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The taxonomy of Fusarium species has been controversial. The controversy surrounding the morphology-based classification, as well as the limitations and advantages of the various tools used to circumvent this problem are discussed as an introduction to the research presented in this thesis. Emphasis in this case was on the F. oxysporum species complex. The body of the research focuses on Fusarium species in Ethiopian agriculture about which little has been published. Results from this study suggest that F. oxysporum and F. solani are the two species most commonly isolated from agricultural soils and plant tissues from Ethiopia. The Ethiopian F. solani isolates were further characterized using AFLPs which showed that these isolates group into two separate clusters. Additional characterization using EF-1á sequence analyses showed that all these isolates belong to one of the three clades previously designated for the F. solani-Nectria haematococca species complex. Nine SSR markers were developed for studying the F. oxysporum complex. These markers are highly polymorphic and should be useful for many different population genetic studies of the F. oxysporum species complex. Ethiopian F. oxysporum isolates, and F. oxysporum isolates obtained from other fungal collections, were characterized using AFLPs, SSRs and DNA sequence analyses. These studies resolved the isolates into three concordant groups that corresponded to the three clades of F. oxysporum previously designated for this species complex. Most of the Ethiopian isolates grouped in one of these three clades. This and the high degree of AFLP- and SSR-based genetic similarity observed among the Ethiopian isolates suggested that these isolates are largely clonal. In addition, a PCR-based diagnostic was developed to allow for the accurate differentiation between F. oxysporum and F. redolens which has proved to be difficult using morphological characters. The studies presented in this thesis contribute to a better understanding of Fusarium species commonly found in Ethiopia. Clearly, there is much that will still need to be done. The research presented in this thesis establishes a foundation for other studies and also provides a stimulus for further studies of these important fungi in Ethiopia. Copyright 2006, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. Please cite as follows: Bogale, MA 2006, Molecular characterization of Fusarium isolates from Ethiopia, PhD thesis, University of Pretoria, Pretoria, viewed yymmdd < http://upetd.up.ac.za/thesis/available/etd-11072006-172206 / > D87/ag / Thesis (PhD)--University of Pretoria, 2007. / Genetics / Unrestricted

Diss. (sammanfattning). Uppsala : Sveriges lantbruksuniv., 2003. / Härtill 3 uppsatser.

Diss. (sammanfattning). Uppsala : Sveriges lantbruksuniversitet, 2005. / Härtill 5 uppsatser.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniversitet, 2008. / Härtill 5 uppsatser.

CoordenaÃÃo de AperfeiÃoamento de NÃvel Superior / A disposiÃÃo dos resÃduos industriais à um dos problemas de maior importÃncia no mundo e, na busca de alternativas sustentÃveis tÃm-se avaliado a possibilidade de aplicaÃÃo destes na agricultura. Para avaliar a potencialidade do uso de resÃduo industrial inorgÃnico e orgÃnico em solos agrÃcolas foram realizados dois estudos. O primeiro para avaliar o comportamento da atividade microbiolÃgica e a mineralizaÃÃo de C no solo com incorporaÃÃo de resÃduos industriais e o segundo, para avaliar alteraÃÃes nas propriedades quÃmicas do solo, apÃs a adiÃÃo dos resÃduos industriais. Utilizou-se para ambos os experimentos o delineamento experimental inteiramente casualizado, sendo os tratamentos no primeiro um fatorial 3 x 2 x 16, referente a trÃs doses de resÃduo inorgÃnico (RI): 0, 2,5 e 5,0 Mg ha-1 e duas doses de resÃduo orgÃnico (RO): ausÃncia e presenÃa, em parcelas divididas em 16 Ãpocas de avaliaÃÃo (3, 6, 9, 12, 15, 21, 28, 35, 42, 49, 56, 63, 70, 77, 84 e 91 dias) apÃs o inÃcio da incorporaÃÃo dos tratamentos com 4 repetiÃÃes. A quantidade de resÃduo orgÃnico foi aplicada em quantidades equivalente a 100 kg de N ha-1 (aproximadamente 20 Mg ha-1 de resÃduo orgÃnico). O segundo, em esquema fatorial 3 x 2 x 4 utilizando trÃs doses RI: 0, 2,5 e 5,0 Mg ha-1 e na presenÃa e ausÃncia do RO aplicado em quantidade equivalente a 100 kg de N ha-1, avaliados aos 0, 30, 60 e 90 dias apÃs incubaÃÃo, com quatro repetiÃÃes. A adiÃÃo do RI nÃo alterou a atividade microbiana do solo, no entanto sendo afetada pela adiÃÃo do RO. O resÃduo orgÃnico apresentou alta recalcitrÃncia. Nas propriedades quÃmicas, a incorporaÃÃo de ambos resÃduos provocou aumento nos valores de pH do solo na fase inicial, mas diminuiu durante o perÃodo avaliado. A adiÃÃo do RI aumentou os valores da CE, os teores de P, Na, Fe, Cu e Mn nas doses estudadas e a presenÃa do RO os teores N, K e Zn. / The disposal of industrial waste is one of the major problems in the world and, in the search for sustainable alternatives have been evaluated the possibility of applying these in agriculture. To evaluate the potential use of industrial waste inorganic and organic in agricultural soils were carried out two studies. The first to assess the behavior of microbial activity and mineralization of soil C with incorporation of industrial waste and second, to assess changes in soil properties after the addition of industrial waste. It was used for both experiments the completely randomized design, with treatments at first a 3 x 2 x 16 factorial, referring to three doses of inorganic waste (RI): 0, 2,5 and 5,0 Mg ha-1 and two doses organic waste (RO): absence and presence in terms divided into 16 times (3, 6, 9, 12, 15, 21, 28, 35, 42, 49, 56, 63, 70, 77, 84 and 91 days) after initiation of incorporation of treatments and 4 replicates. The amount of organic waste was applied in amounts equivalent to 100 kg N ha-1 (approximately 20 Mg ha-1 of organic waste). The second, in factorial 3 x 2 x 4 using three doses RI: 0, 2.5 and 5.0 Mg ha-1 in the presence and absence of RO applied in quantities equivalent to 100 kg N ha-1, evaluated at 0, 30, 60 and 90 days after incubation with four replications. The addition of RI did not alter soil microbial activity, however being affected by adding the RO. The organic waste showed high recalcitrance. In chemical properties, the incorporation of both residues increased the pH of the soil in the initial phase, but decreased during the study period. The addition of RI increased values of CE, the levels of P, Na, Fe, Cu and Mn at the doses studied and the presence of RO levels N, K and Zn.

The aim of this thesis was the experimental evaluation of thermogravimetry (TG) to assess the status of organic matter supply in agricultural soils. TG is an innovative analytical method for recording thermal mass losses (TML) during heating of soil samples from room temperature to 950 °C. The determination of TML in 10 °C temperature increments (TG indicators) is a central method of TG data evaluation. There is a very close correlation between selected temperature ranges and classically determined soil properties (organic carbon, total nitrogen and clay content). The regression parameters of these relationships can be used to estimate soil properties and to assess the quality of SOM.:List of Tables VI List of Figures VII List of Abbreviations VIII Summary 10 Zusammenfassung 13 Chapter One – Synthesis: Thermogravimetry – a promising technique to assess the status of organic matter supply in agricultural soils 16 1 Introduction 16 1.1 Soils and agriculture 16 1.2 The Importance of soil organic matter (SOM) 17 1.3 Current challenges in the assessment of SOM as an indicator of soil quality 18 1.4 Main objectives 20 2 Methodological Approach 22 2.1 General approach 22 2.2 Experimental areas and soil description 22 2.3 Application of thermogravimetric analysis (TG) 28 2.4 Experimental design 29 2.4.1 SOC content determination using TML (chapter two and chapter five) 29 2.4.2 Detectability of thermal stabilities of organic amendments in soil samples using TML (chapter two) 30 2.4.3 Comparison between biological and thermal stability of SOM (chapter two and chapter three) 30 2.4.4 Linking thermogravimetric data with soil properties, thermal stability of SOM and SOC fractions (chapter four and chapter five) 31 3 Results and Discussion 32 3.1 Thermogravimetric-based fingerprint predictions of soil properties and soil organic matter stability (chapter two and chapter three) 32 3.2 Linking thermogravimetric indicators with functional SOC fractions to assess SOM quality (chapter four and chapter five) 35 4. Research needs and perspectives 37 5. Conclusion 40 References 40 Chapter Two: Contribution of organic amendments to soil organic matter detected by thermogravimetry 51 Chapter Three: Detectability of degradable organic matter in agricultural soils by thermogravimetry 52 Chapter Four: Linking soil organic matter thermal stability with contents of clay, bound water, organic carbon and nitrogen 53 Chapter Five: Linking thermogravimetric data with soil organic carbon fractions 54 Appendix 55 List of publications 55 Acknowledgments 56

Potentially toxic elements (PTEs) can be absorbed and accumulated in vegetables organ and tissues, and this is an important channel through which PTEs can enter into the food chain. Soil management may interfere in the behavior of PTEs in the system. So, the study of the dynamics of elements in the soil is fundamental to a better understanding of factors that influence soil-plant transfer. In the state of Pernambuco, Brazil, the production of vegetables is mainly concentrated in small or medium organic and conventional farms located in the Agreste and Sao Francisco regions. Our aims in this research were: i) to determine the contents of PTEs in soil and in vegetables produced under conventional and organic systems in garden soils of Pernambuco; ii) to investigate the forms of the PTEs and their uptake by the vegetables based on different soil-plant transfer factors; iii) to use the calculated transfer factors to assess the human risk exposure; iv) to assess the effect of aging and organic matter (OM) on copper (Cu) desorption in garden soils; v) to determine if manure application to soils increases water soluble Cu concentrations; and vi) to verify the efficiency of machine learning techniques in the classification of vegetables produced under organic and conventional systems. Acid and complexing solutions were employed to extract total contents of PTEs in plants and to extract pseudototal, reactive and bioavailable fractions of the PTEs in soils. Soil-plant transfer factors and human risk assessment were calculated based on the determined levels of PTEs. Kinetic assays were developed using rates of organic composts added to Cu-spiked soils to model the Cu desorption. Water extractable Cu and dissolved organic carbon (DOC) were extracted from soils amended with dairy manure, and the Cu-DOC interactions were studied using spectroscopic techniques. Lettuce (Lactuca sativa) leaves had the highest capacity to accumulate PTEs; conventional system promoted higher PTEs values in soils and plants than the organic production; regardless of the scenario, children and adults in contact to vegetables cropped in organic system have a lower health risk than individuals exposed to lettuce leaves conventionally produced. The addition of OM promoted greater Cu desorption, while aging lead to a reduction in the Cu release. The Fouriertransform infrared spectroscopy spectra showed increase in the presence of aliphatic and carboxylic groups in the extracts from the manure-amended soils. Carboxylic acid functional groups on the DOC formed strong bonds with Cu, which can promote Cu transport as dissolved Cu-organic complexes in the soil profile. The Support Vector Machine had an accuracy over 90% to classify the vegetables in the two groups (organic and conventional); and this high assertiveness rate highlights the potential of using elemental quantification and algorithms as support techniques in the process of authenticity and inspection of organic products. / Elementos potencialmente toxicos (EPTs) podem estar biodisponiveis para serem absorvidos e acumulados nos tecidos e orgaos vegetais, sendo esta uma importante rota de entrada de EPTs na cadeia alimentar. O manejo do solo pode interferir no comportamento dos EPTs no sistema. Desta forma, o estudo da dinamica desses elementos no solo e fundamental para melhor entendimento dos fatores que influenciam a transferencia solo-planta. No estado de Pernambuco, a producao de hortalicas se concentra em intensos cultivos organicos e convencionais localizados em pequenas ou medias propriedades, principalmente na regiao Agreste e Sao Francisco. Nossos objetivos neste trabalho foram: i) determinar os teores de EPTs no solo e nas hortalicas produzidas em sistemas convencionais e organicos em hortas de Pernambuco; ii) investigar as formas de EPTs e sua absorcao pelas hortalicas com base em diferentes fatores de transferencia solo-planta; iii) usar os fatores de transferencia calculados para investigar o risco de exposicao aos humanos; iv) estudar o efeito do tempo e da materia organica (MO) na dessorcao de cobre (Cu) em solos de horta; v) determinar se a aplicacao de esterco aumenta a concentracao de Cu soluvel em agua; e vi) verificar a eficiencia de tecnicas machine learning na classificacao de hortalicas produzidas em sistemas organicos e convencionais. Solucoes acidas e complexantes foram utilizadas para extrair os teores totais de EPTs nas plantas e os teores pseudototal, reativo e biodisponivel dos EPTs no solo. Fatores de transferencia solo-planta e avaliacao de risco humano foram calculados com base nos teores de EPTs. Estudos de cinetica foram desenvolvidos apos adicao de composto organico em solos contaminados com Cu para modelar a dessorcao de Cu. Cu soluvel em agua e carbono organico dissolvido (COD) foram extraidos de solos adubados com esterco, a interacao Cu-COD foi estudada usando tecnicas espectroscopicas. Folhas de alface (Lactuca sativa) apresentaram a maior capacidade de acumular EPTS; o sistema convencional promoveu maiores tores de EPTs nos solos e plantas do que o sistema organico; independentemente do cenario, criancas e adultos em contato com vegetais produzidos em sistema organico tem um menor risco do que os individuos que consomem folhas de alface convencionalmente produzidas. A adicao de MO promoveu maior dessorcao de Cu, enquanto o aumento no tempo de contato reduziu a liberacao de Cu. Os graficos da espectroscopia de infravermelho com transformada de Fourier mostraram um aumento na presenca de grupos funcionais alifaticos e carboxilicos nos extratos de solos adubados com esterco. Esses grupos funcionais no COD formam ligacoes fortes com Cu, o que promove o transporte do elemento na forma de complexos organicos dissolvidos no perfil do solo. O modelo Support Vector Machine apresentou acuracia superior a 90% na classificacao das hortalicas em dois grupos (organicas e convencionais); e a alta taxa de assertividade mostra o potencial do uso de quantificacao elementar e algoritmos como tecnicas auxiliares no processo de autenticidade de inspecao de produtos organicos.

Potentially toxic elements (PTEs) can be absorbed and accumulated in vegetables organ and tissues, and this is an important channel through which PTEs can enter into the food chain. Soil management may interfere in the behavior of PTEs in the system. So, the study of the dynamics of elements in the soil is fundamental to a better understanding of factors that influence soil-plant transfer. In the state of Pernambuco, Brazil, the production of vegetables is mainly concentrated in small or medium organic and conventional farms located in the Agreste and Sao Francisco regions. Our aims in this research were: i) to determine the contents of PTEs in soil and in vegetables produced under conventional and organic systems in garden soils of Pernambuco; ii) to investigate the forms of the PTEs and their uptake by the vegetables based on different soil-plant transfer factors; iii) to use the calculated transfer factors to assess the human risk exposure; iv) to assess the effect of aging and organic matter (OM) on copper (Cu) desorption in garden soils; v) to determine if manure application to soils increases water soluble Cu concentrations; and vi) to verify the efficiency of machine learning techniques in the classification of vegetables produced under organic and conventional systems. Acid and complexing solutions were employed to extract total contents of PTEs in plants and to extract pseudototal, reactive and bioavailable fractions of the PTEs in soils. Soil-plant transfer factors and human risk assessment were calculated based on the determined levels of PTEs. Kinetic assays were developed using rates of organic composts added to Cu-spiked soils to model the Cu desorption. Water extractable Cu and dissolved organic carbon (DOC) were extracted from soils amended with dairy manure, and the Cu-DOC interactions were studied using spectroscopic techniques. Lettuce (Lactuca sativa) leaves had the highest capacity to accumulate PTEs; conventional system promoted higher PTEs values in soils and plants than the organic production; regardless of the scenario, children and adults in contact to vegetables cropped in organic system have a lower health risk than individuals exposed to lettuce leaves conventionally produced. The addition of OM promoted greater Cu desorption, while aging lead to a reduction in the Cu release. The Fouriertransform infrared spectroscopy spectra showed increase in the presence of aliphatic and carboxylic groups in the extracts from the manure-amended soils. Carboxylic acid functional groups on the DOC formed strong bonds with Cu, which can promote Cu transport as dissolved Cu-organic complexes in the soil profile. The Support Vector Machine had an accuracy over 90% to classify the vegetables in the two groups (organic and conventional); and this high assertiveness rate highlights the potential of using elemental quantification and algorithms as support techniques in the process of authenticity and inspection of organic products. / Elementos potencialmente toxicos (EPTs) podem estar biodisponiveis para serem absorvidos e acumulados nos tecidos e orgaos vegetais, sendo esta uma importante rota de entrada de EPTs na cadeia alimentar. O manejo do solo pode interferir no comportamento dos EPTs no sistema. Desta forma, o estudo da dinamica desses elementos no solo e fundamental para melhor entendimento dos fatores que influenciam a transferencia solo-planta. No estado de Pernambuco, a producao de hortalicas se concentra em intensos cultivos organicos e convencionais localizados em pequenas ou medias propriedades, principalmente na regiao Agreste e Sao Francisco. Nossos objetivos neste trabalho foram: i) determinar os teores de EPTs no solo e nas hortalicas produzidas em sistemas convencionais e organicos em hortas de Pernambuco; ii) investigar as formas de EPTs e sua absorcao pelas hortalicas com base em diferentes fatores de transferencia solo-planta; iii) usar os fatores de transferencia calculados para investigar o risco de exposicao aos humanos; iv) estudar o efeito do tempo e da materia organica (MO) na dessorcao de cobre (Cu) em solos de horta; v) determinar se a aplicacao de esterco aumenta a concentracao de Cu soluvel em agua; e vi) verificar a eficiencia de tecnicas machine learning na classificacao de hortalicas produzidas em sistemas organicos e convencionais. Solucoes acidas e complexantes foram utilizadas para extrair os teores totais de EPTs nas plantas e os teores pseudototal, reativo e biodisponivel dos EPTs no solo. Fatores de transferencia solo-planta e avaliacao de risco humano foram calculados com base nos teores de EPTs. Estudos de cinetica foram desenvolvidos apos adicao de composto organico em solos contaminados com Cu para modelar a dessorcao de Cu. Cu soluvel em agua e carbono organico dissolvido (COD) foram extraidos de solos adubados com esterco, a interacao Cu-COD foi estudada usando tecnicas espectroscopicas. Folhas de alface (Lactuca sativa) apresentaram a maior capacidade de acumular EPTS; o sistema convencional promoveu maiores tores de EPTs nos solos e plantas do que o sistema organico; independentemente do cenario, criancas e adultos em contato com vegetais produzidos em sistema organico tem um menor risco do que os individuos que consomem folhas de alface convencionalmente produzidas. A adicao de MO promoveu maior dessorcao de Cu, enquanto o aumento no tempo de contato reduziu a liberacao de Cu. Os graficos da espectroscopia de infravermelho com transformada de Fourier mostraram um aumento na presenca de grupos funcionais alifaticos e carboxilicos nos extratos de solos adubados com esterco. Esses grupos funcionais no COD formam ligacoes fortes com Cu, o que promove o transporte do elemento na forma de complexos organicos dissolvidos no perfil do solo. O modelo Support Vector Machine apresentou acuracia superior a 90% na classificacao das hortalicas em dois grupos (organicas e convencionais); e a alta taxa de assertividade mostra o potencial do uso de quantificacao elementar e algoritmos como tecnicas auxiliares no processo de autenticidade de inspecao de produtos organicos.

Phosphorus (P) loss from agricultural soils has been identified as one of the major causes of eutrophication of surface waters. This study was conducted to evaluate the suitability of various measures of soil P as indicators of risk potential for P loss from agricultural soils to surface waters. To fulfill the research objective, soil samples were collected from six major soil series in southern Ontario, and were subjected to simulated precipitation and to leaching. Relationships between various soil P measures and dissolved reactive P (DRP) concentration in surface runoff and subsurface flow were assessed. Amongst the selected soil test P (STP) and the estimates of degree of P saturation (DPS), DPSM3-2 [Mehlich-3 P/(Mehlich-3 Al + Fe)], DPSM3-3 (Mehlich-3 P/Mehlich-3 Al), and water extractable P (WEP) had the highest correlation with DRP concentration in surface runoff and leachate across all six soil series. The Fe-oxide coated filter paper P (FeO-P) method gave the second best predictor of DRP concentration through a split-line linear model. The Olsen P test was significantly correlated to DRP losses in runoff and leachate but it was generally not as strongly correlated to DRP losses as were other soil P measures. Given that soil WEP concentration can represent risk of soil P loss, a study with a greater range of soils (n=391) suggested that DPSM3-2 and DPSM3-3 tended to overestimate P losses from alkaline soils, especially when soils had high DPSM3-2 or DPSM3-3. In comparison, soil FeO-P and DPSOl-b [Olsen P/(Olsen P + P sorption index)] each were significantly correlated to DRP concentrations in surface runoff, subsurface water and soil WEP concentration, and showed reasonable accuracy. Compared to STP and routine DPS, a detailed soil DPS estimated from P sorption isotherm (DPSsorp) and P buffering capacity (PBC0), could provide reliable predictions of runoff DRP concentration across different soil types. Within each soil type, runoff DRP concentration increased linearly with increasing DPSsorp following a common slope of approximately 1.79, while the common change point was at a PBC0 value of approximately 0.29 L mg-1. A unit change in the PBC0 value resulted in a much greater change in runoff DRP concentration below the change point than above the change point. / The OMAFRA (Ontario Ministry of Agriculture, Food, and Rural Affaires) – MOE (Ontario Ministry of Environment) Nutrient Management Joint Research Program and the University of Guelph-OMAFRA (Environmental Sustainability Research Theme) Research Program.