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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Legionella growth potential of drinking water produced by a reverse osmosis pilot plant
Learbuch, K.L.G. ; Lut, M.C. ; Liu, G. ; Smidt, H. ; Wielen, P.W.J.J. van der - \ 2019
Water Research 157 (2019). - ISSN 0043-1354 - p. 55 - 63.
Drinking water quality - Legionella pneumophila - Regrowth - Reverse osmosis

Treatment processes, such as membrane filtration with reverse osmosis (RO), are used to produce drinking water with a high degree of biostability. To our knowledge, the influence of RO water on biofilm formation and growth of L. pneumophila has not yet been investigated. Therefore, this study aimed (i) to determine the Legionella growth potential of (remineralised) RO-water produced by a pilot plant and to compare this to conventional treated groundwater, and (ii) to determine if different pipe materials, in contact with remineralised RO-water, can cause growth of L. pneumophila. The Legionella growth potential of water was determined with the boiler biofilm monitor (BBM) that mimics the flow of water in a premise plumbing system. The Legionella growth potential of materials in contact with remineralised RO-water was determined by using the biomass production potential (BPP)-test. ATP concentrations in the biofilm on the glass rings from the BBM fed with (remineralised) RO water fluctuated around 100 pg ATP cm −2 . In contrast, BBMs fed with conventionally treated water resulted in ten-fold higher ATP concentrations in the biofilm. Moreover, conventionally treated water had a Legionella growth potential that was 1000-fold higher than that of (remineralised) RO-water. Furthermore, glass, copper and PVC-C had the lowest biofilm concentrations and Legionella growth potential in the BPP-test, followed by PE-Xb, PE-Xc and PE-100. The highest biofilm concentration and Legionella growth potential were with PVC-P. Hence, our study demonstrated that remineralised RO-water did not enhance growth of L. pneumophila in the BBM that mimics the premises plumbing system. However, when PE or PVC-P materials are used growth of L. pneumophila can still occur in the premises plumbing system despite the high quality of the supplied remineralised RO-water.

Photo-stability of a flavonoid dye in presence of aluminium ions
Villela, Alexandre ; Vuuren, Monique S.A. van; Willemen, Hendra M. ; Derksen, Goverdina C.H. ; Beek, Teris A. van - \ 2019
Dyes and Pigments 162 (2019). - ISSN 0143-7208 - p. 222 - 231.
Flavonoid - Light-fastness - Luteolin - Natural dye - Reseda luteola - Weld

The main colouring compounds of the dye plant weld (Reseda luteola L.) are the flavones luteolin (lut), lut-7-O-glucoside and lut-7,3ʹ-O-diglucoside. Alum (an aluminium salt)-premordanted wool dyed with weld leads to yellow colours that are of low resistance to light. The photo-stability of lut in aerated methanol–water 8:2 (v/v) solution upon irradiation with light above 300 nm was studied at different lut–Al3+ ratios. Experiments using extracts of weld to dye wool premordanted with increasing quantities of aluminium salts were also carried out. The photo-stability of lut in the polar protic solvent and the photo-resistance (light-fastness) of the colour of weld-dyed wool decrease with increasing concentrations of aluminium ions. Thus, the lower the [Al3+] used for mordanting the wool, the more light-fast its colour. Lowering the [Al3+] appears to have no negative influence on the wash-fastness of the colour. As the gain in light-fastness by the use of low [Al3+] to premordant the wool is not extensive, however, this does not seem to be a way to meet today's requirement of light-fastness of the colours of dyed textiles by itself. Nevertheless, it may be part of a bigger strategy to address the need for increased light-fastness of the colour of wool dyed with weld. Implementation of this approach by dyers is expected to clarify whether it results in benefits for textile dyeing practice.

Hotspots for selected metal elements and microbes accumulation and the corresponding water quality deterioration potential in an unchlorinated drinking water distribution system
Liu, Gang ; Tao, Yu ; Zhang, Ya Ping ; Lut, Maarten ; Knibbe, Willem Jan ; Wielen, Paul van der; Liu, Wentso ; Medema, Gertjan ; Meer, Walter van der - \ 2017
Water Research 124 (2017). - ISSN 0043-1354 - p. 435 - 445.
Drinking water distribution system - Hotspot - Material accumulation - Next generation sequencing - Quality deterioration potential
Biofilm formation, loose deposit accumulation and water quality deterioration in drinking water distribution systems have been widely reported. However, the accumulation and distribution of harbored elements and microbes in the different niches (loose deposits, PVC-U biofilm, and HDPE biofilm) and their corresponding potential contribution to water quality deterioration remain unknown. This precludes an in-depth understanding of water quality deterioration and the development of proactive management strategies. The present study quantitatively evaluated the distribution of elements, ATP, Aeromonas spp., and bacterial communities in distribution pipes (PVC-U, D = 110 mm, loose deposit and biofilm niches) and household connection pipes (HDPE, D = 32 mm, HDPE biofilm niches) at ten locations in an unchlorinated distribution system. The results show that loose deposits in PVC-U pipes, acting as sinks, constitute a hotspot (highest total amount per meter pipe) for elements, ATP, and target bacteria groups (e.g., Aeromonas spp., Mycobacterium spp., and Legionella spp.). When drinking water distribution system niches with harbored elements and microbes become sources in the event of disturbances, the highest quality deterioration potential (QDP) is that of HDPE biofilm; this can be attributed to its high surface-to-volume ratio. 16s rRNA analysis demonstrates that, at the genus level, the bacterial communities in the water, loose deposits, PVC-U biofilm, and HDPE biofilm were dominated, respectively, by Polaromonas spp. (2–23%), Nitrosipra spp. (1–47%), Flavobacterium spp. (1–36%), and Flavobacterium spp. (5–67%). The combined results of elemental composition and bacterial community analyses indicate that different dominant bio-chemical processes might occur within the different niches—for example, iron-arsenic oxidizing in loose deposits, bio-calumniation in PVC-U biofilm, and methane oxidizing in HDPE biofilm. The release of 20% loose deposits, 20% PVC-U biofilm and 10% HDPE biofilm will cause significant changes of water bacterial community.
Inferring 222Rn soil fluxes from ambient 222Rn activity and eddy covariance measurements of CO2
Laan, Sander van der; Manohar, Swagath ; Vermeulen, Alex ; Bosveld, Fred ; Meijer, Harro ; Manning, Andrew ; Molen, Michiel van der; Laan-Luijkx, Ingrid van der - \ 2016
Atmospheric Measurement Techniques 9 (2016)11. - ISSN 1867-1381 - p. 5523 - 5533.
We present a new methodology, which we call Single Pair of Observations Technique with Eddy Covariance (SPOT-EC), to estimate regional-scale surface fluxes of 222Rn from tower-based observations of 222Rn activity concentration, CO2 mole fractions and direct CO2 flux measurements from eddy covariance. For specific events, the regional (222Rn) surface flux is calculated from short-term changes in ambient (222Rn) activity concentration scaled by the ratio of the mean CO2 surface flux for the specific event to the change in its observed mole fraction. The resulting 222Rn surface emissions are integrated in time (between the moment of observation and the last prior background levels) and space (i.e. over the footprint of the observations). The measurement uncertainty obtained is about ±15 % for diurnal events and about ±10 % for longer-term (e.g. seasonal or annual) means. The method does not provide continuous observations, but reliable daily averages can be obtained. We applied our method to in situ observations from two sites in the Netherlands: Cabauw station (CBW) and Lutjewad station (LUT). For LUT, which is an intensive agricultural site, we estimated a mean 222Rn surface flux of (0.29 ± 0.02) atoms cm−2 s−1 with values  > 0.5 atoms cm−2 s−1 to the south and south-east. For CBW we estimated a mean 222Rn surface flux of (0.63 ± 0.04) atoms cm−2 s−1. The highest values were observed to the south-west, where the soil type is mainly river clay. For both stations good agreement was found between our results and those from measurements with soil chambers and two recently published 222Rn soil flux maps for Europe. At both sites, large spatial and temporal variability of 222Rn surface fluxes were observed which would be impractical to measure with a soil chamber. SPOT-EC, therefore, offers an important new tool for estimating regional-scale 222Rn surface fluxes. Practical applications furthermore include calibration of process-based 222Rn soil flux models, validation of atmospheric transport models and performing regional-scale inversions, e.g. of greenhouse gases via the SPOT 222Rn-tracer method.
Experimental Sentinel-2 LAI estimation using parametric, non-parametric and physical retrieval methods - A comparison
Verrelst, Jochem ; Rivera, Juan Pablo ; Veroustraete, Frank ; Muñoz-Marí, Jordi ; Clevers, J.G.P.W. ; Camps-Valls, Gustau ; Moreno, José - \ 2015
ISPRS Journal of Photogrammetry and Remote Sensing 108 (2015). - ISSN 0924-2716 - p. 260 - 272.
Biophysical variables - Machine learning - Non-parametric - Parametric - Physically-based RTM inversion - Sentinel-2

Given the forthcoming availability of Sentinel-2 (S2) images, this paper provides a systematic comparison of retrieval accuracy and processing speed of a multitude of parametric, non-parametric and physically-based retrieval methods using simulated S2 data. An experimental field dataset (SPARC), collected at the agricultural site of Barrax (Spain), was used to evaluate different retrieval methods on their ability to estimate leaf area index (LAI). With regard to parametric methods, all possible band combinations for several two-band and three-band index formulations and a linear regression fitting function have been evaluated. From a set of over ten thousand indices evaluated, the best performing one was an optimized three-band combination according to (ρ56016102190)/(ρ56016102190) with a 10-fold cross-validation RCV2 of 0.82 (RMSECV: 0.62). This family of methods excel for their fast processing speed, e.g., 0.05s to calibrate and validate the regression function, and 3.8s to map a simulated S2 image. With regard to non-parametric methods, 11 machine learning regression algorithms (MLRAs) have been evaluated. This methodological family has the advantage of making use of the full optical spectrum as well as flexible, nonlinear fitting. Particularly kernel-based MLRAs lead to excellent results, with variational heteroscedastic (VH) Gaussian Processes regression (GPR) as the best performing method, with a RCV2 of 0.90 (RMSECV: 0.44). Additionally, the model is trained and validated relatively fast (1.70s) and the processed image (taking 73.88s) includes associated uncertainty estimates. More challenging is the inversion of a PROSAIL based radiative transfer model (RTM). After the generation of a look-up table (LUT), a multitude of cost functions and regularization options were evaluated. The best performing cost function is Pearson's χ-square. It led to a R2 of 0.74 (RMSE: 0.80) against the validation dataset. While its validation went fast (0.33s), due to a per-pixel LUT solving using a cost function, image processing took considerably more time (01:01:47). Summarizing, when it comes to accurate and sufficiently fast processing of imagery to generate vegetation attributes, this paper concludes that the family of kernel-based MLRAs (e.g. GPR) is the most promising processing approach.

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.
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.
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 - remote sensing - 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.

Growth response of Pterocarpus soyauxii and Lophira alata seedlings to host soil mycorrhizal inocula in relation to land use types.
Onguene, N.A. ; Ngonkeu, L.E.M. ; Kuyper, T.W. - \ 2011
African Journal of Microbiology Research 5 (2011)17. - ISSN 1996-0808 - p. 2391 - 2398.
rain-forest - arbuscular mycorrhizae - tropical forest - south cameroon - plant-growth - fungi - colonization - regeneration - communities
Deficiency in mycorrhizal inoculum in soils due to land use types (LUT) can be alleviated by quantity and quality inoculum addition. A bioassay was carried out to determine how host soil mycorrhizal inoculum influenced mycorrhizal colonization, carbon allocation and partitioning of seedlings of two native timber species of Cameroon humid forest. Seedlings of Pterocarpus soyauxii and Lophira alata were raised for six months on surface soils (0 - 20 cm) collected from early secondary forests and LUT derived from slash-and-burn agriculture and selective logging. Mycorrhizal inoculation effect (MIE) was derived. Seedlings were mainly colonized by members of the Glomaceae and Gigasporaceae, respectively, as shown by molecular typing. They generally performed poorly in soils with indigenous inoculum. But addition of soil inoculum from P. soyauxii trees favored nodulation, significantly increased mycorrhizal colonization and total biomass but decreased root-to-shoot ratios, resulting in large and positive MIE, irrespective of LUT. ln contrast, host soil inoculum of L. alata did not affect fractional mycorrhizal colonization but significantly increased total biomass and resulted in high carbon allocation to roots in low and sometimes negative MIE. Therefore, seedlings' responses to mycorrhizal inoculum depend on host soil inoculum and that could be critical for successful rejuvenation of tropical trees.
Seasonal LAI estimation of irrigated rice using Soil-Leaf-Canopy (SLC) radiative transfer model
Nguyen, Thi Thu Ha ; Verhoef, W. ; Bie, C.A.J.M. de - \ 2011
In: 32nd Asian Conference on Remote Sensing 2011, ACRS 2011. - - p. 327 - 332.
Chlorophyll (Cab) - Inversion - LAI - Look-up table LUT - Rice - Soil-Leaf-Canopy (SLC)
This study compared the use of both the MODIS LAI (MOD15A2) product, which provides directly the 8-day LAI at 1km spatial resolution, and the MODIS 8-day surface reflectance product (MOD09A1) in retrieving and estimating the seasonal variation of LAI for irrigated rice in the Mekong delta, Vietnam. The Soil-Leaf-Canopy (SLC) radiative transfer model was employed to invert MOD09A1 reflectance spectra to get LAI estimates through the look-up table (LUT) approach. The result showed that the dynamic evolution of LAI of irrigated rice during one cropping season could be estimated fairly well by the SLC model (R 2 = 0.69, RMSE= 0.9). This result is a great improvement compared to the retrieved LAI from MOD15A2 (R 2 = 0.07, RMSE = 2.1).
Inversion of a radiative transfer model for estimating vegetation LAI and chlorophyll in a heterogeneous grassland
Darvishzadeh, R. ; Skidmore, A.K. ; Schlerf, M. ; Atzberger, C. - \ 2008
Remote Sensing of Environment 112 (2008)5. - ISSN 0034-4257 - p. 2592 - 2604.
leaf-area index - canopy biophysical variables - remote-sensing data - reflectance data - optical-properties - neural-network - ancillary information - precision agriculture - satellite data - retrieval
Radiative transfer models have seldom been applied for studying heterogeneous grassland canopies. Here, the potential of radiative transfer modeling to predict LAI and leaf and canopy chlorophyll contents in a heterogeneous Mediterranean grassland is investigated. The widely used PROSAIL model was inverted with canopy spectral reflectance measurements by means of a look-up table (LUT). Canopy spectral measurements were acquired in the field using a GER 3700 spectroradiometer, along with simultaneous in situ measurements of LAI and leaf chlorophyll content. We tested the impact of using multiple solutions, stratification (according to species richness), and spectral subsetting on parameter retrieval. To assess the performance of the model inversion, the normalized RMSE and R-2 between independent in situ measurements and estimated parameters were used. Of the three investigated plant characteristics, canopy chlorophyll content was estimated with the highest accuracy (R-2 = 0.70, NRMSE = 0.18). Leaf chlorophyll content, on the other hand, could not be estimated with acceptable accuracy, while LAI was estimated with intermediate accuracy (R-2 = 0.59, NRMSE = 0.18). When only sample plots with up to two species were considered (n = 107), the estimation accuracy for all investigated variables (LAI, canopy chlorophyll content and leaf chlorophyll content) increased (NRMSE=0.14, 0.16, 0.19, respectively). This shows the limits of the PROSAIL radiative transfer model in the case of very heterogeneous conditions. We also found that a carefully selected spectral subset contains sufficient information for a successful model inversion. Our results confirm the potential of model inversion for estimating vegetation biophysical parameters at the canopy scale in (moderately) heterogeneous grasslands using hyperspectral measurements. (C) 2008 Elsevier Inc. All rights reserved.
Ultrafast fluorescence of photosynthetic crystals and light-harvesting complexes
Oort, B.F. van - \ 2008
Wageningen University. Promotor(en): Herbert van Amerongen, co-promotor(en): A.V. Ruban. - [S.l.] : S.n. - ISBN 9789085852056 - 150
fluorescentie - fluorescentie-emissiespectroscopie - fotosynthese - eiwitten - fluorescence - fluorescence emission spectroscopy - photosynthesis - proteins
This thesis focuses on the study of photosynthetic pigment protein complexes using time resolved fluorescence techniques. Fluorescence spectroscopy often requires attaching fluorescent labels to the proteins under investigation. With photosynthetic proteins this is not necessary, because these proteins contain fluorescent pigments. Each pigment’s fluorescence is influenced by its environment, and thereby may provide information on structure and dynamics of pigment protein complexes in vitro and in vivo. Another way to probe protein structure is X ray diffraction of crystals of the pigment protein complexes. In this work fluorescence was measured of crystals of Light Harvesting Complex II (LHCII), of which the structure is known from X ray diffraction on similar crystals. Analysis of spectral properties and structure of the crystals yielded important insights in the process of nonphotochemical quenching (NPQ). The insights were supplemented by studies of aggregated LHCII, and LHCII under high hydrostatic pressure. The largest photosynthetic pigment protein complex to be crystallized to date (PSI LHCI) was also studied. A minor light harvesting complex (CP29), which may be important for NPQ, and which has eluded crystallization, was studied by site directed fluorescent labeling combined with FRET to obtain structural information. This summarizing discussion first treats CP29 (section 7.2), then LHCII and NPQ (section 7.3), and finally PSI (section 7.4). The general conclusions are in section 7.5, followed by the recommendations for future study.

7.1 Streak camera setup: Structure of CP29
A valuable detection method of time resolved fluorescence is the synchroscan streak camera system. Such a setup was built, using a set of lasers and amplifiers of Coherent (U.S.A.), a spectrograph of Chromex (U.S.A.) and a streak camera of Hamamatsu (Japan). Chapter 2 describes the details of the setup, and analysis of the data obtained with it. In Chapter 3 the value of the setup is illustrated for CP29. CP29 is one of the minor light harvesting complexes of PSII. Its exceptionally long N terminal domain1 is phosphorylated2 under cold stress induced photoinhibition3. Phosphorylation leads to spectral changes, that were assigned to conformational changes of the transmembranal part of CP294. Later CP29 was suggested to be a site for quenching during NPQ5, and in Arabidopsis thaliana plants that lack CP29 (and CP24) NPQ is decreased compared to wild type plants6. The structure of CP29 has not been resolved, however the high sequence homology with LHCII, especially in the transmembrane domain, suggests an organization similar to that of LHCII, the structure of which has been obtained at 2.5-2.72 Å7,8. However, no information is available about the organization of the N-terminal domain, which differs completely from that of LHCII. In Chapter 3 specific amino acids in the tail were replaced by a cysteine, which was then labeled with a rhodamine type dye (TAMRA), which can be selectively excited around 530 550 nm. Förster resonance energy transfer was measured from TAMRA to the Chl molecules, providing information about distances between specific sites of the N-terminal domain and the chlorophyll molecules. The N terminal domain seems to fold back to the transmembranal part of CP29. Although these results require further substantiation, the experiments demonstrate the feasibility of this approach to study protein structure.

7.2 Nonphotochemical quenching and LHCII
Nonphotochemical quenching is an important mechanism that plants and algae use to prevent photodamage under conditions of high light intensity9. It has been proposed to take place in LHCII10-13 (or CP295, see above). An unresolved issue is the mechanism of quenching. Currently there are two views: (i) quenching occurs via energy transfer from Chl a to Lut and subsequent rapid relaxation to the ground state13; (ii) quenching occurs via cation radical formation by charge separation in a Chl Zea dimer, and subsequent rapid relaxation to the ground state14. Both candidates have in common that a light harvesting complex (LHC) can switch between a state with a long excited state lifetime, and a state in which this lifetime is reduced. Chapters 1, 4 and 5 describe experiments on this switching in LHCII.

Aggregation of LHCII in vitro leads to fluorescence quenching that is very similar to that observed in vivo under conditions of NPQ15,16. Therefore aggregated LHCII has been used extensively as a model system for studying the role of LHCs in NPQ10,17-20. However, it is still unknown whether LHCII aggregation leads to the formation of quenchers (excitation traps), as proposed for instance by Horton et al.11,19, or that increased connectivity between trimers upon aggregation leads to efficient quenching by a small population of permanently quenched LHCII21,22. If quenchers are formed, the question remains whether strong quenchers form in a small fraction of LHCII18, or whether weaker quenchers form in a large fraction of LHCII11. In Chapter 4 excited state lifetimes of monomers, trimers and aggregates of LHCII are compared. The quenching in aggregates was so strong, that it could not be explained quantitatively by enhanced trapping by quenchers that were present before aggregation. So quenchers are created upon aggregation. These quenching traps do not only trap excitations in the trimer in which they are located, but also excitations originating in complexes that do not contain traps themselves. The fluorescence quenching in monomers was found to be even stronger than that in trimers, suggesting an intramonomeric origin of this process.
In Chapter 5 hydrostatic pressure was used to study the switching between quenched/unquenched states of LHCII. At atmospheric pressure a small fraction of isolated LHCII is quenched, and this fraction is in thermodynamic equilibrium with the bulk unquenched fraction23. Applying high hydrostatic pressure shifts the equilibrium more to the quenched conformation and this allows determination of the energy difference between both states and the change in volume. The volume difference between the two states is very small: 5 ml/mol; less than 0.006% of the volume of one trimeric LHCII complex, which indicates a local conformational switch between the two states. The switch is accompanied by a small change in energy: 7.0 kJ/mol; high enough to keep the quenched state population low under normal conditions, but low enough to switch in a controlled way by environmental changes (such as pH, membrane structure, aggregation) induced by high light intensities.
In addition, at high pressure a state forms that is approximately 100 fold more quenched than the other two states. This state has a fluorescence lifetime of ~25 ps, reflecting the average time to reach an extremely efficient quencher somewhere within the trimer (the excitation equilibration time)24. At 400 MPa (4 kbar) less than 1% of all Chls are highly quenched, whereas in LHCII in which the pigments were uncoupled by detergent treatment this was 47%. These pressure experiments demonstrate that at least two types of quenchers can be formed in LHCII in vitro, very strong and relatively weak ones. In vivo a small number of strong quenchers could quench fluorescence of many connected LHCs. Alternatively a large number of weak quenchers could lead to the same amount of quenching.

A third approach to gain insight in the switching of LHCII between quenched and unquenched states involves the study of crystals of LHCII, as described in Chapter 1 and by Pascal et al.12. The crystal structure of LHCII from spinach at 0.272 nm7 aided in the understanding of its spectroscopic features; extensive modeling based on this structure explained many steady stated and time resolved spectral properties of LHCII in solution25. It is not known a priori, however, whether the structure of LHCII is the same when LHCII is dissolved in buffer, and when it is crystallized. This is particularly relevant, because LHCII has the ability to switch between conformations with different fluorescence lifetimes10,17,18. Fluorescence lifetime imaging microscopy showed that the fluorescence lifetime of LHCII crystals was ~850 ps. When the crystals were dissolved the fluorescence lifetime switched to ~4 ns. Subsequent aggregation switched LHCII back to a quenched state, with a lifetime of ~650 ps (Chapter 1 and ref. 12). Thus, it is clear that the crystal structure does not correspond to the unquenched state of LHCII, but more resembles the quenched state of aggregated LHCII, and/or that of LHCII under hydrostatic pressure. Also the Raman and low temperature fluorescence emission spectra of the crystals differed from those of LHCII in solution12. Those differences indicated a higher degree of homogeneity and stronger twisting of the Neo in the crystals as compared to LHCII in solution. Also the interactions of Chls b and their environment are different. The crystal packing was not dense enough to induce these changes directly by trimer trimer interactions, nor can the quenching be caused by intertrimeric pigment interactions. Therefore the quencher must be sought for inside the trimeric units. Based on the crystal structure7, two sites were proposed: a Chl a dimer in close proximity of a Lut, and a Chl b close to Neo. It was later confirmed that in aggregated LHCII excited state energy is transferred from Chl to Lut, supporting the role of Lut in fluorescence quenching in the crystals13.

7.3 Photosystem I
The structural and spectral differences between LHCII in crystal form and in solution triggered the study of PSI LHCI crystals in Chapter 6. PSI LHCI is a pigment protein complex that is more complicated than LHCII: PSI LHCI binds more pigments (~160 vs. 42), it performs photochemical quenching, and it contains “red Chls”, with an excited state energy lower than that of the reaction centre26. The fluorescence decay is rather complex due to the presence of energetically coupled Chls with very different excited state energies. The excited state energy of the Chls and their coupling may depend on plant species, preparation method and measuring conditions27-33. Consequently, a wide range of fluorescence decay kinetics have been reported over the years27-33. In Chapter 6 it is shown that the picosecond fluorescence of intact crystals is identical to that of dissolved crystals, but differs considerably from most kinetics presented in literature27-33. Caution should therefore be taken in using the crystal structure to model those kinetics.
The data of dissolved crystals were described quantitatively by a simple model that required only two pigment clusters: PSI core and LHCI. This model yielded rates of photosynthetic trapping from the core, and wavelength dependent excitation energy transfer from LCHI to PSI core and vice versa. The model differs from previous models with respect to the reduced number of pigment clusters, and the introduction of the wavelength dependence of the transfer rates. The modeling yields spectra and rate constants that originate specifically from excitation of pigments in PSI core or LHCI, and can therefore serve as a starting point for detailed modeling at the molecular level, using the PSI LHCI crystal structure.
7.4 General conclusions
This thesis presents important information on the mechanisms by which LHCII (or LHCs of PSII in general) can contribute to NPQ. Better understanding of this photoprotective process may in time lead to strategies to increase crop yields and/or plant fitness. It may further aid systems that mimic photosynthesis in vitro, aiming at energy production. The experiments with LCHII crystals showed that its crystal structure was that of a quenched conformation, as compared to LHCII in buffer. Next it was shown that upon aggregation of LHCII quenchers are formed, which consequently also quench fluorescence of LHCII trimers without quenchers. Under high hydrostatic pressure, two quenching mechanisms were observed: (i) Strong quenching, limited by the excitation equilibration time of a trimeric unit; and (ii) weaker quenching, caused by a conformational change that is associated with very small energy and volume changes. These results mark the broad dynamic range of quenching that LHCII can undergo. With CP29, a start has been made to study the structure of its N terminal domain, which is phosphorylated under stress.
This thesis further deals with the aptness of using X ray crystal structures to model spectral properties of pigment protein complexes. Often it is tacitly assumed that the structure of these complexes is the same in solution and in crystal form. For LHCII this assumption is not completely valid, because the fluorescence of LHCII crystals is quenched as compared to that of LHCII in solution. For PSI LHCI the fluorescence decay was identical for crystals and dissolved crystals. The decay was however different from most of those reported before, and the crystal structure may not be suited to model those data. A new type of model provides a simple description of the fluorescence kinetics, based on only two compartments and wavelength dependent excited state energy transfer among them. The experiments on these crystals illustrate the need of caution when using crystal structures to model specific spectral parameters of pigment protein complexes.

7.5 Recommendations
7.5.1 CP29 structure
With regard to the study of the structure of the N terminal tail of CP29 I recommend the following:
1. More detailed structural information can be obtained by using more labeling positions.
2. The effect of the fluorescent label on the structure should be checked, by comparing, for example, (low temperature) linear and circular dichroism, with and without label attached.
3. Another label can be used, for example a smaller fluorescent label, or a paramagnetic label for electron paramagnetic resonance (EPR) experiments.
4. The N terminal domain of CP29 is phosphorylated under stress3. Therefore it would be interesting to study the effect of phosphorylation on the structure of this domain. If in vitro phosphorylation is impossible, its effect may be mimicked by introduction of a negatively charged amino acid.

7.5.2 Nonphotochemical quenching and LHCII
With regard to the study of LHCII as a model system of nonphotochemical quenching in vivo, I recommend the following:
1. Chapter 5 shows that hydrostatic pressure can be used to controllably and reversibly switch LHCII between quenched and unquenched states. This switching can now be studied by many other spectroscopic methods to gain insight in the quenching mechanism.
2. Most experiments on isolated LHCII have been done with micellar systems, where individual monomers or trimers are solubilized by detergent molecules. In vivo LHCII is in a crowded membrane, which is a quite different environment. The in vivo state can be mimicked by reconstitution of LHCII in lipid vesicles (as done by Moya et al.23). The effect of crowding can be studied by changing the protein/lipid ratio of the vesicles. Optical and structural properties of LHCII should be studied in such vesicles. Also the experiments on CP29 could be repeated in lipid vesicles. The structure of the N terminal domain may be affected by the membrane via steric hindrance or electrostatic interactions.
3. In vivo the pH gradient across the photosynthetic membrane is required for full NPQ. Indeed, lowering pH induces fluorescence quenching of isolated LHCII19. However, in vivo the formation and relaxation of qE and ΔpH occur with different kinetics34. With LHCII in lipid vesicles a pH gradient can be applied across the membrane (ideally all LHCII units in a vesicle should be oriented with the same side to the interior). Then the quenching effect of the gradient can be studied in detail in a system that is more in vivo like than LHCII in micelles.
4. Study how connectivity of photosynthetic units in the native membrane influences the effect of quenchers. Native photosynthetic membranes are densely packed35, enabling energy transfer among photosynthetic complexes, which results in migration of excitation energy through multiple complexes. A quencher is more effective in a highly connected network of pigments than in a weakly connected network21. The connectivity is related to the speed of excited state energy migration, but this speed is still under debate36-38, and may change in response to a plant’s environment39,40. Knowledge about the connectivity will therefore help to understand to which extent fluorescence quenching of individual LHCs can contribute to the overall quenching in vivo. Connectivity should be measured (using rapid fluorescence induction41) in unquenched samples and during NPQ formation.

7.5.3 Photosynthetic pigment protein crystals
With regard to the study of crystals of photosynthetic pigment protein complexes, I recommend the following:
1. The use of total internal reflection microscopy instead of confocal microscopy, to avoid reabsorption effects.
2. Study other (optical and electronic) properties than fluorescence lifetimes. A start has been made with measuring Raman and fluorescence spectra of LHCII12, variable fluorescence and electron transfer rates in cyanobacterial PSII cores42, EPR spectroscopy of cyanobacterial PSI43 and PSII44 cores. Such experiments can give more insight in which properties of pigment protein complexes are conserved in crystals and which differ from those of the same complexes in solution. Further experiments are then required to compare those properties with those of the complexes in vivo.
3. “Manipulate” crystals, and measure the effect on optical and electronic properties. For example, it is possible to infiltrate photosynthetic crystals with chemicals such as DCMU42 (which inhibits QA to QB electron transfer). Crystals can be “manipulated” in many other ways, such as by magnetic or electric fields or by light. Also temperature can be varied (note that X ray diffraction experiments are generally performed at cryogenic temperatures). Measurements of pigment protein complex properties under these different conditions can aid the comparison with the complexes in solution and in vivo.

7.5.4 Crystals of biomolecules
The question whether a structure obtained by X ray crystallography is the same as that in solution, is appropriate for many biomolecules, not just photosynthetic proteins. Often it is tacitly assumed that the structure is the same in crystal and solution. This is not always true for pigment protein complexes (see LHCII). Also the fluorescence of several fluorescent proteins of the GFP family is quenched compared to that of the same proteins in solution45. Also the fluorescence of ethidium bromide bound to DNA is quenched more in crystals than in solution45. Therefore a systematic comparison of spectroscopic and structural properties of many types of biomolecules in crystal and in solution can provide valuable missing information.

7.5.5 Photosynthesis research in broader perspective
The production of enough food to feed and energy to power the world’s growing population are key issues of our society. At this moment all food, and most energy, originates from biomass (either directly from “fresh” biomass (~14%) or indirectly from fossil biomass, e.g. oil, coal, gas (~74%)46). The growth of the world’s population and its increasing prosperity, boost the demand for food and energy. Meanwhile the amount of easily accessible natural reserves of fossil fuels is decreasing, and CO2 released by burning fossil fuels is proposed to contribute to climate changes47. Therefore alternative energy sources are required.
A wide range of energy sources is available, for example energy from biomass, wind energy, tidal energy and energy from nuclear fission. Each of these has its own advantages and disadvantages. The main advantages of energy from biomass is that biomass production uses an abundant energy source (the sun) and existing production facilities (i.e. photosynthetic organisms). Disadvantages of biomass production are (i) competition with food production; (ii) requirement of fresh water, which becomes increasingly scarce; and (iii) requirement of large areas of arable land. (Note that the use of algae can overcome some of these disadvantages, but that requires a more complex capital intensive production than the use of plants.)
Most biomass is produced by photosynthesis46. Improving the efficiency of photosynthesis may overcome some of the disadvantages of biomass production. Three paths may lead to such an increase of efficiency: (i) reduction of losses in light-to-fuel conversion; (ii) conversion of solar energy directly into fuel; (iii) realization of artificial devices that perform better than the natural system. Future photosynthesis research should aim at the knowledge required to follow these paths.

Cluster versus grid for operational generation of ATCOR's MODTRAN-based look up tables
Brazile, J. ; Richter, R. ; Schlapfer, D. ; Schaepman, M.E. ; Itten, K.I. - \ 2008
Parallel Computing 34 (2008)1. - ISSN 0167-8191 - p. 32 - 46.
imaging spectrometry data - aviris
A critical step in the product generation of satellite or airborne earth observation data is the correction of atmospheric features. Due to the complexity of the underlying physical model and the amount of coordinated effort required to provide, verify and maintain baseline atmospheric observations, one particular scientific modelling program, modtran, whose ancestor was first released in 1972, has become a de facto basis for such processing. While this provides the basis of per-pixel physical modelling, higher-level algorithms, which rely on the output of potentially thousands of runs of modtran are required for the processing of an entire scene. The widely-used atcor family of atmospheric correction software employs the commonly-used strategy of pre-computing a large look up table (lut) of values, representing modtran input parameter variation in multiple dimensions, to allow for reasonable running times in operation. The computation of this pre-computed look up table has previously taken weeks to produce a dvd (about 4 GB) of output. The motivation for quicker turnaround was introduced when researchers at multiple institutions began collaboration on extending atcor features into more specialized applications. In this setting, a parallel implementation is investigated with the primary goals of: the parallel execution of multiple instances of modtran as opaque third-party software, the consistency of numeric results in a heterogeneous compute environment, the potential to make use of otherwise idle computing resources available to researchers located at multiple institutions, and acceptable total turnaround time. In both grid and cluster environments, parallel generation of a numerically consistent lut is shown to be possible and reduce ten days of computation time on a single, high-end processor to under two days of processing time with as little as eight commodity CPUs. Runs on up to 64 processors are investigated and the advantages and disadvantages of clusters and grids are briefly explored in reference to the their evaluation in a medium-sized collaborative project.
Quantitative cloud analysis using meteorological satellites = [Kwantitatieve analyse van wolken met meteorologische satellieten]
Feijt, A.J. - \ 2000
Agricultural University. Promotor(en): A.A.M. Holtslag; A.C.A.P. van Lammeren. - S.l. : S.n. - ISBN 9789058083159 - 186
wolken - kwantitatieve analyse - satellieten - satellietbeelden - meteorologie - meteorologische instrumenten - clouds - quantitative analysis - satellites - satellite imagery - meteorology - meteorological instruments

This thesis is about observations of clouds from satellite and ground based instruments. The aim is to reconstruct the three dimensional cloud distributions. This information is used both in climate research and operational meteorological applications. In climate research, cloud observations provide a reference to atmospheric models, which enables optimization of cloud parameterizations. For operational meteorologists clouds are symptoms of atmospheric conditions. Cloud observations therefore are helpful in understanding the current weather (nowcasting) and improve the estimate of how of the atmospheric conditions will evolve (forecasting).

In order to obtain cloud field characteristics, analysis environments were developed for the interpretation of meteorological satellite measurements in terms of cloud properties. A large effort was put in the evaluation of the results with synoptic observations and measurements from two measurement campaigns. As a result this thesis comprises three major research topics: Meteosat analysis, AVHRR analysis and combined analysis of ground and satellite observations.

Meteosat analysis

A new cloud detection scheme was developed that includes the use of the surface temperature fields of a Numerical Weather Prediction (NWP) model as a threshold value to distinguish cloudy and cloud free areas. It is shown that also for cloud free conditions, the equivalent black body temperature as measured from satellite is different from the model surface temperature. An innovative part of the scheme is the quantification of this temperature difference, which is used to improve the skill of the cloud detection method. The improvement of the detection efficiency was quantified over land and ocean for 1997 on a 3 hourly basis in a semi-operational setting. As the method optimizes the use of the infrared information it is relatively insensitive to changes of insolation conditions with time of day, location, or season.

AVHRR analysis

The NWP model surface temperatures are also used in the AVHRR analysis environment. For the interpretation of the 0.6μm channel reflectivities, extensive radiative transfer calculations were done with the Doubling-Adding KNMI (DAK) radiative transfer code. The results were put in Look-up tables (LUT). The LUTs are used to obtain the following cloud field properties: cloud cover fraction, cloud top temperature, optical thickness and liquid water path. In order to assess the quality, the retrieved properties were compared to measurements from two campaigns: the Tropospheric Budget Experiment, TEBEX, and the Clouds and Radiation intensive measurement campaigns, CLARA. The comparison shows that the retrieval algorithms yield results that agree with independent ground based measurements for the cases studied.

Combined analysis of satellite and ground observations

Combined analysis of satellite and ground based observations from the TEBEX and CLARA data sets yields information on the quality of the satellite retrieval, but also on the merits of the ground based remote sensing instruments. The study shows that both observational sets have strong points, but a combination is preferred to obtain a good definition of the cloud field. In all comparisons the problem of collocation occurs. The ground based instruments measure continuous in time at one location, while satellites measure a spatial distribution at one moment in time. When comparing ground and satellite derived cloud products it is always questionable which part of the time series corresponds to which part of the spatial distribution. This correlation is studied by comparing variance spectra of time series and spatial distributions of liquid water path derived from microwave radiometer and AVHRR data respectively. It is shown that for two cases with different scaling properties the variance spectrum is similar for a part of the time-series and for a part of the AVHRR image.

This thesis contributes to quantitative use of meteorological satellite data in meteorology and climate research. Furthermore, it advances combined analysis of space born and ground based remote sensing measurements of clouds for routine applications.

Comparative performance analysis of agro-ecosystems
Bie, C.A.J.M. de - \ 2000
Agricultural University. Promotor(en): J. Bouma; P.M. Driessen. - S.l. : S.n. - ISBN 9789058082534 - 232
landevaluatie - landgebruik - landtypen - geografische informatiesystemen - landbouwproductie - agro-ecosystemen - land evaluation - land use - land types - geographical information systems - agricultural production - agroecosystems

Detailed and reliable information on land use systems, as needed for quantitative studies, is scarce and often of low quality. This calls for (guidelines on) data harmonization. Practical concepts to describe and study land use are discussed; the development of the Land Use Database software was instrumental in defining them. Required is that by plot, information on land use purpose(s), on operations and on observations as made by land users is put on record through interviews. To classify land use, three types of classifiers are available: purpose, operation sequence, and context classifiers; using them keeps the possibility to prepare user-defined classification systems open.

Detailed land use descriptions augment Land Use Type (LUT) concepts presented by the FAO Guidelines for Land Evaluation. Biophysical LUT requirements emphasized in land evaluation studies are often crop requirements with management requirements predominantly of a socio-economic nature. The FAO guidelines make insufficient use of information on land use operations that are applied to overcome land aspects that limit yields or reduce production. Proposed is a procedure to evaluate practical technology options to remedy limiting conditions.

Quantitative production functions are not standard output of land evaluation studies. Use of simulation models for quantitative studies is restricted because presently they can not capture the full dynamics of yield limiting and yield reducing factors and can not consider all management options.

Many actual production situations face yield constraints that cause a considerable gap between actual yields and yield levels possible with improved technology. Yield gap studies are essential to identify the biophysical factors and cultural practices that cause the gap. Comparative Performance Analysis (CPA) is an approach to study yield-gaps; it defines quantified yield-gap functions. The key feature of CPA is to relate, after surveying on-farm production situations, differences in land and land use to differences in system performance. CPA complements established land use study methods. The Land Use Database supports it.

Three CPA studies are included. The CPA study on rice identifies priority areas for development. It explains 83% of the yield variability across 63 sites. The CPA study on mango was undertaken to remedy the "trial and error" type of management practised in the study area. It identifies the relative importance of selected production factors, i.e. soil-related (30%), management-related (49%), and crop-related (21%). The CPA study on the impacts of land use on the environment evaluated the merits of four erosion indicators. The indicators could function as Land Quality Indicators to reflect soil loss over time. Pre-rills are promising as an indicator. Their occurrence gave the best correlation to management related site conditions. The relation prepared was not map unit specific and suggested that combined positive conditions reduce the formation of pre-rills exponentially.

An integrated agro-economic and agro-ecological framework for land use planning and policy analysis
Mohamed, A.A. - \ 1999
Agricultural University. Promotor(en): H. van Keulen; M.A. Sharifi. - S.l. : [s.n.] - ISBN 9789058081056 - 188
landgebruiksplanning - landgebruik - ruimtelijke ordening - beleid - analyse - agro-ecologie - land use planning - land use - physical planning - policy - analysis - agroecology

The growing concern about land resource management and the associated decline in land qualities, has led to the realisation that land use planning and policy problems cannot be addressed adequately through a single discipline. This awareness has resulted in renewed attention for integrated, interdisciplinary approaches. It is argued that such an integrated, interdisciplinary approach to problems of land use planning and policy analysis is specifically hampered by lack of an adequate methodology. Although the limitation is increasingly recognised in the various disciplines, relatively little attention has been paid to the question of how to integrate agro-ecological and socio-economic aspects of land use. The study reported here, contributes to development and operationalisation of a land use planning and policy analysis methodology that integrates agro-ecological and agro-economic information in such a way that land use policy options at sub-regional level can be formulated and evaluated with the aim of aiding policy makers.

The study starts with a critical review of the current state of the formal tools of land use planning with particular emphasis on their strengths and weaknesses to integrating bio-physical and socio-economic analysis, stating a need for an alternative integrated methodology, with due recognition of the obstacles and challenges this involves. After a thorough literature search, conceptual and methodological challenges that stand in the way of integration are analysed and described. The basic structure of the framework to a methodology for integrating bio-physical and socio-economic analysis in land use planning and policy analysis is developed and outlined.

The integrated framework derives its conceptual foundation largely from an adaptation of the theory of economic policy of agricultural sector analysis, the systems analytic approach, and the concepts of regional planning, to land use planning and policy analysis. The procedure of building the methodological framework is structured in a set of interrelated blocks (sub-frameworks). Each sub-framework of the methodology actually contains a number of steps, and requires a number of tools and/or methods for its operationalisation. The sub-frameworks of the methodology are further developed and operationaliesd for a case of Amol sub-region in Iran.

After an identification of limitations of existing farm classification procedures, an alternative methodology is developed and outlined. The main purpose for farm classification methodology is to reduce aggregation errors, while integrating farm level with aggregate level of analysis. The methodology combines various clustering methods and proximity measures to group farms on the basis of operational parameters that reflect conditions necessary for exact aggregation. The methodology builds a step-by-step search procedure through a set of possible classifications to identify one that fits the purpose reasonably well. The methodology is illustrated for Amol Township. It allows generating and testing alternative classifications each with different resultant farm types.

The study argues that land has a very strong socio-economic components that are not dealt with in the land unit concept and, therefore, a more integrated unit is defined. For this purpose the concept of "farm type land unit (FTLU)" is introduced. A FTLU is considered to be a farm type's share in a particular land unit or, alternatively, a land unit share in a particular farm type. The concept of FTLU is operationalised by establishing a (partial) link between geographic information system (GIS) and classification models. This link allows mapping of farm types and then linking them spatially with land units.

An integrated approach to definition and description of land use systems, and quantification of their input and output coefficients is presented. The approach presented here considers land use systems as integral systems that include both bio-physical and socio-economic components. The concept ILUS is proposed for a specific form of describing a land use system. The term ILUS is defined as a unique combination of a farm type land unit (FTLU), a land use type (LUT), and a production technique. ILUSs are described in terms of operation sequences. Such a description then serves as a basis for the calculation of the required input-output coefficients. Each unique operation sequence within a ILUS can be interpreted as a specific (land use) activity. Each activity is defined and described quantitatively in terms of input and output coefficients which quantify the relation between inputs of production and the outputs, desired as well as undesired.

Information on bio-physical and socio-economic components of land use systems is then confronted in an integrated land use planning and policy analysis (ILUPPA) model. The linear programming model. ILUPPA is a mathematical programming model in terms of solution technique, however, it is best described as a behavioural simulation model. It attempts to describe how farmers will react to certain classes of policy instruments that may influence their land allocation decisions. ILUPPA generates alternative land use policy options through the definition and description of various land use policy scenarios, corresponding to various policy instruments.

Because the purpose of the model is to generate sustainable land use policy options, various land use scenarios corresponding to different policy instruments are defined. On the basis of these scenarios, the model generates a number of feasible land use policy alternatives with their associated ILUSs and corresponding input and output coefficients. A multi-criteria evaluation technique is applied to rank the set of alternative land use policy scenarios, and hence to assist policy makers in selecting the "best" or the most preferred land use alternative or to facilitate a movement towards a consensus. To take into account the multiple and conflicting views, various preferences or priorities are included in the evaluation.

The rankings of the various policy scenarios, from different policy perspectives, are presented. Results show, that, for the specific situation of Amol sub-region and under the assumed policy views: non-price policy instruments are more effective in bringing about the desired changes and in achieving policy objectives;when more priority is given to environmental protection, the present situation, as reflected by the base scenario, is ranked most unfavourable; and the 'land consolidation' scenario is a good compromise among the different policy views.

In conclusion, the proposed methodology proves to considerably reduce the aggregation errors when compared to the existing modelling approaches in land use planning and policy analysis and is therefore expected to make a significantly positive contribution to improved quality of agricultural planning and policy analysis. Some degree of aggregation is, of course, inevitable to facilitate modelling and to restrict the costs of the analysis to 'reasonable' levels. Implementation of the proposed methodology requires a large database and the gains in precision of the analysis must be balanced against the higher costs of developing and implementing the methodology.

Land use system evaluation: concepts and methodology.
Stomph, T.J. ; Fresco, L.O. ; Keulen, H. van - \ 1994
Agricultural Systems 44 (1994)3. - ISSN 0308-521X - p. 243 - 255.
Analysis of land use systems can be conveniently performed through partial analyses of the bio-physical and the socio-economic sub-systems, followed by their integration. The place of land use practices in both sub-systems is discussed and a format for the description of the bio-physical components of land use practices is proposed. This new operation sequence approach is a deviation from the widely used land utilization type (LUT) concept. Differences and advantages are discussed. The proposed format allows both a more realistic quantitative assessment of the performance of the bio-physical sub-system and a quantitative integration of the bio-physical and socio-economic sub-systems for the overall land use system evaluation.
Land use zones and land use patterns in the Atlantic Zone of Costa Rica : a pattern recognition approach to land use inventory at the sub-regional scale, using remote sensing and GIS, applying an object-oriented and data-driven strategy
Huising, J. - \ 1993
Agricultural University. Promotor(en): M. Molenaar, co-promotor(en): J. Bouma. - S.l. : S.n. - ISBN 9789054851066 - 222
landevaluatie - grondvermogen - bodemgeschiktheid - ruimtelijke ordening - landgebruik - zonering - costa rica - remote sensing - toepassingen - land evaluation - land capability - soil suitability - physical planning - land use - zoning - costa rica - remote sensing - applications

This thesis describes an approach to land use inventory at the sub-regional scale in the Guacimo-Rio Jiménez-Siquirres (GRS) area in the Atlantic Zone of Costa Rica. Therefore, the concept of "land use zones" is introduced. The land use zone (LUZ) plays a central role in the definition of an observational methodology as well for structuring dynamics in land use. Land use is described in terms of the land use pattern (LUP). The LUP denotes the farming systems and land utilization types (LUTs) occurring within a land use zone.

This thesis formulates a methodology for the inventory of land use and land use change that is object-oriented and data-driven. "Object-oriented" means that land use is expressed in terms of a collection of objects (land use zones) with specific geometric and thematic characteristics. A classification system is developed so that each class contains land use zones with a characteristic thematic description, geometry, aggregation structure and dynamics. The handling of such complex object information requires that emphasis is put on the definition of a data model.

For inventory purposes satellite imagery and aerial photos are used. The use of these materials involves pattern recognition. The "data-driven" approach in this case means that the classes to describe land use are not a-priori but inductive, i.e. they result from the inventory process. The data- driven approach is a strategy to gain insight in the sub-regional land use expressed in the land use patterns. The complex land use inventory process is unravelled into a number of sequentially ordered processing steps, described in the various chapters.
This thesis consists of three parts.

The first part of this thesis defines LUZs as a tool for the inventory of land use and land use change. From the comparison of aerial photos of 1948-1952 and 1984 we learn that the LUZs, that belong to the agricultural area, have stable boundaries. This implies that the land use zone may serve as a reference area for monitoring land use change.

Data on farm size distribution and farming system composition of a number of zones were obtained by means of a farm survey. The data show significant differences in the farming system composition, on the basis of which we define the land use patterns. That these clear differences occur indicates that the LUZ serves as a spatial unit for the land use inventory at the sub-regional level. The differences in LUP relate to differences observed in land cover composition and farm size distributions. This relation indicates that information on LUP may be inferred from composite land cover and farm size characteristics, so that satellite imagery and aerial photos can be used as tools for land use inventory, if the proper rules for interpretation are applied.

The correspondence between LUP and composite land cover implies that change in LUP may be inferred from change in land cover composition, under the condition that the geometric characteristics do not change. Change in land cover composition of LUZs between 1986 and 1990 was investigated using satellite imagery. Clear trends in land use change were observed, when the proper interpretation rules are applied. These trends were a decrease in the area for the cultivation of maize and in pasture land, and an increase in the area for banana and macadamia production and reforestation. Besides changes in area of crops, a change in the condition of pastures and banana plantations could be indicated.

The second part describes the pattern recognition process. This concerns the identification and classification of the LUZs. First, the stratification of the GRS area into sub-regions is described. The spatial pattern, which is determined by the size, form and arrangement of the agricultural fields, is used as a key to the aerial photo interpretation and as a criterion to identify the LUZs.

Once the LUZs are identified, their field size characteristics and the land cover composition are determined. A procedure is described for the per pixel land cover classification. This procedure will guide the image analyst in the complex task of defining a set of training classes with statistical properties suitable for the maximum likelihood classification. Emphasis is on the training phases. The procedure presented here makes use of supervised as well as unsupervised approaches.

Special attention has been paid to the definition of LUZ classes. Statistical methods are used to identify and define the different patterns as a key to classification. Field size characteristics of the LUZs were determined. One-way analysis of variance and multiple comparison were used to evaluated differences in mean field size. This resulted in the definition of five classes for mean field size.

A hierarchical cluster analysis was performed to evaluate the difference in land cover composition between the LUZs. To derive the relevant groups of corresponding LUZs from the results (represented by a dendrogram) a critical distance is defined. The critical distance denotes the minimum distance at which LUZs (or groups of LUZs) are considered significantly different with respect to their land cover composition. The critical distance reflects accuracy of data on land cover composition, which is determined by the accuracy of the land cover classification and the geometric accuracy of the land cover map and the LUZ map. The resulting composite land cover classes provide information on land use of the LUZs.

Land use information is obtained by interpretation of the land cover composition and field size characteristics of the LUZs. This interpretation involves the transformation of data classes into information categories by using mapping rules (also termed decision rules). Mapping rules assign a conditional class label to an object, whereby the condition refers to a particular context. The mapping involves complex decisions. Insight in the complex decision structure is gained by putting the decision rules in hierarchical order. The result is a decision tree for the classification of LUZs in terms of LUPs. The decision tree leads to stepwise classification of LUZs. The decision tree provides a formalized description of the decisions in the classification of the LUZs.

In Part Three the land use in the GRS area is evaluated with respect to bio-physical land potentials. The LUZ map and the physiographic soil map were combined. The soil unit boundaries and the land use zone boundaries corresponded to a high degree. But this does not mean that land use is in agreement with the (bio-physical) land potentials. Results show that 18 % of the GRS area is at risk of land degradation, while 51 % of the area is considered to have potential for more intensive use. Expert judgement is used to determine the suitability of the soil types for specific land utilization types (LUTs). However, the exact position of the soil type or the LUT cannot be determined at a sub-regional scale, with units being composite in nature. This introduces a fundamental uncertainty with respect to the statements on land use suitability. The study, therefore, has an exploratory character. The figures denote expectations.

In the last chapter the variation in banana yield within one plantation (representing a particular LUZ) is investigated. Soil survey data explained 67 % of the variation. Combining Landsat-TM and soil data did not provide a better estimation of yields. The explained variation remained 67 %.

Land evaluation for agricultural development : some explorations of land-use systems analysis with particular reference to Latin America
Beek, K.J. - \ 1978
Wageningen University. Promotor(en): J. Bennema; H.A. Luning. - Wageningen : ILRI - 333
economie - grondvermogen - landevaluatie - landgebruik - latijns-amerika - ruimtelijke ordening - bodemgeschiktheid - zonering - economics - land capability - land evaluation - land use - latin america - physical planning - soil suitability - zoning - cum laude

Increases in the demand for agricultural produce and for space to meet non-agricultural needs are provoking rapid changes in the use of land. These changes have stimulated a critical examination of our methods of looking at land. Most useful is a land evaluation that predicts the inputs, outputs, and other favourable as well as adverse effects resulting from specified uses of the land that is being evaluated (Chapter 1).


Thus, relevant uses need to be identified at an early stage (Chapter 2). This has not always been satisfactory. To help in land evaluation, the concept 'land utilization type' (LUT) has been introduced. This is defined as a specific way, actual or alternative, of using the land, described in terms of produce, labour, capital, management, technology and scale of operations. The principal objective of this thesis is to strengthen the philosophical base of land evaluation by explaining the LUT concept. Many similarities exist between this concept in land evaluation and other land-use defining concepts such as production and farming systems. Due to the complicated interactions that occur between their many constituent parts, the analysis of farming systems cannot fully account for the variation in physical land conditions. Land evaluation contributes to solving this problem by making preliminary and partial analyses of the variability of the land and of its influence on the performance of present and alternative land uses. To this end, land use is arbitrarily subdivided into two elements: the land (LU), mostly described by land evaluators in terms of land (mapping) units, and the use (LUT). Thus it should be possible to predict the performance of different LU, LUT combinations, called 'land use systems' (LU S) in this report. Such a 'landuse systems approach' should permit easy extrapolation of the land evaluation results to farming systems research and land use planning.


In agronomy the term 'requirement' is commonly used when referring to the specific land conditions required for the successful growth of a crop or the functioning of an agricultural implement, e.g. the water requirements of wheat or the soil workability requirements of a tractor-driven plough. These land requirements (LR) are the most fundamental aspects of the land utilization types for purposes of land evaluation (Chapter 3). A very critical aspect of land evaluation is the availability of information
about these LRs, especially in developing countries. Most useful are the descriptions of LR expressed in terms of relationships between different levels of specified land conditions and the corresponding levels of output, e.g. a table or graph that relates different levels of soil salinity with yield.

The land requirements of a LUT determine to a great extent which land resources data need to be studied and in how much detail. Early identification of LUTs and their land requirements may considerably reduce the cost and duration of the land resource studies by focussing attention on those land characteristics that may not wholly meet these requirements. In any event, land resource studies result in an enormous amount of data about soil, climate, hydrology etc. But, because of the way data are collected according to the academic discipline of the researcher, important relations and interactions between different land attributes are often overlooked, particularly those between climate and soil. To synthesize the overwhelming volume of data into a more comprehensible form, the construction of simple functional models of the physical environment (LU) is proposed, based on the concept of land qualities. A land quality is a component of the land which acts as a separate factor on the land-use performance. The following broad types of land qualities have been distinguished:

- ecological qualities; e.g. available water, length of growing season;
- management qualities; e.g. the possibility of using specified types of implements or transportation;
- conservation qualities; they represent the land's unique capacities to maintain the status of the land qualities, in particular the productive capacity;
- improvement qualities; land units differ in behaviour when certain physical inputs are applied for their improvement: they have a different 'input application efficiency', e.g. in their response to fertilizers or irrigation water.

There is still much to be achieved in the quantitative measurement of land qualities. They are usually ranked on an ordinal scale: high-medium-low-very low. Statistical methods, such as multiple regression and principal component analysis, are also used as a means of rating land qualities, e.g. soil fertility or soil erosion susceptibility. The success of these statistical methods for describing land qualities seems to be attributable to the small number of factors taken into account. The prospects of using mathematical and analog models for characterizing and simulating dynamic land qualities influenced by the weather, e.g. the soil workability, oxygen contained in the soil, soil nitrogen, are very important. The timing of land-use activities and processes of the LUT - the cropping calender - affects the way in which the time intervals need to be chosen for measuring and simulating dynamic land qualities and component properties.

Land evaluation should be able to predict the impact of land use proposals not only for single land (mapping) units but also for combinations of land units and for the physical environment as a whole. Also, interactions occurring between different land
uses operating on different land units should be foreseen. For this purpose, a distinction is proposed between internal land qualities of individual land units and overall land qualities of major landscape elements, internal land requirements of individual land utilization types and overall land requirements encompassing the sum of individual land requirements made by the different land utilization types that operate simultaneously.


In Chapter 4 the different approaches to land evaluation are presented. At the highest level, a distinction is made between general purpose and specific purpose land evaluation. General purpose land evaluation represents a standardized approach for all lands to evaluate their capability to support a generally defined land use. The best known example is the USDA Land Capability System. Specific purpose land evaluation represents a pragmatic approach: not only the land but also the use possibilities (LUT) are explicitly studied. The use (LUT) becomes as much a determinant of land suitability as the land itself. Many land suitability classifications for specific crops belong to this category.

To compare the performances of different LU-LUT combinations, not only an analysis of the physical factors is needed (physical land evaluation), but also a socioeconomic analysis. The approach to land evaluation that includes socio-economic analysis has been named 'integral land evaluation'.

Application of the proposed concepts and procedures of land evaluation requires close contact with the farmer: his operations need to be observed, and his achievements, attitudes, and expectations taken into account. During field surveys, one should always be on the look-out for potentially constraining land qualities. Observation of present land use and discussions with farmers will improve the correspondence between the real land conditions and their descriptive models in terms of qualities and properties.

To illustrate the above concepts and procedures in land evaluation, methods from Venezuela, Nicaragua, Mexico, Brazil, and Chile are described. In Latin America land evaluation is relied on as a fundamental source of information for agricultural development. Land evaluation methods that evolved in other countries, especially the USDA Land Capability System, have not been rigidly followed. New systems are being developed to suit local needs. The willingness of national scientists to abandon established methods of land capability classification is encouraging the introduction of new approaches that pay more attention to the biological, technical, and socioeconomic aspects of land use, and in particular to the farmer himself, In such specific.purpose land evaluations, the dynamic aspects of land and land use can no longer be ignored; this is making land evaluation more complex, but not insurmountably so, given today's data- handling techniques. This idea is elaborated in Chapter 5, where the possibilities for using systems analysis are explored.


Land-use systems analysis in land evaluation must be understood as 'simulation', defined by De Wit and Goudriaan (1974) as the building of a dynamic model and the study of its behaviour. The land-use model only includes that part of reality that is needed to answer the questions asked: to predict inputs (I), outputs (Y) and changes in the values of land qualities (LQ), on-site or off-site, that would arise if a particular LU were to be combined with a specific LUT.

To be able to provide this information the relation structure of the land-use system must be known. This consists of three fundamental relations:
Y = F(LQ); LQ = F(I); Y = F(I)
These relations are interrelated; one relation can be derived from the two others through the elimination of one variable, usually LQ A graphical method of co-axial analysis is shown for expressing the I-LQY relations.

A further simplification is the tabular presentation of the relation structure of a landuse system, presenting only a few input-land quality-output combinations. Two multiple- entry tables are proposed: the land quality table (Table 5.4A) expressing the input-land quality relations for land units(LU) with different land improvement qualities, and the output table (Table 5.4B) expressing land quality-output relations for land utilization types (LUT) with different land requirements. Combination of the two tables permits the identification of several alternative input-land quality-output combinations for each LU- LUT combination.

A distinction is made between descriptive and prescriptive land-use systems analysis. During the descriptive analysis, physical inputs for ameliorating constraining land qualities, their management and conservation, are compared with their effects on the land qualities and the outputs: 'descriptive input-output analysis'. This information is needed for the next step, when the suitability of a particular land unit (LU) for combination with a particular land utilization type (LUT) is classified: 'prescriptive land suitability classification'. During this second step, for each LUT-LU combination, the input-land quality-output combination is selected which places the land unit in the highest possible land suitability class: a kind of optimization process.


The use of simulation models of specific land use processes and mechanisms holds much promise for land-use systems analysis and is therefore likely to increase, particularly in situations where the physical and/or socio-economic conditions seriously limit a satisfactory matching between land qualities and land requirements.

Such models will probably relate primarily to specific partial land-use problems, e.g. drainage, soil tillage, the behaviour of nitrogen or chemical fertilizers, and to potential yield. In the immediate future the use of mathematical models solely for simulating all input-ouput relations influencing the performance of a land use system will probably remain too complex to satisfy practical land evaluation entirely. Thus land evaluation must compromise between scientific ideals and the limitations posed by data availability, data reliability, and the possibilities for data handling.

Meanwhile land resources inventories should aim increasingly towards the collection of data that explicitly characterize the fundamental environmental regimes (i.e. land qualities) influencing the physiological and agricultural mechanisms and processes, to improve the possibilities for land-use simulation and the prediction of landuse performance.

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