Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production
Kamminga, Tjerko - \ 2017
Wageningen University. Promotor(en): V.A.P. Martins dos Santos, co-promotor(en): P.J. Schaap; J.J.E. Bijlsma. - Wageningen : Wageningen University - ISBN 9789463436519 - 152
interdisciplinary research - molecular biology - mycoplasma hyopneumoniae - vaccines - systems biology - systems analysis - pigs - pneumonia - animals - interdisciplinair onderzoek - moleculaire biologie - mycoplasma hyopneumoniae - vaccins - systeembiologie - systeemanalyse - varkens - longontsteking - dieren
Mycoplasma hyopneumoniae (M. hyopneumoniae) is a bacterial pathogen that has evolved from a gram-positive ancestor and specifically colonizes the lower respiratory tract of pigs where it causes enzootic pneumonia and plays a major role in the development of respiratory disease in pigs. Whole-cell inactivated vaccines are available that lower the severity of disease and are widely applied in pig industry to prevent clinical signs and improve pig herd health. However, production of these vaccines is challenging because it is not known which bacterial components are needed for protection and complex cultivation media are needed because growth requirements are not completely understood. The aim of this thesis was to understand growth and survival strategies of M. hyopneumoniae during infection, to integrate this knowledge with metabolic modeling under conditions used for vaccine production and apply this knowledge to improve the current production process for M. hyopneumoniae vaccines.
Chapter 1 provides a general introduction into the disease, treatment and prevention methods with a focus on vaccines. I then introduce the characteristics of the M. hyopneumoniae genome, transcriptome and review the current knowledge on infectious mechanisms and the response of the pig to infection and vaccination. Finally, I discuss the challenges related to vaccine production and introduce systems biology tools that will be applied in the thesis. In chapter 2 we define a strategy for risk-based process development of bacterial vaccines which provided the framework for future studies performed during this thesis. We propose to integrate the academic workflow for rational strain design with the industry standard for process design. Systems biology tools, especially genome-scale metabolic models, play an essential role in this strategy because application of these tools reduces process risks and increases process understanding. Therefore, in line with this strategy, we created a manually curated genome-scale metabolic model of M. hyopneumoniae which we applied to dynamically model the cultivation step in the vaccine production process (chapter 3). We found that only 16% of cellular energy in a standard fermentation was used for growth and 84% was used for non-growth associated maintenance. By model-driven experimentation we were able to increase the fraction of cellular energy used for growth by addition of pyruvate to the production medium, and showed in dedicated fermentor experiments that the improved process reached a 2.3 times higher biomass yield. Although the metabolic model helped to increase process yield, it did not allow prediction of a defined cultivation medium without components from porcine origin. Therefore, to better understand the dependency of M. hyopneumoniae on host derived components, we performed a functional comparison of 80 mycoplasma genomes and used multivariate and machine-learning algorithms to relate functional capability to the specific host and niche of mycoplasma species (chapter 4). This analysis allowed us to identify protein domains possibly needed for growth and survival in the pig lung. In addition, we found that protein domains expected to be essential for bacterial growth were not persistently present in mycoplasma genomes suggesting that alternative domain configurations exist that bypass their essentiality. To better understand whether the proteins we identified as possibly important for survival in pigs actually play a role during M. hyopneumoniae infection, we sequenced the bacterial mRNA during infection in chapter 5 and compared the in vivo transcriptome to that of broth grown mycoplasma. We found 22 up-regulated and 30 down-regulated genes during infection (FDR<0.01 and fold change >2LOG2) and identified differentially expressed ncRNAs. In chapter 6 we build upon our mycoplasma basis to further analyse the role of ncRNAs in bacterial genomes. We identified an exponential relationship between the AT content of genomes and the number of ncRNAs and propose that this relation is the result of spurious transcription, which is more likely to occur in AT rich genomes. This hypothesis is further substantiated by showing that spurious transcription demands minimal cellular energy and that overexpression of cis-binding ncRNAs in M. pneumoniae did not influence the level of proteins translated from their overlapping mRNAs. Finally, in chapter 7 I discuss four system strategies, identified in this thesis and derived from recent literature, and discuss how these strategies could be integrated in the metabolic model of M. hyopneumoniae. Lastly, I provide an outlook on the next steps needed for improvement of the production process for M. hyopneumoniae vaccines.
In conclusion, this work provided novel insight in the metabolic capability of M. hyopneumoniae based on the proteome domain content, captured in a genome-scale metabolic model and studied under in vitro and in vivo conditions. Biomass yield of the cultivation step for vaccine production was increased and the basis was laid to further improve the production process for M. hyopneumoniae vaccines using model-based experimentation.
Nat zandlandschap van de 21e eeuw : kennisagenda
Schouten, M.G.C. ; Jansen, A.A.M. ; Tweel-Groot, Loekie van - \ 2016
Landschap : tijdschrift voor landschapsecologie en milieukunde 33 (2016)2. - ISSN 0169-6300 - p. 118 - 121.
natuurbeheer - natuurgebieden - biodiversiteit - zandgronden - duurzame ontwikkeling - landschapsecologie - kennismanagement - soortendiversiteit - ecotypen - systeemanalyse - ecosystemen - toegepast onderzoek - bodems van waterrijke gebieden - nature management - natural areas - biodiversity - sandy soils - sustainable development - landscape ecology - knowledge management - species diversity - ecotypes - systems analysis - ecosystems - applied research - wetland soils
Hoe ziet een duurzaam en biodivers nat zandlandschap van de 21e eeuw eruit en hoe ontwikkelen we dat? Dat landschap zal ongetwijfeld een ander zijn dan dat van de 19e en de eerste helft van de 20e eeuw, maar de uitdaging is de totale soortenrijkdom hierin weer voldoende plaats te bieden. Dit artikel biedt een overzicht van de kennis die daartoe ontwikkeld moet worden.
Ecologisch raamwerk voor aquatische ecosystemen
Verdonschot, P.F.M. - \ 2015
Amersfoort : Stowa (Rapport / STOWA 2015-29) - ISBN 9789057737039 - 118
kaderrichtlijn water - aquatische ecologie - ecologische beoordeling - natuurbeleid - waterbeheer - zoetwaterorganismen - ecosystemen - modelleren - systeemanalyse - aquatische ecosystemen - water framework directive - aquatic ecology - ecological assessment - nature conservation policy - water management - freshwater organisms - ecosystems - modeling - systems analysis - aquatic ecosystems
Het doel van de KRW is het in waterlichamen bereiken van de goede ecologische toestand met, vanuit oogpunt van natuurbeleid, een hoge biodiversiteit. Om deze doelen te halen worden maatregelen uitgevoerd. Bij het nemen van maatregelen worden de omstandigheden in oppervlaktewaterecosystemen zo gewijzigd dat een verbetering van de ecologische toestand optreedt. De keuze van maatregelen vraagt kennis van (de toestand van) die factoren en van de achterliggende processen die deze verbetering bewerkstelligen. Om het juiste doel te kunnen bepalen en de juiste maatregelen te kunnen kiezen is begrip nodig van het systeemfunctioneren. Het doel van het ecologisch raamwerk is het geven van een onderbouwing aan de keuze van (kosten-)effectieve en in samenhang probleem-oplossende maatregelen en het afleiden van passende doelen. Om dit doel te bereiken is kennis nodig van de factoren en achterliggende processen die verbetering bewerkstelligen.
Toolkit for a systems analysis framework of the EU bioeconomy : overview of WP2 in the EU FP 7 SAT-BBE project: systems analysis tools framework for the EU Bio-Based Economy Strategy
Leeuwen, M.G.A. van; Meijl, J.C.M. van; Smeets, E.M.W. - \ 2014
Den Haag : LEI Wageningen UR - 30
economische ontwikkeling - monitoring - biobased economy - economische analyse - economische evaluatie - systeemanalyse - analytische methoden - europese unie - economic development - monitoring - biobased economy - economic analysis - economic evaluation - systems analysis - analytical methods - european union
The objective of the SAT-BBE project is to describe, monitor and model the bioeconomy part of the economic system, by the development of an appropriate conceptual toolkit. In WP1, the concepts of bioeconomy and non-bioeconomy sectors have been defined, the major interactions and feedback effects between the bioeconomy and other parts of the system have been identified and analysed. Also, the likely impacts and trade-offs of the bioeconomy drivers (e.g. economic growth, climate change) have been studied. On its turn, the objective of WP 2 in the SAT-BBE project is to provide an inventory of tools for evaluation and monitoring the EU bioeconomy, according to the data bases required, the indicators available, and the quantitative and qualitative models currently used or under development.
Overview of the Systems Analysis Framework for the EU Bioeconomy. Deliverable 1.4 of the EU FP 7 SAT-BBE project Systems Analysis Tools Framework for the EU Bio-Based Economy Strategy (SAT BBE)
Leeuwen, M.G.A. van; Meijl, H. van; Smeets, E.M.W. ; Tabeau-Kowalska, E.W. - \ 2014
Den Haag : SAT-BBE / LEI Wageningen UR (Report Deliverable 1.4) - 23
economische analyse - biobased economy - economische ontwikkeling - analytische methoden - economische evaluatie - systeemanalyse - europese unie - economic analysis - biobased economy - economic development - analytical methods - economic evaluation - systems analysis - european union
In November 2012 the Systems Analysis Tools Framework for the EU Bio-Based Economy Strategy project (SAT-BBE) was launched with the purpose to design an analysis tool useful to monitoring the evolution and impacts of the bioeconomy. In the SAT-BBE project the development of the analysis tool for the EU bioeconomy strategy is structured in three phases: scoping and definition of the systems analysis framework (WP 1); tools for evaluating and monitoring (WP 2); systems analysis protocols (WP 3).
Panarchy rules? : rethinking resilience of agroecosystems
Apeldoorn, D.F. van - \ 2014
Wageningen University. Promotor(en): Ken Giller, co-promotor(en): Kasper Kok; Marthijn Sonneveld. - Wageningen : Wageningen University - ISBN 9789461739179 - 137
agro-ecosystemen - duurzaamheid (sustainability) - bedrijfssystemen - organisch bodemmateriaal - wiskundige modellen - systeemanalyse - nederland - zimbabwe - agroecosystems - sustainability - farming systems - soil organic matter - mathematical models - systems analysis - netherlands - zimbabwe
This thesis explores the applicability of the resilience perspective on agro-ecosystems dynamics. It start out by using the five heuristics of the resilience perspective on intensive agricultural systems. Simulations with a dynamic farm model suggest that conventional farming short cuts the adaptive cycle leading to an ‘incremental adaptation’ trap. Panarchy is therefore claimed as a leading heuristic to understand long-term dynamics and current management characteristics. This interaction of long-term dynamics with current management leads to an asymmetry in the landscape. This asymmetry leads to windows of opportunities for farmers. However, disregarding the cross-scale nature of the asymmetry might also lead to a cascade of events that undermine the resilience of the landscape as whole. The cross-scale interactions of landscape dynamics and farm management suggest a co-evolution of production intensity and landscape pattern. Moreover trajectories of intensification might even be linked to certain tipping points of combinations of landscape characteristics and management. Therefore the landscape asymmetry might yield insight in agro-ecosystem functioning. The landscape asymmetry potentially provides a level of self-organisation above the farm. However, identifying the asymmetry appeared to be problematic. Next to scale issues, the current pattern does not necessary result from current management, leading to a de-coupling of pattern and process. A re-coupling of management and landscape asymmetry can exploit positive feedbacks. I suggest the use of identity to locate asymmetries and to use space-time substitutions to experiment with the typical slow variables that shape the asymmetry.
The theory developed in this thesis is grounded on empirical farm management data and dynamical model simulation of intensive dairy farming in the Netherlands and small-holder systems in Zimbabwe.
Perspectives in hindsight
Rabbinge, R. - \ 2012
Wageningen : Wageningen University, Wageningen UR - ISBN 9789461731654 - 28
systeemanalyse - hulpbronnenbeheer - voedselzekerheid - duurzaamheid (sustainability) - ontwikkeling - landbouwproductie - systems analysis - resource management - food security - sustainability - development - agricultural production
Klimaatbestendig Nederland : systeemanalyse
Koomen, A.J.M. ; Nieuwenhuizen, W. ; Kater, E. ; Maas, G.J. ; Jansen, P. ; Massop, H.T.L. ; Grashof-Bokdam, C.J. ; Boers, J. - \ 2011
Utrecht : Programmabureau Kennis voor Klimaat - 106
klimaatverandering - klimaatadaptatie - watersystemen - systeemanalyse - climatic change - climate adaptation - water systems - systems analysis
De systeemanalyse waar deze rapportage over gaat, probeert antwoorden te vinden op vragen als: hoe is een systeem opgebouwd?; wat zijn de diverse (hiërarchische) schaalniveaus en hoe is de samenhang tussen deze schaalniveaus?; wat zijn de onderdelen en wat zijn de kenmerken daarvan? En ten slotte hoe werkt het systeem (op diverse schaalniveaus)?
Bewogen toestand : systeemdynamica in het groen
Straten, G. van - \ 2011
Wageningen : Wageningen University - ISBN 9789461731586 - 40
automatische regeling - regeltheorie - regelsystemen - systeemanalyse - dynamisch modelleren - agrotechnologie - automatic control - control theory - control systems - systems analysis - dynamic modeling - agrotechnology
Nutriëntenhuishouding in de bodem en het oppervlaktewater van de Drentse Aa : bronnen, routes en sturingsmogelijkheden
Roelsma, J. ; Grift, B. van der; Mulder, H.M. ; Tol-Leenders, T.P. van - \ 2011
Wageningen : Alterra (Reeks monitoring stroomgebieden 25-I) - 82
stroomgebieden - beekdalen - nutriëntenuitspoeling - oppervlaktewaterkwaliteit - bodemchemie - systeemanalyse - drenthe - watersheds - brook valleys - nutrient leaching - surface water quality - soil chemistry - systems analysis - drenthe
Deze rapportage richt zich op het stroomgebied de Drentse Aa. Om zicht te krijgen op de nutriëntenhuishouding in het gebied is er vanaf 2004 aanvullend op het reguliere meetnet van het waterschap in het oppervlaktewater gemeten. Voor de interpretatie van deze meetgegevens en het leggen van relaties om de bronnen en transportroutes van nutriënten in beeld te brengen waren modellen en aanvullende metingen noodzakelijk. In dit syntheserapport wordt de nutriëntenhuishouding in de bodem en het oppervlaktewater van de Drentse Aa beschreven, met als doel het totale systeem te doorgronden (waaronder de bronnen en routes van nutriënten in het systeem) en vanuit die positie de sturingsmogelijkheden om de waterkwaliteit te verbeteren aan te geven.
From food production to food security: developing interdisciplinary, regional-level research
Ingram, J.S.I. - \ 2011
Wageningen University. Promotor(en): Rudy Rabbinge. - [S.l.] : S.n. - ISBN 9789461730022 - 152
voedselproductie - voedselzekerheid - systeemanalyse - interdisciplinair onderzoek - klimaatverandering - landbouwkundig onderzoek - regionale ontwikkeling - multi-stakeholder processen - food production - food security - systems analysis - interdisciplinary research - climatic change - agricultural research - regional development - multi-stakeholder processes
Food security is a condition whereby “all people, at all times, have physical and economic access to sufficient, safe, and nutritious food to meet their dietary needs and food preferences for an active and healthy life” (FAO World Food Summit, 1996). Globally, food production has kept ahead of demand for many years, yet about one billion people currently do not have such access. This is due to a combination of biophysical, socioeconomic and political factors. New research concepts, tools and methods are needed to understand, and improve governance of, the complex interactions between these factors if such food insecurity is to be overcome. This is especially the case at the regional (sub-continental) level where many stakeholder groups and actors are involved in setting policies and taking decisions that affect food security outcomes. Based on six publications, this thesis therefore addresses three questions:
What are the essential characteristics of a research agenda to address food security?
Why is research at the regional level important?
Who needs to be involved in research design and delivery, and how are they best engaged?
The food system concept, which integrates an understanding of the activities of producing, distributing, trading and consuming food with the food security outcomes relating to access, availability and utilisation of food, provides a robust framework for analysis of these questions. A synthesis of the publications reveals an effective food security research agenda needs to not only encompass all these activities and outcomes, but also note the range of biophysical, socioeconomic and political food system drivers across and along spatial, temporal and jurisdictional scales. This is because food insecurity arises from vulnerability of the food system to combinations of stresses induced from changes in these drivers. Analysis in this thesis has shown that the ability to overcome these stresses, and thereby enhance food security, would be increased if policy and technical options were considered more specifically at regional level, in addition to at local and global levels. This is however challenging, due to the diversity of stakeholder groups operating at this level (e.g. government and NGOs; researchers and research funders; and business and civil society) all of whom have their own objectives. Further, there are numerous interactions with higher and lower levels on these scales, and insufficient knowledge and awareness of actions taken at these other levels often leads to ‘scale challenges’. Participatory research methods (e.g. surveys, consultations and scenario exercises) have been found in this research to help overcome these ‘scale challenges’.
Improved understanding of how food systems operate will help food security planning by identifying where, when and how vulnerability arises; and hence what sorts of adaptation interventions are needed, and where and when they would be most effective. Understanding can be enhanced by integrating concepts from production ecology, agroecology and human ecology with concepts of food systems and scales, to develop the notion of ‘food system ecology’. This not only helps identify the many biophysical and socioeconomic interactions across the range of activities and drivers that determine food security, but also provides a framework for two key research avenues: increasing the efficiency with which inputs to the food system are used, and enhancing food system governance.
Le lait, de l'or blanc? : amélioration de la productivité des exploitations mixtes cultures-élevage à travers une meilleure gestion et alimentation des vaches laitières dans la zone de Koutiala, Mali
Sanogo, O. - \ 2011
Wageningen University. Promotor(en): Herman van Keulen; Ken Giller; Nico de Ridder; Mariana Rufino. - S.l. : s.n. - ISBN 9789085859505 - 157
bedrijfssystemen - melkveehouderij - veehouderij - dry farming - dierlijke productie - diervoedering - systeemanalyse - simulatiemodellen - mali - farming systems - dairy farming - livestock farming - dry farming - animal production - animal feeding - systems analysis - simulation models - mali
Goede, D.M. de - \ 2010
In: Over zorgvuldige veehouderij. Veel instrumenten, één concert / Eijsackers, H., Scholten, M., Wageningen : Wageningen UR (Essaybundel 2010 ) - ISBN 9789085858959 - p. 104 - 113.
dierenwelzijn - veehouderij - duurzaamheid (sustainability) - systeemanalyse - diergezondheid - dierlijke productie - animal welfare - livestock farming - sustainability - systems analysis - animal health - animal production
Hoewel de term robuustheid steeds vaker wordt gebruikt om een ‘niet-kwetsbare’ staat van een systeem te omschrijven, blijft de precieze betekenis meestal onduidelijk. Robuustheid heeft betrekking op de relatieve kwetsbaarheid van een systeem in relatie tot een specifieke verstoring. Dit essay gaat in op de conceptualisering van robuustheid in de veehouderij en onderzoekt in hoeverre robuustheid kan bijdragen aan een zorgvuldige veehouderij. Drie verschillende robuustheidtoestanden en -strategieën worden gerelateerd aan één extern en twee interne aspecten van systeemkwetsbaarheid, namelijk blootstelling, weerstand en veerkracht. Dit essay beargumenteert dat robuustheid in de veehouderij als systeemeigenschap in enge zin gebruikt wordt op dierniveau in relatie tot dierenwelzijn en diergezondheid, en dat de robuustheidstrategie zich beperkt tot het dierlijke subsysteem en het sociale duurzaamheidaspect
Exploring the potential of high technological and eco-efficient agriculture
Visser, C.L.M. de; Hengsdijk, H. ; Ittersum, M.K. van; Meijerink, G.W. ; Pol, A. van den; Slingerland, M.A. - \ 2010
Wageningen : Applied Plant Research (PPO publication 395) - 154
landbouwproductie - voedselzekerheid - populatiegroei - landbouwkundig onderzoek - duurzaamheid (sustainability) - systeemanalyse - agro-ecologie - agricultural production - food security - population growth - agricultural research - sustainability - systems analysis - agroecology
A framework to introduce flexibility in crop modelling: from conceptual modelling to software engineering and back
Adam, M.Y.O. - \ 2010
Wageningen University. Promotor(en): Herman van Keulen; J. Wery, co-promotor(en): F.A. Ewert; Peter Leffelaar. - [S.l. : S.n. - ISBN 9789085857648 - 190
systeemanalyse - computersimulatie - wiskundige modellen - computer software - engineering - gewasproductie - gewasopbrengst - systems analysis - computer simulation - mathematical models - computer software - engineering - crop production - crop yield
Keywords: model structure, uncertainty, modularity, software design patterns, good modelling practices, crop growth and development.
This thesis is an account of the development and use of a framework to introduce flexibility in crop modelling. The construction of such a framework is supported by two main beams: the implementation and the modelling beam. Since the beginning of the 1990s, the implementation beam has gained increasing attention in the crop modelling field, notably with the development of APSIM (Agricultural Production Systems sIMulator) in Australia, OMS (Object Modelling System) in the United States, and APES (Agricultural Production and Externalities Simulator) in Europe. The main focus of this thesis is on the modelling beam and how to combine it with the implementation beam. I first explain how flexibility is adopted in crop modelling and what is required for the implementation beam of the framework, namely libraries of modules representing the basic crop growth and development processes and of crop models (i.e. modelling solutions). Then, I define how to deal with this flexibility (i.e. modelling beam) and more specifically I describe systematic approaches to facilitate the selection of the appropriate model structure (i.e. a combination of modules) for a specific simulation objective. While developing the framework, I stress the need for better documentation of the underlying assumptions of the modules and of the criteria applied in the selection of these modules for a particular simulation objective. Such documentation should help to point out the sources of uncertainties associated with the development of crop models and to reinforce the role of the crop modeller as an intermediary between the software engineer, coding the modules, and the end users, using the model for a specific objective. Finally, I draw conclusions for the prospects of such a framework in the crop modelling field. I see its main contribution to (i) a better understanding in crop physiology through easier testing of alternatives hypotheses, and (ii) integrated studies by facilitating model reuse.
Kennisleemten in de concept-kennisagenda gezien door de bril van systeeminnovatie: de Uitvoeringsagenda centraal
Spoelstra, S.F. - \ 2010
Lelystad : Wageningen UR Livestock Research (Rapport / Wageningen UR Livestock Research 351) - 28
duurzame veehouderij - veehouderij - duurzaamheid (sustainability) - systeemanalyse - kennismanagement - wetenschappelijke methode - innovaties - sustainable animal husbandry - livestock farming - sustainability - systems analysis - knowledge management - scientific method - innovations
An overview is given of 1. research that supports the policies of the Ministry towards sustainable livestock production and 2. initiatives mentioned in the policy agenda. Sustainable Livestock. Based on these overviews gaps in knowledge are identified including system analyses to identify chances and barriers for sustainable development, formulation of concrete visions of integral sustainable livestock production and performance of "real world" experiments to advance sustainable development
29th Benelux Meeting on Systems and Control - Book of Abstracts, Heeze, The Netherlands, 30 March-1 April 2010
Stigter, J.D. ; Meinsma, G. - \ 2010
Wageningen : Wageningen University - ISBN 9789085856726 - 301
automatische regeling - systeemanalyse - systemen - regeltechniek - regeltheorie - regelsystemen - automatic control - systems analysis - systems - control engineering - control theory - control systems
Adaptation science for agriculture : solutions for a changing planet
Meinke, H.B. - \ 2010
Wageningen : Wageningen UR - ISBN 9789085852711 - 32
gewasproductie - plantenfysiologie - plantenecologie - systeemanalyse - agro-ecologie - agro-ecosystemen - crop production - plant physiology - plant ecology - systems analysis - agroecology - agroecosystems
A road to food? : efficacy of nutrient management options targeted to heterogeneous soilscapes in the Teso farming system, Uganda
Ebanyat, P. - \ 2009
Wageningen University. Promotor(en): Ken Giller, co-promotor(en): Nico de Ridder. - [S.l. : S.n. - ISBN 9789085854227 - 218
bodemvruchtbaarheid - landgebruik - bedrijfssystemen - rotaties - plantenvoeding - gebruiksefficiëntie - systeemanalyse - uganda - nutrientenbeheer - soil fertility - land use - farming systems - rotations - plant nutrition - use efficiency - systems analysis - uganda - nutrient management
Key words: Land use change; Heterogeneity in soil fertility; Targeting; Integrated soil fertility management; Nutrient use efficiencies; Rehabilitation of degraded fields; Fertiliser requirements, Finger millet; QUEFTS model; Smallholder systems; sub-Saharan Africa.
Poor soil fertility in smallholder farming systems in sub-Saharan Africa is recognised as a major factor responsible for low per capita food production and escalating food insecurity. Increasing food production in most smallholder farming systems requires intensification with nutrient inputs. Targeting nutrient management interventions to heterogeneity can greatly enhance the use efficiency of the scarce nutrient inputs and can help in identification of ‘best fits’ (most suitable options for niches within the systems). This thesis aimed at contributing to understanding how to target nutrient management options to heterogeneity for improved crop production in the Teso farming system in eastern Uganda.
Land use change analysis between 1960 and 2001 showed that 48-78% more land was brought into cultivation and disappearance of communal grazing lands. Productivity of the farming system is also low. Population growth, political-instability-mediated collapse of institutions that supported production and marketing of cotton, and cattle rustling account for the changes in land use and productivity of the system. Balances of N, P and K were positive on larger farms (LF) and negative on the medium farms (MF), small farms with cattle (SF1) and without cattle (SF2), but were negative at the crop scale on all the farm types. Livestock, crop yield, labour availability and access to off farm income are the sustainability indicators in the system.
There were no topographic-gradients in soil pH, SOC, total N, Exch. Mg, Exch. Ca, Exch. K, CEC, sand and clay in the two villages with different geo-morphological features characterised except for extractable P which was 3 - 5 times higher in the in the top soils of the profiles in the valley bottoms than those in the upper landscape position of the toposequences. Soil organic carbon (SOC) concentrations significantly differed (P<0.05) in surface soil properties between landscape positions and even significantly much larger (P<0.001) between field types. Fields classified as of good, medium and poor soil fertility by farmers had average SOC concentrations of respectively 9.3-15 g kg–1, 6.6-11 g kg–1, 5.5-7.0 g kg–1. In contrast with other studies in smallholder farming systems in sub-Saharan Africa, spatial analysis did not reveal a particular generalized pattern in variability in soil fertility across farms. Within-farms, larger contents of SOC were associated with larger amounts of silt + clay and on locations of former kraals. The field scale, which is easily recognised by farmers, is an important entry point for targeting soil fertility management technologies.
Heterogeneity in soil fertility affected performance of legumes established with and without P and their residual effect on subsequent finger millet crops. Legume biomass and N accumulation differed significantly (P<0.001) between villages, landscape position, field type and P application rate. Mucuna accumulated the most biomass (4.8-10.9 Mg ha–1) and groundnut the least (1.0-3.4 Mg ha–1) on both good and poor fields in the upper and middle landscape positions. N accumulation and amounts of N2-fixed by the legumes followed a similar trend as biomass, and was increased significantly by application of P. Grain yields of finger millet were significantly (P<0.001) higher in the first season after incorporation of legume biomass than in the second season after incorporation. Finger millet also produced significantly more grain yield in good fields (0.62-2.15 Mg ha–1) compared with poor fields (0.29-1.49 Mg ha–1). Farmers preferred growing groundnut and were not interested in growing pigeonpea and mucuna. They preferentially targeted grain legumes to good fields except for mucuna and pigeonpea to poor fields. Benefit-cost ratios indicated that legume-millet rotations without P application were only profitable on good fields. Green grams, cowpea and soyabean without P can be targeted to good fields on both upper and middle landscape positions in both villages but mucuna without P to poor fields on the middle landscape position in Chelekura village and cowpea without P to poor fields on the upper landscape position in Onamudian village.
Application of N, P fertilisers alone (0, 30, 60, 90 kg ha–1), N+P at equal rates of single application, and manure (3 t ha–1) supplemented with N (0, 30, 60 and 90 kg ha–1) to degraded fields closed the within farm yield gap in finger millet by only 24%-43 %. The inability of the options to close the yield differences was because of poor nutrient use efficiencies (<25%) and other nutrient limitations (S and K) and physical limitations due to surface crusting. With large heterogeneity in soil fertility within smallholder farming systems, blanket recommendations are of limited value.
Using the Quantitative Evaluation of Fertility of Tropical Soils (QUEFTS) model calibrated for finger millet, balanced fertiliser requirements for a target millet yield of 2000 kg ha–1 was estimated at 83 kg N ha–1 and 52 kg P ha–1 and 56 kg K ha–1 for the sandy loam soils of Chelekura village and 64 kg N ha–1 and 31 kg P ha–1 and 40 kg K ha–1 for the sandy clay loam soils in Onamudian village. Targeting nutrient management options can result in larger benefits from nutrient management interventions and specific attention can be afforded to specific constraints to avoid wastage of resources. Combining organic resources and mineral fertilisers is needed for higher crop yields and nutrient use efficiencies. However, the SOC thresholds for higher mineral fertiliser use efficiencies need to be determined for different soil types (silt + clay) and crops as well as making farm/ system scale reconfigurations of cropping systems that will enhance efficiency in resource use. Supportive policy frameworks should be put in place to enhance investment in soil fertility management and thus increase food production.
Cassava and soil fertility in intensifying smallholder farming systems of East Africa
Fermont, A.M. van - \ 2009
Wageningen University. Promotor(en): Ken Giller, co-promotor(en): Mark van Wijk; Pablo Tittonell. - [S.l. : S.n. - ISBN 9789085853992 - 196
manihot esculenta - cassave - bodemvruchtbaarheid - agronomie - bedrijfssystemen - systeemanalyse - voedselzekerheid - kunstmeststoffen - kenya - uganda - manihot esculenta - cassava - soil fertility - agronomy - farming systems - systems analysis - food security - fertilizers - kenya - uganda
Keywords: Cost-benefits, Crop management, Farming systems, Fertilizer, Food security, Generalizations, Income, Labour, Land pressure, Niche, Rainfall, Sub-Saharan Africa, System analysis, Yield gap.
Cassava is an important crop in Africa. This thesis focuses on cassava production in the mid altitude zone of East Africa, an area characterized by high population densities, bimodal rainfall patterns and relatively poor soils. The overall aim was to better understand the roles and production constraints of cassava in order to explore opportunities to improve the productivity and sustainability of intensifying cassava-based smallholder farming systems in East Africa. Increasing land pressure has changed agricultural landscapes from traditional millet-, cotton-, sugarcane- or banana-based systems with an important fallow component to continuously, cultivated cassava-based systems. Cassava cultivation on cropped fields increased from 1-11 to 16-55% in three to four decades as farmers believe that cassava improves soil fertility for the subsequent crop and increasingly target cassava to low fertility soils when land pressure increases. The substantial increase in cassava cultivation has allowed farmers to postpone intensification of crop management, but it seems that the elasticity of the traditionally low-input systems is coming to an end as production of the two most important crops (cassava and maize) is limited by nutrients. Farmers in areas of high land pressure have started to adopt fertilizer and manure and to improve crop management.
Contrary to existing generalizations, cassava is not a food security crop for poorer farmers in East Africa, but an important food and cash crop for farmers from all wealth classes. Average farm income was not less than in other farming systems in the region, while average food security was higher (>10 months year-1) than in maize-based systems. Cassava is also not predominantly grown as an intercrop, as is often thought, nor is it grown without inputs, because farmers commonly use hired labour and improved genotypes. In addition, its labour requirements are higher than commonly assumed (287 man days ha-1), due to large requirements for weed control. Existing generalizations concerning cassava are therefore either false or half truths and a continued belief in them will hamper the effectiveness of policy and development efforts aimed at improving cassava production. Efforts to increase cassava production in cassava-based farming systems will, for example, improve its scope for commercialization, but will not significantly enhance food security.
Average farmer yields for cassava (7-12 t ha-1) are far below attainable yields on farm (30-50 t ha-1). Still, on-farm yields are highly variable. Largest yields were obtained on farms with high labour availability, fertile soils, good weed management and timely (not too early) harvesting. An improved technology package more than doubled
average yields in farmer fields, whereby the largest yield increase for a single technology was observed with 100-22-83 kg ha-1 N-P-K fertilizer. Multivariate analysis identified soil fertility, rainfall and weed management as the most important production constraints, while biotic factors were less important. Many fields were affected by multiple and interacting production constraints. Fertilizer responses were governed by the same, interacting factors influencing unfertilized cassava production. Genotype and biotic factors did not influence fertilizer response. Closing the considerable yield gap between actual and attainable cassava yields at farm level, can not be achieved by integrated pest management and breeding alone. Instead, research and development organizations should focus on addressing the whole range of interacting production constraints through the development and evaluation of integrated management packages. Improving cassava production will be more difficult for poorer than for wealthier farmers, as the first have less social and financial capital and less fertile soils and are therefore more likely to face multiple production constraints.
The positive impact of cassava on soil fertility perceived by farmers is supported by model simulations and nutrient balances that indicate that cassava may improve SOC contents of low fertility soils compared with maize and contribute to higher N recycling through crop residues. Adoption of higher yielding genotypes and improved production practices will improve yields and increase nutrient removal rates, but may simultaneously have a positive effect on SOC contents and nutrient recycling rates. Improving cassava stem management after harvesting seems an interesting option to improve sustainability of the system.
This thesis concludes that there is an urgent need to invest in agronomy and ISFM research and to reform existing research for developments programmes with a strong emphasis on breeding and IPM into integrated programmes that are able to address the multiple production constraints of cassava and thereby significantly contribute to improving the livelihoods of smallholder cassava farmers.