Diversity of the soil microbial community and its functional aspects were investigated in man-influenced environments, such as colliery spoil heaps in post mining sites and upland pasture used for outdoor cattle husbandry. The study was based on the cultivation of bacteria and streptomycetes as well as culture-independent approaches. Cultivated bacteria and streptomycetes were characterized by phenotypic and genotypic means. The culture-independent approaches were based on an analysis of environmental DNA in terms of both qualitative and quantitative parameters.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Atualmente, uma das maiores preocupações da humanidade é com a disponibilidade e qualidade da água. A exploração inadequada das fontes acarreta a contaminação das águas superficiais e subterrâneas que se tornam um risco para a saúde pública. Dentre as fontes biológicas de contaminação da água, incluem-se as bactérias, que são responsáveis por inúmeras doenças, sendo frequentemente tratadas com antimicrobianos. O amplo uso de antimicrobianos na medicina humana e na produção animal tem resultado no aumento do número de bactérias comensais e patogênicas resistentes a agentes antimicrobianos, fato que nos últimos anos vem se tornando um dos principais problemas de saúde pública. O presente trabalho resulta do interesse pelo estudo da qualidade da água consumida pelos alunos de 20 escolas estaduais da rede pública de Boa Vista RR, bem como obter o perfil de resistência a antimicrobianos de bactérias isoladas a partir de diferentes amostras de águas, coletadas nessas escolas. No período de outubro de 2010 a abril de 2011, foram coletas 40 amostras de águas de torneiras das copas e 40 amostras de águas de bebedouros, as quais foram submetidas à avaliação microbiológica. A determinação dos coliformes totais e termotolerantes foi realizada por meio da técnica dos tubos múltiplos com 3 diluições e série de 5 tubos. Para a detecção de bactérias heterotróficas uso-se o método pour plate, de acordo com as normas preconizadas no Standard Methods for the Examination of Water and Wastwater. O isolamento e a identificação dos isolados bacteriano foi realizada no LACEN-RR utilizando-se a série bioquímica. Para a avaliação da resistência aos antimicrobianos, utilizou-se a metodologia de difusão de disco, seguindo as normas estabelecidas pelo CLSI. Das amostras de águas que recebem tratamento completo, 10% apresentaram resultados positivos para coliformes totais e nas amostras de água clorada, 20% apresentaram resultados positivos para coliformes totais e 2,5% resultado positivo para coliformes termotolerantes, o que as tornam imprópria para o consumo humano. A contagem de bactérias heterotróficas variou de 1,4 x 10 a 3,6 x 102 UFC/mL de água, não ultrapassando o estabelecido pela Portaria 518/2004/MS. Foram identificadas as seguintes bactérias Gram-negativas (66,7%): Acinetobacter spp., C. violacea, Cocobacilos spp., E. aerogenes, E. coli, K. ozaenae, Leptothrix ssp. e Bacilo Gram-negativo não fermentador de glicose, as bactérias Gram-positivas (33,3%), identificadas foram: B. subtilis, Micrococcus spp., S. aureus e Staphylococcus spp. Os resultados dos testes de sensibilidade aos antibióticos revelaram que a maioria das bactérias isoladas foi resistente a ampicilina (68,2%), 27,3% apresentaram resistência a oxacilina e 22,7% foram resistentes a eritromicina e meropenem. As cepas de S. aureus isoladas das amostras de águas apresentaram maior índice MAR (0,61) entre as bactérias Gram-positivas, enquanto que nas bactérias Gram-negativas, as cepas que apresentaram maior índice MAR foram as cepas de E. coli, com índice 0,61. Os resultados comprovam a ocorrência de instabilidade no padrão de qualidade da água fornecida a população de Boa Vista RR seja no tratamento, na distribuição ou no armazenamento da água. Além de constatar a presença de bactérias multirresistentes a antibióticos, o que representa risco à população. / One of the main concerns of humanity nowadays is water: its availability and its quality. An inadequate exploitation of the sources results in the contamination of both superficial and deep waters, which become a public health hazard. Bacteria are one of these biological sources of water contamination, responsible for countless diseases which are treated with antimicrobials. The widely spread use of antimicrobials in human medicine along with animal production had resulted in a steady increase in the number of pathogenic and commensal bacteria resistant to antimicrobial agents, which in recent years are becoming one of the main problems of public health. This paper is a result of an interest in studying the quality of water consumed by the students of 20 state schools of the public school system of Boa Vista RR, as well as trying to obtain a profile of antimicrobial resistance of the bacteria isolated in different water samples collected at these schools. Between October 2010 and April 2011, 40 water samples were collected from taps in lunchrooms, along with 40 samples from drinking wells, and all of them were submitted to microbiological examination. Using the multiple tubes technique, with 3 dilutions and a series of 5 tubes, we determined the total number of coliforms and thermotolerant coliforms. In agreement with the rules of the Standard Methods for the Examination of Water and Wastewater, the pour plate method was used at the CBio UFRR to detect heterotrophic bacteria. Isolation and identification of microorganisms was done at LACEN RR, using the biochemical series. In evaluating the resistance to antimicrobials, disk diffusion methods were used, in agreement with the established rules of the CLSI. In water samples that receive full treatment, 10% tested positive for total coliforms and, in chlorinated water samples, 20% tested positive for total coliforms and 2,5% for thermo-tolerant coliforms, which makes them inadequate for human consume. The counting of heterotrophic bacteria went from 1,4 x 10 to 3,6 x 10 CFU/mL of water, not surpassing what is established in the ordinance 518/2004/MS. The following Gram-negative bacteria (66,7%) were identified: Acinetobacter spp., C. violacea, Cocobacilos spp., E. aerogenes, E. coli, K. ozaenae, Leptothrix ssp. and Gram-negative glucose non fermenting bacillus. The Gram-positive bacteria identified were: B. subtilis, Micrococcus spp., S. aureus and Staphylococcus spp. The results of antibiotic sensibility tests revealed that most of the isolated bacteria were resistant to ampicilin (68,2%), 22,3% showed resistance to oxacilin and 22,7% were resistant to both eritromicin and meropenem. In Gram-positive bacteria, the growths of S. aureus isolated from water samples showed the greatest MAR index (0,61), while E. coli growths were the ones who showed the greatest MAR index in Gram-negative bacteria (also 6,1%). Results prove a great instability in the quality of water provided to the Boa Vista - RR population, being in its treatment, distribution or containment, as well as showing the presence of bacteria resistant to multiple antibiotics, which is a health hazard to the public.

La croissance hétérotrophe de l’hypocotyle est une étape clé pour la réussite de la levée. La présente étude est focalisée sur le déterminisme génétique de l’allongement de cet organe à l’obscurité chez Medicago truncatula en analysant le nombre et la longueur des cellules de l’épiderme, tissu gouvernant l’allongement des organes. Une grande variabilité génétique du nombre de cellules a été révélée dans les graines de 15 génotypes représentatifs de la diversité génétique de l’espèce. La stabilité de ce caractère dans des graines provenant de différentes productions suggère qu’il est sous contrôle génétique fort. Il a été montré que ce nombre de cellules, préétabli dans les graines, est le principal déterminant de la variation génotypique de la longueur de hypocotyle en conditions optimales de croissance. Par contre, l'élongation cellulaire devient le déterminant majeur des différences génotypiques observées sous stress abiotiques (basse température, déficit hydrique).Des loci contrôlant le nombre de cellules de l’épiderme et leur longueur maximale à basse température ont ensuite été identifiés dans une population de lignées recombinantes. Ceux ayant un impact sur l’élongation de l’hypocotyle à basse température ont été mis en évidence. Enfin, deux génotypes présentant un nombre de cellules similaire mais des capacités d’allongement cellulaire contrastées ont été plus finement comparés. Des protéines ayant un rôle dans la formation et l’organisation du cytosquelette et dans la modification des parois cellulaires ont été révélées en lien avec les différences d’allongeme / The heterotrophic growth of hypocotyl is a crucial process for successful seedling emergence. The present study is focused on the genetic determinism of its elongation in darkness in Medicago truncatula by analyzing the number and the length of cells of epidermis, the tissue controlling organ elongation.A large genetic variability of the epidermal cell number of the hypocotyl in seeds of 15 genotypes representative of the genetic diversity of the species was revealed. The stability of this trait in the seeds collected from different productions suggests it is under strong genetic control. This cell number was shown to be the main contributor of genotypic variation of hypocotyl length in optimal conditions. On the other hand, cell elongation becomes the major determinant of the genotypic differences observed under abiotic stresses (low temperature, water deficit).Quantitative Trait Loci (QTLs) controlling the number of epidermal cells and their maximal length at low temperature were then identified using a recombinant inbred lines population, and those impacting hypocotyl elongation at low temperature were highlighted.Finally, two genotypes sharing a similar cell number but contrasted capacities of cell elongation were compared more in detail. Proteins playing a role in the formation and organization of cytoskeleton and in the modification of the cell wall were revealed in connection with the differences in cellular elongation between genotypes. Moreover, differences in the cell wall sugar composition, in the degree of methylation of pectins and in a potential inhibito

Une approche in situ et expérimentale sont menées en baie de Marseille. Des mesures simultanées de PB, de RB, de la phosphatase alcaline (phos) et de la protéase (prot) sont réalisées. Des gradients de températures (12-32°C) de ces 4 activités sont effectués. Les résultats montrent que 1) les températures optimales et les Q10 varient saisonnièrement, 2) le BGE ne diminue pas nécessairement lorsque la température augmente et 3) quelles que soit les conditions in situ, l'assemblage bactérien possède un BGE à la température in situ proche de sa température optimale. Des expériences d'enrichissements en PO4 et glucose incubées à température in situ et température in situ + 3°C montrent que la nature de l'interaction entre la température et les ressources est principalement synergétique. L'hypothèse d'un scénario supposant des changements relatifs de PB, prot et phos lors d'un changement de température suggère que les taux prot/PB et phos/PB diminuent lors d'un réchauffement et augmentent lors d'un refroidissement. Enfin, ces expériences témoignent que la température et la disponibilité du PO4 sont les principaux facteurs limitant les activités hétérotrophes. L'étude du mode d'apport de la MO (pulsé ou en continu) menée sur 4 cultures saisonnières montre que selon les conditions environnementales et le mode d'apport de la MO, l'AB, la PB et la RB varient significativement. Toutefois, l'AB, la PB, la RB et le BGE ne montrent pas de différences significatives entre les réservoirs d'ajouts pulsés et d'ajouts continus de MO suggérant des communautés bactériennes peu sensibles à la nature de la perturbation nutritionnelle alors que leurs activités en sont fortement dépendantes. / In this work, in situ and experimental approaches have been carried out in Marseilles' Bay. Simultaneous measurements of bacterial production (BP), bacterial respiration (BR), alkaline phosphatase activity (phos) and protease activity (prot) have been performed. Kinetic temperatures (12-32°C) of these 4 activities have been also conducted. The results demonstrate that i) the optimum temperature and Q10 values vary seasonally, ii) BGE value does not necessarily decrease with increasing temperature and iii) whatever the in situ conditions, the bacterial assemblage has a in situ temperature BGE value close to its optimal temperature. Enrichments experiments in PO4 and glucose incubated at in situ temperature and in situ temperature + 3°C allow to observe that the synergistic nature of the interaction between temperature and resources. The assumption of a scenario assuming that BP, prot and phos changes during a temperature change suggests that prot:BP and phos:BP ratios decrease with a warming and increase with a cooling. Finally, these experiments show that temperature and PO4 availability are the main factors controlling heterotrophic activities. The study on OM availability and associated timing (pulsed or continuous) conducted during 4 seasonal cultures demonstrates that at different seasons and according to the delivery mode of OM, BA, BP and BR are varying significantly. However, the BA, BP and the BR does not show significant differences between the tanks with pulse OM addition and continuous OM addition suggesting that predominant bacterial communities are insensitive to the nature of nutritional disturbance whereas bacterial activities are highly dependent.

No description available.

La germination et la croissance hétérotrophe sont des phases clés de l'établissement des plantes. Ils sont sous contrôle génétique et affectés par la température. L'objectif de cette thèse est d'analyser la variabilité inter et intra-spécifique de cinq espèces prairiales dans leurs réponses à la température pendant la germination et la croissance hétérotrophe. Trente-deux populations de Lolium perenne, Festuca arundinacea, Dactylis glomerata, Medicago sativa, et Onobrychis viciifolia ont été évalués sous huit températures constantes entre 5 et 40°C.La nouveauté de ce travail vient de la large gamme de températures et le nombre de populations évaluées. Il a été observé que, au sein des espèces, la réaction des populations à la température indique une forte variabilité et des différences significatives. La germination n'a été pas observée à 40°C pour l'une des 23 graminées, l'O. viciifolia germé peu tandis que les variétés de M. sativa ont été peu affectées. La croissance hétérotrophe des 32 populations a été affectée par la température. La croissance des axes fortement fiable ou nulle à 40°C. Les courbes de réponse du taux de croissance maximale de l'axe sont asymétriques en forme de cloche.Des interactions significatives entre la température et la population ont été détectées pour la germination et la croissance hétérotrophe. La germination des populations des sites froids est renforcée par des températures plus chaudes et limité par les plus froids et vice-versa pour les populations chaudes adaptées. / Germination and heterotrophic growth are key phases for plant establishment. They are under genetic control and affected by temperature. The objective of this thesis was to analyse the inter- and intra-specific variability of five pasture species in their responses to temperature during germination and heterotrophic growth.Thirty two populations of Lolium perenne, Festuca arundinacea, Dactylis glomerata, Medicago sativa, and Onobrychis viciifolia were evaluated under eight constant temperatures between 5 and 40°C.The novelty of this work comes from the wide range of temperatures and the number of populations evaluated. It was observed that, within species, the response of populations to temperature shows high variability and significant differences. No germination was observed at 40°C for any of the 23 grasses, O. viciifolia germinated poorly while M. sativa varieties were little affected. Heterotrophic growth of the 32 populations was affected by temperature. The growths of the axes were negligible or lethal at 40°C. Response curves of maximum growth rate of the axis were asymmetric bell-shaped.Significant interactions between temperature and population were detected for germination and heterotrophic growth. Germination of populations from cold sites is enhanced by warmer temperatures and limited by colder ones and vice versa for warm-adapted populations. This study demonstrates that genetic variability does exist within the five studied species. This variability could be exploited to breed new varieties adapted to the future climate.

Partial Nitritation/Anammox process (deammonification process), by which occurs oxidation of ammonium to nitrogen gas by autotrophic bacteria in anaerobic conditions, considered to be cost-effective and environmentally friendly method of nitrogen removal. Present research work focuses on achieving a high nitrogen removal degree, thanks to Anammox bacteria, while providing the best performance of the ongoing process. Integrated fixed-film activated sludge (IFAS) reactor was supplied with the main stream of the wastewater after UASB reactor, characterized by low concentration of nitrogen and organic matter. The bacteria ability to accommodate, were tested in the biofilm and in the activated sludge, depending on the different stages in which the process were being conducted. Batch test, such as Specific Anammox Activity (SAA), Nitrate Uptake Rate (NUR) and Oxygen Uptake Rate (OUR), were used for the evaluation of activity of various groups of bacteria. On the basis of laboratory analysis verified the values obtained from the batch tests. It was determined that a high degree of nitrogen removal (92% of NH4-N) was achieved thanks to the dominant activity of the Anammox bacteria, with low participation of other groups of bacteria. It was also proved, that Anammox bacteria activity were overwhelming in the biofilm. Dominant role of Ammonium Oxidizing Bacteria (AOB) was associated with high activity of Anammox bacteria, which together satisfyingly out-competed Nitrite Oxidizing Bacteria (NOB) and heterotrophic bacteria. It has been shown that Anammox bacteria quickly adapt to the new conditions and they are able to assume a dominant role, even in the case of inoculation of the reactor with the sludge from SBR. This allows conclude, that in the case of operational problems, the reactor can be supplied from another source, in order not to inhibit the process.