La bio-augmentation des stations d’épuration est parfois envisagée pour faire face à des situations transitoires au cours desquelles la capacité nitrifiante des boues activées est insuffisante pour traiter efficacement la charge reçue par l’installation. Le succès de cettestratégie repose sur l’activité nitrifiante de la biomasse ajoutée ainsi que sur sa capacitéd’adaptation et de maintien dans les boues activées en place.L’objectif de ce travail était d’évaluer la possibilité d’adaptation des micro-organismes d’une solution commerciale nitrifiante dans une station d’épuration municipale à très faible charge.Les populations nitrifiantes composant la solution étudiée ont été comparées à celles des boues activées de treize stations d’épurations, échantillonnées en été et en hiver. Une démarche couplant des outils de la biologie moléculaire et du génie des procédés a été mise en oeuvre afin d’analyser et de comparer ces populations selon trois axes : diversité, abondance et activité. Cette comparaison a été complétée par une expérience de bio-augmentation en réacteur fermé. D’après les profils obtenus en DGGE, les communautés nitrosantes des stations d’épuration à très faible charge sont généralement dominées par une même espèce appartenant au groupe Nitrosomonas oligotropha.Les biomasses nitrosantes et nitratantes ont été chacune estimées entre 0,5 et 3,5 % de la biomasse totale des boues activées par marquage FISH. La solution commerciale comporteune seule espèce nitrosante, du groupe N. europaea, qui représente 45 % de sa biomasse.Les analyses cinétiques, réalisées par suivi direct des vitesses de réaction (analyses chimiques) et/ou par respirométrie, indiquent que N. europaea adopte une stratégie de type –r contrairement aux bactéries autochtones des boues activées (stratégie de type –K). Ces résultats expérimentaux laissent supposer une faible capacité d’adaptation de la biomasse nitrifiante de cette solution commerciale aux conditions environnementales des stationsd’épuration à très faible charge. En revanche, l’expérience de bio-augmentation a montré sa capacité d’intégration aux flocs, et le maintien de son activité lors de son mélange à des boues activées. / Bio-augmentation is sometimes proposed to cope with transient situations in wastewatertreatment plants, when the nitrifying capacity of the autochthonous biomass is insufficient totreat the nitrogen load.The success of such a strategy is conditioned by the nitrifying activity of the added biomass,its adaptation to local conditions and its residence time in the system.This work aimed at evaluating the adaptation of nitrifying microorganisms from a commercialsolution in very low loaded municipal wastewater treatment plant. Nitrifying populations ofthe studied solution were compared to those of thirteen wastewater treatment plants (activatedsludge), observed in summer and in winter. The analysis and the comparison of the biomasseswere performed using tools from two disciplines: molecular biology and processengineering. Three points were especially characterised: the diversity, abundance and activityof the biomasses. A bio-augmentation experiment performed in a batch reactor completed thecomparison. DGGE profiles showed that Ammonia Oxidising Bacteria (AOB) communities from lowloaded wastewater treatment plants are mostly dominated by the same species related to theNitrosomonas oligotropha.The abundance of ammonia oxidising bacteria and of nitrite oxidising bacteria, estimatedusing the FISH technique, was almost similar, ranging from 0.5 to 3.5 % of the total biomass.The AOB species present in the commercial solution is identified as Nitrosomonas europaea,and represents 45 % of the solution’s total biomass.Kinetic analyses carried out by chemical analysis and/or by respirometry indicate that N.europaea behave as –r strategist, whereas activated sludge’s bacteria are –K strategist. These results suggest a slight adaptation capacity of the commercial solution’s nitrifyingbiomass to environmental conditions prevailing in low loaded municipal wastewater treatmentplants. On the other hand, bio-augmentation experiment showed the capacity of the addedmicroorganisms to integrate the activated sludge flocs and to maintain its activity when addedto activated sludge.

A presente investigação teve como objetivo avaliar a prática de cirurgiões dentistas em uma unidade de terapia intensiva (UTI) de um hospital militar, o estabelecimento de um protocolo de higiene oral e os seus efeitos sobre a redução de pneumonias associadas à ventilação mecânica (PAVM). As percepções da equipe da UTI sobre as atividades dos cirurgiões dentistas também foram avaliadas por meio de um questionário. O perfil de colonização microbiana da mucosa oral antes e depois do estabelecimento das medidas de higiene oral também foi avaliado tanto por diluição e plaqueamento em meios de cultura microbiológicos seletivos e enriquecidos e através da amplificação pelo método de PCR e eletroforese em gel desnaturante em gradiente (DGGE), subsequente ao sequenciamento dos amplicons. A carga microbiana foi avaliada após a contagem de placas de agar e através da amplificação por PCR em tempo real (qPCR) do gene rrs nas amostras. O protocolo de higiene oral, realizado pelos cirurgiões dentistas, foi capaz de reduzir a incidência de PAVM (p <0,05). O questionário revelou que a modificação da halitose foi percebida por 93,33% dos participantes. A redução da ocorrência das úlceras orais e dos lábios durante a internação dos pacientes foi observada por 80% da equipe da UTI. Foi observada a redução da produção das secreções nasais e bucais por 70% da equipe dos profissionais da UTI. Para 86,66% dos participantes a assistência aos pacientes tornou-se mais agradável após a instituição dos cuidados bucais. O protocolo, realizado com a utilização de solução 0,12% de clorexidina, não foi capaz de evitar a colonização da mucosa oral por patógenos microbianos usualmente encontrados no ambiente hospitalar tais como os bastonetes Gram-negativos entéricos e não fermentadores, nem foi capaz de eliminá-los quando tais micro-organismos já se encontravam presentes antes dos procedimentos de higiene bucal. Alguns Bastonetes Gram-positivos (Lactobacillus sp e corinebactérias) e Staphylococcus epidermidis permaneceram após a realização dos procedimentos. O protocolo de higiene oral permitiu a redução da carga microbiana na mucosa oral de 50% dos pacientes considerando-se o método de contagem microbiana e para 35% dos pacientes pela avaliação dos números de cópias de genes rrs através de qPCR. Em conclusão, o protocolo de higiene oral desenvolvido pelos cirurgiões dentistas foi capaz de reduzir a incidência de PAV na UTI, embora não tenha sido capaz de prevenir a colonização da mucosa oral por supostos patógenos microbianos. O protocolo de higiene oral com a participação ativa dos cirurgiões dentistas foi bem aceito pelos profissionais da UTI e foi capaz de melhorar a qualidade da assistência aos pacientes críticos. / This investigation aimed to evaluate the practice of dentists in an intensive care unit (ICU) of a military hospital, the establishment of a protocol for oral hygiene, and the effect of the protocol on the reduction of ventilator associated pneumonia (VAP) after the introduction of the oral hygiene protocol. The opinion of the ICU staff about the activity of the dentists was also evaluated by means of a questionnaire. In addition, the microbial colonization profile of the oral mucosa before and after the establishment of the oral hygiene measures was evaluated by means of both dilution and plating the samples in microbiological culture mediums (both selective and rich agar media) and DGGE technique, with sequencing of amplicons. The microbial load was evaluated after counting agar plates and by real time rrs gene PCR amplification (qPCR) in the samples. The oral hygiene protocol performed by dentists was capable to reduce the incidence of VAP (p< 0.05). The questionnaire revealed that the change of the oral odor was noticed by 93.33% of the participants. The reduction of oral and lip ulcers during the hospitalization of the patients was observed by 80% of the staff. The patients were observed to reduce the production of oral and nasal secretions after the establishment of the oral hygiene procedures by 70% of the ICU professionals. The approach to the patients developed by the staff became more pleasant after the establishment of the oral protocol for 86.66%. The protocol, with the use of 0,12% chlorhexidine solution, was not capable to avoid the colonization of the oral mucosa by the microbial pathogens usually found in nosocomial environment, in especial Gram-negative enteric and non-fermentative rods, nor eliminated these organisms previously found before the oral care procedures. Gram-positive rods (Lactobacillus sp, and corynebacteria) and Staphylococcus epidermidis remained after the procedures. The protocol reduced the microbial load in the oral mucosa of 50% of the patients considering the microbial counting and in 35% of the patients evaluated by the numbers of copies of rrs genes by qPCR. In conclusion, the oral hygiene protocol developed by dentists was capable to reduce the incidence of VAP in the studied ICU, though was not capable to prevent the colonization of oral mucosa by putative microbial pathogens. The oral hygiene protocol with active participation of dentists was well accepted by the ICU professionals and was capable to improve the quality of assistance to critically ill patients.

Made available in DSpace on 2016-06-02T19:26:22Z (GMT). No. of bitstreams: 1 SOARES_Lais_2013.pdf: 1502301 bytes, checksum: 5eb3bd554b98070bc2586ad2fed479d4 (MD5) Previous issue date: 2013-05-17 / Universidade Federal de Sao Carlos / This work aimed to quantifier the archaeal and bacterial communities by real time PCR, that shown the number of copies of 16S gene, rDNA into the water samples and to compare the archaeal and bacterial profiles on the PCR/DGGE technique as well as relate them with environmental variables in two points, dam and input on the Itupararanga reservoir, Sorocaba s basin. The bacterial density on the sediment (6,09 x108 e 2,56 x 109, dam and input, respectively) was more than water column (6,79 x 107 e 6,55 x 107, dam and input, respectively) this can be attributed to increase of the nutrients concentration from the surface to bottom. The bacterial (6,09 x 108 e 2,56 x 109 dam and input, respectively ) and archaeal (2,31 x 102 e 4,49 x 102 dam and input, respectively) quantities on the reservoir were more in the water column than in the sediment, which can be caused by the higher nutrients concentration in the top and the lees nutrients concentration in the bottom of Itupararanga reservoir. Since the canonical correspondence analysis has been possible, identify that the archaeal community has correlated with profundity and ammonia concentration suggesting ammonia oxidizing archaea s presence and abundance. The bacterial community quantity has correlated with physical chemical properties like pH and dissolved oxygen suggesting the environmental variables influence the group s abundance. Richness has correlated with nutrients distribution like orthophosphate concentration suggesting that the resources may limit the communities. / Com este trabalho objetivou-se quantificar a comunidade de bactérias e arqueias por meio de PCR em tempo real que determina o número de cópias do gene 16S de rDNA presentes nas amostras ambientais e comparar as comunidades de arqueia e bactérias em um perfil de bandas de PCR/DGGE, bem como relacioná-las às variáveis ambientais de dois pontos, Entrada e Barragem do reservatório de Itupararanga, bacia do rio Sorocaba. A quantidade de bactérias (6,09 x 108 e 2,56 x 109 barragem e entrada, respectivamente) e de arqueias (2,31 x 102 e 4,49 x 102 barragem e entrada, respectivamente) no sedimento foi maior do que na coluna d água o que pode ser atribuído ao aumento da concentração de nutrientes da superfície para o fundo do reservatório. A partir de análise de correspondência canônica foi possível observar que a quantidade de arqueias relacionou-se a profundidade e à concentração de íons amônio indicando possível presença e abundância de arqueias amônio oxidantes (AOA), enquanto que as bactérias foram mais relacionadas às variáveis físico-químicas, como temperatura e oxigênio dissolvido indicando que este grupo é mais sensível às variações ambientais. A riqueza de ambos os grupos foi relacionada à disponibilidade de nutrientes, indicando que os recursos podem ser limitantes às comunidades.

A presente investigação teve como objetivo avaliar a prática de cirurgiões dentistas em uma unidade de terapia intensiva (UTI) de um hospital militar, o estabelecimento de um protocolo de higiene oral e os seus efeitos sobre a redução de pneumonias associadas à ventilação mecânica (PAVM). As percepções da equipe da UTI sobre as atividades dos cirurgiões dentistas também foram avaliadas por meio de um questionário. O perfil de colonização microbiana da mucosa oral antes e depois do estabelecimento das medidas de higiene oral também foi avaliado tanto por diluição e plaqueamento em meios de cultura microbiológicos seletivos e enriquecidos e através da amplificação pelo método de PCR e eletroforese em gel desnaturante em gradiente (DGGE), subsequente ao sequenciamento dos amplicons. A carga microbiana foi avaliada após a contagem de placas de agar e através da amplificação por PCR em tempo real (qPCR) do gene rrs nas amostras. O protocolo de higiene oral, realizado pelos cirurgiões dentistas, foi capaz de reduzir a incidência de PAVM (p <0,05). O questionário revelou que a modificação da halitose foi percebida por 93,33% dos participantes. A redução da ocorrência das úlceras orais e dos lábios durante a internação dos pacientes foi observada por 80% da equipe da UTI. Foi observada a redução da produção das secreções nasais e bucais por 70% da equipe dos profissionais da UTI. Para 86,66% dos participantes a assistência aos pacientes tornou-se mais agradável após a instituição dos cuidados bucais. O protocolo, realizado com a utilização de solução 0,12% de clorexidina, não foi capaz de evitar a colonização da mucosa oral por patógenos microbianos usualmente encontrados no ambiente hospitalar tais como os bastonetes Gram-negativos entéricos e não fermentadores, nem foi capaz de eliminá-los quando tais micro-organismos já se encontravam presentes antes dos procedimentos de higiene bucal. Alguns Bastonetes Gram-positivos (Lactobacillus sp e corinebactérias) e Staphylococcus epidermidis permaneceram após a realização dos procedimentos. O protocolo de higiene oral permitiu a redução da carga microbiana na mucosa oral de 50% dos pacientes considerando-se o método de contagem microbiana e para 35% dos pacientes pela avaliação dos números de cópias de genes rrs através de qPCR. Em conclusão, o protocolo de higiene oral desenvolvido pelos cirurgiões dentistas foi capaz de reduzir a incidência de PAV na UTI, embora não tenha sido capaz de prevenir a colonização da mucosa oral por supostos patógenos microbianos. O protocolo de higiene oral com a participação ativa dos cirurgiões dentistas foi bem aceito pelos profissionais da UTI e foi capaz de melhorar a qualidade da assistência aos pacientes críticos. / This investigation aimed to evaluate the practice of dentists in an intensive care unit (ICU) of a military hospital, the establishment of a protocol for oral hygiene, and the effect of the protocol on the reduction of ventilator associated pneumonia (VAP) after the introduction of the oral hygiene protocol. The opinion of the ICU staff about the activity of the dentists was also evaluated by means of a questionnaire. In addition, the microbial colonization profile of the oral mucosa before and after the establishment of the oral hygiene measures was evaluated by means of both dilution and plating the samples in microbiological culture mediums (both selective and rich agar media) and DGGE technique, with sequencing of amplicons. The microbial load was evaluated after counting agar plates and by real time rrs gene PCR amplification (qPCR) in the samples. The oral hygiene protocol performed by dentists was capable to reduce the incidence of VAP (p< 0.05). The questionnaire revealed that the change of the oral odor was noticed by 93.33% of the participants. The reduction of oral and lip ulcers during the hospitalization of the patients was observed by 80% of the staff. The patients were observed to reduce the production of oral and nasal secretions after the establishment of the oral hygiene procedures by 70% of the ICU professionals. The approach to the patients developed by the staff became more pleasant after the establishment of the oral protocol for 86.66%. The protocol, with the use of 0,12% chlorhexidine solution, was not capable to avoid the colonization of the oral mucosa by the microbial pathogens usually found in nosocomial environment, in especial Gram-negative enteric and non-fermentative rods, nor eliminated these organisms previously found before the oral care procedures. Gram-positive rods (Lactobacillus sp, and corynebacteria) and Staphylococcus epidermidis remained after the procedures. The protocol reduced the microbial load in the oral mucosa of 50% of the patients considering the microbial counting and in 35% of the patients evaluated by the numbers of copies of rrs genes by qPCR. In conclusion, the oral hygiene protocol developed by dentists was capable to reduce the incidence of VAP in the studied ICU, though was not capable to prevent the colonization of oral mucosa by putative microbial pathogens. The oral hygiene protocol with active participation of dentists was well accepted by the ICU professionals and was capable to improve the quality of assistance to critically ill patients.

O histórico agronômico da cultura, em geral, explica a comunidade microbiana presente na massa ensilada, entretanto, a diversidade e o grau de contaminação da população microbiana epifítica pode auxiliar na compreensão do padrão de fermentação da silagem e da estabilidade desse produto quando em exposição ao ambiente aeróbio. No presente trabalho, foram avaliados a influência do genótipo, maturidade e período de estocagem na composição da comunidade bacteriana em silagens de grãos de milho. Para isso, dois cultivares de milho AG 1051 (\"dent\") e IAC 8390 (\"flint\") foram colhidos em três estágios de maturidade (ponto de silagem de planta inteira, ponto de silagem de grão úmido e ponto de grão seco), moídos e ensilados por 0, 7 e 120 dias. Atualmente, a aplicação de técnicas de microbiologia molecular permite acessar alterações causadas nestas comunidades de maneira independente do cultivo bacteriano, por esse motivo, a comunidade bacteriana foi avaliada por meio da técnica de Eletroforese em Gel de Gradiente Desnaturante (DGGE) e sequenciamento dos produtos de PCR via sistema MiSeqTM Illumina. Foi demonstrado que em silagens de grãos de milho contendo alta umidade, os diferentes estágios de desenvolvimento da cultura, e por conseguinte, do grão, são os principais determinantes da composição da comunidade bacteriana deste, sendo menos importantes o genótipo das plantas e os tempos de estocagem das silagens. Aos 120 dias de estocagem nas amostras de grão seco reconstituído, as sequências afiliadas ao gênero Clostridium representaram total de aproximadamente 40% das sequências afiliadas aos gêneros encontrados, enquanto o gênero Lactobacillus representou menos de 7% das sequências afiliadas a este gênero. Provavelmente, grãos secos sofrem mais estresse a campo, o que consequentemente, pode interferir na qualidade higiênico sanitária das silagens desses grãos. Com base nestes resultados fica evidenciada a possibilidade de realização de recomendações potenciais de aditivos específicos para ensilagem de grãos de milho, direcionados para cada ponto de maturidade da cultura. / The agronomic background of crops in general, explains the microbial community present in silage, however, diversity and contamination status may help on understanding the silage fermentation profile and aerobic stability. In the present work, the influence of factors such as different genotypes, different stages of plants development and storage time in the composition of bacterial communities were evaluated. On this way, maize cultivars AG 1051 (\"dent\") and IAC 8390 (\"flint\") were harvested in three physiological stages (whole plant silage, wet grain silage and dry grain), the grain were grounded and ensiled for 0, 7 and 120 days. Nowadays, the applications of techniques of molecular microbiology allow assessing the shifts caused on these communities by a culture independent approach, therefore, bacterial community were evaluated by Denaturing Gradient Gel Electrophoresis technique (DGGE), and PCR products were sequenced by Illumina MiSeqTM System. It was demonstrated that in high moisture corn silage, different stages of plants development are main determinants of bacterial community composition rather than the plants genotypes and storage time. In addition in the samples of reconstituted dry grain, it was demonstrated that after 120 days of storage, sequences affiliated to the gender Clostridium accounted for a total of approximately 40% of total sequences affiliated to genera found, while the genus Lactobacillus represented less than 7% of sequences affiliated to this gender. Probably dried grains suffer more stress at field conditions, which in turn can interfere with the sanitary hygienic quality of silages obtained from these grains. At least, based on these results it is clear the possibility of performing potential specific additives recommendations, unique at each stage of maize plants development.

Les compartiments géologiques profonds suscitent un intérêt grandissant dans la communauté scientifique depuis les 50 dernières années. Néanmoins, ces écosystèmes demeurent largement méconnus du fait de leur difficulté d’accès. Le forage profond réalisé par l’ANDRA dans le Bassin parisien en 2008 a offert une opportunité unique de les étudier. Dans ce cadre, cette thèse avait deux objectifs majeurs ; i) caractériser, d’un point de vue microbiologique, quatre formations sédimentaires terrestres triasiques situées entre 1700 et 2000 m de profondeur et ii) étudier les effets combinés des paramètres de température, pression et salinité ainsi que de leur interaction sur l’activité métabolique de procaryotes anaérobies afin de mieux appréhender leur comportement au cours d’un enfouissement géologique.Malgré la recherche de microorganisme par la réalisation d’une gamme de milieux de culture diversifiée, ciblant préférentiellement les types trophiques fréquemment rencontrés en subsurface (méthanogènes, fermentaires, réducteurs de composés soufrés), aucun microorganisme viable et cultivable n’ait été isolé. En parallèle, une approche moléculaire complémentaire, composée (i) de l’étude comparative de l’efficacité de différentes méthodes d’extraction directe d’ADN et (ii) de l’analyse de la diversité bactérienne par la réalisation d’inventaires moléculaires, par DGGE (Denaturing Gel Gradient Electrophoresis) et clonage, a été réalisée sur le coeur des carottes de roches, conservées à pression atmosphérique ou sous pression, dans leurs états initiaux et post-incubation. L’exploration de ces formations sédimentaires profondes a indiqué la présence d’une très faible biomasse et d’une biodiversité microbienne pauvre principalement composée de membres aérobies et mésophiles appartenant au domaine Bacteria. Cette communauté bactérienne inattendue car a priori peu adaptée aux conditions régnant in-situ, également retrouvée dans divers écosystèmes de subsurface ainsi que dans des biotopes extrêmes, pourrait provenir en partie d’une paléo-recharge de l’aquifère du Trias par des eaux froides dérivées de la fonte des glaces formées lors de la dernière glaciation du Pléistocène.Le second objectif a été abordé à travers l’élaboration d’un plan factoriel complet dans le but d’identifier les effets des paramètres sur les activités microbiennes. Ainsi, les activités métaboliques de huit souches microbiennes halophiles et thermo-tolérantes ont été mesurées sous trente conditions distinctes de température (40, 55 et 70°C), pression (1, 90 et 180 bars) et salinité (13, 50, 110, 180 et 260 g.l-1). Toutes les souches originaires d’environnements profonds se sont révélées être au minimum piézo-tolérantes et capables de maintenir leur activité métabolique sous pressions hydrostatiques. Les métabolismes fermentaires (Thermovirga lienii et Halothermothrix orenii) et thiosulfato-réducteurs (Petrotoga mexicana et Thermosipho japonicus) se sont avérés particulièrement bien adaptées, d’un point de vue métabolique, aux hautes pressions, les plus hautes activités ayant été détectées sous pression. Certaines souches ont montré une résistance accrue aux hautes températures sous pression (Petrotoga mexicana). Toutefois une résistance variable à la salinité dans les différentes conditions de température et de pression a été observée pour chacune des souches, suggérant que certains mécanismes de résistance contre la pression osmotique seraient également efficaces pour lutter contre les températures et les pressions hydrostatiques élevées.Ce travail souligne que l’étude des écosystèmes terrestres profonds d’un point de vue microbiologique ne doit pas se restreindre à la recherche et à l’analyse de la diversité présente. L’étude des activités métaboliques de souches de subsurface en conditions profondes ouvre la voie à une meilleure compréhension des rôles joués par les communautés microbiennes en milieu extrême. / Over the past 50 years, the scientific community has shown a growing interest for deep geological compartments. However, these ecosystems remain largely unknown due to their inaccessibility. The aim of the present thesis was double; the first aim was to characterize, from a microbiological perspective, four terrestrial Triassic sedimentary formations located between 1700 and 2000 m depth in the Parisian Basin and collected by the ANDRA during a deep drilling campaign in 2008, and the second aim was to study the combined effects of temperature, pressure and salinity on the metabolic activity of anaerobic prokaryotes in order to predict their reaction to geological burial.Incubations in a large variety of media were carried out in order to stimulate the growth of the main trophic types found in such environments such as methanogens, fermenters and bacteria reducing sulphur compounds, however, no viable and cultivable microorganisms could be isolated. In parallel, a molecular approach was used to i) compare the efficacy of several DNA extractions methods and ii) analyse the bacterial diversity, using DGGE (Denaturing Gel Gradient Electrophoresis) and cloning, present in rock inner cores conserved either at atmospheric pressure or under pressure, in their initial states and following incubations in various media. The genetic exploration of these samples revealed a very low biomass and a poor diversity composed mainly of aerobic and mesophilic members of the Bacteria domain, a priori unadapted to such a deep, hot, saline and anoxic environment. This unexpected microbial community also found in many subsurface ecosystems as well as in extreme ecosystems could have partially originated from a paleorecharge of the Trias aquifer with cold waters coming from the melting of ice formed during the last Pleistocene glaciation.The second objective was to study the combined effects of temperature (40, 55 and 70°C), pressure (1, 90 and 180 bars) and salinity (13, 50, 110, 180 and 260 g.l-1) on the metabolic activity of anaerobic prokaryotes. In order to identify effects of parameters on microbial activities, a complete factorial plan was constructed from the metabolic activities measured for eight halophile and thermo-tolerant bacterial strains exposed to 30 distinct temperature, pressure and salinity conditions. All the strains issued from deep environments were at the least piezo-tolerant and capable of maintaining their activity under hydrostatic pressures. The fermenting (Thermovirga lienii and Halothermothrix orenii) and thiosulfate reducing strains (Petrotoga mexicana and Thermiosipho japonicus) were particularly well adapted, from a metabolic point of view, to high pressures; indeed the highest activities were measured under pressure. Also, several strains (such as Petrotoga mexicana) showed an increased resistance to high temperatures under pressure. However, resistance to an increase in salinity was variable for each strain under the different temperature and pressure conditions. This suggests that the resistance mechanisms for osmotic pressure also enable resistance to high temperatures and hydrostatic pressures.This work underlines that the microbiological characterization of deep terrestrial ecosystems must not be limited to the search and analyses of the existing diversity. Moreover, such upstream studies of the metabolic activities of subsurface bacterial strains in deep terrestrial conditions are a necessary beginning towards understanding the role of microbial communities in extreme environments.

Mikrobielle Prozesse spielen eine wichtige Rolle im Sediment von Talsperren und Seen. Demgegenüber stehen nur unzureichende Erkenntnisse über die Zusammensetzung mikrobieller Biozönosen in Sedimenten sowie deren Aktivität zur Verfügung. Das Ziel dieser Studie war die Untersuchung und der Vergleich der Zusammensetzung und der Struktur mikrobieller Gemeinschaften in Sedimenten um eine Abschätzung der mikrobiellen Diversität in Talsperrensedimenten unterschiedlicher Trophie zu erreichen. Durch die Kombination der in dieser Arbeit verwendeten Methoden (Vergleichende 16S rDNA Analyse, Fingerprinttechniken, klassische Methoden) konnte eine Charakterisierung der mikrobiellen Zusammensetzung der obersten 5 cm von den Talsperrensedimenten Neunzehnhain, Muldenberg, Quitzdorf und Saidenbach erzielt werden. Die vergleichende 16S rDNA Analyse offenbarte in 2541 analysierten rekombinanten Klonen 528 verschiedene Sequenztypen, welche zu 293 OTUs zusammengefaßt werden konnten. Obwohl die Gemeinschaften der verschiedenen Talsperren nur schwach auf der Ebene der phylogenetischen Gruppen differierten, konnte durch die Verwendung von Ähnlichkeitsindices gezeigt werden, dass jede Talsperre eine spezifische mikrobielle Sedimentgemeinschaft aufweist. Über 60% aller Klone zeigten Ähnlichkeiten von mehr als 97% zu 16S rDNA-Sequenzen kultivierter Organismen oder phylogenetisch eingeordneten Sequenzen (14 bekannte phylogenetische Gruppen). Alle anderen Klone zeigten hohe Sequenzhomologien zu unidentifizierten, phylogenetisch bisher nicht eingeordneten Bakterien. Diese Bakterien waren mit Anteilen zwischen 19,8% (Muldenberg) und 54,6% (Saidenbach) in den 16S rDNA Bibliotheken repräsentiert. Mittels Fingerprinttechniken (DGGE, T-RFLP, ARISA) konnten komplexe Muster der mikrobiellen Diversität erzeugt werden. Dabei konnten die Ergebnisse der 16S rDNA Analyse bestätigt werden. Durch die verwendeten Methoden konnte eine komplexe mikrobielle Diversität in den Sedimenten aufgedeckt werden und die Ergebnisse weisen darauf hin, dass die mikrobielle Diversität in Sedimenten wesentlich höher ist als bisher angenommen.

Soil nematodes play an important role in indication for assessing soil environments and ecosystems. Previous studies of nematode community analyses based on molecular identification have shown to be useful for assessing soil environments. Here we applied PCR-DGGE method for molecular analysis of five soil nematode communities (designed as S1 to S5) collected from four provinces in Southeastern Vietnam (Binh Duong, Ba Ria Vung Tau, Binh Phuoc and Dong Nai) based on SSU gene. By sequencing DNA bands derived from S5 community sample, our data show 15 species containing soil nematode, other nematode and non-nematode (fungi) species. Genus Meloidogyne was found as abundant one. The genetic relationship of soil nematode species in S5 community were determined by Maximum Likelihood tree re-construction based on SSU gene. This molecular approach is applied for the first time in Vietnam for identification of soil nematode communities. / Tuyến trùng đất đóng vai trò chỉ thị quan trọng trong công tác đánh giá môi trường và hệ sinh thái đất. Các nghiên cứu trước đây đã cho thấy lợi ích của việc phân tích cộng đồng tuyến trùng đất bằng định danh sinh học phân tử đối với việc đánh giá môi trường đất. Ở đây, chúng tôi ứng dụng phương pháp PCR-DGGE dựa trên gene SSU để phân tích năm (ký hiệu từ S1 đến S5) cộng đồng tuyến trùng đất thuộc các vùng trồng chuyên canh cây hồ tiêu ở miền nam Việt Nam (Bình Dương, Bà Rịa Vũng Tàu, Bình Phước và Đồng Nai). Bằng cách giải trình tự các vạch của mẫu tuyến trùng S5, kết quả cho thấy cộng đồng tuyến trùng này có 15 loài gồm nhóm tuyến trùng đất, nhóm các loại tuyến trùng khác và nhóm không phải tuyến trùng (nấm) và trong đó Meloidogyne là giống ưu thế. Mối quan hệ di truyền của các các loài tuyến trùng đất thuộc cộng đồng S5 được xác định bằng việc thiết lập cây phát sinh loài Maximum Likelihood dựa trên gene SSU. Đây là nghiên cứu đầu tiên ở Việt Nam sử dụng kỹ thuật PCR-DGGE để phân tích các cộng đồng tuyến trùng đất trồng hồ tiêu.

Die bei der Biogasproduktion anfallenden Gärreste werden als organische Dünger im Pflanzenbau eingesetzt. Infolge des Vergärungsprozesses unterscheiden sich Gärreste von herkömmlichen organischen Düngern. Daraus könnten sich spezifische positive oder negative Wirkungen auf Bodenfruchtbarkeit und Pflanzen ergeben, die Gegenstand dieser Arbeit sind. In einem sechsjährigen Feldversuch (Energiepflanzenfruchtfolge, sandiger Boden) wur- den die Düngeeffekte von fünf verschiedenen Gärresten mit denen von Rindergülle, Stallmist und mineralischem Dünger (KAS) verglichen. Zur umfassenden Charakterisie- rung der Bodenfruchtbarkeit erfolgten Untersuchungen aus den Bereichen Bodenchemie, -physik, -mikrobiologie und Pflanzenbau, wobei die Humusdynamik einen Schwerpunkt bildete. Die Mengenkalkulation der Düngung basierte auf der gleichen Gabe organi- schem C mit einem N-Ausgleich durch KAS. Es ergaben sich für Gärreste gegenüber KAS überwiegend positive Effekte auf Hu- musgehalt, Aggregatstabilität und bakterielle Aktivität und Diversität. Diese Effekte waren denen von Rindergülle und Stallmist ähnlich. Möglicherweise besteht aber durch Gärrestdüngung ein erhöhtes Risiko von P- und K-Überschüssen sowie N-Verlusten. Eine erhöhte Benetzungshemmung wurde nicht gefunden. Die mikrobielle Gemeinschaft des Bodens zeigte eine spezifische Beeinflussung durch die Gärreste in der funktionellen, jedoch nicht in der genetischen Struktur. Die N-Verfügbarkeit war deutlich geringer als die von KAS, wodurch sich für Grünroggen Mindererträge ergaben. Für Silomais und Sorghum fand sich bei kombinierter Anwendung mit KAS ein zu KAS ähnliches Ertragsniveau. Gärreste haben analog zu herkömmlichen organischen Düngern bei effizientem Einsatz das Potential zu KAS vergleichbare Erträge zu erzielen und gleichzeitig die Bodenfrucht- barkeit zu fördern. Diese Schlussfolgerung ist im Kontext der spezifischen Standort- und Versuchsbedingungen zu sehen und sollte durch eine längere Versuchszeit abgesichert werden. / Digestates arising during biogas production are used as organic fertilizers in agriculture. Due to the fermentation process, digestates have different properties from traditional organic fertilizers. This may result in specific positive or negative effects on soil fertility and plants, which are subject of this work. In a six year field experiment (energy crop rotation, sandy soil) fertilizer effects of five different digestates were compared with cattle slurry, farm yard manure and mineral fertilizer (KAS). For a comprehensive characterization of soil fertility effects, methods from the fields of soil chemistry, physics, microbiology and plant science were applied. One special focus of these investigations was humus dynamics. Manure doses were based on the same dose of organic carbon, resulting different N-doses were compensated by KAS. Compared with KAS, digestates showed predominantly positive effects on humus con- tent, soil aggregate stability and bacterial activity and diversity. These effects of di- gestates were similar to those of cattle slurry and farm yard manure. There may be an increased risk of P and K oversupply and N losses as a result of digestate fertilization. An increased soil water repellency was not found. The soil bacterial community was specifically influenced by digestates regarding its functional, but not regarding its genetic structure. Saprotrophic fungy were reduced by some digestates in comparison to KAS. N availability was considerably lower than of KAS, resulting in yield depressions of forage rye. For silage maize and sorghum, digestates combined with KAS equaled the yield level of KAS. If efficiently applied, digestates have like other organic fertilizers the potential to produce equal yields as KAS whilst enhancing soil fertility. This conclusion is restricted to the specific conditions of experimental site and design and must be verified during a longer experimental period.

La fertilisation phosphatée est très répandue dans les pratiques agricoles Nord-Américaines. Bien que généralement très efficace pour augmenter la production végétale, son utilisation peut engendrer certaines contaminations environnementales. Afin de diminuer ce problème, plusieurs pratiques de gestion sont envisagées. Parmi celles-ci, on retrouve l’intéressante possibilité de manipuler la flore microbienne car cette dernière est reconnue pour son implication dans bons nombres de processus fondamentaux liés à la fertilité du sol. Cette étude a démontré que lors d’essais en champs, la forme de fertilisant ajouté au sol ainsi que la dose de phosphore (P) appliquée avaient un impact sur la distribution des microorganismes dans les différentes parcelles. Une première expérience menée sur une culture de luzerne en prairie semi-aride a montré que les échantillons provenant de parcelles ayant reçu différentes doses de P présentaient des différences significatives dans leurs communautés bactériennes et fongiques. La communauté de CMA est restée similaire entre les différents traitements. Une deuxième expérience fut menée pendant trois saisons consécutives afin de déterminer l’effet de différentes formes de fertilisation organiques et minérale ajustées selon une dose unique de P sur les populations bactériennes et fongiques d’une culture intensive de maïs en rotation avec du soja. Les résultats des analyses ont montrés que les populations varient selon le type de fertilisation reçu et que les changements sont indépendants du type de végétaux cultivé. Par contre, les populations microbiennes subissent une variation plus marquée au cours de la saison de culture. La technique de DGGE a permis d’observer les changements frappant la diversité microbienne du sol mais n’a permis d’identifier qu’une faible proportion des organismes en cause. Parallèlement à cette deuxième étude, une seconde expérience au même site fut menée sur la communauté de champignons mycorhiziens à arbuscules (CMA) puisqu’il s’agit d’organismes vivant en symbiose mutualiste avec la majorité des plantes et favorisant la nutrition de même que l’augmentation de la résistance aux stress de l’hôte. Ceci permit d’identifier et de comparer les différents CMA présents dans des échantillons de sol et de racines de maïs et soja. Contrairement aux bactéries et aux champignons en général, les CMA présentaient une diversité très stable lors des différents traitements. Par contre, au cours des trois années expérimentales, il a été noté que certains ribotypes étaient significativement plus liés au sol ou aux racines. Finalement, l’ensemble de l’étude a démontré que la fertilisation phosphatée affecte la structure des communautés microbiennes du sol dans les systèmes évalués. Cependant, lors de chaque expérience, la date d’échantillonnage jouait également un rôle prépondérant sur la distribution des organismes. Plusieurs paramètres du sol furent aussi mesurés et ils présentaient aussi une variation au cours de la saison. L’ensemble des interactions possibles entre ces différents paramètres qui, dans certains cas, variaient selon le traitement appliqué, aurait alors probablement plus d’impact sur la biodiversité microbienne que la seule fertilisation. / Phosphorus fertilization is a widespread practice in North American agriculture. Although it is generally efficient to increase yields, its use can also induce some environmental contaminations. Several management practices are considered in order to decrease this problem. Among these possibilities there is the challenging one of manipulating microbial flora, which is well known for its implication in many processes related to soil fertility. We have demonstrated in field trials that both the form of fertilizer added to soil and the applied P amounts impact microbial distribution in plots. A first experiment performed on alfalfa monocultures in semi-arid prairie conditions demonstrated that samples coming from plots that had received different doses of P fertilizer presented significant differences on their bacterial and fungal communities. AMF population remained stable between treatments. A second experiment was conducted over three growing season of an intensive maize/soybean rotation cropping system. It aimed to determine the effect of different organic and mineral fertilizers containing equal P amount on bacterial and fungal populations. It was demonstrated that these communities varied according to the fertilizer type applied. Changes are independent from the grown crop. However, microbial populations have undergone greater variation within each growing season. DGGE approach allowed to observe changes occurring in soil microbial diversity but have only permit to identify a small proportion of organisms. A second experiment in the latter study was performed on the same site and focused on arbuscular mycorrhizal fungi (AMF) as they are organisms living in a mutualistic symbiosis with most land plants and increasing host nutrition and resistance to stresses. It led to the identification and comparison of the different AMF found in maize and soybean soil and root samples. In opposition to what was observed with bacteria and fungi previously, AMF presented a very stable diversity between the different treatments. However, some ribotypes were significantly more present in soil or roots during each growing season. Finally, our whole project demonstrated that P fertilization affected microbial community structure on studied sites. Nevertheless, in each experiment, sampling time also played a substantial role in the organism distribution. Many soil parameters were also monitored and presented a seasonal variation. The sum of possible interactions between these parameters, which in some cases varied according to treatment, would thus have more impact on microbial diversity that the sole fertilization.