by inverse modelling, especially when small spatial scales are examined. Sensitivity tests have been carried out to estimate the impact of the measurement network and the advantage of higher horizontal resolution in transport models. The large differences found between methane flux estimates inferred in these different configurations highly question the consistency of transport model errors in current inverse systems. Future inversions should include more accurately prescribed observation covariances matrices in order to limit the impact of transport model errors on estimated methane fluxes.
Global atmospheric carbon budget: results from an ensemble of atmospheric CO2 inversions.
Peylin, P. ; Law, R.M. ; Gurney, K.R. ; Chevallier, F. ; Jacobsen, A.R. ; Maki, T. ; Niwa, Y. ; Patra, P.K. ; Peters, W. ; Rayner, P.J. ; Rödenbeck, C. ; Laan-Luijkx, I.T. van der; Zhang, X. - \ 2013
Biogeosciences 10 (2013). - ISSN 1726-4170 - p. 6699 - 6720.
interannual variability - dioxide exchange - transport model - sinks - fluxes - sensitivity - ocean - land - cycle - emissions
Atmospheric CO2 inversions estimate surface carbon fluxes from an optimal fit to atmospheric CO2 measurements, usually including prior constraints on the flux estimates. Eleven sets of carbon flux estimates are compared, generated by different inversions systems that vary in their inversions methods, choice of atmospheric data, transport model and prior information. The inversions were run for at least 5 yr in the period between 1990 and 2010. Mean fluxes for 2001-2004, seasonal cycles, interannual variability and trends are compared for the tropics and northern and southern extra-tropics, and separately for land and ocean. Some continental/basin-scale subdivisions are also considered where the atmospheric network is denser. Four-year mean fluxes are reasonably consistent across inversions at global/latitudinal scale, with a large total (land plus ocean) carbon uptake in the north (-3.4 Pg C yr(-1) (+/- 0.5 Pg C yr(-1) standard deviation), with slightly more uptake over land than over ocean), a significant although more variable source over the tropics (1.6 +/- 0.9 Pg C yr(-1)) and a compensatory sink of similar magnitude in the south (-1.4 +/- 0.5 Pg C yr(-1)) corresponding mainly to an ocean sink. Largest differences across inversions occur in the balance between tropical land sources and southern land sinks. Interannual variability (IAV) in carbon fluxes is larger for land than ocean regions (standard deviation around 1.06 versus 0.33 Pg C yr(-1) for the 1996-2007 period), with much higher consistency among the inversions for the land. While the tropical land explains most of the IAV (standard deviation similar to 0.65 Pg C yr(-1)), the northern and southern land also contribute (standard deviation similar to 0.39 Pg C yr(-1)). Most inversions tend to indicate an increase of the northern land carbon uptake from late 1990s to 2008 (around 0.1 Pg C yr(-1)), predominantly in North Asia. The mean seasonal cycle appears to be well constrained by the atmospheric data over the northern land (at the continental scale), but still highly dependent on the prior flux seasonality over the ocean. Finally we provide recommendations to interpret the regional fluxes, along with the uncertainty estimates.
Letter tot the editor: Iconic CO2 Time Series at Risk
Houweling, S. ; Badawy, B. ; Baker, D.F. ; Basu, S. ; Belikov, D. ; Bergamaschi, P. ; Bousquet, P. ; Broquet, G. ; Butler, T. ; Canadell, J.G. ; Chen, J. ; Chevallier, F. ; Ciais, P. ; Collatz, G.J. ; Denning, S. ; Engelen, R. ; Enting, I.G. ; Fischer, M.L. ; Fraser, A. ; Gerbig, C. ; Gloor, M. ; Jacobson, A.R. ; Jones, D.B.A. ; Heimann, M. ; Khalil, A. ; Kaminski, T. ; Kasibhatla, P.S. ; Krakauer, N.Y. ; Krol, M. ; Maki, T. ; Maksyutov, S. ; Manning, A. ; Meesters, A. ; Miller, J.B. ; Palmer, P.I. ; Patra, P. ; Peters, W. ; Peylin, P. ; Poussi, Z. ; Prather, M.J. ; Randerson, J.T. ; Rockmann, T. ; Rodenbeck, C. ; Sarmiento, J.L. ; Schimel, D.S. ; Scholze, M. ; Schuh, A. ; Suntharalingam, P. ; Takahashi, T. ; Turnbull, J. ; Yurganov, L. ; Vermeulen, A. - \ 2012
Science 337 (2012)6098. - ISSN 0036-8075 - p. 1038 - 1040.
TransCom model simulations of CH4 and related species: linking transport, surface flux and chemical loss with CH4 variability in the troposphere and lower stratosphere
Patra, P.K. ; Houweling, S. ; Krol, M.C. ; Bousquet, P. ; Belikov, D. - \ 2011
Atmospheric Chemistry and Physics 11 (2011)24. - ISSN 1680-7316 - p. 12813 - 12837.
general-circulation model - biomass burning emissions - atmospheric methane - growth-rate - interannual variability - methyl chloroform - tracer transport - sf6 - gases - co2
A chemistry-transport model (CTM) intercomparison experiment (TransCom-CH4) has been designed to investigate the roles of surface emissions, transport and chemical loss in simulating the global methane distribution. Model simulations were conducted using twelve models and four model variants and results were archived for the period of 1990–2007. All but one model transports were driven by reanalysis products from 3 different meteorological agencies. The transport and removal of CH4 in six different emission scenarios were simulated, with net global emissions of 513±9 and 514±14 TgCH4 yr-1 for the 1990s and 2000s, respectively. Additionally, sulfur hexafluoride (SF6) was simulated to check the interhemispheric transport, radon (222Rn) to check the subgrid scale transport, and methyl chloroform (CH3CCl3) to check the chemical removal by the tropospheric hydroxyl radical (OH). The results are compared to monthly or annual mean time series of CH4, SF6 and CH3CCl3 measurements from 8 selected background sites, and to satellite observations of CH4 in the upper troposphere and stratosphere. Most models adequately capture the vertical gradients in the stratosphere, the average long-term trends, seasonal cycles, interannual variations (IAVs) and interhemispheric (IH) gradients at the surface sites for SF6, CH3CCl3 and CH4. The vertical gradients of all tracers between the surface and the upper troposphere are consistent within the models, revealing vertical transport differences between models. An average IH exchange time of 1.39±0.18 yr is derived from SF6 time series. Sensitivity simulations suggest that the estimated trends in exchange time, over the period of 1996–2007, are caused by a change of SF6 emissions towards the tropics. Using six sets of emission scenarios, we show that the decadal average CH4 growth rate likely reached equilibrium in the early 2000s due to the flattening of anthropogenic emission growth since the late 1990s. Up to 60% of the IAVs in the observed CH4 concentrations can be explained by accounting for the IAVs in emissions, from biomass burning and wetlands, as well as meteorology in the forward models. The modeled CH4 budget is shown to depend strongly on the troposphere-stratosphere exchange rate and thus on the model’s vertical grid structure and circulation in the lower stratosphere. The 15-model median CH4 and CH3CCl3 atmospheric lifetimes are estimated to be 9.99±0.08 and 4.61±0.13 yr, respectively, with little IAV due to transport and temperature.
TransCom model simulations of hourly atmospheric CO2: Analysis of synoptic-scale variations for the period 2002-2003
Patra, P.K. ; Law, R.M. ; Peters, W. ; Krol, M.C. - \ 2008
Global Biogeochemical Cycles 22 (2008). - ISSN 0886-6236 - 16
klimaatverandering - kooldioxide - emissie - simulatiemodellen - climatic change - carbon dioxide - emission - simulation models - carbon-dioxide - transport models - tall tower - inversions - sinks - variability - delta-c-13 - europe - trends - cycle
The ability to reliably estimate CO2 fluxes from current in situ atmospheric CO2 measurements and future satellite CO2 measurements is dependent on transport model performance at synoptic and shorter timescales. The TransCom continuous experiment was designed to evaluate the performance of forward transport model simulations at hourly, daily, and synoptic timescales, and we focus on the latter two in this paper. Twenty-five transport models or model variants submitted hourly time series of nine predetermined tracers (seven for CO2) at 280 locations. We extracted synoptic-scale variability from daily averaged CO2 time series using a digital filter and analyzed the results by comparing them to atmospheric measurements at 35 locations. The correlations between modeled and observed synoptic CO2 variabilities were almost always largest with zero time lag and statistically significant for most models and most locations. Generally, the model results using diurnally varying land fluxes were closer to the observations compared to those obtained using monthly mean or daily average fluxes, and winter was often better simulated than summer. Model results at higher spatial resolution compared better with observations, mostly because these models were able to sample closer to the measurement site location. The amplitude and correlation of model-data variability is strongly model and season dependent. Overall similarity in modeled synoptic CO2 variability suggests that the first-order transport mechanisms are fairly well parameterized in the models, and no clear distinction was found between the meteorological analyses in capturing the synoptic-scale dynamics.
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