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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    Substantial Reductions in Cloud Cover and Moisture Transport by Dynamic Plant Responses
    Sikma, Martin ; Vilà-Guerau de Arellano, Jordi - \ 2019
    Geophysical Research Letters 46 (2019)3. - ISSN 0094-8276 - p. 1870 - 1878.
    cloud shading - heterogeneity - land-atmosphere interactions - LES - plant stomatal responses - wind

    Cumulus clouds make a significant contribution to the Earth's energy balance and hydrological cycle and are a major source of uncertainty in climate projections. Reducing uncertainty by expanding our understanding of the processes that drive cumulus convection is vital to the accurate identification of future global and regional climate impacts. Here we adopt an interdisciplinary approach that integrates interrelated scales from plant physiology to atmospheric turbulence. Our explicit simulations mimic the land-atmosphere approach implemented in current numerical weather prediction, and global climate models enable us to conclude that neglecting local plant dynamic responses leads to misrepresentations in the cloud cover and midtropospheric moisture convection of up to 21% and 56%, respectively. Our approach offers insights into the key role played by the active vegetation on atmospheric convective mixing that has recently been identified as the source of half of the variance in global warming projections (i.e., equilibrium climate sensitivity).

    Economics of Sustainable Development and the Bioeconomy
    Zilberman, David ; Gordon, Ben ; Hochman, Gal ; Wesseler, J.H.H. - \ 2018
    Applied Economic Perspectives and Policy 40 (2018)1. - ISSN 2040-5790 - p. 22 - 37.
    Sustainable development - bioeconomy - dynamics - heterogeneity - adoption - renewable resources
    Sustainable development can be attained by policies that are derived by analyses that integrate biophysical considerations into economic models. We show that policies and incentives that correct market failure can attain sustainable resources, and development of the bioeconomy, which relies on biological processes and feed-stock to produce renewable products. The design of sustainable development policies and analysis of the bioeconomy pose new challenges to applied economists, who are uniquely qualified to integrate economic analysis with biophysical considerations.
    The evolution of the MasAgro hubs : responsiveness and serendipity as drivers of agricultural innovation in a dynamic and heterogeneous context
    Camacho-Villa, Tania Carolina ; Almekinders, Conny ; Hellin, Jon ; Martinez-Cruz, Tania Eulalia ; Rendon-Medel, Roberto ; Guevara-Hernández, Francisco ; Beuchelt, Tina D. ; Govaerts, Bram - \ 2016
    The Journal of Agricultural Education and Extension 22 (2016)5. - ISSN 1389-224X - p. 455 - 470.
    adaptive management - Agricultural innovation - heterogeneity - MasAgro - Mexico

    Purpose: Little is known about effective ways to operationalize agricultural innovation processes. We use the MasAgro program in Mexico (which aims to increase maize and wheat productivity, profitability and sustainability), and the experiences of middle level ‘hub managers’, to understand how innovation processes occur in heterogeneous and changing contexts. Design/methodology/approach: We use a comparative case study analysis involving research tools such as documentary review, key informant interviews, focus group discussions, and reflection workshops with key actors. Findings: Our research shows how a program, that initially had a relatively narrow technology focus, evolved towards an innovation system approach. The adaptive management of such a process was in response to context-specific challenges and opportunities. In the heterogeneous context of Mexico this results in diverse ways of operationalization at the hub level, leading to different collaborating partners and technology portfolios. Practical implications: MasAgro experiences merit analysis in the light of national public efforts to transform agricultural advisory services and accommodate pluralistic agricultural extension approaches in Latin America. Such efforts need long-term coherent macro level visions, frameworks and support, while the serendipitous nature of the process requires meso-level implementers to respond and adapt to and move the innovation process forward. Originality/value: This paper contributes to the debate on how to operationalize large programs by showing that the innovation support arrangements enacted in the field should allow for diversity and have a degree of flexibility to accommodate heterogeneous demands from farmers in different contexts as well as continuous changes in the politico- institutional environment.

    Quantitative and ecological aspects of Listeria monocytogenes population heterogeneity
    Metselaar, K.I. - \ 2016
    Wageningen University. Promotor(en): Marcel Zwietering; Tjakko Abee, co-promotor(en): Heidy den Besten. - Wageningen : Wageningen University - ISBN 9789462577664 - 173
    listeria - listeria monocytogenes - stress - stress tolerance - ribosomes - proteins - lactobacillus plantarum - behaviour - ecological assessment - genome analysis - dna sequencing - resistance - heterogeneity - listeria - listeria monocytogenes - stress - stresstolerantie - ribosomen - eiwitten - lactobacillus plantarum - gedrag - ecologische beoordeling - genoomanalyse - dna-sequencing - weerstand - heterogeniteit

    Bacterial stress response and heterogeneity therein is one of the biggest challenges posed by minimal processing. Heterogeneity and resulting tailing representing a more resistant fraction of the population, can have several causes and can be transient or stably in nature. Stable increased stress resistance is caused by alterations in the genome and therefore inheritable and is referred to as stable stress resistant variants. Also L. monocytogenes exhibits a heterogeneous response upon stress exposure which can be partially attributed to the presence of stable stress resistant variants. Adverse environments were shown to select for stable stress resistant variants. The objective of the research described in this thesis was to evaluate if L. monocytogenes population diversity and the presence of stable resistant variants is a general phenomenon that is observed upon different types of stress exposure, to get more insight in the mechanisms leading to increased resistance and to evaluate the ecological behaviour and potential impact on food safety of these stable resistant variants. Acid stress was chosen as it is an important hurdle both in food preservation, as well as in stomach survival.

    First, the non-linear inactivation kinetics of L. monocytogenes upon acid exposure were quantitatively described. A commonly used biphasic inactivation model was reparameterized, which improved the statistical performance of the model and resulted in more accurate estimation of the resistant fraction within L. monocytogenes WT populations. The observed tailing suggested that stable stress resistant variants might also be found upon acid exposure. Indeed, 23 stable acid resistant variants of L. monocytogenes LO28 were isolated from the tail after exposure of late-exponential phase cells to pH 3.5 for 90 min, with different degrees of acid resistance amongst them. Increased acid resistance showed to be significantly correlated to reduced growth rate. Studying the growth boundaries of the WT and a representative set of variants indicated that the increased resistance of the variants was only related to survival of severe pH stress but did not allow for better growth or survival at mild pH stress.
    A set of variants were further characterized phenotypically and cluster analysis was performed. This resulted in three clusters and four individual variants and revealed multiple-stress resistance, with both unique and overlapping features related to stress resistance, growth, motility, biofilm formation and virulence indicators. A higher glutamate decarboxylase (GAD) activity correlated with increased acid resistance. Whole genome sequencing of a set of variants was performed and revealed mutations in rpsU, encoding ribosomal protein S21. This rpsU mutation was found in all 11 variants comprising the largest phenotypic cluster, indicating a potential role of this ribosomal protein in stress resistance. Mutations in ctsR, which were previously shown to be responsible for increased resistance of heat and HHP resistant variants, were not found in the acid resistant variants. This underlined that large population diversity exists within one L. monocytogenes strain and that different adverse conditions drive selection for different variants.

    Next, the performance in mixed species biofilms with Lactobacillus plantarum was evaluated, as well as their benzalkonium chloride (BAC) resistance in these biofilms. It was hypothesized that the acid resistant variants might also show better survival in biofilms with L. plantarum, which provide an acidic environment by lactose fermentation with pH values below the growth boundary of L. monocytogenes when biofilms mature. L. monocytogenes LO28 WT and eight acid resistant variants were capable of forming mixed biofilms with L. plantarum at 20°C and 30°C in BHI supplemented with manganese and glucose. Some of the variants were able to withstand the low pH in the mixed biofilms for a longer time than the WT and there were clear differences in survival between the variants which could not be correlated to (lactic) acid resistance alone. Adaptation to mild pH of liquid cultures during growth to stationary phase increased the acid resistance of some variants to a greater extent than of others, which could be correlated to increased survival in the mixed biofilms. There were no clear differences in BAC resistance between the wild type and variants in mixed biofilms.

    Lastly, a set of robustness and fitness parameters of WT and variants was obtained and used to model their growth behaviour under combined mild stress conditions and to model their performance in a simulated food chain. This gave more insight in the trade-off between increased stress resistance and growth capacity. Predictions of performance were validated in single and mixed cultures by plate counts and by qPCR in which WT and an rpsU deletion variant were distinguished by specific primers. Growth predictions for WT and rpsU deletion variant were matching the experimental data generally well. Globally, the variants are more robust than the WT but the WT grows faster than most variants. Validation of performance in a simulated food chain consisting of subsequent growth and inactivation steps, confirmed the trend of higher growth fitness and lower stress robustness for the WT compared to the rpsU variant. This quantitative data set provides insights into the conditions which can select for stress resistant variants in industrial settings and their potential persistence in food processing environments.

    In conclusion, the work presented in this thesis highlights the population diversity of L. monocytogenes and the impact of environmental conditions on the population composition, which is of great importance for minimal processing. The work of this thesis resulted in more insight in the mechanisms underlying increased resistance of stress resistant variants and quantitative data on the behaviour of stress resistant variants which can be implemented in predictive microbiology and quantitative risk assessments aiming at finding the balance between food safety and food quality.

    Variation in elevation and sward height facilitate coexistence of goose species through allometric responses in wetlands
    Zhang, Yong ; Prins, Herbert H.T. ; Cao, Lei ; Zhao, Meijuan ; Boer, Fred de - \ 2016
    Waterbirds 39 (2016)1. - ISSN 1524-4695 - p. 34 - 44.
    Anser albifrons - Anser fabalis - Bean Goose - body size - forage quality - forage quantity - grassland - Greater White-fronted Goose - habitat selection - heterogeneity

    Allometric scaling law predicts that herbivores respond differently to the availability of resources, mediated by body size. However, studies of allometric responses have often focused on animals with a relatively large difference in body size. Here, using a correlative field study, habitat use by two herbivorous species, the Bean Goose (Anser fabalis) and the Greater White-fronted Goose (A. albifrons), with a relatively small difference in body size was investigated during the wintering period. Both a generalized linear mixed model and a mixed logistic regression model showed that both species selected lower lying areas that were recently exposed, and, as expected, the smaller Greater White-fronted Goose showed a stronger selection of foraging habitat than the larger Bean Goose. Sward height also influenced habitat selection by both species, and the smaller species selected shorter swards than the larger species. In terms of forage quality, both models failed to detect a significant effect of nitrogen content on goose habitat selection. A logistic regression model showed that structural heterogeneity of the sward negatively correlated with the patch selection of the smaller species, but for the larger species such a correlation was not found. In agreement with our hypotheses, our results provide some preliminary indication that coexistence of the two goose species studied here might be mediated by an allometric response even if the difference in body size is relatively small.

    Genetic analysis of within-litter variation in piglets’ birth weight using genomic or pedigree relationship matrices
    Sell, E.B. ; Wang, Q. ; Mulder, H.A. ; Knol, E.F. - \ 2015
    Journal of Animal Science 93 (2015)4. - ISSN 0021-8812 - p. 1471 - 1480.
    generalized linear-models - single nucleotide polymorphism - environmental variance - broiler-chickens - residual variance - individual birth - breeding values - parameters - heterogeneity - selection
    The objective of this study was to estimate the genetic variance for within-litter variation of birth weight (BW0) using genomic (GRM) or pedigree relationship matrices (PRM) and to compare the accuracy of estimated breeding values (EBV) for within-litter variation of BW0 using GRM and PRM. The BW0 and residual variance of BW0 were modeled by the double hierarchical generalized linear model using GRM or PRM. Data came from 2 dam lines: Landrace and Large White. After editing, the data set in Landrace consisted of 748 sows with 1,938 litters and 29,430 piglets and in Large White of 989 sows with 3,320 litters and 51,818 piglets. To construct GRM, 46,466 (Landrace) and 44,826 (Large White) single nucleotide polymorphisms were used, whereas to construct PRM, 5 generations of pedigree were used. The accuracy of EBV with GRM was estimated with 8-fold cross-validation and compared to PRM. Estimated variance components were highly similar for GRM and PRM. The maternal genetic variance in residual variance of BW0 in Landrace was 0.05 with GRM and 0.06 with PRM. In Large White these were 0.04 with GRM and 0.05 with PRM. The genetic coefficient of variation (GCVSDe) was about 0.10 in both dam lines. This indicates a change of 10% in residual SD of BW0 when achieving a genetic response of 1 genetic standard deviation. The genetic correlation between birth weight and its residual variance was about 0.6 in both dam lines. The accuracies of selection for within-litter variation of birth weight were 0.35 with GRM and 0.23 with PRM in Landrace and 0.29 with GRM and 0.34 with PRM in Large White. In this case, using GRM did not significantly increase accuracies of selection. Results, however, show good opportunities to select for reduced within-litter variation of BW0. Genomic selection can increase accuracy of selection when reference populations contain at least 2,000 sows
    Trade-offs between pasture production and farmland bird conservation: exploration of options using a dynamic farm model
    Sabatier, R. ; Teillard, F. ; Rossing, W.A.H. ; Doyen, L. ; Tichit, M. - \ 2015
    Animal 9 (2015)5. - ISSN 1751-7311 - p. 899 - 907.
    grassland agroecosystem - viability model - management - biodiversity - heterogeneity - populations - habitat - waders
    In European grassland landscapes, grazing and mowing play a key role for the maintenance of high-quality habitats that host important bird populations. As grasslands are also key resources for cattle feeding, there is a need to develop management strategies that achieve the double objective of production and biodiversity conservation. The objective of this study was to use a modelling approach to generate recognisable patterns of bird dynamics in farms composed of different land use proportions, and to compare their production and ecological dimensions. We developed a dynamic model, which linked grassland management to bird population dynamics at the field and farm levels. The model was parameterised for two types of suckling farms corresponding to contrasting levels of grassland intensification and for two bird species of high conservation value. A viability algorithm was used to define and assess viable management strategies for production and ecological performance so as to draw the shape of the relationship between both types of performances for the two types of farms. Our results indicated that, at the farm level, there was a farming system effect with a negative and non-linear relationship linking performance. Improving bird population maintenance was less costly in extensive farms compared with intensive farms. At the field level, the model predicted the timing and intensity of land use, maximising either production or ecological performance. The results suggested that multi-objective grassland management would benefit from public policies that consider levels of organisation higher than the field level, such as the farm or the landscape.
    Combining multi-dimensional scaling and cluster analysis to describe the diversity of rural households
    Pacini, G.C. ; Colucci, D. ; Baudron, F. ; Righi, E. ; Corbeels, M. ; Tittonell, P.A. ; Stefanini, F.M. - \ 2014
    Experimental Agriculture 50 (2014)3. - ISSN 0014-4797 - p. 376 - 397.
    farms - management - heterogeneity - assemblages - typologies - indicators - region - spain
    Capturing agricultural heterogeneity through the analysis of farm typologies is key with regard to the design of sustainable policies and to the adoptability of new technologies. An optimal balance needs to be found between, on the one hand, the requirement to consider local stakeholder and expert knowledge for typology identification, and on the other hand, the need to identify typologies that transcend the local boundaries of single studies and can be used for comparisons. In this paper, we propose a method that supports expert-driven identification of farm typologies, while at the same time keeping the characteristics of objectivity and reproducibility of statistical tools. The method uses a range of multivariate analysis techniques and it is based on a protocol that favours the use of stakeholder and expert knowledge in the process of typology identification by means of visualization of farm groups and relevant statistics. Results of two studies in Zimbabwe and Kenya are shown. Findings obtained with the method proposed are contrasted with those obtained through a parametric method based on latent class analysis. The method is compared to alternative approaches with regard to stakeholder-orientation and statistical reliability.
    Sensor-based farming : Mogelijkheden voor bollen- en vaste planten
    Baltissen, Ton - \ 2014
    precision agriculture - heterogeneity - crop growth stage - crop density - geographical information systems - spot spraying - plant protection - chemical control - ornamental bulbs - ornamental crops - field crops - outdoor cropping - cropping systems - fertilizer application
    Ercella succinigenes gen. nov., sp. nov., an anaerobic succinate-producing bacterium
    Gelder, A.H. van; Sousa, D.Z. ; Rijpstra, W.I. ; Damsté, J.S. ; Stams, A.J.M. ; Sanchez Andrea, I. - \ 2014
    International Journal of Systematic and Evolutionary Microbiology 64 (2014)7. - ISSN 1466-5026 - p. 2449 - 2454.
    ribosomal-rna genes - acid - heterogeneity - fermentation - sequences - biofuels - glycerol - industry - operons - genomes
    A novel anaerobic succinate-producing bacterium, strain ZWBT, was isolated from sludge collected from a biogas desulfurization bioreactor (Eerbeek, the Netherlands). Cells were non-spore-forming, motile, slightly curved rods (0.4–0.5 µm in diameter and 2–3 µm in length), and stained Gram-negative. The temperature range for growth was 25–40 °C, with an optimum at 37 °C. The pH range for growth was 7.0–9.0, with an optimum at pH 7.5. Strain ZWBT was able to ferment glycerol and several carbohydrates mainly to H2, succinate and acetate. Sulfur and fumarate could be used as electron acceptors by strain ZWBT. The G+C content of the genomic DNA was 37.6 mol%. The most abundant fatty acids were iso-C14¿:¿0 and iso-C16¿:¿0 DMA. On the basis of 16S rRNA gene sequence similarity, strain ZWBT belongs to the family Ruminococcaceae and it is distantly related to Saccharofermentans acetigenes JCM 14006T (92.1¿%). Based on the physiological features and phylogenetic analysis, strain ZWBT represents a novel species of a new genus, for which the name Ercella succinigenes gen. nov., sp. nov. is proposed. The type strain of Ercella succinigenes is ZWBT (¿=¿DSM 27333T¿=¿JCM 19283T).
    Using agronomic tools to improve pineapple quality and its uniformity in Benin
    Fassinou Hotegni, V.N. - \ 2014
    Wageningen University. Promotor(en): Paul Struik; Jack van der Vorst, co-promotor(en): Willemien Lommen. - Wageningen : Wageningen University - ISBN 9789462570382 - 302
    ananas comosus - ananassen - fruitteelt - gewaskwaliteit - plantmateriaal - heterogeniteit - verbetering - gewasfysiologie - benin - ananas comosus - pineapples - fruit growing - crop quality - planting stock - heterogeneity - improvement - crop physiology - benin

    Keywords: Ananas comosus; Benin; cultural practices; fruit quality; hapas; heterogeneity; planting material; slips; suckers; supply chain; variation in quality; variation within crop; vigour.

    Poor average quality and uniformity in quality have become major issues in agri-food chains. This is also the case in the pineapple sector in Benin where less than 2% of the fresh pineapple is exported to international markets. The average quality of pineapple delivered to other markets, local and regional, is poor. The present thesis studied the improvement options in the pineapple sector which will help pineapple producers to produce higher pineapple quality for different markets, including international ones. This thesis aimed at (1) understanding how fresh pineapple supply chains are organised in Benin and identifying the bottlenecks for delivering the right pineapple to the right market; (2) increasing our knowledge on the agronomic tools used by pineapple producers to produce pineapple fruits; (3) understanding how agronomic factors affect pineapple quality and harvesting time, and (4) proposing and discussing the trade-offs between cultural practices. Research included analysis of supply chains and cropping systems and field experimentation.

    To understand how fresh pineapple supply chains are organised, 54 semi-structured interviews were held with key informants and 173 structured interviews with actor groups. Results indicated six main actor groups in the fresh pineapple chains: primary producers, exporters, wholesalers (those selling at local markets and those selling at regional markets), processors, retailers, and middlemen. Two pineapple cultivars were grown: Sugarloaf and Smooth Cayenne, with Sugarloaf being dominant in local and regional markets and Smooth Cayenne in European markets. The main constraints hampering the effectivity of the chains were: the non-controlled conditions under which the pineapple was transported from one actor group to another, the lack of appropriate storage facilities at wholesaler’s and processor’s levels, the unavailability of boxes for export and the non-concordance between actor groups in which quality attributes and criteria they valued most. In addition, most respondents interviewed affirmed that the pineapple quality was highly heterogeneous, emphasising the need to understand how pineapple is grown in Benin and what the constraints for producing high pineapple quality are.

    To find out the agronomic tools in use by pineapple producers in Benin, interviews were held with 100 producers in the pineapple production areas. Pineapple production practices proved diverse for both cultivars in planting density, flowering induction practice and fertiliser application. The production systems of the two pineapple cultivars differed in planting material used (slips in cv. Sugarloaf; hapas plus suckers in cv. Smooth Cayenne); the use of K2SO4 (not commonly used in cv. Sugarloaf and commonly used in cv. Smooth Cayenne); the number of fertiliser applications (lower in cv. Sugarloaf than in cv. Smooth Cayenne) and in the maturity synchronisation practice by means of Ethephon (not commonly used in cv. Sugarloaf and commonly used in cv. Smooth Cayenne). Constraints for high quality production were the unavailability of planting material, unavailability and high costs of fertilisers and the heterogeneity in planting material weight.

    To understand how agronomic factors affect pineapple quality and harvesting time, four on-farm experiments were conducted in commercial pineapple fields. Results first indicated that the heterogeneity in fruit weight was a consequence of the heterogeneity in plant vigour at artificial flowering induction time. The plant vigour at flowering induction was mainly related with the infructescence weight and less or not with crown weight. Second, results indicated that artificial flowering induction gave fruits with lower infructescence weight and heavier crown than natural flowering induction. Artificial maturity induction reduced the total soluble solids (TSS) concentration in the fruits. Finally, results showed that the reason why a high proportion of fruits in cv. Sugarloaf was not exportable to Europe was the high value in the ratio crown: infructescence height (above 1.5); in cv. Smooth Cayenne, reasons were a ratio crown: infructescence height as well as a TSS below 12 ºBrix.

    To come up with improvement options for high pineapple quality production with low heterogeneity in quality, the possibility of pruning slips on selective plants as means to improve uniformity in fruit quality was evaluated through two on-farm experiments on commercial fields with cv. Sugarloaf. Results revealed that pruning of slips did not significantly improve average fruit quality attributes and was not successful in achieving more uniform fruit quality at harvesting time. Through one experiment per pineapple cultivar, we investigated how fruit quality and its variation were affected by weight (in both pineapple cultivars) and type (in cv. Smooth Cayenne only) of planting material. Results showed that fruits from heavy planting material had heavier infructescence and fruit weights, longer infructescence height, but shorter crown height and smaller ratio crown: infructescence height than those from light planting material. In cv. Sugarloaf fruits from heavy planting material had higher variation in crown weight and lower variation in infructescence height than fruits from light and mixed (light plus heavy) planting materials. In cv. Smooth Cayenne, fruits from heavy planting material had a lower variation in fruit height than fruits from other classes of planting material. The type of planting material (in cv. Smooth Cayenne) had no effect on the average fruit quality attributes except on the crown height where fruits from hapas had shorter crowns than those from suckers. The type of planting material had in overall no significant effect on the variation in the fruit quality attributes.

    The present study is a step towards the improvement of the whole pineapple sector in Benin. It identified constraints for high pineapple quality production but also tested and proposed improvement options for high pineapple quality production.

    Livelihood strategies, resilience and transformability in African agroecosystems
    Tittonell, P.A. - \ 2014
    Agricultural Systems 126 (2014). - ISSN 0308-521X - p. 3 - 14.
    soil fertility management - social-ecological systems - western kenya - exploring diversity - makanya catchment - smallholder farms - poverty traps - heterogeneity - agriculture - tanzania
    Aiming to translate resilience thinking theory into farming systems design practice, this paper examines fundamental properties of complex systems dynamics and their relation with the mechanisms that govern resilience and transformability in African smallholder agriculture. Agroecosystems dynamics emerge from the aggregation of diverse livelihood strategies in response to changes in the agroecosystem context, and are characterised by non-linearity, irreversibility, convergence/divergence and hysteresis. I examine a number of case studies from Africa to verify three guiding hypotheses in connection to the diversity of rural livelihood strategies: (1) diversity as alternative system regimes; (2) diversity as the result of transformability; (3) diversity determined by changing agricultural contexts. The hierarchy of constraints that determine the space for manoeuvring in agroecosystems is described through the analogy of the Matryoshka nesting dolls: each system level confines and is confined by their immediate sub- and supra-systems. Agricultural contexts, as defined by agro-ecological potential, demography and market connectivity are also dynamic and their trajectory can be described as shifts across stability domains. An example from Kenya shows that household diversity can be described as alternative system regimes, through hysteretic rather than continuous, reversible models. In some particular cases diversity emerges from divergent pathways that may have implied radical transformations in the past, as shown here for rural livelihoods in northern Cameroun. A comparative analysis of East African agroecosystems shows that thresholds in specific variables that may point to the existence of possible tipping points are rather elusive and largely site specific, requiring systematic categorisation of agricultural contexts. While agroecology needs to provide the knowledge base for the ecological intensification of smallholder landscapes, policy and market developments are needed to deal with the Matryoshka effect – or with interactions that are presumably panarchical in certain cases. Desirable shifts in farming systems can only be stimulated by working on both ends simultaneously.
    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.
    Reconstructing grazer assemblages for protected area restoration
    Venter, J.A. ; Prins, H.H.T. ; Slotow, R. - \ 2014
    PLoS ONE 9 (2014)3. - ISSN 1932-6203 - 10 p.
    south-african savanna - middle stone-age - conservation management - distribution patterns - foraging behavior - landscape-scale - herbivore - fire - heterogeneity - biodiversity
    Protected area management agencies often struggle to reliably reconstruct grazer assemblages due to a lack of historical distribution data for their regions. Wrong predictions of grazing assemblages could potentially affect biodiversity negatively. The objective of the study was to determine how well grazing herbivores have become established since introduction to the Mkambati Nature Reserve, South Africa, how this was influenced by facilitation and competition, and how indigenous grazer assemblages can best be predicted for effective ecological restoration. Population trends of several grazing species were investigated in in order to determine how well they have become established since introduction. Five different conceivable grazing assemblages reflecting a range of approaches that are commonly encountered during conservation planning and management decision making were assessed. Species packing was used to predict whether facilitation, competition or co-existence were more likely to occur, and the species packing of the different assemblages were assessed using ANCOVA. Reconstructing a species assemblage using biogeographic and biological information provides the opportunity for a grazer assemblage that allows for facilitatory effects, which in turn leads to an ecosystem that is able to maintain its grazer assemblage structure. The strength of this approach lies in the ability to overcome the problem of depauperate grazer assemblages, resulting from a lack of historical data, by using biogeographical and biological processes, to assist in more effectively reconstructing grazer assemblages. Adaptive management of grazer assemblage restoration through reintroduction, using this approach would further mitigate management risks.
    Vegetation factors influencing density and distribution of wild large herbivores in a southern African savannah
    Gandiwa, E. - \ 2014
    African Journal of Ecology 52 (2014)3. - ISSN 0141-6707 - p. 274 - 283.
    gonarezhou-national-park - distribution patterns - ungulate diversity - semiarid savanna - water sources - zimbabwe - heterogeneity - populations - elephant - habitat
    Understanding factors influencing large herbivore densities and distribution in terrestrial ecosystems is a fundamental goal of ecology. This study examined environmental factors influencing the density and distribution of wild large herbivores in Gonarezhou National Park, Zimbabwe. Vegetation and surface water were predicted to have a stronger influence than anthropogenic-related disturbances (livestock grazing, fires, settlements and poaching) on the density and distribution of wild large herbivores. Aerial survey data for seven common wild large herbivores conducted in 2007 and 2009 and environmental data were collected. Only grass cover explained a significant proportion of the variation in large herbivore densities and distribution. Moreover, only two species densities significantly differed across the Gonarezhou, namely impala and zebra. In contrast, buffalo, elephant, giraffe, kudu and nyala densities did not differ significantly across the Gonarezhou. Overall, the findings only partly support the study prediction. The study results suggest the need to further investigate the roles of environmental factors at smaller scales in order to tease out their relative strengths in influencing density and distribution of large herbivores.
    Institutions and Bank Performance; A Stochastic Frontier Analysis
    Lensink, B.W. ; Meesters, A. - \ 2014
    Oxford Bulletin of Economics and Statistics 76 (2014)1. - ISSN 0305-9049 - p. 67 - 92.
    spanish savings banks - financial institutions - economic-development - efficiency - growth - deregulation - law - intermediation - heterogeneity - endowments
    This article investigates the impact of institutions on bank efficiency and technology, using a stochastic frontier analysis of a data set of 7,959 banks across 136 countries over 10 years. The results confirm the importance of well-developed institutions for the efficient operation of commercial banks. Furthermore, the insights reveal the impact of institutional reforms in improving bank efficiency. The results are robust to adjustments in country-specific effects, achieved by including country dummies, as well as across different risk profiles. Moreover, they provide empirical evidence in support of the public view of the banking sector.
    The influence of spatiotemporal variability and adaptations to hypoxia on empirical relationships between soil acidity and vegetation
    Cirkel, D.G. ; Witte, J.P.M. ; Bodegom, P.M. van; Nijp, J.J. ; Zee, S.E.A.T.M. van der - \ 2014
    Ecohydrology 7 (2014)1. - ISSN 1936-0584 - p. 21 - 32.
    bodemchemie - bodemaciditeit - vegetatietypen - bodem-plant relaties - soortensamenstelling - plantenfysiologie - rizosfeer - wetlands - heterogeniteit - ecohydrologie - ruimtelijke variatie - soil chemistry - soil acidity - vegetation types - soil plant relationships - species composition - plant physiology - rhizosphere - wetlands - heterogeneity - ecohydrology - spatial variation - ellenberg indicator values - field-measurements - plant ecology - ph changes - iron - regression - diversity - diffusion - oxidation
    Soil acidity is well known to affect the species composition of natural vegetation. The physiological adaptations of plants to soil acidity and related toxicity effects and nutrient deficiencies are, however, complex, manifold and hard to measure. Therefore, generally applicable quantifications of mechanistic plant responses to soil acidity are still not available. An alternative is the semi-quantitative and integrated response variable ‘indicator value for soil acidity’ (Rm). Although relationships between measured soil pH and Rm from various studies are usually strong, they often show systematic bias and still contain high residual variances. On the basis of a well-documented national dataset consisting of 91 vegetation plots and a dataset with detailed, within-plot, pH measurements taken at three periods during the growing season, it is shown that strong spatiotemporal variation of soil pH can be a critical source of systematic errors and statistical noise. The larger part of variation, however, could be explained by the moisture status of plots. For instance, Spearman's rho decreased from 93% for dry plots and 87% for moist plots to 59% for wet plots. The loss of relation between soil pH and Rm in the moderately acid to alkaline range at increasingly wetter plots is probably due to the establishment of aerenchyma-containing species, which are able to control their rhizosphere acidity. Adaptation to one site factor (oxygen deficit) apparently may induce indifference for other environmental factors (Fe2+, soil pH). For predictions of vegetation response to soil acidity, it is thus important to take the wetness of plots into account
    Efficiency of and interference among multiple Aquifer Thermal Energy Storage systems; A Dutch case study
    Bakr, M. ; Oostrom, N. van; Sommer, W.T. - \ 2013
    Renewable Energy 60 (2013). - ISSN 0960-1481 - p. 53 - 62.
    ground-water - heat - heterogeneity - transport - solute - model
    This paper describes the analysis of a real case of multiple Aquifer Thermal Energy Storage systems. The Hague, the capital city of the province of South Holland in the Netherlands, is densely populated with many ATES systems. A total of 19 ATES systems are installed in an area of 3.8 km(2) with a total of 76 functioning wells. The analysis focuses on the development of a coupled groundwater flow and heat transfer model over a period of 10 years. Results are then post-processed to evaluate efficiency of each individual well and system. Efficiency of the ATES systems has ranged between 68% and 87%. The analysis showed that efficiency tends, in general, to increase over time and stabilize at an asymptotic value after few years. Analysis of interference among individual wells of an ATES system and wells of other systems showed that interference could, in fact, have a positive impact on the efficiency of a well/system. Interference can increase efficiency of an ATES system since it can help in trapping energy (cold or warm) within the capture zone of all operating ATES systems. In the study area, the interference phenomenon affects efficiency, in general, positively where it increases the efficiency of individually operating wells by a maximum of 20%. However, the phenomenon also affects efficiency of some wells negatively where it reduces the efficiency of individually operating wells by a maximum of 25%. In average, systems in the study area are positively affected by interferences among each other with an overall average of 3.2% for all wells (over the 10 years operation period). (C) 2013 Elsevier Ltd. All rights reserved.
    Proton binding to soil humic and fulvic acids: Experiments and NICA-Donnan modelling
    Tan, W. ; Xiong, J. ; Li, Y. ; Wang, M. ; Weng, L. ; Koopal, L.K. - \ 2013
    Colloids and Surfaces. A: Physicochemical and Engineering Aspects 436 (2013). - ISSN 0927-7757 - p. 1152 - 1158.
    natural organic-matter - metal-ion binding - potentiometric titrations - affinity distributions - base properties - substances - heterogeneity - parameters - adsorption
    Proton binding to one soil fulvic acid (JGFA), two soil humic acids (JGHA, JLHA) and a lignite-based humic acid (PAHA) was investigated. The results were fitted to NICA-Donnan model and compared directly with the predictions using the generic parameters. NICA-Donnan model can describe proton binding satisfactorily when parameter fitting is allowed for humic substance (HS). However, predictions based on the generic parameter sets deviate for soil samples in a non-systematic way from the measured results. Replacing Qmax,H1 in generic parameter sets with material-specific values improves the predictions for soil HA significantly. For JGFA, the agreement between the model prediction and data is still not satisfactory after substitution. This is due to a very different pattern of site distribution of JGFA from that of generic FA. For two other soil FAs (FH-14, FH-22 of Milne's database) the generic predictions can be improved significantly with material-specific Qmax,H1. Adjusting also Qmax,H2 to HS material-specific value improves the prediction only slightly further. In practice, Qmax,H1 and Qmax,H2 of HS can be obtained in a relatively simple way by performing one acid–base titration at a given ionic strength and applying the procedure of Lenoir et al. to fit data to NICA equation. Introduction of thus obtained Qmax,H1 and Qmax,H2 into generic parameter sets improves the generic predictions significantly. The functional group contents as obtained by SG-method are not adequate for this purpose.
    Genetic variance in micro-environmental sensitivity for milk and milk quality in Walloon Holstein cattle
    Vandenplas, J. ; Bastin, C. ; Gengler, N. ; Mulder, H.A. - \ 2013
    Journal of Dairy Science 96 (2013)9. - ISSN 0022-0302 - p. 5977 - 5990.
    generalized linear-models - residual variance - breeding values - fatty-acids - production traits - bovine-milk - heterogeneity - variability - prediction - components
    Animals that are robust to environmental changes are desirable in the current dairy industry. Genetic differences in micro-environmental sensitivity can be studied through heterogeneity of residual variance between animals. However, residual variance between animals is usually assumed to be homogeneous in traditional genetic evaluations. The aim of this study was to investigate genetic heterogeneity of residual variance by estimating variance components in residual variance for milk yield, somatic cell score, contents in milk (g/dL) of 2 groups of milk fatty acids (i.e., saturated and unsaturated fatty acids), and the content in milk of one individual fatty acid (i.e., oleic acid, C18:1 cis-9), for first-parity Holstein cows in the Walloon Region of Belgium. A total of 146,027 test-day records from 26,887 cows in 747 herds were available. All cows had at least 3 records and a known sire. These sires had at least 10 cows with records and each herd × test-day had at least 5 cows. The 5 traits were analyzed separately based on fixed lactation curve and random regression test-day models for the mean. Estimation of variance components was performed by running iteratively expectation maximization-REML algorithm by the implementation of double hierarchical generalized linear models. Based on fixed lactation curve test-day mean models, heritability for residual variances ranged between 1.01 × 10-3 and 4.17 × 10-3 for all traits. The genetic standard deviation in residual variance (i.e., approximately the genetic coefficient of variation of residual variance) ranged between 0.12 and 0.17. Therefore, some genetic variance in micro-environmental sensitivity existed in the Walloon Holstein dairy cattle for the 5 studied traits. The standard deviations due to herd × test-day and permanent environment in residual variance ranged between 0.36 and 0.45 for herd × test-day effect and between 0.55 and 0.97 for permanent environmental effect. Therefore, nongenetic effects also contributed substantially to micro-environmental sensitivity. Addition of random regressions to the mean model did not reduce heterogeneity in residual variance and that genetic heterogeneity of residual variance was not simply an effect of an incomplete mean model.
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