Thesis (Ph. D.)--Oregon State University, . / Printout. Includes bibliographical references. Also available on the World Wide Web.

Master of Science / Department of Agronomy / Charles W. Rice / Declining soil health is the underlying cause of decreasing agricultural productivity and environmental degradation. To address this challenge, research was conducted to determine how: (1) cover crops affect soil health in Kansas, USA and (2) direct seeding mulch–based cropping (DMC) systems affect soil health in Nyankpala, Ghana. Soil health indicators assessed include: biomass yield (kg ha[superscript]-1), soil microbial respiration (SMR), soil microbial C and N (MBC & MBN), potentially mineralizable N (PMN), dissolved organic carbon (DOC), soil organic C (SOC), soil total nitrogen (TN), phospholipid fatty acid analysis (PLFA), water stable aggregate (WSA), bulk density, pH, N, P, K, Ca and Mg. DMC systems from Ghana yielded significantly greater biomass compared to the control. High biomass produced by DMC systems did not increase SOC and PMN relative to the control. Fertilizer application had a significant impact on biomass production, which resulted in a significant increase in SOC and PMN in the 0-5 cm soil layer. Soil pH was significantly reduced by cropping systems and fertilizer in the 0-5 cm soil layer. Microbial biomass N, TN, SMR, N, P, Ca and Mg were not affected by the DMC cropping systems. Application of mineral fertilizer increased SMR, MBN, TN, N, and P. Soil K was also significantly affected by cropping systems and mineral fertilizer. The combination of mineral fertilizer and plant residues would be needed to improve soil health and increase crop productivity in the Guinea Savanna Zone of Ghana. Liming would be required to address low soil pH. In the USA, of all the soil health indicators examined, actinomycetes, gram-positive bacteria, fungi-bacteria ratio (F:B), SMR, MBN and WSA, were those significantly influenced by cover crops. The interactive effect of cover cops and N fertilizer also affected gram-positive bacteria, total PLFA, MBN, F:B ratio and WSA. Cover crop residues contributed to the observed differences in these indicators. The low response of soil health indicators suggest further evaluations are needed to determine the effectiveness of the indicators.

京都大学 / 0048 / 新制・課程博士 / 博士(地球環境学) / 甲第22022号 / 地環博第186号 / 新制||地||96(附属図書館) / 京都大学大学院地球環境学舎地球環境学専攻 / (主査)准教授 岡田 直紀, 教授 舟川 晋也, 准教授 真常 仁志 / 学位規則第4条第1項該当 / Doctor of Global Environmental Studies / Kyoto University / DGAM

No description available.

Fusarium graminearum est un champignon pathogène des plantes, responsable de la fusariose de l'épi (plus connue sous le nom de Fusarium Head Blight : FHB) sur céréales, notamment sur le blé et le maïs. En interaction avec la plante, le champignon produit des mycotoxines, parmi lesquellse le déoxynivalénol (DON), dont la finalité pour le champignon producteur est méconnue mais qui sont toxiques pour les humains et les animaux. Ainsi la qualité des grains contribue fortement aux pertes de rendement observées et les résidus contaminés restent au champ. Une première revue bibliographique (Leplat et al 2012) a mis en évidence l'importance des résidus de culture (habitat écologique) pour la survie saprophyte du champignon, pour sa reproduction sexuée et pour l'établissement de l'inoculum primaire susceptible d'infecter la prochaine culture. Une seconde revue bibliographique a souligné les lacunes en ce qui concerne le rôle que les mycotoxines pourraient jouer dans la survie de F. graminearum dans un cet habitat. L'objectif principal de cette thèse était donc de vérifier si la présence de mycotoxines dans les résidus de récolte donne un avantage compétitif à F. graminearum vis-à-vis des composantes biotiques du sol et des résidus et notamment les champignons, les bactéries, les protozoaires, les nématodes et les vers de terre. L'impact du DON sur ces différentes communautés a été évalué dans des résidus de maïs et de blé, au champ et en microcosmes, en condition de labour et de travail superficiel du sol. Le développement de la maladie et ses conséquences sur le rendement ont été observés dans l'expérience de terrain à l'Unité Expérimentale de l'INRA de Dijon.Au cours de cette étude, la survie et les dynamiques de développement de la souche modèle d'étude F. graminearum MIAE00376 et des communautés fongiques et bactériennes ont été mesurées en utilisant la réaction de polymérisation en chaîne en temps réel (Q-PCR) ainsi que par comptage sur boîtes. Dans le même temps, l'évolution des structures des communautés microbiennes a été déterminée par analyse du polymorphisme de longueur des fragments de restriction terminaux (T-RFLP). Les nématodes et les vers de terre ont été quantifiés par extraction et observations à l'œil ou a la loupe binoculaire. Le DON introduit dans le sol et les résidus a été extrait et quantifié au cours du temps par chromatographie liquide haute performance (CLHP). Des dynamiques de population de la souche MIAE00376 associée à différents microorganismes isolés de paille en décomposition et sélectionnés pour leur résistance au DON, à des bactéries fixatrice d'azote et à des Fusarium sp. appartenant au complexe fongique du FHB ont été mesurées en microcosmes de paille en présence ou non de DONLes résultats suggèrent que le DON dans les résidus de culture a une incidence sur les composantes biotiques du sol, mais l'impact dépend des communautés et de la localisation des résidus (en surface ou incorporés dans le sol). La biomasse moléculaire montre que les densités bactériennes et fongiques ont été significativement affectées par la présence de DON. La présence de DON a joué un rôle significatif sur la structure des communautés bactériennes et protozoaires, plus faible sur les communautés fongiques et nul sur les nématodes voire positif sur les vers de terre.Il est conclu que le DON est rapidement inaccessible en profondeur et un peu moins rapidement en surface (immobilisation ou dégradation), qu'il ne confère pas d'avantage compétitif au champignon producteur et que la gestion de l'habitat privilégié que constituent les résidus de culture pour F. graminearum peut être envisagée par le travail du sol en favorisant la décomposition rapide des résidus, par le labour ou l'utilisation d'organismes décomposeurs indigènes ou introduits. / Fusarium graminearum is a plant pathogenic fungus, causing devastating disease “Fusarium head blight” (FHB) in cereals including wheat and maize. It also contaminates the grains with mycotoxins including deoxynivalenol (DON) which are toxic to human and animals. This disease has resulted in the serious losses in grain yield and quality. We established through a first bibliographic review that during off season fungus survives saprophytically on the crop residues (ecological habitat) and serves as primary inoculum for the next season crop. However, we noticed also that the literature was poor about the role mycotoxins could play in the establishment of F. graminearum in such a habitat. The main aim of this thesis was therefore to test whether the presence of mycotoxins in the crop residues gives an advantage to F. graminearum to survive and develop a primary inoculum in the presence of the whole soil biota including fungi, bacteria, protozoa, nematodes and earthworms. We studied the impact of DON on the soil communities in the field as well as in microcosms, in wheat as well as in maize residues under tillage and no-tillage conditions. The disease development and the yield were noted in the field experiment. Some DON resistant active fungal decomposers and nitrogen fixing bacteria were picked and the dynamics of F. graminearum was observed by accelerating decomposition of crop residue in their presence, in the presence or absence of DON.During this study, the dynamic and survival of F. graminearum and total fungal and bacterial communities were examined by using quantitative real time polymerase chain reaction (qPCR) as well as by plate counting. At the same time, the structures of microbial communities were determined by using terminal restriction fragment length polymorphism analysis (T-RFLP). The DON resistance of isolated fungal decomposers and nitrogen fixers was tested by using minimal inhibitory concentration test (MIC). Nematodes and earthworms were quantified through binocular observations. The fate of DON was determined by quantifying the mycotoxin by high performance liquid chromatography (HPLC).The results suggested that DON in crop residues showed an impact on the biotic components of the soil but the impact depended on the communities and on the location of the residues (on surface or incorporated in the soil). The molecular biomass shows that the fungal and bacterial densities were significantly affected by the presence of DON. The presence of DON played significant role on the structure of bacterial and protozoan community while the nematodes and fungal communities remained unaffected. MIC results showed that the susceptibility of some competitive fungal strains towards DON was dependent on the dose of mycotoxin. The earthworms (Lumbricus terrestris) were not affected by the presence of mycotoxin. The degradation of DON in the residues was dependent on the time, the location of residues and the soil biota. The quantification of F. graminearum suggested that the presence of DON gave no advantage in the survival and development of primary inoculum during the decomposition of crop residues in the soil. We conclude that fungal decomposers can be selected on their enzymatic potential towards organic matter more than on the DON resistance to increase the degradation of the straw left at the surface and limit the subsequent development of F. graminearum.

A agropecuária brasileira apresenta relevante papel sócio-econômico para o país, e constantemente busca novas tecnologias para alcançar uma agricultura sustentável. Com as mudanças que vêm ocorrendo no uso da terra, principalmente nas regiões tropical e subtropical, o Brasil vem sendo apontado como um grande emissor dos gases do efeito estufa. A conversão de florestas em sistemas agrícolas pode levar a um rápido aumento dos fluxos de CO2, CH4 e N2O no ambiente, além de potencializar o efeito estufa e ameaçar os diferentes ecossistemas. Em busca de sistemas mais conservacionistas, que possam mitigar o efeito estufa, os sistemas convencional, plantio direto, integração lavoura-pecuária e pastagem com histórico bem definido, foram selecionados nesse estudo para melhor compreensão e discernimento das possíveis mudanças oriundas dos sistemas avaliados no bioma do Cerrado. Em um segundo momento avaliamos o potencial da elevada concentração de CO2 aquecimento das parcelas em sistema sob temperature freeair controlled enhancement e carbon dioxide free-air enrichment (T-FACE) para avaliar as alterações funcionais e composição microbiana do solo. Os objetivos desse estudo foram: determinar a quantidade de células total dos genes 16S rRNA bactéria, archaea e dos genes funcionais amoA, nirS, nirK, cnorB, nosZ, presentes em diferentes sistemas de manejo do solo. Bem como, possíveis alterações na comunidade microbiana do solo sob elevada concentração de CO2 e aquecimento das parcelas. Para acessar o número de cópias dos genes foi utilizado o PCR quantitativo, a estrutura da comunidade microbiana foi determinada pela técnica de T-RFLP e a composição microbiana pelo sequenciamento de terceira geração. Os resultados dos sistemas de plantio direto e integração lavoura-pecuária revelaram importante capacidade de controlarem as emissões de N2O. Notoriamente, o número de cópias do gene nosZ teve sua densidade incrementada nos dois sistemas de plantio direto e integração lavoura-pecuária, este gene apresenta alto potencial para monitorar a desnitrificaçnao completa do N2O a N2. Adicionalmente, a elevada concentração de CO2 e elevada temperatura incrementaram o número de cópias dos genes nifH, AOB e nosZ ao longo do experimento. A análise da diversidade dos grupos taxinômicos e funcional revelou que a diversidade funcional foi alterada nas parcelas com maior emissão de N2O, apresentando maior abundância de genes (2-3 vezes) envolvidos na desnitrificação, acarretando possivelmente essas maiores emissões de N2O pela microbiota do solo. / Agriculture activities have large an important socio-economic role for a country, and are constantly searching for new technologies to achieve sustainable agriculture. Changes have occurred in land use, especially in tropical and subtropical regions and Brazil has been considered as a large emitter of greenhouse gases from agricultural systems. The conversion of forests to agricultural systems can lead to a fast increase of CO2 streams, CH4 and N2O for atmosphere, which enhances the greenhouse effect and threaten the ecosystem. In search of more conservation systems that can mitigate the greenhouse gas, the conventional, no-tillage, integrated crop-livestock and pasture systems with well defined historical management were selected in this study to better understand and decifer the possibles changes resulting in the biome Cerrado. In a second study, it was evaluated the potential of high concentration of CO2 and warming plots on system under increased temperature free-air controlled enhancement e carbon dioxide freeair enrichment (T-FACE) to assess the functional changes and microbial composition in the soil. The objectives of this study were to determine the total amount of the 16S rRNA Bacteria, Archaea and the functional genes amoA, nirS, nirK, cnorB, nosZ present under different soil management and evaluate the possible changes in the soil microbial community under high CO2 concentration and warming in the plots. To access the number of copies genes we used quantitative PCR, with the microbial community structure determined by T-RFLP and the microbial composition by Illumina next-generation sequencing. No-tillage and integrated crop-livestock revealed important capability to control N2O emissions. Notably, the high number of nosZ gene copies was found under no-tillage and integrated crop-livestock systems. This gene has a high potential to monitor the oxidation of N2O to N2. In addition, high CO2 concentration and elevated temperature increased 2-3 folds the number of copies of the nifH genes, and AOB nosZ throughout the experiment. The analysis of the diversity of functional taxonomic groups revealed that functional diversity has changed in plots with high N2O emissions, and showed a greater abundance of genes involved in denitrification, which possibly has stimulated the emissions of N2O from soil microbiota.

Title from first page of PDF document. Includes bibliographical references (p. 22-27).

A agropecuária brasileira apresenta relevante papel sócio-econômico para o país, e constantemente busca novas tecnologias para alcançar uma agricultura sustentável. Com as mudanças que vêm ocorrendo no uso da terra, principalmente nas regiões tropical e subtropical, o Brasil vem sendo apontado como um grande emissor dos gases do efeito estufa. A conversão de florestas em sistemas agrícolas pode levar a um rápido aumento dos fluxos de CO2, CH4 e N2O no ambiente, além de potencializar o efeito estufa e ameaçar os diferentes ecossistemas. Em busca de sistemas mais conservacionistas, que possam mitigar o efeito estufa, os sistemas convencional, plantio direto, integração lavoura-pecuária e pastagem com histórico bem definido, foram selecionados nesse estudo para melhor compreensão e discernimento das possíveis mudanças oriundas dos sistemas avaliados no bioma do Cerrado. Em um segundo momento avaliamos o potencial da elevada concentração de CO2 aquecimento das parcelas em sistema sob temperature freeair controlled enhancement e carbon dioxide free-air enrichment (T-FACE) para avaliar as alterações funcionais e composição microbiana do solo. Os objetivos desse estudo foram: determinar a quantidade de células total dos genes 16S rRNA bactéria, archaea e dos genes funcionais amoA, nirS, nirK, cnorB, nosZ, presentes em diferentes sistemas de manejo do solo. Bem como, possíveis alterações na comunidade microbiana do solo sob elevada concentração de CO2 e aquecimento das parcelas. Para acessar o número de cópias dos genes foi utilizado o PCR quantitativo, a estrutura da comunidade microbiana foi determinada pela técnica de T-RFLP e a composição microbiana pelo sequenciamento de terceira geração. Os resultados dos sistemas de plantio direto e integração lavoura-pecuária revelaram importante capacidade de controlarem as emissões de N2O. Notoriamente, o número de cópias do gene nosZ teve sua densidade incrementada nos dois sistemas de plantio direto e integração lavoura-pecuária, este gene apresenta alto potencial para monitorar a desnitrificaçnao completa do N2O a N2. Adicionalmente, a elevada concentração de CO2 e elevada temperatura incrementaram o número de cópias dos genes nifH, AOB e nosZ ao longo do experimento. A análise da diversidade dos grupos taxinômicos e funcional revelou que a diversidade funcional foi alterada nas parcelas com maior emissão de N2O, apresentando maior abundância de genes (2-3 vezes) envolvidos na desnitrificação, acarretando possivelmente essas maiores emissões de N2O pela microbiota do solo. / Agriculture activities have large an important socio-economic role for a country, and are constantly searching for new technologies to achieve sustainable agriculture. Changes have occurred in land use, especially in tropical and subtropical regions and Brazil has been considered as a large emitter of greenhouse gases from agricultural systems. The conversion of forests to agricultural systems can lead to a fast increase of CO2 streams, CH4 and N2O for atmosphere, which enhances the greenhouse effect and threaten the ecosystem. In search of more conservation systems that can mitigate the greenhouse gas, the conventional, no-tillage, integrated crop-livestock and pasture systems with well defined historical management were selected in this study to better understand and decifer the possibles changes resulting in the biome Cerrado. In a second study, it was evaluated the potential of high concentration of CO2 and warming plots on system under increased temperature free-air controlled enhancement e carbon dioxide freeair enrichment (T-FACE) to assess the functional changes and microbial composition in the soil. The objectives of this study were to determine the total amount of the 16S rRNA Bacteria, Archaea and the functional genes amoA, nirS, nirK, cnorB, nosZ present under different soil management and evaluate the possible changes in the soil microbial community under high CO2 concentration and warming in the plots. To access the number of copies genes we used quantitative PCR, with the microbial community structure determined by T-RFLP and the microbial composition by Illumina next-generation sequencing. No-tillage and integrated crop-livestock revealed important capability to control N2O emissions. Notably, the high number of nosZ gene copies was found under no-tillage and integrated crop-livestock systems. This gene has a high potential to monitor the oxidation of N2O to N2. In addition, high CO2 concentration and elevated temperature increased 2-3 folds the number of copies of the nifH genes, and AOB nosZ throughout the experiment. The analysis of the diversity of functional taxonomic groups revealed that functional diversity has changed in plots with high N2O emissions, and showed a greater abundance of genes involved in denitrification, which possibly has stimulated the emissions of N2O from soil microbiota.

Forest harvest can have significant impacts on forest ecosystems that may influence the capacity of soils to sequester carbon (C). The microbial community controls decomposition, which is a critical process in partitioning litter- and root-C between CO₂ and storage in semi-permanent soil-C pools. The objectives of this study were to determine the effect of clear-cutting and stand age on: 1) temporal dynamics of soil microbial community (SMC) structure and physiological status; and 2) shifts among microbial functional groups in taking up ¹³C-labeled plant materials during decomposition. The experiment was conducted in Douglas-fir ecosystems within the Gifford Pinchot National Forest, Washington. We chose stands of three different ages: old-growth where trees are between 300 and 500 years old; an 8-year old stand; and a 25-year old stand. Phospholipid fatty acid (PLFA) profiling and ¹³C-PLFA labeling techniques along with the ratio of saturated to monounsaturated PLFAs and the ratios of cyclopropyl PLFAs to their monoenoic precursors as microbial physiological stress markers were utilized. Microbial PLFA profiles showed that SMC structure and physiological status was most affected by season and secondarily by time since clear-cutting. Total microbial biomass and bacterial and fungal biomass were significantly reduced in CC8 but not in CC25 sites relative to old-growth sites. Total microbial biomass concentration was lowest and the stress indicators were highest in August, which corresponded to low soil moisture and high temperatures. The relative amount of ¹³C incorporated into PLFAs was also influenced by stand age and ¹³C source (¹³C-labeled litter vs. ¹³C-labeled root material). A significantly greater amount of ¹³C was incorporated in CC8 samples compared to OG1 samples in five out of the seven sample dates. Additionally, a significantly greater proportion of ¹³C was incorporated into soil samples containing the ¹³C-labeled litter material relative to samples containing ¹³C-labeled root material in four out of the seven dates. In general, 18:lω9 and 18:2ω6,9 (common fungal biomarkers) had the greatest amount of ¹³C incorporation throughout the study period in both clear-cut and old-growth sites, indicating the important role of fungi in the decomposition of litter and root material and translocation of C within soil layers. / Graduation date: 2006

Pollution by toxic compounds is one of the most relevant environmental damages to ecosystems produced by human activity and, therefore, it must be considered in environmental protection and restoration of contaminated sites. According to this purposes, the main goal of this doctoral thesis has been to analyse the impact of several chlorophenols and heavy metals on the microbial communities of two typical Mediterranean soils. The ecological risk concentrations of each pollutant, which have been determined according to respirometric activity and changes in the microbial community composition, and the factors that influence on their effective toxic concentrations (bioavailable pollutants) have been analysed in order to predict their potential impact on different soil ecosystems and provide scientific data for the regulation of the soil protection policies. Moreover, resistant microorganisms with pollutant removal capacities have been isolated from artificially contaminated soil microcosms and tested in axenic cultures, to infer their potential usefulness for bioremediation. / La contaminació amb compostos tòxics antropogènics és un dels perjudicis ambientals més rellevants per als ecosistemes i, per tant, cal tenir-ho en compte en la protecció ambiental i la restauració de llocs contaminats. Amb aquests propòsits, l’objectiu principal d’aquesta tesi doctoral ha estat analitzar l’impacte de clorofenols i metalls pesants sobre la microbiota de dos sòls típicament mediterranis. S’han analitzat les concentracions de risc ecològic de cada contaminant, determinades segons activitat respiromètrica i canvis en la composició de la comunitat microbiana, i els factors que influeixen en les seves concentracions tòxiques efectives (contaminants biodisponibles), per predir l’impacte potencial sobre diferents ecosistemes edàfics i proporcionar evidències científiques per a les polítiques de protecció del sòl. D’altra banda, a partir de microcosmos edàfics contaminats artificialment, es van aïllar també microorganismes resistents amb capacitat per eliminar els contaminants, que van ser analitzats en cultius purs per avaluar-ne la utilitat potencial en bioremediació.