Ecosystems currently face widespread biodiversity losses and other environmental disturbances, such as climate warming, related to increased anthropogenic activities. Within this context, scientists consider the effects of such changes on the biodiversity, and hence on the activity, of soil microorganisms. Indeed, soil microorganisms mediate a wide range of soil processes. Currently, knowledge on soil microbial diversity is still limited, partially due to technical limitations. The advent of molecular-based analyses now allows studying the soil microbial diversity. These advances in the study of soil microbial communities have lead to a growing evidence of the critical role played by the microbial community in ecosystem functioning. This relationship is supposed to be relevant for narrow processes, regulated by a restricted group of microorganisms, such as the nitrification process. This PhD thesis aimed at studying ammonia oxidizing bacteria (AOB) community structure and richness as an integrated part of soil functioning. This research aimed at investigating the effect of aboveground plant diversity on ammonia oxidizing bacteria diversity and function in forest and grassland soils with focus on the influence of (a) functional group identity of grassland plants (legumes, grasses, forbs), (b) grassland plant species richness and (c) tree species, on AOB diversity and function. Another objective of this research was to study the effect of a 3°C increase in air temperature on AOB diversity and function. The link between AOB diversity and function (potential nitrification) is also investigated. For grassland ecosystems, a microcosm experiment was realized. An experimental platform containing 288 assembled grassland communities was established in Wilrijk (Belgium). Grassland species were grown in 12 sunlit, climate controlled chambers. Each chamber contained 24 communities of variable species richness (S) (9 S=1, 9 S=3 and 6 S=9).The grassland species belonged to three functional groups: three species of each grasses (Dactylis glomerata L., Festuca arundinacea SCHREB., Lolium perenne L.), forbs (non-N-fixing dicots; Bellis perennis L., Rumex acetosa L., Plantagolanceolata L.), and legumes (N-fixing dicots; Trifolium repens L., Medicago sativa L., Lotus corniculatus L.). Half of these chambers were exposed to ambient temperature and the other half were exposed to (ambient +3°C) temperature. One ambient and one (ambient+3°C) chambers were destructively harvested 4, 16 and 28 months after the start of the experiment. The influence of plant functional group identity on the nitrification process and on AOB community structure and richness (AOB diversity) was assessed in soils collected from the first two destructive amplings (chapter 2). The effect of plant species richness on AOB diversity and function was considered for soils sampled after 16 and 28 months (chapter 3). AOB function was determined by potential nitrification. AOB community structure and richness were assessed by polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) and sequencing of excised DGGE bands. I found that functional group identity can affect AOB community structure. In particular, the presence of legumes, both in monoculture or in mixture with forbs and grasses, lead to AOB community composition changes towards AOB clusters tolerating higher ammonium concentrations. This change in AOB community structure was only linked to increased potential nitrification under monocultures of legumes, when ammonium was supposed to be not limiting. This study revealed that physiological attributes of AOB and resource availability may be important factors in controlling the nitrification process. This research showed that the impact of plant species richness on the nitrification process could be mediated by the interactions between plants and AOB, through competition for substrate. A 3°C increase in air temperature did not affect AOB community structure, richness or function. In forest ecosystems, we studied the effect of tree species in forest sites located in Belgian and in the Grand-Duchy of Luxembourg covered each by several deciduous or coniferous tree species (Fagus sylvatica L., Quercus petraea (Mattuschka) Lieblein, Picea abies (L.) Karst, Pseudotsuga menziesii (Mirbel) Franco). We investigated the influence of these tree species on microbial processes (chapter 5) related to C and N cycling, particularly with emphasize on the nitrification process and on the diversity of AOB (chapter 6). The results showed that the effect of tree species on net N mineralization was likely to be mediated through their effect on soil microbial biomass, reflecting their influence on organic matter content and carbon availability. Influence of tree species on nitrification (potential and relative) might be related to the presence of ground vegetation through its influence on soil ammonium and labile C availability. AOB community structure was more site-specific than tree specific. However, within sites, AOB community structure under broadleaved trees differed from the one under coniferous trees. The effect on tree species on AOB was likely to be driven by the influence of tree species on net N mineralization, which regulates the substrate availability for AOB. The results also demonstrated that the relationship between AOB diversity and function might be related both to AOB abundance and AOB community structure and richness. This thesis showed no clear relationship between AOB community structure or richness and AOB function. However, we revealed that aboveground grassland plant richness, grassland plant functional groups and tree species influence AOB community structure and richness. Actuellement, les écosystèmes sont soumis à dimportantes pressions anthropiques et environnementales, pouvant aboutir à des pertes massives de biodiversité. Les scientifiques sinterrogent sur limpact de ces perturbations sur la diversité et, par conséquent, sur lactivité des microorganismes du sol. En effet, ceux-ci régulent de nombreux processus du sol. Actuellement, de nombreuses lacunes subsistent dans la connaissance de la diversité microbienne du sol. Celles-ci peuvent être partiellement attribuées aux difficultés méthodologiques associées à l'étude des micro-organismes du sol. Lavènement des techniques moléculaires nous permet de combler ces lacunes. Les avancées réalisées dans l'étude des communautés microbiennes du sol ont mis en évidence le rôle crucial joué par les communautés microbiennes dans le fonctionnement des écosystèmes. De plus, il semblerait que les processus régulés par un groupe restreint dorganismes, tel le processus de nitrification, soient plus sensibles à toute altération de la communauté. Lobjectif de cette thèse était détudier la structure de la communauté ainsi que la richesse (nombre de bandes DGGE) des bactéries oxydant lammoniac (AOB) comme une partie intégrante du fonctionnement des sols. Notre étude se focalisait sur linfluence de (a) différents groupes fonctionnels de plantes (graminées, légumineuses, dicotylédones), (b) communautés de plantes présentant une richesse spécifique croissante et (c) différentes essences forestières, sur la diversité (structure de la communauté et richesse des AOB) et la fonction des AOB. Cette recherche étudiait également limpact dune augmentation de température de 3°C sur ces paramètres. Létablissement dun lien éventuel entre la diversité et la fonction (nitrification potentielle) des AOB a aussi été envisagé. Concernant les écosystèmes prairiaux, nous avons réalisé une étude en microcosmes. Une plateforme expérimentale comprenant 288 communautés artificielles de plantes a été établie à Wilrijk (Belgique). Cette plateforme consistait en 12 chambres, dont une moitié était à température ambiante et la seconde était à température ambiante augmentée de 3°C. Chaque chambre contient 24 communautés de plantes de richesse spécifique variable (9 S=1, 9 S=3 et 6 S=9). Les communautés de plantes sont créées avec 9 espèces de plantes appartenant à trois groupes fonctionnels : 3 espèces de graminées (Dactylis glomerata L., Festuca arundinacea SCHREB., Lolium perenne L.), de légumineuses (dicotylédones fixatrices dazote ;Trifolim repens L., Medicago sativa L., Lotus corniculatus L.), et de dicotylédones non fixatrices dazote (Bellis perennis L., Rumex acetosa L., Plantago lanceolata L.). Les sols issus dune chambre à température ambiante et dune chambre à température ambiante augmentée de 3°C ont été échantillonnés, respectivement, 4, 16 et 28 mois après le début de lexpérimentation. Linfluence des groupes fonctionnels de plantes sur le processus de nitrification ainsi que sur la structure de la communauté et la richesse des AOB a été mesuré sur les sols issus des deux premiers échantillonnages (chapitre 2). Nous avons mesuré leffet de la richesse croissante en plantes sur la diversité et lactivité des AOB sur les sols échantillonnés après 16 et 28 mois dexpérimentation (chapitre 3). La structure de la communauté ainsi que la richesse des AOB ont été évaluées à laide dune amplification spécifique par réaction de polymérisation en chaîne (PCR) de lADN génomique extrait du sol suivie par une séparation par électrophorèse sur gel dacrylamide en présence dun gradient dénaturant (DGGE). Nous avons identifié les différentes AOB présentes par séquençage des bandes DGGE excisées. Nos résultats ont montré que les différents groupes fonctionnels peuvent affecter la structure de la communauté des AOB. En particulier, la présence de légumineuses, aussi bien en monoculture quen mélange avec des graminées ou des dicotylédones non fixatrices dazote, provoque des changements au sein de la structure de la communauté des AOB, favorisant la présence de clusters tolérants des concentrations en ammonium plus élevées. Ces changements de la structure de la communauté des AOB sont liés à des augmentations de la production potentielle de nitrates (nitrification potentielle) quand lammonium est supposé être non limitant. Cette étude révèle que la physiologie des AOB ainsi que la disponibilité en substrat peuvent être des facteurs majeurs intervenant dans le contrôle du processus de nitrification. Cette recherche montre que linfluence de la richesse spécifique des plantes sur la nitrification pourrait dépendre des interactions entre les plantes et les AOB via la compétition pour le substrat. Une augmentation de la température de lair de 3°C na pas influencé les richesse, structure de la communauté ou les fonctions des AOB. Pour les écosystèmes forestiers, nous aborderons leffet de différentes essences forestières (Picea abies (L.) KARST, Fagus sylvatica L., Quercus petraea LIEBLEIN ; Pseudotsuga menziezii (MIRB.) FRANCO) dans différents peuplements au Grand Duché du Luxembourg et en Belgique. Nous avons étudié l'influence de ces essences forestières sur les processus microbiens (chapitre 5) liés aux cycles du carbone et de lazote, en particulier leur effet sur le processus de nitrification et la diversité des AOB (chapitre 6). Notre étude révèle que linfluence des essences forestières sur la minéralisation nette de lazote pourrait être attribuable à leur effet sur la biomasse microbienne, reflétant ainsi leur effet sur la teneur en matière organique et la disponibilité en carbone. Limpact des essences forestières sur la nitrification (à la fois sur la nitrification relative et sur la nitrification potentielle) serait conditionné par la présence de végétation au sol, en raison de linfluence de celle-ci sur la disponibilité en ammonium et en carbone labile. Nous avons observé que la structure de la communauté des AOB était plus spécifique aux sites quaux essences forestières. Cependant, au sein dun site, elle différait sous feuillus et sous conifères. Les essences forestières influenceraient la structure de la communauté des AOB au travers de limpact quelles ont sur la minéralisation nette de lazote qui régule, quant à elle, la disponibilité en ammonium. Cette recherche démontre que le lien observé entre la diversité et la fonction dépendrait la fois de labondance, de la structure de la communauté et de la richesse des AOB. Cette thèse na révélé aucune relation claire entre la structure de la communauté ou la richesse des AOB et leur fonction. Par contre, nous avons observé que la richesse spécifique et les groupes fonctionnels de plantes prairiales et les essences forestières affectent la structure de la communauté et la richesse des AOB.

Made available in DSpace on 2014-07-29T14:52:08Z (GMT). No. of bitstreams: 1 Tese cicero agronomia.pdf: 980115 bytes, checksum: fc39630e9c5fb7bef0bb3944a6ce5081 (MD5) Previous issue date: 2009-04-16 / Different soil organic matter pools under management systems and natural Cerrado vegetation were studied. These pools were estimated using their carbon and nitrogen contents. Total soil organic carbon and total nitrogen (COT and NT), carbon and nitrogen of particulate organic matter (COP and NP), mineral-associated organic carbon and nitrogen (COM and NM), particulate organic carbon associated with different aggregates size classes (COPA), microbial biomass carbon and nitrogen contents (CBM and NBM) and their relations, and basal respiration as a measure of microbial activity, were determined in this study. Eight treatments were used: seven soil management systems and an undisturbed area of Savanna type vegetation, Cerrado, as a reference. They were: heavy disk harrow and legume species cultivation during twelve years (GP); disk plow and legume species cultivation during twelve years (AD); minimum tillage with chisel plow starting five years after installing the experiment (ESC); no-tillage with biennial crop rotation: grass and legume species as cover crop (PD1); no-tillage with crop rotation and annual cover crops (PD2), no-tillage with annual crop rotation of grass and legume species (PD3), permanent pasture (PAST) and natural savanna vegetation, cerrado (CER). The experiment was established in a randomized blocks design with three replicates to study soil tillage and crop rotation dynamics, with temporal and spatial alternation. Soil samples were taken at five depths: 0-5, 5-10, 10-20, 20-30 and 30-40 cm. Soil samples were collected in February, 2008, at soybean flowering stage. The soil management systems cause changes on soil organic carbon contents mainly on particulate organic matter (> 53 μm) and microbial biomass fractions as compared to the Cerrado vegetation. The annual use of plow discs to soil tillage causes increase of associated minerals-organic matter levels. In soil and climatic conditions of Cerrado, the use of no-till system preceded by soil chemical and structural correction has promote a more uniform distribution of particulate organic matter in the profile. The microbial biomass is responsive to changes caused by different soil management systems in the Cerrado / Foram estudados diferentes compartimentos da matéria orgânica do solo sob sistemas de manejo e vegetação natural de Cerrado. Esses compartimentos foram estimados por meio de seus conteúdos de carbono e nitrogênio. Determinaram-se: carbono orgânico e nitrogênio total do solo (COT e NT, respectivamente); carbono e nitrogênio da matéria orgânica particulada (> 53 μm) (COP e NP, respectivamente); carbono e nitrogênio orgânicos associados a minerais (COM e NM, respectivamente); carbono orgânico particulado associado a classes de agregados (COPA); carbono e nitrogênio da biomassa microbiana (CBM e NBM, respectivamente) e suas relações; e respiração basal como medida da atividade microbiana. Utilizaram-se oito tratamentos: sete com sistemas de manejo do solo e um com vegetação natural de Cerrado, como referência. Os sistemas estudados foram: uso de grade pesada e cultivado com leguminosas há doze anos (GP); uso de arado de discos e cultivado com leguminosas há doze anos (AD); preparo mínimo com escarificador a partir do quinto ano de experimento (ESC); plantio direto com alternância bienal de gramíneas e leguminosas (PD1); plantio direto com rotação bienal e safrinha (PD2); plantio direto com alternância anual de gramíneas e leguminosas (PD3); pastagem permanente (PAST); e cerrado nativo (CER). O experimento foi projetado para estudar a dinâmica de sistemas de preparo do solo e a rotação de culturas, com alternância no tempo e no espaço. O delineamento experimental utilizado foi o de blocos ao acaso com três repetições. As amostras de solo foram coletadas em cinco profundidades: 0-5, 5-10, 10-20, 20-30 e 30-40 cm. A amostragem de solo foi realizada em fevereiro de 2008, por ocasião da floração da soja. Alterações nos teores de carbono orgânico pelo uso do solo no Cerrado ocorreram, principalmente, na fração particulada da matéria orgânica (> 53 μm) e na fração microbiana do solo (CBM), quando comparadas ao cerrado nativo. Com o uso freqüente de arado de discos no preparo do solo, ocorre aumento dos teores de matéria orgânica associada aos minerais. Nas condições edafoclimáticas do Cerrado, o uso do sistema de plantio direto, precedido de correção química e estrutural do solo, promove uma distribuição mais uniforme da matéria orgânica particulada no perfil. A biomassa microbiana é sensível às mudanças causadas pelos diferentes sistemas de manejo do solo no Cerrado

Made available in DSpace on 2017-07-10T19:23:56Z (GMT). No. of bitstreams: 1 TESE_ FRANCIELI .pdf: 3210488 bytes, checksum: 139233665a2fb9191412af6ecba0f292 (MD5) Previous issue date: 2015-02-06 / The composting process has been used as the main way to stabilize agro-industrial waste from the broiler production chain. These wastes are generated in the run-fattening stage and during the slaughtering and processing of meat, originally inadequate to composting process due to its high levels of nitrogen. The objective of this research was to evaluate different lignocellulosic materials available regionally as a carbon source to be added to the composting process. The lignocellulosic materials were carding cotton waste, pruning of urban trees, sawdust, crushed sugarcane bagasse and crushed napier grass, which mixed with other wastes (reproductive poultry bedding, hatchery waste, flotation sludge, sausage skins and coal from boilers), constituted the treatments. Five windrows were set up and monitored, with C:N ratio of around 30. The windrows were turned twice a week in the first month and once a week in the following months until stabilization, confirmed by the decline of the windrow temperature until it reaches values of room temperature. At every turning, moisture was adjusted to 60%. The time of composting was evaluated, as well as mass reductions and volume (parameters related to optimization of the composting area); losses of N, P and K; concentration of N, P and K and the ratio of humic to fulvic acid - HA / FA that to characterize the agronomic value of the final compost, in addition to monitoring of microbiological parameters such as basal respiration and activity enzymatic β-glucosidase, cellulase, acid and alkaline phosphatase. With the aid of techniques of Multivariate Analysis (Cluster Analysis and Principal Component), it was concluded that the treatment which used the carding cotton waste as a carbon source allowed optimizing the use of composting area and provided the production of a organic compost with greater agronomic value. Regarding the microbiological parameters, these were most intense in the thermophilic phase, being the cellulase activity most accentuated. / O processo de compostagem é utilizado como principal forma de estabilizar resíduos agroindustriais provenientes da cadeia produtiva do frango de corte. Trata-se dos resíduos gerados no período que antecede a fase de engorda e durante o abate e industrialização da carne, originalmente inadequados ao processo de compostagem por apresentarem altos teores de nitrogênio. Objetivou-se avaliar diferentes materiais lignocelulósicos disponíveis regionalmente como fonte de carbono a ser adicionado na compostagem destes resíduos. Os materiais lignocelulósicos avaliados foram: resíduos da desfibrilação do algodão, podas de árvores urbanas, serragem, bagaço de cana moído e capim napier triturado, que em mistura com os demais resíduos (cama de matrizeiro, resíduos de incubatório, lodo de flotador, tripa celulósica e carvão), constituíram os tratamentos. Foram montadas e monitoradas cinco leiras, com relação C:N em torno de 30. As leiras foram revolvidas duas vezes por semana no primeiro mês e uma vez por semana nos meses seguintes até a estabilização, confirmada pelo declínio da temperatura da leira até atingir os valores da temperatura ambiente. A cada revolvimento, a umidade foi corrigida para 60%. Os parâmetros avaliados foram o tempo de compostagem e as reduções de massa e volume (parâmetros relacionados à otimização do pátio de compostagem); perdas de N, P e K, concentração de N, P e K e relação ácidos húmicos:ácidos/fúlvicos AH/AF que permitiram caracterizar o valor agronômico do composto final. Monitorou-se os parâmetros microbiológicos, como a respiração basal e a atividade enzimática de β-glucosidase, celulase, fosfatase ácida e alcalina. Com auxílio de técnicas da Análise Multivariada (Análise de Agrupamento e de Componentes Principais), concluiu-se que o tratamento em que se utilizou o resíduo da desfibrilação de algodão como fonte de carbono permite otimizar a utilização do pátio de compostagem e proporciona a produção de um composto orgânico com maior valor agronômico. Com relação aos parâmetros microbiológicos, estes foram mais intensos na fase termofílica, sendo a atividade de celulase a mais pronunciada