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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Turbulent exchange of energy, momentum, and reactive gases between high vegetation and the atmospheric boundary layer
Shapkalijevski, M.M. - \ 2017
Wageningen University. Promotor(en): Maarten Krol; Jordi Vila-Guerau de Arellano, co-promotor(en): Arnold Moene; H.G. Ouwersloot. - Wageningen : Wageningen University - ISBN 9789463430845 - 163
vegetation - atmospheric boundary-layer - atmosphere - energy exchange - gases - canopy - meteorology - vegetatie - atmosferische grenslaag - atmosfeer - energie-uitwisseling - gassen - kroondak - meteorologie

This thesis deals with the representation of the exchange of energy, momentum and chemically reactive compounds between the land, covered by high vegetation, and the lowest part of the atmosphere, named as atmospheric boundary layer (ABL).

The study presented in this thesis introduces the roughness sublayer (RSL), the layer just above the tall vegetation canopy in which the atmospheric flow is directly affected by the presence of roughness elements, as an important part of the ABL system. Our focus is on the exchange of the thermodynamic, as well as the chemical properties of the boundary layer. Our methodology combines observational analysis using high resolution meteorological and chemistry measurements from the Canopy Horizontal Array Turbulence Study (CHATS) and modelling framework of the soil-vegetation-atmospheric boundary layer system. The systematic investigation in this thesis showed the relevance of the RSL for the turbulent exchange processes between the atmosphere and the land surface characterized by high vegetation. More specifically, we explained and discussed how the turbulence parameterization within the roughness sublayer is strongly dependent on canopy-phenology (canopy leaf state) and atmospheric-stability changes, and provided parameterization formulations for . Our modelling analysis further showed that the CHATS boundary-layer dynamics are mainly affected and controlled by the large-scale processes (advection and subsidence), while the effect of the canopy and the roughness sublayer were relatively small. Near the canopy top however, the the canopy had a significant impact on the modelled boundary layer state variables (wind speed, potential temperature and specific humidity) and the corresponding turbulent transfer coefficients (drag coefficients for momentum and scalars), as supported by the observations. With respect to the exchange of reactive compounds, we diagnosed twice-larger magnitude of the ozone deposition fluxes when the roughness sublayer effects are taken into account in the flux-gradient relationship, compared to the method which neglects these effects. Thus, neglecting the roughness sublayer effects in the surface flux parameterization schemes of ozone in atmosphere-chemistry models can lead to significant overestimation of the ozone diurnal mixing ratio in the boundary layer.

By studying the high vegetation-atmosphere exchange processes, their quantification, and testing methods for their parameterization, we contribute to improve our understanding and representation of the roughness sublayer-atmospheric boundary-layer system.

Dynamic photosynthesis under a fluctuating environment: a modelling-based analysis
Morales Sierra, Alejandro - \ 2017
Wageningen University. Promotor(en): Paul Struik; Jaap Molenaar, co-promotor(en): Xinyou Yin; Jeremy Harbinson. - Wageningen : Wageningen University - ISBN 9789463430456 - 282
photosynthesis - modeling - analysis - environmental factors - light - canopy - leaves - crop physiology - metabolism - fotosynthese - modelleren - analyse - milieufactoren - licht - kroondak - bladeren - gewasfysiologie - metabolisme

In their natural environment, leaves are exposed to rapid fluctuations of irradiance. Research on CO2 assimilation under fluctuating irradiance often relies on measurements of gas exchange during transients where irradiance is rapidly increased or decreased, after the leaf has adapted to a particular set of environmental conditions. In the field, such increases and decreases occur mostly because of sunflecks (rapid increases in irradiance on a low irradiance background) created by gaps in the canopy and plant movement by wind, and cloudflecks (rapid decreases in irradiance on a high irradiance background) generated by clouds that transiently block the sun.

In this dissertation, the metabolic regulation of photosynthesis and how this may limit dynamic CO2 assimilation is studied in silico with the development and application of simulation models. In order to support the development of the models, a review of the literature was performed as well as an experiment designed to generate data on dynamic CO2 assimilation for different photosynthetic mutants of Arabidopsis thaliana. In addition to providing these models to the research community, this dissertation also identifies multiple targets that may be used for improving dynamic CO2 assimilation in plants. It further demonstrates that the dynamic responses of CO2 assimilation to changes in irradiance has a significant effect on canopy CO2 assimilation, even for dense canopies exposed to open skies, resembling the conditions of commercial crops.

In Chapter 1, the context of this dissertation is presented. The societal relevance of this research is argued, making reference to the role that photosynthesis could play in addressing global problems such as food and energy security. The necessary background on the physiology of photosynthesis is provided, with special emphasis on the terminology and concepts required to understand the rest of the dissertation, with the aim of making the contents more accessible to a wider audience. Then, prior literature on the specific topics of this dissertation (i.e., photosynthesis in a dynamic environment and its mathematical modelling) is presented, with a chronological approach that analyses the evolution of ideas and methodologies up to the present.

In Chapter 2, the current literature on dynamic CO2 assimilation is reviewed, with an emphasis on the effects of environmental conditions ([CO2], temperature, and air humidity) on the rates of photosynthetic induction and loss of induction. This review reveals major knowledge gaps, especially on the loss of induction. The little data available indicates that rates of photosynthetic induction increase with [CO2], which could be explained by a weak effect on Rubisco activation and a strong effect on stomatal opening. Increases in temperature also increase the rates of photosynthetic induction, up to an optimum, beyond which a strong negative effect can be observed, which could be attributed to deactivation of Rubisco activase.

In Chapter 3, an experiment is presented that makes use of several photosynthetic mutants of A. thaliana. Downregulating non-photochemical quenching and sucrose synthesis did not have any significant effect on dynamic CO2 assimilation, whereas CO2 diffusion and Rubisco activation exerted stronger limitations. Further analysis reveals that whether stomatal opening limits CO2 assimilation after an increase in irradiance depends on the stomatal conductance prior to the change in irradiance. A threshold value of 0.12 mol m−2 s−1 (defined for fluxes of water vapour) could be defined, above which stomata did not affect the rates of photosynthetic induction. The comparison of measurements across irradiance levels also indicated that the apparent rate constant of Rubisco activation is irradiance-dependent, at least for irradiance levels below 150 μmol m−2 s−1.

In Chapter 4, a phenomenological model of leaf-level CO2 assimilation is presented. The model is described in detail and all the parameters are first estimated with published data, and later refined by fitting the model to the data from Chapter 3. Additional data from the experiment in Chapter 3 is used to validate predictions of CO2 assimilation under lightflecks for the different photosynthetic mutants. The model predicts accurately dynamic CO2 assimilation for the different photosynthetic mutants by only modifying those parameters that are affected by the mutation. This demonstrates that the model has a high predictive power and that the equations, although phenomenological in nature, have a solid physiological basis.

The model is further used to analyse, in silico, the limitations imposed by different photosynthetic processes on dynamic CO2 assimilation at the leaf and canopy level, allowing a more in depth analysis than in Chapter 3. The analysis demonstrates that results obtained at the leaf level should not be extrapolated directly to the canopy level, as the spatial and temporal distribution of irradiance within a canopy is more complex than what is achieved in experimental protocols. Both at the leaf and canopy level, CO2 diffusion is strongly limiting, followed by photoinhibition, chloroplast movements and Rubisco activation.

In Chapter 5, a mechanistic model of the dynamic, metabolic regulation of the electron transport chain is presented. The model is described in detail and all the parameters are estimated from published literature, using measurements on A. thaliana when available. Predictions of the model are tested with steady-state and dynamic measurements of gas exchange, chlorophyll fluorescence and absorbance spectroscopy on A. thaliana, with success.

The analysis in silico indicates that a significant amount of alternative electron transport is required to couple ATP and NADPH production and demand, and most of it is associated with nitrogen assimilation and export of redox power through the malate shuttle. The analysis also reveals that the relationship between ATP synthesis and the proton motive force is highly regulated by the concentrations of substrates (ADP, ATP and inorganic phosphate), and this regulation facilitates an increase in non-photochemical quenching under conditions of low metabolic activity in the stroma.

In Chapter 6, the findings of Chapters 2–5 are summarised and employed to answer in detail the four research questions formulated in Chapter 1. Of great interest is the identification of six potential targets that may be used to improve dynamic CO2 assimilation. These targets are: (i) regulation of Rubisco activity through changes in the amount or regulation of Rubisco activase, (ii) acceleration of stomatal opening and closure, (iii) a lower /ATP for ATP synthesis, (iv) faster relaxation of non-photochemical quenching, (v) reduced chloroplast movements, and (vi) reduced photoinhibition by increased rates of repair of Photosystem II.

Boomkronen afleiden uit het Actueel Hoogtebestand Nederland : kwaliteitsaspecten rondom het geautomatiseerd in kaart brengen van bomen op basis van het AHN2-bestand
Meijer, M. ; Rip, Frans ; Benthem, R. van; Clement, J. ; Sande, C. van der - \ 2015
Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2671) - 85
bomen - kroondak - kroon - gegevensanalyse - gegevens verzamelen - methodologie - remote sensing - hoogteligging - cartografie - nederland - trees - canopy - crown - data analysis - data collection - methodology - altitude - mapping - netherlands
Alom wordt erkend dat bomen belangrijk zijn. Zowel voor de mens, de natuur als het klimaat. Recentelijk is een procedure ontwikkeld om op basis van het nationale Nederlandse hoogtebestand AHN2 een bestand te genereren met alle boomkronen in Nederland, genaamd ‘CP’. Een dergelijk bestand kan onder andere het groenbeheer van de gemeenten in Nederland vereenvoudigen en helpen bij het inventariseren van landschapselementen. De vraag is echter: hoe goed is dit bestand? In dit rapport wordt voor een drietal verschillende gebieden onderzocht wat de kwaliteit is van CP. Verder wordt mede op basis van de ervaringen die tijdens het kwaliteitsonderzoek zijn gedaan een standaard kwaliteitsraamwerk opgezet voor het controleren van nieuwe versies van het boomkronenbestand. Daarnaast is dit document er ook op gericht om de potentiële gebruiker een beter beeld van de kwaliteit te geven.
Spatial boundary of urban ‘acid islands’ in China
Du, E. ; Vries, W. de; Liu, X. ; Fang, J. ; Galloway, J.N. ; Jiang, Y. - \ 2015
Scientific Reports 5 (2015). - ISSN 2045-2322 - 9 p.
atmospheric deposition - nitrogen deposition - air-pollution - soil acidification - emissions - canopy - forest - rain - ecosystems - cities
Elevated emissions of sulfur dioxide, nitrogen oxides and ammonia in China have resulted in high levels of sulfur and nitrogen deposition, being contributors to soil acidification, especially in and near large cities. However, knowledge gaps still exist in the way that large cities shape spatial patterns of acid deposition. Here, we assessed the patterns of pH, sulfate, nitrate and ammonium in bulk precipitation and throughfall in southern China’s forests by synthesizing data from published literature. Concentrations and fluxes of sulfate, nitrate and ammonium in bulk precipitation and throughfall exhibited a power-law increase with a closer distance to the nearest large cities, and accordingly pH showed a logarithmic decline. Our findings indicate the occurrence of urban ‘acid islands’ with a critical radius of approximately 70¿km in southern China, receiving potential acid loads of more than 2 keq ha-1 yr-1. These urban acid islands covered an area of 0.70¿million km2, accounting for nearly 30% of the land area in southern China. Despite a significant capacity to neutralize acids in precipitation, our analysis highlights a substantial contribution of ammonium to potential acid load. Our results suggest a joint control on emissions of multiple acid precursors from urban areas in southern China
What drives the vital rates of secondary hemiepiphytes? A first assessment for three species of Heteropsis (Araceae) in the Colombian Amazon
Balcázar-Vargas, M.P. ; Andel, T.R. van; Westers, P. ; Zuidema, P. - \ 2015
Journal of Tropical Ecology 31 (2015)3. - ISSN 0266-4674 - p. 251 - 265.
neotropical rain-forest - liana machaerium-cuspidatum - eastern brazilian amazon - life-history diversity - physical damage - montane forest - national-park - growth - canopy - size
Secondary hemiepiphytes rely on other plants (hosts) to grow vertically. After germinating on the forest floor, their seedlings search a host to ascend. We recorded information on survival, growth, reproduction and vegetative propagation of three Heteropsis species, to evaluate what drives their vital rates. We measured 700 individuals of each study species between 2007 and 2009 in the southern Colombian Amazon. A gradual increase in stem length, leaf size, number of roots and plagiotropic branches was found with increasing height of Heteropsis individuals on their hosts. Survival of leafless non-climbing seedlings was very low (28% annually); increasing substantially (84–94%) once the seedling had ascended a host. The three Heteropsis species presented slow height growth rates (c. 2–8 cm y-1) with large variation, while a substantial percentage of the stems (31–62%) did not grow or dried out. Vegetative propagation in Heteropsis may act as a dispersion-propagation strategy to find a suitable host and reach the canopy again after falling. The slow growth rates suggest that Heteropsis individuals that have reached the canopy are rather old. Once plants have reached the tree crowns, their longevity is largely determined by the survival of the host tree.
Estimation of Aerodynamic Roughness Length over Oasis in the Heihe River Basin by Utilizing Remote Sensing and Ground Data
Chen, Q. ; Jia, L. ; Hutjes, R.W.A. ; Menenti, M. - \ 2015
Remote Sensing 7 (2015)4. - ISSN 2072-4292 - p. 3690 - 3709.
laser altimeter measurements - time-series analysis - leaf-area index - surface-roughness - vegetation - parameters - canopy - forest - lidar - displacement
Most land surface models require information on aerodynamic roughness length and its temporal and spatial variability. This research presents a practical approach for determining the aerodynamic roughness length at fine temporal and spatial resolution over the landscape by combining remote sensing and ground measurements. The basic framework of Raupach, with the bulk surface parameters redefined by Jasinski et al., has been applied to optical remote sensing data collected by the HJ-1A/1B satellites. In addition, a method for estimating vegetation height was introduced to derive the aerodynamic roughness length, which is preferred by users over the height-normalized form. Finally, mapping different vegetation classes was validated taking advantage of the data-dense field experiments conducted in the Heihe Watershed Allied Telemetry Experimental Research (HiWATER) project. Overall, the roughness model performed well against the measurements collected at most HiWATER flux tower sites. However, deviations still occurred at some sites, which have been further analyzed.
An Improved Method For Retrieving Land Surface Albedo Over Rugged Terrain
Gao, B. ; Jia, L. ; Menenti, M. - \ 2014
IEEE Geoscience and Remote Sensing Letters 11 (2014)2. - ISSN 1545-598X - p. 554 - 558.
digital elevation data - bidirectional reflectance - canopy - models
Land surface albedo is a very important parameter, which can be derived from a bidirectional reflectance distribution function (BRDF) model with angular integration of BRDF in a particular distribution of downward solar irradiance. The Algorithm for MODIS Bidirectional Reflectance Anisotropic of Land Surface (AMBRALS) utilizes a kernel-driven BRDF model to retrieve land surface albedo, but it does not take into account the topographic effect. This letter proposed an improved method by adding topographic factor to the AMBRALS, which removes the topographic effect on land surface reflectance and considers the topographic effect in retrieving land surface albedo. This method is applied to the HJ-1A/B CCD land surface reflectance data to retrieve the land surface albedo. The results are compared with those from the AMBRALS and with the ground measurements. The comparison results show that the proposed method performs well in general and better than the AMBRALS over rugged area.
On the relation between tree crown morphology and particulate matter deposition on urban tree leaves: a ground-based LiDAR approach
Hofman, J. ; Bartholomeus, H. ; Calders, K. ; Wittenberghe, S. van; Wuyts, K. ; Samson, R. - \ 2014
Atmospheric Environment 99 (2014). - ISSN 1352-2310 - p. 130 - 139.
air-quality - marquardt algorithm - magnetic-properties - leaf surfaces - street canyon - pollution - particles - canopy - accumulation - vegetation
Urban dwellers often breathe air that does not meet the European and WHO standards. Next to legislative initiatives to lower atmospheric pollutants, much research has been conducted on the potential of urban trees as mitigation tool for atmospheric particles. While leaf-deposited dust has shown to vary significantly throughout single tree crowns, this study evaluated the influence of micro-scale tree crown morphology (leaf density) on the amount of leaf-deposited dust. Using a ground-based LiDAR approach, the three-dimensional tree crown morphology was obtained and compared to gravimetric measurements of leaf-deposited dust within three different size fractions (>10, 3–10 and 0.2–3 µm). To our knowledge, this is the first application of ground-based LiDAR for comparison with gravimetric results of leaf-deposited particulate matter. Overall, an increasing leaf density appears to reduce leaf-deposition of atmospheric particles. This might be explained by a reduced wind velocity, suppressing turbulent deposition of atmospheric particles through impaction. Nevertheless, the effect of tree crown morphology on particulate deposition appears almost negligible (7% AIC decrease) compared to the influence of physical factors like height, azimuth and tree position.
Implications of sensor configuration and topography on vertical plant profiles derived from terrestrial LiDAR
Calders, K. ; Armston, J. ; Newnham, G. ; Herold, M. ; Goodwin, N. - \ 2014
Agricultural and Forest Meteorology 194 (2014). - ISSN 0168-1923 - p. 104 - 117.
ground-based lidar - pulsed-laser systems - wave-form lidar - tropical forests - deciduous forest - leaf-area - canopy - airborne - heterogeneity - environments
The vertical distribution of plant constituents is a key parameter to describe vegetation structure and influences several processes, such as radiation interception, growth and habitat. Terrestrial laser scanning (TLS), also referred to as terrestrial LiDAR, has the potential to measure the canopy structure with high spatial detail and accuracy. Vertical plant profiles, which describe the plant area per unit volume (PAVD) as a function of height, are often used to quantify the vertical structure. However, most studies do not account for topography, use registered multiple TLS scans or use a detailed airborne LiDAR digital terrain model to account for this variation in ground height. Airborne LiDAR is often not available or expensive to acquire. Here, we present an approach that facilitates rapid, robust and automated assessment of the vertical structure of vegetation. We use single scans and local plane fitting to correct for topographic effects in vertical plant profiles and test our approach in five different Australian forest types with different topography and understorey. We validate our approach with topography-corrected vertical plant profiles with digital terrain models derived from airborne LiDAR. Our results demonstrate that not correcting for topography can lead to significant errors in the vertical distribution of plant constituents (CV(RMSE) up to 66.2%, typically ranging from 4.2% to 13.8%). This error decreases significantly when topography is accounted for with TLS plane fitting (CV(RMSE) up to 20.6%, typically ranging from 1.5% to 12.6%). We demonstrate that height metrics from vertical plant profiles that are not corrected for topography depart significantly from those that are inferred from the reference profile. The effect is most noticeable for canopy top height and the peak PAVD height. Correcting topography with a TLS plane fitting approach reduces the error in canopy top height by at least 77% and up to 100%, and reduces the error in peak PAVD height by 83.3% and up to 100%. We also show the advantage of a multiple return over a first return TLS instrument. The definition of the ground returns with a first return instrument might be problematic in environments with dense herbaceous understorey and there is an overall trend of lower height metrics compared to multiple return instruments. We present a data-driven approach that is based on single scan TLS data. The latter is of importance for large area sampling as it allows more sites to be sampled from existing resources and facilitate consistent processing of archived TLS data, which is often single scan data with no survey control.
Crown depth as a result of evolutionary games: decreasing solar angle should lead to shallower, not deeper crowns
Vermeulen, P.J. - \ 2014
New Phytologist 202 (2014)4. - ISSN 0028-646X - p. 1249 - 1256.
nitrogen-use efficiency - carbon allocation - adaptive significance - plant monocultures - light interception - height growth - fagus-crenata - tree height - rain-forest - canopy
There is a general notion in the literature that, with increasing latitude, trees have deeper crowns as a result of a lower solar elevation angle. However, these predictions are based on models that did not include the effects of competition for light between individuals. Here, I argue that there should be selection for trees to increase the height of the crown base, as this decreases shading by neighbouring trees, leading to an evolutionarily stable strategy (ESS). Because the level of between-tree shading increases with decreasing solar angle, the predicted ESS will shift to higher crown base height. This argument is supported by a simulation model to check for the effects of crown shape and the change of light intensity that occurs with changing solar angle on model outcomes. So, the lower solar angle at higher latitudes would tend to select for shallower, and not deeper, crowns. This casts doubt on the common belief that a decreasing solar angle increases crown depth. More importantly, it shows that different assumptions about what should be optimized can lead to different predictions, not just for absolute trait values, but for the direction of selection itself.
Conservation in a crowded place : forest and people on Mount Elgon Uganda
Sassen, M. - \ 2014
Wageningen University. Promotor(en): Ken Giller, co-promotor(en): D. Sheil. - Wageningen : Wageningen University - ISBN 9789461737847 - 200
bossen - landbouw - brandhout - houtsoorten - natuurbescherming - natuurbeheer - kroondak - verstoorde bossen - biomassa - biodiversiteit - oost-afrika - uganda - forests - agriculture - fuelwood - timbers - nature conservation - nature management - canopy - disturbed forests - biomass - biodiversity - east africa

Key words: tropical forest, conservation management, local livelihoods, forest cover change, disturbance, fuelwood, forest structure, species richness, biomass, Mount Elgon

A growing world population has important consequences for forests. In this study I investigate how conflicting goals by different actors under different historical contexts impacted the protected area of Mt Elgon, Uganda, and I consider what this means for conservation. Mt Elgon is an important water catchment area for Uganda and Kenya with important biodiversity values. The forest on Mt Elgon is also a source of agricultural land, timber, fuel wood and other forest resources for local communities. In this study I explore the factors that influenced local people’s motivations for forest clearing, the impacts of local forest use, including as a source of fuelwood, on Mt Elgon, Uganda. I also evaluate the use of radar satellite data to estimate above ground biomass on Mt Elgon. Finally I discuss the implications for the design of interventions that seek to reconcile the needs of local people and forest conservation.

A major wave of deforestation on Mt Elgon, Uganda took place in the 1970s and 1980s and by 2009, 25% of the forest on Mt Elgon was lost. However, locally, there were areas of recovery. This study demonstrated that agricultural expansion on Mt Elgon cannot simply be linked to individual drivers such as population or high crop prices, and these were not always associated with increased deforestation. By analysing local variations, I found that it is the context (institutional, social, political) under which drivers such as population, wealth or commodity prices operate, rather than the drivers per se, that influences outcomes for forest cover.

I found that local forest uses strongly influenced forest structure, even where people had a collaborative management agreement with the park authorities. The type of resources collected varied with the land use systems around the park: small stem-harvesting affected regeneration in areas where people grew crops that require supports such as bananas and climbing beans, and seedlings were almost absent where in-forest cattle grazing was important. Studying the characteristics and impacts of fuelwood harvesting revealed high levels of fuelwood collection and depletion of dead wood on the edge of the park. Human impacts affected highly preferred and used tree species. Allowing the collection of fuelwood or other non-timber products creates opportunities for more destructive activities such as timber harvesting or charcoal making. On the other hand it helps to improve relations between local people and park staff, which this study showed helps limit agricultural encroachment. I also found indications that trees on people’s own land can provide alternative sources of fuel.

Mt Elgon has a history of conservation and development projects in an attempt to better reconcile local livelihood improvement and forest conservation. The most recent include pilot REDD+ schemes both inside and outside the protected area. Such schemes need consistent biomass estimations. I used a cost-effective field method for direct basal area estimation that yielded consistent estimates of above ground biomass (AGB), which reached above 800Mg/ ha on Mt Elgon’s northern slopes. Radar (ALOS PALSAR) data produced realistic classifications of the different vegetation types. However, using radar backscatter values in combination with field estimated AGB data to produce a biomass map had limited success. This was likely linked to the sampling strategy and topography.

Our study showed that simple theoretical models based on single drivers of deforestation cannot explain local variation, nor can simple models that lead to “simplified institutional prescriptions” lead to sustainable solutions, as they do not reflect complex local social and ecological realities. This has important implications for the design of more locally adapted and ecologically and socially sustainable management arrangements on Mt Elgon and elsewhere. These are necessary because current practices appear to lead to forest degradation and resource depletion. Building trust between stakeholders and developing alternative resources are vital to support more sustainable forest management. Both international conservation actors, as well as forest management authorities need to recognise that incentives that influence people’s motivation for action vary locally and can therefore not be designed globally.

Bayesian object-based estimation of LAI and chlorophyll from a simulated Sentinel-2 top-of-atmosphere radiance image
Laurent, V.C.E. ; Schaepman, M.E. ; Verhoef, W. ; Weyermann, J. ; Chavez Oyanadel, R.O. - \ 2014
Remote Sensing of Environment 140 (2014). - ISSN 0034-4257 - p. 318 - 329.
radiative-transfer models - high-spatial-resolution - remote-sensing data - red-edge bands - reflectance model - global products - leaf-area - inversion - canopy - vegetation
Leaf area index (LAI) and chlorophyll content (Cab) are important vegetation variables which can be monitored using remote sensing (RS). Physically-based approaches have higher transferability and are therefore better suited than empirically-based approaches for estimating LAI and Cab at global scales. These approaches, however, require the inversion of radiative transfer (RT) models, which is an ill-posed and underdetermined problem. Four regularization methods have been proposed, allowing finding stable solutions: 1) model coupling, 2) using a priori information (e.g. Bayesian approaches), 3) spatial constraints (e.g. using objects), and 4) temporal constraints. For mono-temporal data, only the first three methods can be applied. In an earlier study, we presented a Bayesian object-based algorithm for inverting the SLC-MODTRAN4 coupled canopy-atmosphere RT model, and compared it with a Bayesian LUT inversion. The results showed that the object-based approach provided more accurate LAI estimates. This study, however, heavily relied on expert knowledge about the objects and vegetation classes. Therefore, in this new contribution, we investigated the applicability of the Bayesian object-based inversion of the SLC-MODTRAN4 model to a situation where no such knowledge was available. The case study used a 16 × 22 km2 simulated top-of-atmosphere image of the upcoming Sentinel-2 sensor, covering the area near the city of Zurich, Switzerland. Seven APEX radiance images were nadir-normalized using the parametric Li–Ross model, spectrally and spatially resampled to Sentinel-2 specifications, geometrically corrected, and mosaicked. The atmospheric effects between APEX flight height and top-of-atmosphere level were added based on two MODTRAN4 simulations. The vegetation objects were identified and delineated using a segmentation algorithm, and classified in four levels of brightness in the visible domain. The LAI and Cab maps obtained from the Bayesian object-based inversion of the coupled SLC-MODTRAN4 model presented realistic spatial patterns. The impact of the parametric Li–Ross nadir-normalization was evaluated by comparing 1) the angular signatures of the SLC-MODTRAN4 and Li–Ross models, and 2) the LAI and Cab maps obtained from a Li–Ross nadir-normalized image (using nadir viewing geometry) and from the original image (using the original viewing geometry). The differences in angular signatures were small but systematic, and the differences between the LAI and Cab maps increased from the center towards the edges of the across-track direction. The results of this study contribute to preparing the RS community for the arrival of Sentinel-2 data in the near future, and generalize the applicability of the Bayesian object-based approach for estimating vegetation variables to cases where no field data are available.
Dynamics of nitrogen oxides and ozone above and within a mixed hardwood forest in Northern Michigan
Seok, B. ; Helmig, D. ; Ganzeveld, L.N. ; Williams, W. ; vogel, C.S. - \ 2013
Atmospheric Chemistry and Physics 13 (2013). - ISSN 1680-7316 - p. 7301 - 7320.
reactive oxidized nitrogen - volatile organic-compounds - nitric-acid photolysis - biogenic nox emissions - gas-phase chemistry - dry deposition - atmospheric chemistry - tropospheric ozone - global-model - canopy
The dynamic behavior of nitrogen oxides (NOx=NO+NO2) and ozone (O3) above and within the canopy at the University of Michigan Biological Station AmeriFlux (UMBS Flux) site was investigated by continuous multi-height vertical gradient measurements during the summer and the fall of 2008. A daily maximum in nitric oxide (NO) mixing ratios was consistently observed during the morning hours between 06:00 and 09:00 EST above the canopy. Daily NO maxima ranged between 0.1 and 2 ppbv (with a median of 0.3 ppbv), which were 2 to 20 times above the atmospheric background. The sources and causes of the morning NO maximum were evaluated using NOx and O3 measurements and synoptic and micrometeorological data. Numerical simulations with a multi-layer canopy-exchange model were done to further support this analysis. The observations indicated that the morning NO maximum was caused by the photolysis of NO2 from non-local air masses, which were transported into the canopy from aloft during the morning breakup of the nocturnal boundary layer. The analysis of simulated process tendencies indicated that the downward turbulent transport of NOx into the canopy compensates for the removal of NOx through chemistry and dry deposition. The sensitivity of NOx and O3 concentrations to soil and foliage NOx emissions was also assessed with the model. Uncertainties associated with the emissions of NOx from the soil or from leaf-surface nitrate photolysis did not explain the observed diurnal behavior in NOx (and O3) and, in particular, the morning peak in NOx mixing ratios. However, a 30% increase in early morning NOx and NO peak mixing ratios was simulated when a foliage exchange NO2 compensation point was considered. This increase suggests the potential importance of leaf-level, bidirectional exchange of NO2 in understanding the observed temporal variability in NOx at UMBS.
Towards a climate-dependent paradigm of ammonia emission and deposition
Sutton, M.A. ; Reis, S. ; Riddick, S.N. ; Dragosits, U. ; Nemitz, E. ; Theobald, M.R. ; Tang, Y.S. ; Vries, W. de - \ 2013
Philosophical Transactions of the Royal Society B. Biological sciences 368 (2013)1621. - ISSN 0962-8436 - 13 p.
plant-atmosphere exchange - gas-particle interactions - compensation point - managed grassland - dutch heathland - model - volatilization - nitrogen - canopy - soil
Existing descriptions of bi-directional ammonia (NH3) land–atmosphere exchange incorporate temperature and moisture controls, and are beginning to be used in regional chemical transport models. However, such models have typically applied simpler emission factors to upscale the main NH3 emission terms. While this approach has successfully simulated the main spatial patterns on local to global scales, it fails to address the environment- and climate-dependence of emissions. To handle these issues, we outline the basis for a new modelling paradigm where both NH3 emissions and deposition are calculated online according to diurnal, seasonal and spatial differences in meteorology. We show how measurements reveal a strong, but complex pattern of climatic dependence, which is increasingly being characterized using ground-based NH3 monitoring and satellite observations, while advances in process-based modelling are illustrated for agricultural and natural sources, including a global application for seabird colonies. A future architecture for NH3 emission–deposition modelling is proposed that integrates the spatio-temporal interactions, and provides the necessary foundation to assess the consequences of climate change. Based on available measurements, a first empirical estimate suggests that 58C warming would increase emissions by 42 per cent (28–67%). Together with increased anthropogenic activity, global NH3 emissions may increase from 65 (45–85) Tg N in 2008 to reach 132 (89–179) Tg by 2100.
Assessing water stress of desert Tamarugo trees using in situ data and very high spatial resolution remote sensing
Chávez Oyanadel, R.O. ; Clevers, J.G.P.W. ; Herold, M. ; Acevedo, E. ; Ortiz, M. - \ 2013
Remote Sensing 5 (2013)10. - ISSN 2072-4292 - p. 5064 - 5088.
oriented image-analysis - northern chile - red edge - chlorophyll concentration - canopy - plants - soil - reflectance - vegetation - photoinhibition
The hyper-arid Atacama Desert is one of the most extreme environments for life and only few species have evolved to survive its aridness. One such species is the tree Prosopis tamarugo Phil. Because Tamarugo completely depends on groundwater, it is being threatened by the high water demand from the Chilean mining industry and the human consumption. In this paper, we identified the most important biophysical variables to assess the water status of Tamarugo trees and tested the potential of WorldView2 satellite images to retrieve these variables. We propose green canopy fraction (GCF) and green drip line leaf area index (DLLAIgreen) as best variables and a value of 0.25 GCF as a critical threshold for Tamarugo survival. Using the WorldView2 spectral bands and an object-based image analysis, we showed that the NDVI and the Red-edge Chlorophyll Index (CIRed-edge) have good potential to retrieve GCF and DLLAIgreen. The NDVI performed best for DLLAIgreen (RMSE = 0.4) while the CIRed-edge was best for GCF (RMSE = 0.1). However, both indices were affected by Tamarugo leaf movements (leaves avoid facing direct solar radiation at the hottest time of the day). Thus, monitoring systems based on these indices should consider the time of the day and the season of the year at which the satellite images are acquired.
A Bayesian object-based approach for estimating vegetation biophysical and biochemical variables from APEX at-sensor radiance data
Laurent, V.C.E. ; Verhoef, W. ; Damm, A. ; Schaepman, M.E. ; Clevers, J.G.P.W. - \ 2013
Remote Sensing of Environment 139 (2013). - ISSN 0034-4257 - p. 6 - 17.
radiative-transfer models - leaf-area index - sun-induced fluorescence - remote-sensing data - reflectance data - global products - brdf model - inversion - canopy - lai
Vegetation variables such as leaf area index (LAI) and leaf chlorophyll content (Cab) are important inputs for vegetation growth models. LAI and Cab can be estimated from remote sensing data using either empirical or physically-based approaches. The latter are more generally applicable because they can easily be adapted to different sensors, acquisition geometries, and vegetation types. They estimate vegetation variables through inversion of radiative transfer models. Such inversions are ill-posed but can be regularized by coupling models, by using a priori information, and spatial and/or temporal constraints. Striving to improve the accuracy of LAI and Cab estimates from single remote sensing images, this contribution proposes a Bayesian object-based approach to invert at-sensor radiance data, combining the strengths of regularization by model coupling, as well as using a priori data and object-level spatial constraints. The approach was applied to a study area consisting of homogeneous agricultural fields, which were used as objects for applying the spatial constraints. LAI and Cab were estimated from at-sensor radiance data of the Airborne Prism EXperiment (APEX) imaging spectrometer by inverting the coupled SLC-MODTRAN4 canopy-atmosphere model. The estimation was implemented in two steps. In the first step, up to six variables were estimated for each object using a Bayesian optimization algorithm. In the second step, a look-up-table (WT) was built for each object with only LAI and Cab as free variables, constraining the values of all other variables to the values obtained in the first step. The results indicated that the Bayesian object-based approach estimated LAI more accurately (R-2 = 0.45 and RMSE = 1.0) than a LUT with a Bayesian cost function (LUT-BCF) approach (R-2 = 022 and RMSE = 2.1), and Cab with a smaller absolute bias (-9 versus -23 mu g/cm(2)). The results of this study are an important contribution to further improve the regularization of ill-posed RT model inversions. The proposed approach allows reducing uncertainties of estimated vegetation variables, which is essential to support various environmental applications. The definition of objects and a priori data in cases where less extensive ground data are available, as well as the definition of the observation covariance matrix, are critical issues which require further research. (C) 2013 Elsevier Inc All rights reserved.
Runoff and Sediment load of the Yan River, China: changes over the last 60 yr
Wang, F. ; Mu, X. ; Hessel, R. ; Zhang, W. ; Ritsema, C.J. ; Li, R. - \ 2013
Hydrology and Earth System Sciences 17 (2013). - ISSN 1027-5606 - p. 2515 - 2527.
lower yellow-river - loess plateau - agricultural catchment - impacts - interception - rainfall - dynamics - erosion - canopy - trends
Runoff and sediment load changes are affected by climate change and human activities in an integrated way. Historical insight into these effects can not only improve the knowledge of river processes, but also promote more effective land and water management. In this study, we looked at runoff and sediment change in the Yan River basin, Loess Plateau, China, using data sets on land use and land cover (LUC), monthly data of precipitation and temperature, and observed data on runoff and sediment load from 1952 to 2010 at the Ganguyi Hydrologic Station. Available data on soil and water conservation structures and their effect were also studied. Five main findings emerged from the data analysis. (1) The annual runoff and sediment load varied greatly during the last 60 yr, and both had coefficients of variation that were much larger than those of precipitation and temperature. (2) Annual runoff and sediment load both showed a significant trend of linear decline over the period studied. The climate data showed a non-significant decline in precipitation over the same period, and a very significant increase in temperature; both can help explain the observed declines in runoff and soil loss. (3) Based on a mass curve analysis with anomalies of normalized runoff and sediment load, 4 stages in the change of runoff and soil loss were identified: 1951 to 1971 (Stage I), 1972 to 1986 (Stage II), 1987 to 1996 (Stage III) and 1997 to 2010 (Stage IV). (4)When years were paired based on similar precipitation and temperature condition (SPTC) and used to assess the impacts of human activities, it was found that 6 sets of paired years out of 12 (50 %) showed a decline in runoff, 8 (67 %) a decline in sediment load, and 9 (75 %) a decline in sediment concentration. The other sets show an increasing change with time. It showed the complexity of human impacts. (5) Human impacts relating to LUC change and soil and water measures in this basin were significant because of both the transfer of sloping cropland into non-food vegetation or terraces, and the siltation in the reservoirs and behind check dams. Data indicated that about 56 Mt of sediment was deposited annually from 1960– 1999 as a result of the soil and water conservation structures, which is significantly more than the average 42 Mt, leaving the Yan River basin as sediment load each year. Although the effects of climate change and human action could not be separated, analysis of the data indicated that both had a significant impact on runoff and sediment load in the area.
Measurement methods and variability assessment of the Norway spruce total leaf area: Implications for remote sensing
Homolova, L. ; Lukes, P. ; Malenovsky, Z. ; Lhotakova, Z. ; Kaplan, V. ; Hanus, J. - \ 2013
Trees-Structure and Function 27 (2013)1. - ISSN 0931-1890 - p. 111 - 121.
chlorophyll-a - light-interception - hyperspectral data - picea-abies - imaging spectroscopy - conifer needles - surface-area - gas-exchange - canopy - biochemistry
Estimation of total leaf area (LAT) is important to express biochemical properties in plant ecology and remote sensing studies. A measurement of LAT is easy in broadleaf species, but it remains challenging in coniferous canopies. We proposed a new geometrical model to estimate Norway spruce LAT and compared its accuracy with other five published methods. Further, we assessed variability of the total to projected leaf area conversion factor (CF) within a crown and examined its implications for remotely sensed estimates of leaf chlorophyll content (Cab). We measured morphological and biochemical properties of three most recent needle age classes in three vertical canopy layers of a 30 and 100-year-old spruce stands. Newly introduced geometrical model and the parallelepiped model predicted spruce LAT with an error >5 % of the average needle LAT, whereas two models based on an elliptic approximation of a needle shape underestimated LAT by up to 60 %. The total to projected leaf area conversion factor varied from 2. 5 for shaded to 3. 9 for sun exposed needles and remained invariant with needle age class and forest stand age. Erroneous estimation of an average crown CF by 0. 2 introduced an error of 2-3 µg cm-2 into the crown averaged Cab content. In our study, this error represents 10-15 % of observed crown averaged Cab range (33-53 µg cm-2). Our results demonstrate the importance of accurate LAT estimates for validation of remotely sensed estimates of Cab content in Norway spruce canopies.
Coupled canopy-atmosphere modelling for radiance-based estimation of vegetation properties
Laurent, V.C.E. - \ 2013
Wageningen University. Promotor(en): Michael Schaepman, co-promotor(en): Wouter Verhoef; Jan Clevers. - [S.l.] : s.n. - ISBN 9789461735393
vegetatie - modelleren - kroondak - atmosfeer - remote sensing - meting - methodologie - vegetation - modeling - canopy - atmosphere - measurement - methodology

Vegetation is an important component of the Earth’s biosphere and therefore plays a crucial role in the carbon exchange of terrestrial ecosystems. Vegetation variables, such as leaf area index (LAI) and leaf chlorophyll content (Cab), can be monitored at global scale using remote sensing (RS). There are two main categories of approaches for estimating the vegetation variables from RS data: empirical and physically-based approaches. Physically-based approaches are more widely applicable because they rely on radiative transfer (RT) models, which can be adapted to the observation conditions and to the observed vegetation. For estimating the vegetation variables, however, the RT model has to be inverted, and this inversion is usually an ill-posed and under-determined problem. Several regularization methods have been proposed to allow finding stable and unique solutions: model coupling, using multi-angular data, using a priori information, as well as applying spatial or temporal constraints.

Traditionally, radiance data measured at top-of the atmosphere (TOA) are pre-processed to top-of-canopy (TOC) reflectances. Corrections for atmospheric effects, and, if needed, for adjacency, directional, or topographic effects are usually applied sequentially and independently. Physically, however, these effects are inter-related, and each correction introduces errors. These errors propagate to the TOC reflectance data, which are used to invert the canopy RT model. The performance of the TOC approach is therefore limited by the errors introduced in the data during the pre-processing steps.

This thesis proposes to minimize these errors by directly using measured TOA radiance data. In such a TOA approach, the atmospheric RT model, which is normally inverted to perform the atmospheric correction, is coupled to the canopy RT model. The coupled canopy-atmosphere model is inverted directly using the measured radiance data. Adjacency, directional and topographic effects can then be included in the coupled RT model. The same regularization methods as used for TOC approaches can be applied to obtain stable and unique estimates. The TOA approach was tested using four case studies based on mono-temporal data.

A) The performance of the TOA approach was compared to a TOC approach for three Norway spruce stands in the Czech Republic, using near-nadir Compact High Resolution Imaging Spectrometer (CHRIS) data. The coupled model included canopy directional effects and simulated the CHRIS radiance data with similar accuracy as the canopy model simulated the atmospherically-corrected CHRIS data. Local sensitivity analyses showed that the atmospheric parameters had much less influence on the simulations than the vegetation parameters, and that the sensitivity profiles of the latter were very similar for both TOC and TOA approaches. The dimensionality of the estimation problem was evaluated to be 3 for both approaches. Canopy cover (Cv), fraction of bark material (fB), Cab, and leaf dry matter content (Cdm) were estimated using look-up tables (LUT) with similar accuracy with both approaches.

B) Regularization using multi-angular data was tested for the TOA approach, using four angular CHRIS datasets, for the same three stands as used in A). The coupled model provided good simulations for all angles. The dimensionality increased from 3 to 6 when using all four angles. Two LUTs were built for each stand: a 4-variable LUT with fB, Cv, Cdm, and Cab, and a 7-variable LUT where leaf brown pigment concentration (Cs), dissociation factor (D), and tree shape factor (Zeta) were added. The results did not fully match the expectation that the more angles used, the more accurate the estimates become. Although their exploitation remains challenging, multi-angular data have higher potential than mono-angular data at TOA level.

C) A Bayesian object-based approach was developed and tested on at-sensor Airborne Prism Experiment (APEX) radiance data for an agricultural area in Switzerland. This approach consists of two steps. First, up to six variables were estimated for each crop field object using a Bayesian optimization algorithm, using a priori information. Second, a LUT was built for each object with only LAI and Cab as free variables, thus spatially constraining the values of all other variables to the values obtained in the first step. The Bayesian object-based approach estimated LAI more accurately than a LUT with a Bayesian cost function approach. This case study relied on extensive field data allowing defining the objects and a priori data.

D) The Bayesian object-based approach proposed in C) was applied to a simulated TOA Sentinel-2 scene, covering the area around Zurich, Switzerland. The simulated scene was mosaicked using seven APEX flight lines, which allowed including all spatial and spectral characteristics of Sentinel-2. Automatic multi-resolution segmentation and classification of the vegetated objects in four levels of brightness in the visible domain enabled defining the objects and a priori data without field data, allowing successful implementation of the Bayesian object-based approach.

The research conducted in this thesis contributes to the improvement of the use of regularization methods in ill-posed RT model inversions. Three major areas were identified for further research: 1) inclusion of adjacency and topography effects in the coupled model, 2) addition of temporal constraints in the inversion, and 3) better inclusion of observation and model uncertainties in the cost function. The TOA approach proposed here will facilitate the exploitation of multi-angular, multi-temporal and multi-sensor data, leading to more accurate RS vegetation products. These higher quality products will support many vegetation-related applications.

Post-harvesting silvicultural treatments in logging gaps: A comparison between enrichment planting and tending of natural regeneration
Schwartz, G. ; Lopes, J.C.A. ; Mohren, G.M.J. ; Peña-Claros, M. - \ 2013
Forest Ecology and Management 293 (2013). - ISSN 0378-1127 - p. 57 - 64.
bolivian tropical forests - neotropical rain-forest - long-term impacts - reduced-impact - eastern amazon - brazilian amazon - dry forest - management - growth - canopy
Despite greatly improved forest management in recent decades, long-term assessments show that if current harvesting volumes and cutting cycles are maintained, future volume yields of commercial species will decrease. A possible solution is to apply post-harvesting silvicultural treatments to increase the number of valuable trees. In this study we compared during 4 years two treatments: tending naturally established seedlings/saplings of commercial species in logging gaps, and enrichment planting + tending seedlings of commercial species. In both treatments, competition was artificially reduced by liberating each focal seedling/sapling from competitors (i.e. other tree seedlings/saplings, lianas, or herbs). The experiment was carried out in an area of ombrophilous dense forest managed by the Orsa Florestal forestry company in Jari Valley, eastern Amazon, Brazil (01°09'S and 52°38'W). The company applies reduced-impact logging in a polycyclic silvicultural system. We sampled 64 2-year-old logging gaps (average area 427.2 m2). Thirty-four gaps were used for the planting + tending, 15 gaps underwent the tending treatment, and there were 15 gaps in the control treatment (i.e. no intervention). The tending treatment showed lower mortality rate, faster growth rate, and required less liberation from overstorey plants and lianas than the other two treatments. Half of the species responded positively to tending: the long-lived pioneers Goupia glabra and Laetia procera, and the partially shade-tolerant Dinizia excelsa, Tachigali myrmecophila, and Trattinnickia sp. Similarly to tending, individuals subjected to the enrichment planting + tending treatment also presented higher growth rates. Based on these results we recommend tending be applied to areas with sufficient natural regeneration of commercial species. Enrichment planting + tending should be applied when regeneration of commercial species is scare, ideally using species that have high initial growth rates, and high commercial or conservation value.
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