Dissertations / Theses: 'Bacterial taxonomy'

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Kim, Bongcheol. "Polyphasic taxonomy of thermophilic actinomycetes." Thesis, University of Newcastle Upon Tyne, 1999. http://hdl.handle.net/10443/1757.

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Molecular systematic methods were applied in a series of studies designed to resolve the taxonomic relationships of thermophilic actinomycetes known to be difficult to classify using standard taxonomic procedures. The test strains included representatives of clusters defined in an extensiven umerical phenetic survey of thermophilic streptomycetesa nd twelve marker strains. The resultant genotypic data together with the results of corresponding phenotypic studies were used to highlight novel taxa and to improve the circumscription of validly described species. The most comprehensive study was undertaken to clarify relationships within and between representative alkalitolerant, thermophilic and neutrophilic, thermophilic streptomycetes isolated from soil and appropriate marker strains. The resultant data, notably those from DNA: DNA relatedness studies, supported the taxonomic integrity of the validly described species Streptomyces thermodiastaticus, Streptomyces thermoviolaceus and Streptomyces thermovulgaris. However, the genotypic and phenotypic data clearly show that Streptomyces thermonitrificans Desai and Dhala 1967 and Streptomyces thermovulgaris (Henssen 1957) Goodfellow et al. 1987 represent a single species. On the basis of the priority, Streptomyces thermonitrificans is a later subjective synonym of Streptomyces thermovulgaris. Similarly, eight out of eleven representative alkalitolerant, thermophilic isolates and three out of sixteen representative neutrophilic, thermophilic isolates had a combination of properties consistent with their classification as Streptomyces thermovulgaris. One of the remaining alkalitolerant, thermophilic isolate, Streptomyces strain TA56, merited species status. The name Streptomyces thermoalcalitolerans sp. nov. is proposed for this strain. A neutrophilic, thermophilic isolate, Streptomyces strain NAR85, was identified as Streptomyces thermodiastaticus. Four other neutrophilic thermophilic isolates assigned to a numerical phenetic cluster and a thermophilic isolates from poultry faeces were also considered to warrant species status; the names Streptomyces eurythermophilus sp. nov. and Streptomyces thermocoprophilus sp. nov. are proposed to accommodate these strains. It was also concluded that additional comparative taxonomic studies are required to clarify the relationships between additional thermophilic streptomycete strains included in the present investigation. A corresponding polyphasic approach was used to clarify the taxonomy of six thermophilic isolates provisionally assigned to either the genera Amycolatopsis or Excellospora. Two of the isolates, strain NT202 and NT303, had properties consistent with their classification in the genus Amycolatopsis. However, the genotypic and phenotypic data also showed that these strains formed a new centre of taxonomic variation for which the name Amycolatopsis eurythermus sp. nov. is proposed. Similarly, the four remaining strains formed two new centre of taxonomic variation within the genus Excellospora. It is proposed that isolates TA113 and TA114 be designated Excellospora alcalithermophilus sp. nov. Similarly, the name Excellospora thermoalcalitolerans sp. nov. is proposed for strains TA86 and TA111. An emended description is also given for the genus Excellospora.

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Brady, Carrie Louise. "Taxonomy of Pantoea associated with bacterial blight of Eucalyptus." Pretoria : [s.n.], 2005. http://upetd.up.ac.za/thesis/available/etd-02092006-110117.

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Cosgaya, Castro Clara. "Not the usual suspects: membrane translocation, pathogenic potential and bacterial species of the Acinetobacter baumannii group." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/668097.

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The most clinically relevant species of the Acinetobacter genus are comprised within the Acinetobacter baumannii group (Ab group, i. e. A. baumannii, Acinetobacter nosocomialis, Acinetobacter pittii, Acinetobacter seifertii and A. pittii-like/A. dijskhoorniae). Among these species A. baumannii is the most prevalent and usually shows multidrug resistance. This, and the fact that the Ab group species cannot be distinguished by phenotypic methods, has led to the misidentification of the species of the Ab group as A. baumannii in the clinical settings. Nevertheless, in the last years the incidence of the other species of the Ab group has risen, partly due to the use of molecular techniques and mass spectrometry tools. This thesis has characterised, using both genotypic (rpoB-based and MLSA phylogenetic analyses, and whole genome sequence analysis) and phenotypic (carbon utilisation assays and MALDI-TOF MS) techniques, a group of strains mainly recovered from human samples that represents a new bacterial species within the Ab group for which the name of Acinetobacter dijkshoorniae has been proposed. The genome of the type strain of the novel species has been sequenced and the identification of the species of the Ab group by MALDI-TOF MS has been optimised, since the novel species (A. dijkshoorniae and A. seifertii) could not be identified by this technique prior to this study. MALDI-TOF MS was shown to be rapid and accurate in the discrimination of all the species of the Ab group, indicating its suitability for the implementation of this technique in the clinical settings. In addition, the use of MALDI- TOF MS allowed the identification of members of the Ab group in market meat from Peru, leading to the first identification of A. dijkshoorniae from food and in South America. We also evaluated the differences among the species of the Ab group beyond those at the taxonomic level and found that while A. baumannii still presents the higher rates of antimicrobial resistance, this species and A. nosocomialis, which usually are more prevalent in our hospitals and have worst outcomes, showed a minor pathogenicity in terms of biofilm formation and virulence in the Caenorhabditis elegans infection model. In contrast, A. pittii, A. seifertii and A. dijkshoorniae presented a higher pathogenicity in the phenotypes studied. This data suggests the emergence of the non-baumannii species of the Ab group as well as different degrees of adaptation to the human host and the need of studying them as distinct entities. The rise on the antimicrobial resistance of A. baumannii has drastically reduced the therapeutic options left to treat infections caused by this pathogen. In view of the lack of effective antimicrobial drugs there is an urgent need for novel therapeutic approaches. In order to find novel targets for the development of antimicrobial drugs against A. baumannii, we evaluated the dual role of transport-related proteins in antimicrobial resistance and virulence using a transposon mutant strain collection derived from the A. baumannii AB5075 strain. The antimicrobial susceptibility of the mutant strains was compared against the wild- type strain and led to the identification of novel antimicrobial substrates for known efflux pumps and uncharacterised transport-related proteins which seem to participate in the transport of antibiotics across membranes. The evaluation of the virulence in the Galleria mellonella infection model also identified transport-related proteins putatively involved in the virulence of A. baumannii. This results are still preliminary but show the dual role of transport- related proteins in the antimicrobial resistance and pathogenicity of A. baumannii and open a new line of research that might help to gain further knowledge about the virulence of this pathogen while finding novel targets for the development of new antimicrobial drugs against A. baumannii.
Dentro del género Acinetobacter, las especies del grupo Acinetobacter baumannii (Ab) (i. e. A. baumannii, Acinetobacter nosocomialis, Acinetobacter pittii y Acinetobacter seifertii y A. pittii-like/A. dijskhoorniae) destacan por su gran relevancia clínica, siendo A. baumannii el patógeno del grupo Ab de mayor importancia debido a su frecuente aislamiento y su usual fenotipo de multirresistencia. Esto, sumado a que las especies del grupo Ab son indistinguibles a nivel fenotípico, ha conllevado que habitualmente hayan sido erróneamente identificadas en el ámbito clínico como A. baumannii. Sin embargo, en los últimos años se ha observado un aumento en la incidencia de las otras especies del grupo Ab, en parte gracias a las técnicas moleculares, que han revolucionado la taxonomía de este género, y también al uso de la espectrometría de masas MALDI-ToF (EM MALDI-TOF). Este estudio proporciona las pruebas fenotípicas y genotípicas que respaldan la delineación de una nueva especie dentro del grupo Ab, para la cual se ha propuesto el nombre de Acinetobacter dijkshoorniae. El genoma de la cepa tipo de esta nueva especie ha sido secuenciado, y se ha puesto a punto la identificación mediante EM MALDI-TOF de los nuevos miembros del grupo Ab (A. dijkshoorniae y A. seifertii) así como ha sido optimizado para el resto de especies del grupo. Rasgos como la formación de biofilm o la virulencia en el modelo animal de Caenhorabditis elegans muestran que A. baumannii, junto con A. nosocomialis, presentan menor potencial patogénico que las otras especies del grupo Ab, y que A. dijkshoorniae es especialmente virulenta. Estos datos sugieren diferentes niveles de adaptación al ámbito hospitalario, y remarca la necesidad de identificar y estudiar las especies del grupo Ab individualmente. Además, a nivel de susceptibilidad antimicrobiana, A. baumannii sigue siendo la especie que presenta mayores tasas de resistencia. Finalmente, hemos hallado nuevas proteínas implicadas en el transporte de membrana que, de manera preliminar, parecen participar en la resistencia a antibióticos y virulencia de A. baumannii, y cuya caracterización podría aportar nuevas dianas para el desarrollo de fármacos antimicrobianos para tratar las infecciones causadas por A. baumannii multirresistente.

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Albarral, Ávila Vicenta. "Diversidad intraespecífica y factores de virulencia en el “complejo de especies de Aeromonas hydrophila” (A. Hydrophila, A. Salmonicida, A. Bestiarum)." Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/125472.

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The genus Aeromonas comprises 26 currently recognized species, some of them divided in to several subspecies. They are ubiquitous in fresh water, but found in chlorinated, brackish and marine water. Aeromonas strains are obtained from a wide variety of foods, as well as clinical samples. Aeromonas species are the cause of intestinal and extra-intestinal infections although the mechanisms that cause bacterial diarrhoea are not yet clearly established. The “A. hydrophila complex” (A. hydrophila, A. salmonicida, A. bestiarum, A. piscicola and A. popoffii), includes A. salmonicida, an important pathogen of fish, and A. hydrophila, an opportunistic pathogen in humans. The virulence of these species is multifactorial and involves complex pathogenic mechanisms associated with toxins (cytotoxic and cytotonic), proteases, haemolysins, lipases, adhesins, agglutinins, pili, etc. A phylogenetic study was performed from a collection of 128 strains belonging to the “A. hydrophila complex", determining partial sequences of dnaJ, cpn60, gyrB and rpoD genes, this analysis allowed us to clarify the taxonomy of this group of Aeromonas species, showing a polyphyletic origin that challenges the existence of the group as such. The population analysis of the studied strains revealed as strong linkage disequilibrium, typical of a clonal population, and a high genetic diversity. We also studied the prevalence and distribution of different virulence factors in the population to establish its pathogenic potential. For this purpose, we determined several enzymatic activities and the antibiotic sensitivity profile of these strains. We also detected the presence of act (aerolysin), alt (cytotonic toxin) and ast (cytotonic toxin) genes by PCR as well as the adhesion capacity and cytopathic effect of the strains on the Caco-2 cell line. The results obtained revealed a high pathogenic of potential the studied Aeromonas strains, regardless of their origin.
El género Aeromonas está constituido actualmente por 26 especies reconocidas, algunas de las cuales incluyen varias subespecies. Son habitantes ubicuos del agua dulce, pero también de aguas cloradas, salobres y marinas. Se han obtenido cepas de Aeromonas de una amplia variedad de alimentos, y se han aislado de muestras clínicas. Algunas especies de Aeromonas son causantes de infecciones intestinales y extraintestinales aunque los mecanismos por los que causan diarreas bacterianas no están todavía establecidos de manera clara. Dentro del “complejo A. hydrophila” (A. hydrophila, A. salmonicida, A. bestiarum, A. piscicola y A. popoffii), hay que destacar A. salmonicida como patógeno importante de peces y A. hydrophila como patógeno oportunista de humanos. La virulencia de estas especies es multifactorial e implica mecanismos de patogenicidad complejos asociados a toxinas (citotóxicas y citotónicas), proteasas, hemolisinas, lipasas, adhesinas, aglutininas, pili, etc. A partir de una colección de 128 de cepas del “complejo A. hydrophila”, se ha realizado un estudio filogenético, poblacional y de factores de patogenicidad. El estudio filogenético con las secuencias parciales de los genes cpn60, dnaJ, gyrB, y rpoD, ha permitido clarificar la taxonomía de las especies del “complejo A. hydrophila”, demostrándose que posee un origen polifilético que cuestionaría la posible existencia del grupo como tal. El análisis de la población de las cepas estudiadas revela un fuerte desequilibrio de ligamiento, típico de una población clonal, y una elevada diversidad genética. También se ha estudiado la prevalencia y distribución de diversos factores de virulencia en la población estudiada para poder establecer su potencial patogénico. Para ello se han determinado actividades enzimáticas, el perfil de sensibilidad a antibióticos, la detección por PCR de los genes act (aerolisina/hemolisina), alt (toxina citotónica) y ast (toxina citotónica), y la capacidad de adherencia y efecto citopático de las cepas en la línea celular Caco-2. Los resultados obtenidos revelan un elevado potencial patogénico de las cepas de Aeromonas estudiadas, independientemente de su origen.

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Tian, Long. "Tackling the current limitations of bacterial taxonomy with genome-based classification and identification on a crowdsourcing Web service." Diss., Virginia Tech, 2019. http://hdl.handle.net/10919/103055.

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Bacterial taxonomy is the science of classifying, naming, and identifying bacteria. The scope and practice of taxonomy has evolved through history with our understanding of life and our growing and changing needs in research, medicine, and industry. As in animal and plant taxonomy, the species is the fundamental unit of taxonomy, but the genetic and phenotypic diversity that exists within a single bacterial species is substantially higher compared to animal or plant species. Therefore, the current "type"-centered classification scheme that describes a species based on a single type strain is not sufficient to classify bacterial diversity, in particular in regard to human, animal, and plant pathogens, for which it is necessary to trace disease outbreaks back to their source. Here we discuss the current needs and limitations of classic bacterial taxonomy and introduce LINbase, a Web service that not only implements current species-based bacterial taxonomy but complements its limitations by providing a new framework for genome sequence-based classification and identification independently of the type-centric species. LINbase uses a sequence similarity-based framework to cluster bacteria into hierarchical taxa, which we call LINgroups, at multiple levels of relatedness and crowdsources users' expertise by encouraging them to circumscribe these groups as taxa from the genus-level to the intraspecies-level. Circumscribing a group of bacteria as a LINgroup, adding a phenotypic description, and giving the LINgroup a name using the LINbase Web interface allows users to instantly share new taxa and complements the lengthy and laborious process of publishing a named species. Furthermore, unknown isolates can be identified immediately as members of a newly described LINgroup with fast and precise algorithms based on their genome sequences, allowing species- and intraspecies-level identification. The employed algorithms are based on a combination of the alignment-based algorithm BLASTN and the alignment-free method Sourmash, which is based on k-mers, and the MinHash algorithm. The potential of LINbase is shown by using examples of plant pathogenic bacteria.
Doctor of Philosophy

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Pradhanang, Prakash Man. "Bacterial wilt of potato caused by Ralstonia solanacearum biovar 2A : a study of the ecology and taxonomy of the pathogen in Nepal." Thesis, University of Reading, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.245336.

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Rouli, Laetitia. "Etude systématique des génomes bactériens." Thesis, Aix-Marseille, 2014. http://www.theses.fr/2014AIXM5038.

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Débutée en 2005, l'ère du pangénome a connu un important essor ces dernières années, notamment grâce aux progrès des techniques de séquençage haut débit. Le pangénome, qui est divisé en deux grandes parties, le core génome et le génome accessoire, offre un grand éventail d'utilisation. Au cours de ces trois dernières années, nous avons étudié cette gamme de possibilités en nous basant sur des pathogènes humains tel que Coxiella burnetii, Kingella kingae et Bacillus anthracis. Ainsi, outre la découverte d'une nouvelle espèce de Kingella et l'étude de quelques génomes spécifiques, nous nous sommes attardés sur le lien entre pangénome et pathogénicité, sur l'importance des SNPs (Single Nucleotide Polymorphism), ainsi que sur la corrélation entre pangénome et taxonomie et donc, par extension, nous avons étudié la notion d'espèce bactérienne
The pangenome area began in 2005 and had known a huge increase thanks to the improvement of the Next Generation Sequencing methods. The pangenome, which is divided into two parts, the core and the accessory genome, offer a large panel of uses. During the last three years, we have studied all these possibilities. We based our work on human pathogens as Coxiella burnetii, Kingella kingae and Bacillus anthracis. Thus, in addition to the discovery of a new Kingella species and the study of some specific genomes, we studied in details the link between pangenome and pathogenicity, the importance of SNPs (Single Nucleotide Polymorphism) and the correlation between pangenome and taxonomy. Finally, we worked on the bacterial species definition

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Bautista, Guerrero Hector Hugo. "Phylogenomic study and specific diversity depiction of frankia genus : special focus on non-cultivable strains and ecological implications." Phd thesis, Université Claude Bernard - Lyon I, 2010. http://tel.archives-ouvertes.fr/tel-00838567.

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The depiction of the phylogenetic structure of the genus Frankia is still troublesome and the evolutionary forces guiding the speciation, dispersion and diversity are not well documented. The current phylogeny has been defined on the basis of the comparative analysis of the 16S rRNA gene sequence while de genomospecies definition is still subjected to DNA-DNA hybridization trials. Aiming to bring to light the genomic variability of the genus and its translation into the ecological and specific diversity, our studies consisted in, firstly, evaluating the specific diversity within the genus and the ability of the Amplified Fragment Length Polymorphism technique (AFLP) to describe Frankia genomospecies and their phylogenetic liaisons. Moreover this technique was also tested for the study of the non isolated Frankia directly in the actinorhizal nodules. Secondly, we defined a MLSA (Multilocus Sequence analysis) scheme which allowed us to establish a phylogeny of the genus by using a hundred of strains and for the first time to describe the phylogenetic divergence of a group of non culturable strains exhibiting the particular ability (phenotype) of sporulating in planta (Sp+). The Sp+ strains are distributed into two divergent clades whose structure is highly correlated to the host genotype. The importance of genetic markers having impact over ecology of the strains has been revised. In this regard we have studied the phylogenetic analysis and the occurrence of the genetic components for the siderophore production and of the sodF gene in Frankia.

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Souza, Danilo Tosta. "Exploração da diversidade bacteriana de esponjas marinhas por abordagens dependente e independente de cultivo." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/11/11138/tde-06012017-113512/.

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Este estudo descreve a diversidade e composição das comunidades bacterianas associadas a cinco esponjas marinhas, e o potencial destes microrganismos como produtores de substâncias bioativas com propriedades fungicidas. As esponjas vivem em simbiose com microrganismos que apresentam alto interesse ecológico, evolutivo e biotecnológico. Contudo, este sistema microbiano permanece pobremente entendido. Para totalmente compreender a biologia desses animais é necessário descrever os fatores ecológicos e evolutivos influenciando a estrutura e dinâmica de sua microbiota. Nesta tese é defendida a hipótese de que a composição taxonômica e estrutura das comunidades bacterianas se correlaciona com o parentesco filogenético de seus hospedeiros. Neste trabalho, as comunidades bacterianas associadas às esponjas Aplysina fulva, Aiolochroia crassa, Chondrosia collectrix, Didiscus oxeata e Scopalina ruetzleri foram examinadas usando a plataforma Ion torrent para sequenciamento parcial do gene 16S rRNA. A água do mar circundante aos espécimes foram coletadas para comparações com a microbiota de esponjas. As análises detectaram um complexo e específico sistema microbiano vivendo em esponjas, com as unidades taxonômicas operacionais dominantes classificadas nos filos: Acidobacteria, Actinobacteria, Chloroflexi, Proteobacteria e Gemmatimonadetes. Apesar da ocorrência simpátrica dos espécimes, as comunidades bacterianas diferiram significativamente entre as espécies de esponjas e a água do mar. Contudo, foi observado que as comunidades bacterianas habitando esponjas filogeneticamente mais próximas (A. fulva e A. crassa) são mais similares uma para com a outra, do que quando comparado com as comunidades em um táxon mais distante filogenitacamente (C. collectrix). O isolamento de bactérias foi realizado nas esponjas D. oxeata e S. ruetzleri. Cinquenta e seis linhagens foram isoladas e classificadas em três filos: Actinobacteria, Proteobacteria e Firmicutes. As análises filogenéticas indicaram cinco possíveis novas espécies bacterianas. Com base na taxonomia polifásica, um dos isolados, denominado ASPSP 40, foi caracterizado como pertencente a uma nova espécie do gênero Saccharopolyspora, para qual o nome Saccharopolyspora spongiae sp. nov. foi proposto. Dois isolados bacterianos demonstraram forte atividade antagônica contra as seguintes espécies de Pythium: P. aphanidermatum, P. graminicola e P. ultimum. Os metabólitos secundários desses isolados, assim identificados como pertencentes aos gêneros Terrabacter sp. ASPSP 140 e Bacillus sp. ASPSP 434, foram identificados por LC-MS/MS como sendo uma mistura de dipepitídeos cíclicos pertencentes à classe das dicetopiperazinas (DKP). Este é o primeiro relato da atividade fungicida e, consequentemente, a detecção de DKP a partir do gênero Terrabacter.
This study describes the diversity of associated bacterial communities to five marine sponges, and the potential of these microorganisms as producers of bioactive substances with fungicidal properties. Sponges live in symbiosis with microorganisms that have a high ecological interest, evolutionary and biotechnological. However, this microbial system remains poorly understood. To fully understand sponge biology, it is necessary to describe the ecological and evolutionary factors that influence the structure and dynamics of their microbial communities. In this work, it is supported the hypothesis that the taxonomic composition and structure of bacterial communities correlate with phylogenetic relatedness of their corresponding hosts. Bacterial communities associated with the sponges Aplysina fulva, Aiolochroia crassa, Chondrosia collectrix, Didiscus oxeata and Scopalina ruetzleri were examined using the Ion Torrent platform for partial sequencing of the 16S rRNA gene. Seawater surrounding specimens were collected for comparisons. The analysis detected a complex and specific microbial system living in sponges, with the operational taxonomic units dominant classified in the phyla: Acidobacteria, Actinobacteria, Chloroflexi, Proteobacteria and Gemmatimonadetes. Despite sympatric occurrence of the specimens, the studied sponges presented different bacterial compositions that differed from those observed in seawater. However, lower dissimilarities in bacterial communities were clearly observed within sponges from the same phylogenetic group (A. fulva and A. crassa). Isolation of bacteria was done from the sponges D. oxeata and S. ruetzleri. Fifty-six strains were isolated and classified into three phyla: Actinobacteria, Proteobacteria and Firmicutes. Phylogenetic analysis indicated five possible novel bacterial species. Based in a polyphasic taxonomy approach, one of the isolates denominated ASPSP 40 was identified as belonging to a novel species of the genus Saccharopolyspora for which the name, Saccharopolyspora spongiae sp. nov. has been proposed. All bacterial isolates were evaluated by their antagonisms against Pythium species. Two of them, Terrabacter sp. ASPSP 140 and Bacillus sp. ASPSP 434 demonstrated strong potential in inhibiting the following species P. aphanidermatum, P. ultimum and P. graminicola. The bioactive secondary metabolites of both, characterized by LC-MS/MS, were identified as a mixture of cyclic dipepitides belonging to the class of diketopiperazine (DKP). This is the first report of fungicidal activity, and thus the detection of DKP of the genus Terrabacter.

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Diop, Awa. "Analyse des séquences des génomes bactériens en tant que source d'information taxonomique." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0276/document.

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L’Identification rapide et la classification microbienne précise sont cruciales en microbiologie médicale pour la surveillance de la santé humaine et animale, établir un diagnostic clinique approprié et choisir des mesures thérapeutiques et de contrôle optimales. Cependant, les seuils universels utilisés pour la définition des espèces ne sont pas applicables à de nombreux genres bactériens. C'est notamment le cas des espèces du genre Rickettsia, qui expriment peu de caractéristiques phénotypiques distinctives. Compte tenu de la disponibilité des séquences de près de 100 génomes de Rickettsia, nous avons voulu évaluer une gamme de paramètres taxonomiques basés sur l’analyse des séquences génomiques afin de mettre au point des recommandations pour la classification des isolats au niveau de l’espèce et du genre. En comparant le degré de similarité des séquences de 78 génomes de Rickettsia et 61 génomes de 3 genres étroitement apparentés en utilisant 4 paramètres génomiques, nous avons montré que les outils taxonomiques basés sur les séquences génomiques sont simples à utiliser et rapides, et permettent une classification taxonomique fiable et reproductible des isolats de rickettsies avec des seuils spécifiques. Les résultats obtenus nous ont permis d'élaborer des recommandations pour la classification des isolats de rickettsies au niveau du genre et de l'espèce. À l'aide de la taxono-génomique, nous avons également pu décrire 17 nouvelles espèces bactériennes associées à l'homme. L'utilisation des outils génomiques est donc parfaitement adaptée à la classification taxonomique et peut changer radicalement notre vision de la taxonomie et de l'évolution bactérienne à l'avenir
Rapid identification and precise microbial classification are crucial in medical microbiology for human and animal health monitoring, appropriate clinical diagnosis and selection of optimal therapeutic and control measures. Indeed, the universal used for the definition of species are not applicable to many bacterial genera. This is particularly true of species of the genus Rickettsia which are strictly intracellular alpha-proteobacteria that express few phenotypic characteristics. Given the availability of genomic sequences of nearly 100 rickettsial genomes, we wanted to evaluate a range of taxonomic parameters based on genomic sequence analysis, to develop guidelines for the classification of Rickettsia isolates at the genus and species levels. By comparing the degree of similarity of the sequences of 78 genomes from Rickettsia species and 61 genomes from 3 closely related genera using several genomic parameters, we have shown that genome-based taxonomic tools are simple to use and fast, and allow for a reliable and reproducible taxonomic classification of isolates within species of the genus Rickettsia, with specific thresholds. The obtained results enabled us to develop guidelines for classifying rickettsial isolates at the genus and species levels. Using taxono-genomics, we have also been able to describe 17 new human-associated bacterial species on the basis of a combination of genomic analysis and phenotypic properties. The use of genomic tools is therefore perfectly adapted to taxonomic classification and can dramatically change our vision of taxonomy and bacterial evolution in the future

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Groenewald, Willem Hermanus. "Taxonomy of species of Alicyclobacillus from South African orchards and fruit concentrate manufacturing environments and the prevention of fruit juice contamination." Thesis, Stellenbosch: University of Stellenbosch, 2009. http://hdl.handle.net/10019.1/1253.

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Thesis (PhD (Food Science))--University of Stellenbosch, 2009.
ENGLISH ABSTRACT: Species of Alicyclobacillus are acid-tolerant and heat-resistant bacteria that cause spoilage of heat-treated fruit juices stored at room temperature. During the past decade, Alicyclobacillus spp. have become a major cause of spoilage in pasteurised fruit juices leading to significant economic losses world-wide. Spoilage has been reported in apple, pear, orange, peach, mango and white grape juice, as well as in fruit juice blends, fruit juice containing drinks and tomato products, such as tomato juice and canned tomatoes. Spoilage is characterised by a medicinal smell and guaiacol production. These endospore-formers have been shown to survive pasteurisation conditions of 95 °C for 2 min, grow at temperatures between 25° and 60 °C and a pH range of 2.5 to 6.0. Knowledge of this organism is limited, both locally and internationally and the route of contamination to the final product is not well established. In this study the fruit concentrate processing environment was investigated as a potential source and route of contamination for the final product. Species of Alicyclobacillus were isolated from orchard soil, various stages during processing and from fruit juice and concentrates. The isolates were identified based on morpholological, biochemical and physiological properties. Identification to species level was done by 16S ribosomal RNA gene sequencing and strain differentiation by RAPD-PCR. Results indicate that species of A. acidoterrestris and Alicyclobacillus acidocaldarius were found in orchard soil and throughout the processing environment. This is the first report on the isolation of these species from orchard soil, vinegar flies and the fruit processing environment. The 16 isolates identified as A. acidoterrestris grouped into four clusters based on RAPD-PCR banding patterns, suggesting that they belong to at least four genotypic groups. Isolates from the fruit concentrate, wash water and soil located outside of the fruit processing plant grouped into one cluster. Concluded from these results, A. acidoterrestris found in the wash water and soil outside of the factory could act as a potential reservoir of organisms for the contamination of the final fruit concentrate. Thus good manufacturing practices play an essential role in controlling incidence of spoilage caused by these bacteria. Fruit juices can be treated using ultraviolet (UV-C) light with a wavelength of 254 nm, which has a germicidal effect against micro-organisms. Alicyclobacillus acidoterrestris spores were inoculated into tap water, used wash water from a fruit processing plant and grape juice concentrate. Ultraviolet dosage levels (J L−1) of 0, 61, 122, 183, 244, 305 and 367 were applied using a novel UV-C turbulent flow system. The UV treatment method was shown to reliably achieve in excess of a 4 log10 reduction (99.99%) per 0.5 kJ L-1 of UV-C dosage in all the liquids inoculated with A. acidoterrestris. The applied novel UV technology could serve as an alternative to thermal treatments of fruit juices for the inactivation of Alicyclobacillus spores or in the treatment of contaminated processing wash water. Finally, the thermal inactivation at 95 °C for two strains of A. acidoterrestris isolated from contaminated fruit juice concentrates were investigated in a 0.1% (m/v) peptone buffer solution (pH 7.04) and grape juice (pH 4.02, 15.5 °Brix). The thermal inactivation of A. acidoterrestris spores followed first-order kinetics, suggesting that as the microbial population is exposed to a specific high temperature, the spores inactivated at a constant rate. D-values determined in the buffer solution were calculated to be 1.92 min and 2.29 min, while in grape juice D-values were found to be 2.25 min and 2.58 min for the two strains tested. From this study it is clear that the D-value is dependant on the strain tested, but also on the soluble solids of the solution the cells are suspended in. The results indicated that the spores of A. acidoterrestris isolated from South African fruit juice concentrate may survive after the pasteurisation treatment commonly applied during manufacturing.
AFRIKAANSE OPSOMMING: Spesies van Alicyclobacillus is suur-tolerante en hittebestande bakterieë wat bederf veroorsaak in hitte-behandelde vrugtesappe wat teen kamertemperatuur gestoor word. Gedurende die afgelope dekade het Alicyclobacillus spp. ‘n belangrike oorsaak van bederf in gepasteuriseerde vrugtesappe geword en beduidende ekonomiese verliese wêreldwyd veroorsaak. Bederf is aangeteken in appel-, peer-, lemoen-, perske-, mango- en witdruiwesap, sowel as in vrugtesapversnitte, vrugtesapbevattende drankies en in tamatieprodukte soos tamatiesap en ingemaakte tamaties. Bederf word gekenmerk deur ’n medisinale reuk en guaiacol produksie. Daar is gevind dat hierdie endospoorvormers pasteurisasie teen 95 °C vir 2 min kan oorleef en kan groei by temperature tussen 25° en 60 °C en ‘n pH van 2.5 to 6.0. Plaaslik sowel as internasionaal is kennis van hierdie organisme beperk en die roete van kontaminasie van produkte is nog nie goed vasgestel nie. In hierdie studie is die vrugtekonsentraat-verwerkingsmilieu ondersoek as ‘n moontlike bron en roete van kontaminasie van die finale produk. Spesies van Alicyclobacillus is vanuit vrugteboordgrond, verskeie verwerkingstadia en van vrugtesap en vrugtesapkonsentraat geïsoleer. Die isolate is op grond van morfologiese, biochemiese en fisiologiese eienskappe geïdentifiseer. Identifikasie tot spesiesvlak is deur 16S rDNS sekwensering gedoen en stam differensiasie deur RAPD-PKR. Resultate het aangetoon dat A. acidoterrestris en A. acidocaldarius in vrugteboordgrond sowel as in alle stadia van die verwerkingsmilieu voorkom. Dit is die eerste verslag van die isolering van hierdie spesies uit die Suid-Afrikaanse vrugteverwerkingsmilieu, vrugteboordgrond en asynvlieë. Die 16 isolate, geïdentifiseer as A. acidoterrestris en in vier groepe geplaas op grond van hul RAPD-PKR bandpatrone, dui aan dat hulle aan minstens vier genotipiese groepe behoort. Isolate afkomstig van die vrugtekonsentraat, waswater en die grond buitekant die vrugteverwerkingsaanleg het een groep gevorm. Uit hierdie resultate kan afgelei word dat A. acidoterrestris, wat in die waswater en grond buite die aanleg voorkom, as ‘n moontlike bron van organismes vir die kontaminering van die finale vrugtekonsentraat kan dien. Goeie vervaardigingspraktyke speel dus ‘n noodsaaklike rol in die beheer van bederf veroorsaak deur hierdie bakterieë. Vrugtesappe kan behandel word met ultravioletlig (UV-C) met ‘n golflengte van 254 nm wat ‘n dodende effek op mikro-organismes het. Kraanwater, gebruikte waswater van ‘n vrugtesapvervaardigingsaanleg en druiwesapkonsentraat is met A. acidoterrestris spore geïnokuleer. Ultraviolet toedieningsvlakke (J L−1) van 0, 61, 122, 183, 244, 305 en 367 is aangewend met behulp van ‘n nuwe UV-C drukvloei stelsel. Daar is aangetoon dat die UV-behandelingsmetode ‘n betroubare vermindering (99.99%) van meer as 4 log10 per 0.5 kJ L-1 van ‘n UV-C dosis gee in al die vloeistowwe wat geïnokuleer is met A. acidoterrestris. Die toegepaste nuwe UV-tegnologie kan gebruik word as ‘n alternatief tot die hittebehandeling van vrugtesap vir die deaktivering van Alicyclobacillus spore of in die behandeling van gekontamineerde waswater. Ten slotte is hitte-deaktivering teen 95 °C van twee stamme van A. acidoterrestris, geïsoleer uit gekontamineerde vrugtesapkonsentraat, in ‘n 0.1% (m/v) peptoonbufferoplossing (pH 7.04) en druiwesap (pH 4.02, 15.5 °Brix), ondersoek. Die hitte-deaktivering van A. acidoterrestris spore het eerste-orde kinetika gevolg, wat aandui dat die mikrobe-populasie teen ‘n konstante tempo afsterf, wanneer blootgestel aan ‘n spesifieke hoë temperatuur. Die D-waardes in die bufferoplossing is bereken as 1.92 min en 2.29 min, terwyl daar gevind is dat die D-waardes in druiwesap 2.25 min en 2.58 min is vir die twee betrokke stamme. Vanuit hierdie studie is dit duidelik dat die D-waardes afhang van die betrokke stam, maar ook van die oplosbare vaste stowwe van die oplossing waarin die selle opgelos is. Die resultate dui daarop dat die spore van A. acidoterrestris, wat geïsoleer is uit Suid-Afrikaanse vrugtesapkonsentraat, die pasteurisasiebehandeling wat algemeen tydens vervaardiging toegepas word, kan oorleef. Aangesien die toepassing van strenger hittebehandeling om spore van A. acidoterrestris te deaktiveer onaanvaarbare organoleptiese veranderinge in die produk tot gevolg het, word dit aanbeveel dat die risiko van bederf verminder behoort te word deur die gebruik van goeie vervaardigingspraktyke gedurende vrugteverwerking.

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12

Toboli, Abubakr Salem. "Taxonomy of acid-fast bacteria." Thesis, University of Newcastle Upon Tyne, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.387481.

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13

Carrión, Fonseca Ornella. "Caracterización de una nueva bacteria antártica, y estudio de una nueva vía de producción de dimetilsulfuro." Doctoral thesis, Universitat de Barcelona, 2014. http://hdl.handle.net/10803/283547.

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A partir de una muestra de sedimento marino procedente de la Antártida se aisló una cepa adaptada al frío que llamaba la atención por el aspecto mucoso de sus colonias, lo cual sugería la producción de material extracelular. Esta cepa también destacó por desprender un olor característico que se atribuyó a la producción de compuestos orgánicos volátiles de azufre (VOSCs). Con el objetivo de caracterizar el nuevo aislamiento antártico, se procedió a realizar su clasificación taxonómica polifásica mediante pruebas genéticas, fenotípicas y quimiotaxonómicas. Posteriormente, se caracterizó el material extracelular producido por la nueva bacteria antártica a nivel estructural y químico. También se estudiaron sus propiedades, principalmente su capacidad emulsionante, crioprotectora y osmoprotectora, con el fin de explorar posibles aplicaciones biotecnológicas. En la última parte de este estudio, se analizaron los VOSCs producidos por el nuevo aislamiento antártico y se identificó el dimetilsulfuro (DMS) como el principal de ellos. El DMS es un gas de gran importancia debido a que es la mayor fuente de origen biológico que se transfiere desde los océanos a la atmósfera en el ciclo global del azufre. Además, es un potente quimioatrayente para aves, crustáceos y mamíferos marinos y ha sido ampliamente estudiado por su posible efecto en la regulación del clima. Se estudiaron los posibles sustratos para la producción de DMS en esta bacteria adaptada al frío y se identificó y caracterizó una nueva ruta de síntesis de DMS a partir de metanotiol (MeSH) e independiente de dimetilsulfoniopropionato (DMSP). Se identificó el gen implicado en la producción de DMS a partir de MeSH y se demostró que su expresión no estaba afectada por ninguno de los sustratos o condiciones ensayadas y tampoco estaba localizado cerca de ningún gen relacionado con el metabolismo del azufre. Este gen codifica una proteína con 4-6 dominios transmembrana que sin embargo se localiza en agregrados fibrilares citoplasmáticos que están ausentes en el mutante. Además, esta proteína está presente en una amplia variedad de importantes grupos taxonómicos incluyendo Pseudomonas sp., múltiples cepas de actinobacterias de los géneros Gordonia, Rhodococcus y Mycobacterium, incluyendo a los patógenos M.tuberculosis y M.avium; miembros de los rhizobiales incluyendo los fijadores de N2 Bradyrhizobium y Mesorhizobium y cianobacterias fijadoras de N2 incluyendo Cyanothece sp., Pseudoanabaena sp., y Nodosilinea sp. Finalmente, la proteína que cataliza la conversión de MeSH en DMS, está presente en la mayoría de metagenomas consultados, aunque se observan abundancias relativas más elevadas en ambientes terrestres, particularmente en metagenomas de suelo.
A cold-adapted bacterial strain was isolated from an Antarctic marine sediment sample. This strain caught the attention because of the mucous appearance of its colonies, which indicated the production of extracellular material. Notably, this isolate produced a characteristic smell that was apportioned to volatile organic sulfurous compounds (VOSCs). With the aim of characterising the new Antarctic isolate, its polyphasic taxonomy classification was performed by genetic, phenotypic and chemotaxonomic analyses. The extracellular material produced by the Antarctic strain was also chemically and structurally characterised and its properties were studied, focusing on its emulsifying, cryoprotectant and osmoprotectant capacities to evaluate its potential biotechnological applications. In the final component of this study, the VOSCs produced by the new Antarctic isolate were analysed and dimethylsulfide (DMS) was identified as the main compound. DMS is a very important gas because it is the most abundant biogenically derived form of sulfur transferred from the sea to the air in the global sulfur cycle. Also, it is a potent chemoattractant for birds, crustaceans and marine mammals and it has been widely studied for its potential effects on climate regulation. Possible substrates for DMS production were studied and a novel pathway for DMS synthesis from methanetiol (MeSH) and independent of dimethylsulfoniopropionate (DMSP) was identified and characterised in this new Antarctic strain. The gene involved in DMS production from MeSH was identified and it was shown that is not regulated in response to none of the substrates and conditions tested, and neither is it located near any genes related to sulfur metabolism. This gene encodes a protein with 4-6 transmembrane domains but localises in cytoplasmic fibers that are absent in the mutant. Moreover, this protein is present in many varied and important taxonomic groups including Pseudomonas sp., multiple strains of actinobacteria of the genus Mycobacterium, including the pathogens M. tuberculosis and M. avium, Gordonia and Rhodoccocus; rhizobiales members including the N2-fixing Bradyrhizobium and Mesorhizobium and N2-fixing cyanobacteria such as Cyanothece sp., Pseudoanabaena sp., and Nodosilinea sp. Finally, the protein that catalyses the conversion of MeSH into DMS, is present in most of the metagenomes analysed, but higher relative abundances are seen in terrestrial environments, particularly in soil metagenomes.

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Gosink, John J. "Taxonomy, biogeography, and evolution of polar gas vacuolate bacteria /." Thesis, Connect to this title online; UW restricted, 1996. http://hdl.handle.net/1773/11511.

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15

Ramos, Patrícia Locosque. "Taxonomia do gênero Stenotrophomonas através de Multi Locus Sequence Analysis (MLSA)." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-26012012-170618/.

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As Stenotrophomonas são comumente encontradas no trato respiratório de pacientes com doenças pulmonares crônicas e também na rizosfera de plantas. Esse gênero apresenta resistência a diversos antibióticos, promove o crescimento de plantas e algumas espécies apresentam a capacidade de fixar o nitrogênio atmosférico. O Multi Locus Sequence Analysis (MLSA) é uma metodologia baseada em genes constitutivos para definição e alocação taxonômica de novas espécies. O objetivo geral do presente trabalho foi caracterizar taxonomicamente uma coleção ampla de Stenotrophomonas composta por isolados endófitos, linhagens-tipo e de referência. Para tanto, foi estabelecido um sistema de classificação e identificação de Stenotrophomonas por meio de MLSA. Foi possível através da metodologia de MLSA definir 9 novas espécies, detectar a presença de um novo gênero e estabelecer um sistema online de taxonomia para Stenotrophomonas.
The genus Stenotrophomonas is found in the respiratory treatment of patients with chronic pulmonary and also in the rizhosfera of plants. It presents resistance to several antibiotics, promotes the growth of plants and some species present the ability to fix atmospheric nitrogen. The Multi Locus Sequence Analysis (MLSA) is a methodology based on constitutive genes for definition and taxonomic allocation of new species. The general objective of the present work was to characterize a wide collection constituted by Stenotrophomonas from isolated endophytic, type and reference strains. In such a way, a system of classification and identification of Stenotrophomonas by means of MLSA was established. It was possible through the MLSA methodology to define 9 new species, to detect the presence of a new genus and to establish an online system for Stenotrophomonas taxonomy.

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16

Hutt, Lee Philip. "Taxonomy, physiology and biochemistry of the sulfur bacteria." Thesis, University of Plymouth, 2017. http://hdl.handle.net/10026.1/8612.

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Inorganic sulfur-oxidising Bacteria are present throughout the Proteobacteria and inhabit all environments of Earth. Despite these facts they are still poorly understood in terms of taxonomy, physiology, biochemistry and genetics. Using phylogenetic and chemotaxonomic analysis two species that were erroneously classified as Thiobacillus trautweinii spp. in 1921 and 1934 are in fact novel chemolithoheterotrophic species for which the names Pseudomonas trautweiniana sp. nov. and Achromobacter starkeyanus sp. nov. are proposed, respectively. These species were found to oxidise thiosulfate in a “fortuitous” manor when grown in continuous culture and increases in maximum theoretical growth yield (YMAX) and maximum specific growth rate (μMAX) were observed. Cytochrome c linked thiosulfate-dependent ATP production was confirmed in both species, confirming “true” chemolithoheterotrophy. Evidence is presented that the ATP concentration governs the benefits of chemolithoheterotrophy. There were significant changes in enzyme activities, including enzymes of the TCA cycle that might be affecting amino acid synthesis. This is strong evidence that chemolithoheterotrophy gives a strong physiological boost and evolutionary advantage over strictly heterotrophic species. An autotrophic species that was historically placed in Thiobacillus was also shown to be a novel species for which the name Thermithiobacillus parkerianus sp. nov. is proposed. The enzyme profiles of Thermithiobacillus parkerianus differed significantly between different inorganic sulfur growth substrates and was the first time all TCA cycle enzymes were assayed in a member of the Acidithiobacillia. The properties of thiosulfate dehydrogenase varied significantly between Pseudomonas sp. Strain T, Achromobacter sp. Strain B and Thermithiobacillus sp. ParkerM both in terms of optimal parameters and the effect of inhibitors. This evidence adds to the increasing body of work indicating there to be at least two thiosulfate dehydrogenases present in the Bacteria.

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17

Bobowski, S. "The serology of sulphate-reducing bacteria." Thesis, University of Essex, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.376722.

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18

El, Semary Nermin Adel Hussein. "Anabaena and associated bacteria : molecular approaches to studying microbial community structure and taxonomy." Thesis, University of Bristol, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.420889.

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19

Chan, Yuen-piu. "Taxonomic analysis of a haloacid degrading Burkholderia species MBA4." Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/B36096374.

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20

Kaji, Denise Akiko. "Taxonomia molecular de Bacillus entomopatogenicos." [s.n.], 1993. http://repositorio.unicamp.br/jspui/handle/REPOSIP/255729.

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Orientador : Vanderlei Perez Canhos
Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos
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Resumo: Foi efetuado um estudo taxômico de 15 isolados entomopatogênicos de mostras de solos e insetos do Brasil com características de bactérias aeróbias, formadoras de endosporos e presença de cristal. Treze isolados acarretaram 100 % de mortalidade a larvas de Aedes fluviatilis em leituras observadas a 24 h. Os resultados dos testes de caracterização morfológica, bioquímica e fisiológica indicaram que 14 isolados pertencem a espécie Bacillus thuringiensis (B.t.) enquanto que o 15° foi determinado como Bacillus sphaericus (B.s.). Através dos perfis eletroforéticos de proteínas totais 11 B.t. isolados foram identificados como subespécie israelensis (sorotipo H-14, incluindo duas linhagens não sorotipadas), 1 como kurstaki (soro tipo H3a, 3b) e 1 como morT!isoni (sorotipo H8a, 8b). As linhagens de B. thuringiensis subsp. israelensis (B.t.i.) formaram um grupo homogêneo distinto das linhagens de referências tóxicas. a lepidópteros e coleópteros. O isolado identificado como B. sphaericus demonstrou alta similaridade com a linhagem 2362 através de testes de atividade larVicida; fagotipagem (fagotipo 3) e sorologia (H5). Os 11 isolados identificados como B.t.i. pela sorologia e/ou perfIS eletroforéticos de proteínas totais não apresentaram polimorflsmo quanto aos fragmentos de restrição, quando foram utilizadas sondas do gene 16S rRNA e do cristal de B.t.i.. A sonda do gene toxigêniro de B.t.i. demonstrou ser bastante específica para a subespécie israelensis, não apresentando hibridizaçóes Com outras subespécies. O gene do cristal de B.t.i. de referência IPS82 e isolados identificados como B.t.i. foram amplificados através da reação em cadeia da polimerase (PCR), digeridos com Sau3AI e separados por eletroforese. Os perfis de restrição destes fragmentos foram idênticos. Esses resultados indicam que os B.t.i. isolados no Brasil formam uni grupo. homogêneo e de organização genética bastante conservada. Outras 28 linhagens de referência representando 12 subespécies de B.t. com 9 sorotipos diferentes, 4 B. cereus e 4 B. anthracis foram incluídas na análise do perfil de hibridização com o gene 16S rRNA Os dados obtidos mostraram correspondência com os testes de sorologia (DE BARJAC & FRACHON, 1990) e a taxonomia numérica (PRIEST et ai., 1988)
Abstract: Fifteen bacterial isolates from Brazilian soil and insects with aerobic, endospores and crystal characteristics were taxonomically analysed. Thirteen strains were shown to be pathogenic to Aedes fluviatilis larvae causing 100 % mortality in 24 hours and two strains were non-pathogenic. The results of morphological, biochemical and physiological tests indicated that 14 strains belong B. thuringiensis (8.t.) while the remaining strain was identified as B. sphaericus. Electrophoresis ofwhole celI protein patterns helped in the identification of eleven isolates as israelensis (serotype H-14, including two non-serotypable strains), 1 as kurstaki (serotype H3a, 3b) and 1 as morrisoni (serotype H8a, 8b). Moreover, it was shown that alI B. thuringiensis subsp. israelensis (8.t.i.) strains. formed a homogenous group distinct from reference strains toxic for Lepidoptera or Coleoptera. The isolate identified as B. sphaericus presented high similarity with strain 2362 by larvicidal tests, phagotyping (group 3) and serotyping (H5). The is.olates identified as subspecies israelensis by serology and/or electrophoresis of whole cell proteins patterns showed the same patterns using restriction fragments length polymorphisms (RFLPs) analysis with the 16S rRNA and the crystal gene of B.t.i. as probes. The crystal gene of B.t.i. used as the probe was specific only to the subspecies israelensis. The crystal gene of B.t.i. reference (IPS82) and isolated strains of B.t.i. were amplified by Polymerase Chain Reaction (PCR), digested with Sau3AI and electrophoresed in agarose gel. The restriction fragment patterns obtained were identical. It confirmed as stated above that the B.t.i. isolates used in this study are a highly homogenous group with a conserva tive. genetic organization. Furthermore, 28B.t. reference strains representing 12 subspecies (with 9 different serotypes), 4 B. cereus and 4. B. anthracis were compared with regard to their ribosomal RNA gene restriction patterns. The results obtained match the serological tests (DEBARJAC & FRACHON, 1990) and numerical taxonomy studies (PRIEST et al., 1988). The results in this study suggest that the techniques could be an altemative to serological tests
Doutorado
Doutor em Ciência de Alimentos

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21

Pelantová, Lucie. "Klasifikace bakterií pomocí markerových genů." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2020. http://www.nusl.cz/ntk/nusl-433568.

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The aim of this work is proposal of new method for bacteria classification based on sequences of marker genes. For this purpose was chosen 10 marker genes. Resulting MultiGene classifier processes data set by dividing it in several groups and choosing gene for each group which can distinguish this group with best results. This work describes implementation of MultiGene classifier and its results in comparison with other bacteria classifiers and with classification based entirely on gene 16S rRNA.

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22

Thompson, I. P. "Bacterial population changes during decay of basidiomycetes : a numerical taxonomic study." Thesis, University of Essex, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.370495.

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23

Gonçalves, Edmilson Ricardo. "Xanthomonas axonopodis pv. passiflorae : taxonomia polifasica, filogenia e detecção." [s.n.], 2000. http://repositorio.unicamp.br/jspui/handle/REPOSIP/317428.

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Orientador: Yoko Bomura Rosato
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Doutorado

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24

Humphry, David Robert. "Taxonomy of the psychrophile Flavobacterium frigidarium and the mesophile Cellvibrio japonicus, and comparative analyses of their xylanolytic and laminarinolytic activities." Thesis, University of Sunderland, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269167.

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25

Chan, Yuen-piu, and 陳源標. "Taxonomic analysis of a haloacid degrading Burkholderia species MBA4." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B36096374.

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26

Hervé, Vincent. "Bacterial-fungal interactions in wood decay : from wood physicochemical properties to taxonomic and functional diversity of Phanerochaete chrysosporium-associated bacterial communities." Thesis, Université de Lorraine, 2014. http://www.theses.fr/2014LORR0041/document.

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Dans les écosystèmes forestiers, la décomposition du bois est un processus majeur, notamment impliqué dans le cycle du carbone et des nutriments. Les champignons basidiomycètes saprotrophes, incluant les pourritures blanches, sont les principaux agents de cette décomposition dans les forêts tempérées. Bien que peu étudiées, des communautés bactériennes sont également présentes dans le bois en décomposition et cohabitent avec ces communautés fongiques. L'impact des interactions bactéries-champignons sur le fonctionnement d'une niche écologique a été décrit dans de nombreux environnements. Cependant, leur rôle dans le processus de décomposition du bois n'a été que très peu investigué. A partir d'expériences en microcosme et en utilisant une approche non cultivable, il a été démontré que la présence du champignon Phanerochaete chrysosporium influençait significativement la structure et la diversité des communautés bactériennes associées au processus de décomposition du hêtre (Fagus sylvatica). Par une approche cultivable, cet effet mycosphère a été confirmé, se traduisant par une augmentation de la densité des communautés bactériennes en présence du champignon ainsi que par une modification de la diversité fonctionnelle de ces communautés. Enfin, une approche polyphasique a été développée, combinant l'analyse des propriétés physico-chimiques du bois et des activités enzymatiques extracellulaires. Les résultats de cette expérience ont révélé que l'association de P. chrysosporium avec une communauté bactérienne issue de la mycosphère de ce dernier aboutissait à une dégradation plus importante du matériau bois par rapport à la dégradation par le champignon seul, démontrant pour la première fois des interactions bactéries-champignons synergiques dans le bois en décomposition
Wood decomposition is an important process in forest ecosystems in terms of their carbon and nutrient cycles. In temperate forests, saprotrophic basidiomycetes such as white-rot fungi are the main wood decomposers. While they have been less studied, bacterial communities also colonise decaying wood and coexist with these fungal communities. Although the impact of bacterial-fungal interactions on niche functioning has been highlighted in a wide range of environments, little is known about their role in wood decay. Based on microcosm experiments and using a culture-independent approach, we showed that the presence of the white-rot fungus Phanerochaete chrysosporium significantly modified the structure and diversity of the bacterial communities associated with the degradation of beech wood (Fagus sylvatica). Using a culture-dependent approach, it was confirmed that in the presence of the fungus the mycosphere effect resulted in increased bacterial abundance and modified the functional diversity of the fungal-associated bacterial communities. Lastly, a polyphasic approach simultaneously analysing wood physicochemical properties and extracellular enzyme activities was developed. This approach revealed that P. chrysosporium associated with a bacterial community isolated from its mycosphere was more efficient in degrading wood compared to the fungus on its own, highlighting for the first time synergistic bacterial-fungal interactions in decaying wood

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27

Rueda, Maria Aguirre. "Molecular taxonomic studies on lactic acid bacteria from human clinical infections." Thesis, University of Reading, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.321272.

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Aziz, Saefuddin [Verfasser]. "Chemical and Taxonomic Investigation of Indonesian Soil-dwelling Bacteria / Saefuddin Aziz." Tübingen : Universitätsbibliothek Tübingen, 2021. http://d-nb.info/1237684595/34.

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29

Padmanabhan, Babu roshan. "Taxano-genomics, a strategy incorporating genomic data into the taxonomic description of human bacteria." Thesis, Aix-Marseille, 2014. http://www.theses.fr/2014AIXM5056.

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Mon projet de doctorat était de créer un pipeline pour taxono-génomique pour la comparaison de plusieurs génomes bactériens. Deuxièmement, je automatisé le processus d'assemblage (NGS) et annotation à l'aide de divers logiciels open source ainsi que la création de scripts de maison pour le laboratoire. Enfin, nous avons intégré le pipeline dans la description de plusieurs espèces bactériennes de laboratoire sur. Cette thèse est divisée principalement en Taxono- génomique et Microbiogenomics. Les avis de la section taxono-génomique, décrit sur les avancées technologiques en génomique et métagénomique pertinentes dans le domaine de la microbiologie médicale et décrit la stratégie taxono-génomique en détail et comment la stratégie polyphasique avec des approches génomiques sont reformatage de la définition de la taxonomie bactérienne. Les articles décrivent les bactéries cliniquement importantes, leur séquençage complet du génome et les études génomiques comparatives, génomiques et taxono-génomique de ces bactéries. Dans cette thèse, j'ai inclus les articles décrivant ces organismes: Megasphaera massiliensis, Corynebacterium ihumii, Collinsella massiliensis, Clostridium dakarense. Bacillus dielmoensis, jeddahense, Occidentia Massiliensis, Necropsobacter rosorum et Pantoea septica. Oceanobacillus
My PhD project was to create a pipeline for taxono-genomics for the comparison of multiple bacterial genomes. Secondly I automated the process of assembly (NGS) and annotation using various open source softwares as well as creating in house scripts for the lab. Finally we incorporated the pipeline in describing several bacterial species from out lab. This thesis is subdivided mainly into Taxono-genomics and Microbiogenomics. The reviews in taxono-genomics section, describes about the technological advances in genomics and metagenomics relevant to the field of medical microbiology and describes the strategy taxono-genomics in detail and how polyphasic strategy along with genomic approaches are reformatting the definition of bacterial taxonomy. The articles describes clinically important bacteria, their whole genome sequencing and the genomic, comparative genomic and taxono-genomic studies of these bacteria

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BOUVET-BOUVIER, ANNE. "Les streptocoques deficients : ultrastructure, taxonomie, pouvoir pathogene experimental." Paris 7, 1987. http://www.theses.fr/1987PA077196.

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31

Mollet, Christophe. "Utilisation du gene rpob pour la phylogenie et l'identification des bacteries." Aix-Marseille 2, 1997. http://www.theses.fr/1997AIX20666.

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32

Valešová, Nikola. "Bioinformatický nástroj pro klasifikaci bakterií do taxonomických kategorií na základě sekvence genu 16S rRNA." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2019. http://www.nusl.cz/ntk/nusl-403138.

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Tato práce se zabývá problematikou automatizované klasifikace a rozpoznávání bakterií po získání jejich DNA procesem sekvenování. V rámci této práce je navržena a popsána nová metoda klasifikace založená na základě segmentu 16S rRNA. Představený princip je vytvořen podle stromové struktury taxonomických kategorií a používá známé algoritmy strojového učení pro klasifikaci bakterií do jedné ze tříd na nižší taxonomické úrovni. Součástí práce je dále implementace popsaného algoritmu a vyhodnocení jeho přesnosti predikce. Přesnost klasifikace různých typů klasifikátorů a jejich nastavení je prozkoumána a je určeno nastavení, které dosahuje nejlepších výsledků. Přesnost implementovaného algoritmu je také porovnána s několika existujícími metodami. Během validace dosáhla implementovaná aplikace KTC více než 45% přesnosti při predikci rodu na datových sadách BLAST 16S i BLAST V4. Na závěr je zmíněno i několik možností vylepšení a rozšíření stávající implementace algoritmu.

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Elawad, Sami A. "Studies on the taxonomy and the biology of a newly isolated species of Steinernema (Nematoda: Steinernematidae) from the tropics and its associated bacteria." Thesis, University of Reading, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.394486.

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Pascual, Ramos Christina. "Molecular taxonomic studies on some high G+C content gram-positive bacteria from human and animal sources." Thesis, University of Reading, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312538.

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Neves, Juliana Teixeira de Magalhães. "Características moleculares e identificação de Lactobacillus delbrueckii UFV H2b20." Universidade Federal de Viçosa, 2003. http://www.locus.ufv.br/handle/123456789/10679.

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Submitted by Nathália Faria da Silva (nathaliafsilva.ufv@gmail.com) on 2017-06-13T18:17:32Z No. of bitstreams: 1 resumo.pdf: 17263 bytes, checksum: 8e51a65fe7d8eecb448411acb64cf05b (MD5)
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Fundação de Amparo a Pesquisa do Estado de Minas Gerais
A estirpe probiótica Lactobacillus UFV H2b20, previamente classificada como Lactobacillus acidophilus por suas características de fermentação de açúcares, apresentou-se mais semelhante à espécie Lactobacillus delbrueckii, quanto à seqüência de rDNA 16S, o que levou ao questionamento acerca da identidade da linhagem. Para o esclarecimento da real classificação da linhagem, o método de hibridização DNA-DNA foi empregado. A linhagem apresentou 75,2% e 77,4% de reassociação com L. delbrueckii subsp. lactis (ATCC 12315) e L. delbrueckii subsp. delbrueckii (ATCC 9649), respectivamente. Dado que a homologia de 70% ou mais, por esse método, tem sido usada como padrão para agrupamento de bactérias em uma mesma espécie, sugere-se, aqui, que Lactobacillus UFV H2b20 seja, daqui para frente, denominado L. delbrueckii UFV H2b20. Identificada a linhagem, outro objetivo do trabalho era desenvolver um protocolo para detecção in situ de L. delbrueckii. Uma sonda de 26 nucleotídeos (SA) foi construída e testada com outras espécies de Lactobacillus relacionadas geneticamente entre si. Estes estudos demonstraram que a seqüência de assinatura (SA) estava presente em L. delbrueckii UFV H2b20, L. delbrueckii UFV H2b21, L. delbrueckii subsp. delbrueckii e L. delbrueckii subsp. lactis, o que indica ser ela eficaz para ser usada como sonda para rRNA 16S espécie-específica pelo método de FISH. A hipótese de existência de polimorfismos, levantada em trabalhos prévios no rDNA 16S da linhagem, foi confirmada após as análises dos segmentos de DNA clonados e selecionados do banco genômico construído para a linhagem L. delbrueckii UFV H2b20. As seqüências analisadas demonstraram, também, presença de segmentos correspondentes a quatro genes codificadores de rRNA 16S distintos, e seis segmentos distintos para uma mesma região de rRNA 23S, indicando seis operons putativos. Há evidência de, pelo menos, um operon putativo completo seguido de região codificadora de seis tRNAs. Não se detectou região espaçadora longa entre rDNA 16 e 23S.
Lactobacillus UFV H2b20, a probiotic strain, previously identified as Lactobacillus acidophilus due to its sugar fermentation pattern, was found to be more closely related to Lactobacillus delbrueckii regarding its 16S rDNA sequence. It was demonstrated by DNA-DNA hybridization that this strain presented 75.2% and 77.4% of reassociation with L. delbrueckii subsp. lactis ATCC 12315 and L. delbrueckii subsp. delbrueckii ATCC 9649, respectively. These results place Lactobacillus UFV H2b20 within the L. delbrueckii species, for 70% reassociation as measured by the method used has been a standard to cluster bacteria within the same species. A protocol for in situ detection of L. delbrueckii was developed by means of Fluorescent in situ Hybridization, FISH. A probe consisting of 26 nucleotides labeled with rhodamine was designed based on the signature sequence within the rDNA, and was tested against genetically related Lactobacillus species. A species- specific method was obtained capable of discriminating L. delbrueckii strains from other Lactobacillus species. Previous studies raised the hypothesis of polymorphism among the copies of 16S rDNA in L. delbrueckii UFV H2b20. This was confirmed by sequence analysis of rDNA from a gene library of this strain cloned in phage lambda and subcloned in pBluescript. Sequence analyses of cloned fragments demonstrated the presence of at least four distinct genes encoding 16S rRNAs. Distinct fragments containing 23S rRNA related genes indicated six putative rrn operons. One complete putative rrn operon displays a region encoding 6 different tRNAs. Long spacer regions between 16S and 23S rDNA were not detected.

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Daffé, Mamadou Madani. "Les lipides dans la taxonomie des mycobacteries : application a l'etude de mycobacterium leprae." Toulouse 3, 1986. http://www.theses.fr/1986TOU30138.

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Montes, López María Jesús. "Estudio taxonómico polifásico de bacterias procedentes de ambientes antártidos: descripción de cuatro nuevas especies." Doctoral thesis, Universitat de Barcelona, 2005. http://hdl.handle.net/10803/2394.

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EN CASTELLANO:

Se presenta un estudio basado en la caracterización morfológica, fisiológica, quimiotaxonómica y análisis filogenético de 16 aislamientos obtenidos a partir de muestras procedentes de la Isla del Rey Jorge y la Isla de Livingston. Ambas son las islas de mayor superficie de las Shetland del Sur en la Antártida. Las muestras fueron proporcionadas por científicos españoles en el transcurso de las campañas científicas llevadas a cabo durante los veranos australes de los años 1987-88, 1988-1989 y 1990-91.

El contenido de este trabajo se inicia con un recorrido histórico de la taxonomía bacteriana desde sus orígenes, los grandes hitos que han marcado su avance así como las perspectivas actuales de esta disciplina. Se señalan las aportaciones de Müller, Ehrenberg, Cohn, Migula, Orla-Jensen, Lehmann y Neumann, Buchanan, Bergey, Prévot, Krassilnikov, Murria, Kimura, Woese y Stackebrandt, entre otros.

Como resultado de este estudio polifásico se ha logrado establecer la posición taxonómica de estos 16 aislamientos. Tres de las cepas aisladas (NF12, NF22 y NF24) corresponden a bacilos Gram negativos, psicrotrofos, móviles mediante flagelación polar monotrica y anaerobios facultativos. La composición de bases del DNA presenta un valor entre 41-42 mol % (G+C). En cuanto al perfil de ácidos grasos es similar al perfil que presentan otras especies del género Shewanella. Todas las cepas contienen ubiquinonas, menaquinonas y pequeñas cantidades de metilmenaquinonas al igual que otras shewanellas. Los estudios filogenéticos basados en la secuenciación del rRNA 16S y los experimentos de hibridación DNA-DNA confirman que estos aislamientos pertenecen al género Shewanella. Dos de ellos (NF12 y NF24) se ubican a nivel de la especie Shewanella firigidimarina mientras que NF22T ocupa una posición separada de las especies conocidas en el género Shewanella, corresponde por tanto a una nueva especie a la que se ha designado como Shewanella livingstonensis.

El segundo grupo caracterizado comprende 11 biotipos que corresponden a cocobacilos Gram negativos, halotolerantes, inmóviles y con un metabolismo estrictamente oxidativo. El contenido en G+C presenta un rango entre 44-47 mol %. El perfil de ácidos grasos predominantes que se ha detectado concuerda con el presentado por el género Psychrobacter. Los estudios filogenéticos basados en la composición del rRNA 16S confirman que estas cepas pertenecen al género Psychrobacter. En cuanto a los experimentos basados en las hibridaciones DNA-DNA entre estos 11 biotipos y las especies de Psychrobacter filogenéticamente más próximas, nos han permitido establecer grupos de homología y concluir que 5 de los aislamientos (NF18, NF19, NF20, EN1 y EN2) se sitúan a nivel de Psychrobacter immobilis, 3 aislamientos (NF1, NF7 y NF8) corresponden a representantes de Psychrobacter glacincola y los otros 3 aislamientos corresponden a nuevas especies del género Psychrobactera las que se ha denominado Psychrobacter luti (NF11T) y Psychrobacter fozii(NF23T y EN4).

El último grupo estudiado está constituido por los biotipos 20CM y 20CO, aislados a partir de sedimentos e identificados como miembros del género Paenibacillus. Estos microorganismos psicrotolerantes, aerobios o facultativos, presentan un Gram variable y forman endosporas ovales, terminales o subterminales, deformantes del esporangio. El perfil de ácidos grasos coincide con el descrito para el género Paenibacillus, siendo el ácido graso saturado C15:0 el mayoritario. La composición de bases del DNA es de 40.7 mol % (G+C). Los estudios basados en la secuencia del rRNA 16S sitúan la cepa 20CMT en el género Paenibacillus, con un índice de similitud del 99.5 % respecto a la especie Paenibacillus macquariensis DSM 2T. Sin embargo, los estudios de hibridación DNA-DNA entre ambas cepas dan unos niveles de reasociación muy bajos (47 %), lo que nos permite confirmar que el biotipo 20CMT corresponde a una nueva especie del género Paenibacillus para la que hemos propuesto el nombre de Paenibacillus antarcticus.
This Doctoral Memory presents a study based on evaluation of morphological, physiological, chemotaxonomic and phylogenetic analyses of 16 isolates from samples collected in the South Shetland Islands (Antarctica) by a Spanish scientific expeditions during the Antarctic summers of 1987-88, 1988-89 y 1990-91.

The content of this work begins with an historical overview and taxonomic bacteriology perspectives also. Pointing out the contribution of Müller, Ehrenberg, Cohn, Migula, Orla-Jensen, Lehmann and Neumann, Buchanan, Bergey, Prévot, Krassilnikov, Murray, Kimura, Woese, Stackebrandt and others.

As a result from this study we establish the taxonomic position of these bacteria. Three strains (NF12, NF22 and NF24) of psychrophilic bacteria isolated from Antarctic coastal marine environments were Gram-negative rods, facultatively anaerobic and motile by means of a single polar flagellum. The DNA base content of these bacteria was 41-42 mol % (G+C). The fatty acid profiles of the bacterial isolates were similar to the profiles of other "Shewanella" species. All the strains contained both ubiquinones and menaquinones, like "Shewanella" species. 16S rRNA gene analysis and DNA-DNA hibridization experiments confirmed that isolated strains belonged to the genus "Shewanella" and two of them specifically to "Shewanella frigidimarina" (NF12 and NF24), the other strain (NF22T) occupies a separate position in the genus "Shewanella" and is proposed as a new species, designated "Shewanella livingstonensis sp. nov".

Another group of eleven psychrophilic bacteria isolated correspond to Gram-negative coccobacilli, halotolerant, non-motile with a strictly oxidative metabolism. The DNA (G+C) content ranged from 44 to 47 mol %. The predominant cellular fatty acids detected were typical of the genus Psychrobacter. 16S rRNA gene sequence analysis confirmed that the strains isolated belonged to the genus "Psychrobacter". DNA-DNA hybridization experiments showed six homology groups. The results of the study assigned five isolates (NF18, NF19, NF20, EN1 and EN2) to "Psychrobacter immobilis" LMG 7203T, three isolates (NF1, NF7 and NF8) to "Psychrobacter glacincola" LMG 21282T and three isolates to novel "Psychrobacter" species designated as a Psychrobacter luti sp. nov. (NF11T) and "Psychrobacter fozii sp. nov." (NF23T and EN4).

The last group, constituted by 20CO and 20CM strains, was isolated from sediment and identified as a members of the genus "Paenibacillus". These organisms stained Gram-variable, produced ellipsoidal spores and were facultatively anaerobic. These isolates were psychrotolerant and the fatty acid profile was in accordance with that given in the description of the genus "Paenibacillus", anteiso-branched saturated C15:0 is the predominant fatty acid found. The DNA (G+C) content was 40.7 mol %. Studies based on 16S rRNA gene sequence analysis placed strain 20CMT within the Panibacillus cluster, with a similarity value of 99.5 % to "Paenibacillus macquariensis" DSM 2T. The low DNA-DNA reassociation value of 47 % between these two strains confirmed the distinct position of strain 20CMT within the genus "Paenibacillus". The name "Paenibacillus antarcticus sp. nov". is proposed to the type strain 20CMT.

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Blank, Carrine E., Hong Cui, Lisa R. Moore, and Ramona L. Walls. "MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions." BIOMED CENTRAL LTD, 2016. http://hdl.handle.net/10150/614758.

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Background: MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life, capture the diversity of synonyms and information contained in the taxonomic literature, and relate microbiological entities and processes to terms in a large number of other ontologies, most particularly the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI). We thus constructed MicrO to be rich in logical axioms and synonyms gathered from the taxonomic literature. Results: MicrO currently has similar to 14550 classes (similar to 2550 of which are new, the remainder being microbiologically-relevant classes imported from other ontologies), connected by similar to 24,130 logical axioms (5,446 of which are new), and is available at (http://purl.obolibrary.org/obo/MicrO.owl) and on the project website at https://github.com/carrineblank/MicrO. MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes. Term requests and user feedback can be made using MicrO's Issue Tracker in GitHub. We designed MicrO such that it can support the ongoing and future development of algorithms that can leverage the controlled vocabulary and logical inference power provided by the ontology. Conclusions: By connecting microbial classes with large numbers of chemical entities, material entities, biological processes, molecular functions, and qualities using a dense array of logical axioms, we intend MicrO to be a powerful new tool to increase the computing power of bioinformatics tools such as the automated text mining of prokaryotic taxonomic descriptions using natural language processing. We also intend MicrO to support the development of new bioinformatics tools that aim to develop new connections between microbial phenotypes and genotypes (i.e., the gene content in genomes). Future ontology development will include incorporation of pathogenic phenotypes and prokaryotic habitats.

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Herrera, Rodríguez Daniel. "Exploring the Presence and Characteristics of Antibiotic Resistance Genes and Bacteria Present in Water Environments of Uppsala, Sweden." Thesis, Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-416251.

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Antibiotics are one of the greatest discoveries in medicine, and emerged resistances have become a global threat. It is theorized that a big part of the antibiotic resistance genes come from the environment, and wastewater treatment plants and hospitals are considered a great breeding ground for the spread of these. The aim of this project is to analyse the microbiome and resistome of the wastewater of Uppsala and to evaluate the efficiency in the elimination of antibiotic resistance genes and bacteria. Samples from the University Hospital and the influents, sand filter and effluent of the Wastewater Treatment Plant were collected, DNA was extracted and sequenced to be analysed through metagenomics to explore them taxonomically and looking for resistance genes. Bacteria were also isolated, and their resistances were analysed. Taxonomical differences became noticeable in Order, Family, Genus and Species, with an increase of diversity in the Effluent samples. A total of 233 resistance genes were found in all the samples. There was a clear reduction in the number of resistance genes in the Effluent samples. However, there was an important number of genes carried in these and some prevail through all the path. Within all the isolates collected, from a total of 11, three E. coli isolates, one C. freundii and one E. cloacae presented resistances. Our study shows that the effluent of the wastewater treatment plant of Uppsala is potentially causing a negative impact on the environment, flushing out water not completely free of antibiotic resistance genes and resistant bacteria.

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Triadó, i. Margarit Xavier. "Diversitat de Bacteris Verds del Sofre en llacunes salines i osmoadaptació amb N(epsilon)-acetil-ß-lisina." Doctoral thesis, Universitat de Girona, 2008. http://hdl.handle.net/10803/7872.

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L'objectiu principal del treball de recerca és aprofundir en el coneixement del grup de Bacteris Verds del Sofre (BVS) des del punt de vista de la relació amb la salinitat. L'estudi s'ha restringit als representants halotolerants o halòfils del grup amb tres línies de treball que corresponen a diferents àmbits de coneixement, com són la descripció del biòtop i la riquesa específica de les comunitats de BVS en els ambients naturals, l'avaluació de la significació taxonòmica de la capacitat de desenvolupament en ambients salins en el marc de discussió de la taxonomia-filogenètica del grup, i l'anàlisi de les estratègies fisiològiques desenvolupades per a l'osmoadaptació en medi salí.
The aim of this work is to extend the knowledge of Green Sulfur Bacteria (GSB), specifically those halotolerant and/or halophilic members of the group found in saline environments. The study has been carried out from three different perspectives, corresponding to different knowledge areas: describing the specific richness of GSB communities and environmentally relevant parameters of their habitats, evaluating the taxonomic significance of the requirements and tolerance of salts in the media and discussing the group's classification criteria, and analyzing the physiological responses developed for the osmoadaptation (in particular those related to the accumulation of compatible solutes) in saline media.

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Waldmann, Jost [Verfasser], Frank Oliver [Akademischer Betreuer] Glöckner, Peter [Akademischer Betreuer] Baumann, Hanno [Akademischer Betreuer] Teeling, and Christian [Akademischer Betreuer] Jogler. "Reliable taxonomic classification of metagenome fragments from varying marine bacterial communities / Jost Waldmann. Betreuer: Frank Oliver Glöckner. Gutachter: Frank Oliver Glöckner ; Peter Baumann ; Hanno Teeling ; Christian Jogler." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2016. http://d-nb.info/1098532783/34.

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MELO, Liany Figuerêdo de Andrade. "Screening farmacológico e diversidade bacteriana do muco de Palythoa caribaeorum (Cnidaria, Anthozoa) da praia de Porto de Galinhas-PE, Brasil." Universidade Federal de Pernambuco, 2017. https://repositorio.ufpe.br/handle/123456789/27694.

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Palythoa caribaeorum (baba-de-boi) é um cnidário marinho que secreta um muco viscoso o qual apresenta propriedades farmacológicas e abriga uma série de bactérias com potencial de aplicação biotecnológica. No presente trabalho, objetivou-se obtenção desses micro-organismos associados ao muco de populações do zoantídeo oriundas da praia de Porto de Galinhas, litoral sul de Pernambuco, para fins de prospecção de produtos naturais. Foram isoladas 281 bactérias das quais 55 cepas se mantiveram viáveis após o subcultivo e preservação. A identificação dos isolados foi realizada a partir do sequenciamento dos genes 16S rDNA e rpoB, resultando na obtenção de 18 espécies pertencentes aos filos Firmicutes (37 isolados, 67%), Actinobacteria (11 isolados, 20%), Proteobacteria (5 isolados, 9%) e Bacteroidetes (2 isolados, 4%). Exiguobacterium aurantiacum correspondeu à espécie mais abundante com 9 isolados, enquanto o gênero Bacillus se apresentou como o mais diverso, totalizando 19 isolados distribuídos em 8 espécies distintas. Os isolados de Bacillus spp. foram selecionados para investigação do potencial de produção de 8 enzimas em meio sólido. Todas as cepas produziram pelo menos 4 das enzimas investigadas, com gelatinase sendo a mais frequente (19 isolados), seguida por esterase (18), caseinase (17), amilase (12), poligalacturonase (12), pectato liase (12), celulase (11) e lipase (11). Os isolados B. thuringiensis BCLTHR-01 e B. subtilis BCLSUB-02, 03 e 04 foram os melhores produtores enzimáticos, com resultados positivos em todos os ensaios. A cepa BCLTHR-01 também foi investigada quanto ao potencial biolarvicida contra Aedes aegypti. Para produção das toxinas, foi desenvolvido um processo fermentativo em biorreator operando em batelada com um meio de cultura desprovido de carboidratos como fonte de carbono. A biomassa tóxica concentrada (10⁹ UFC/mL) obtida após 48h de fermentação mostrou atividade biológica com valores de CL₅₀ de 0,849 ppm (intervalo de 0,792 a 0,900 ppm) e de CL₉₀ de 1,285 ppm (intervalo de 1,190 a 1,434 ppm), comprovando o potencial de aplicação deste isolado para o controle do vetor. As bactérias marinhas associadas a P. caribaeorum são potencialmente excelentes fontes de metabólitos bioativos. A presença de espécies capazes de degradar hidrocarbonetos, fixar nitrogênio, metabolizar enxofre e produzir enzimas e toxinas com diversas propriedades sugere que o zoantídeo se beneficia através da assimilação de compostos complementares ao seu metabolismo e através da aquisição de um mecanismo adicional de defesa contra patógenos. A complexidade do ambiente marinho induz à adaptação dos micro-organismos, resultando na produção de uma diversidade de moléculas com propriedades únicas que lhes permitem suportar as condições severas dos processos industriais, tornando-as interessantes objetos para aplicação industrial e biotecnológica.
Palythoa caribaeorum (baba-de-boi) is a marine cnidarian that secretes a viscous mucus which presents pharmacological properties and harbors several bacteria with potential for biotechnological application. In the present work, we aimed to obtain these microorganisms associated with the mucus of zoanthid populations from the beach of Porto de Galinhas, south coast of Pernambuco, to prospect for natural products. 281 bacteria were isolated, of which 55 strains remained viable after subculture and preservation. The identification of the isolates was done by sequencing the 16S rDNA and rpoB genes, resulting in 18 species belonging to the Firmicutes (37 isolates, 67%), Actinobacteria (11 isolates, 20%), Proteobacteria (5 isolates, 9 %) and Bacteroidetes (2 isolates, 4%). Exiguobacterium aurantiacum corresponded to the most abundant species with 9 isolates, while the genus Bacillus was the most diverse, totaling 19 isolates distributed in 8 different species. The isolates of Bacillus spp. were selected to investigate the potential to produce 8 enzymes in solid medium. All strains produced at least 4 of the investigated enzymes, with gelatinase being the most frequent (19 isolates), followed by esterase (18), caseinase (17), amylase (12), polygalacturonase (12), pectate lyase (12), cellulase (11) and lipase (11). The isolates B. thuringiensis BCLTHR-01 and B. subtilis BCLSUB-02, 03 and 04 were the best enzymatic producers, displaying positive results in all the assays. The strain BCLTHR-01 was also investigated for its biolarvicidal potential against Aedes aegypti. To produce the toxins, a fermentation process was developed in bioreactor batching with a culture medium devoid of carbohydrates as carbon source. The concentrated toxic biomass (10⁹ CFU/mL) obtained after 48h of fermentation showed biological activity with LC₅₀ value of 0.849 ppm (range of 0.792 to 0.900 ppm) and CL₉₀ value of 1.285 ppm (range of 1.190 to 1.434 ppm), proving the application potential of this isolate for vector control. Marine bacteria associated with P. caribaeorum are potentially excellent sources of bioactive metabolites. The presence of species capable of degrading hydrocarbons, fixing nitrogen, metabolizing sulfur and producing enzymes and toxins with different properties suggests that the zoanthide benefits through the assimilation of compounds complementary to its metabolism and through the acquisition of an additional mechanism of defense against pathogens. The complexity of the marine environment induces the adaptation of microorganisms, resulting in the production of a diversity of molecules with unique properties that allow them to withstand the harsh conditions of industrial processes, making them interesting objects for industrial and biotechnological application.

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Vilmi, A. (Annika). "Assessing freshwater biodiversity:insights from different spatial contexts, taxonomic groups and response metrics." Doctoral thesis, Oulun yliopisto, 2017. http://urn.fi/urn:isbn:9789526216669.

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Abstract Freshwater ecosystems are severely threatened by a variety of anthropogenic stressors. In order to keep track with at least part of the changes, it is important to efficiently assess and monitor freshwater biological diversity. Biological assessment programs are developed to detect human-induced changes in the ecological state of aquatic systems. These programs typically rely on the assumption that environmental conditions are the sole drivers of biological communities occupying a site and, thus, these local communities would correctly inform about environmental conditions. Recently, this background principle of current bioassessment methods has faced some criticism, stemming from the idea that community structuring is a more complex process than just a mere result of local environmental conditions. In this thesis, I studied the natural and anthropogenic drivers of freshwater biodiversity. I was particularly interested if the various biodiversity metrics studied showed any spatial patterns and if so, for which reasons these patterns might occur. To obtain a comprehensive picture of spatial patterns in biodiversity, I studied multiple spatial contexts, biological groups and indices. I found that environmental conditions were not the only drivers of freshwater biodiversity. Instead, different spatial patterns, likely stemming from dispersal processes, were surprisingly powerful drivers of aquatic communities and index values derived from them. The spatial context (i.e. spatial extent and connectivity) of the aquatic study systems likely played a major role in structuring biodiversity. I also found that the distinct biological groups and indices studied were partly related to different predictor variables. The findings of this thesis are of importance to the development of new bioassessment methods. The results of this thesis also suggest that the spatial context of the study setting should be acknowledged when interpreting results based on current bioassessment methods
Tiivistelmä Makeanveden ekosysteemit ovat hyvin alttiita ihmistoiminnalle. Ekosysteemissä mahdollisesti tapahtuvien muutosten havaitseminen vaatii tehokkaita vesistöjen ekologisen tilan ja luonnon monimuotoisuuden arviointi- ja seurantamenetelmiä. Näiden menetelmien toimintaperiaatteen yleisenä tausta-ajatuksena on, että biologiset yhteisöt määräytyvät paikallisten ympäristöolojen mukaan. Tietyn paikan yhteisön oletetaan siis heijastavan kyseisen paikan ympäristön tilaa. Viime aikoina tausta-ajatus paikallisten ympäristöolojen merkityksestä ainoana eliöyhteisöjä muovaavana tekijänä on kuitenkin kohdannut kritiikkiä. Kriitikot painottavat, että biologisten yhteisöjen rakenteeseen vaikuttavat monet muutkin asiat kuin paikalliset ympäristöolosuhteet ja niissä tapahtuvat ihmisperäiset muutokset. Väitöskirjassani tutkin sisävesien luonnon monimuotoisuuteen vaikuttavia tekijöitä. Olin erityisen kiinnostunut siitä, näkyykö tutkituissa biologisissa parametreissa maantieteellisessä tilassa ilmeneviä spatiaalisia säännönmukaisuuksia. Saadakseni mahdollisimman laaja-alaisen käsityksen luonnon monimuotoisuudessa esiintyvistä spatiaalisista säännönmukaisuuksista, tutkin useaa spatiaalista kontekstia, eliöryhmää ja indeksiä. Tutkimuksessa selvisi, että paikalliset ympäristöolosuhteet eivät ole ainoita luonnon monimuotoisuuteen vaikuttavia tekijöitä. Erilaiset spatiaaliset säännönmukaisuudet, todennäköisesti eliöiden levittäytymiseen liittyvien seikkojen aiheuttamina, olivat yllättävän yleisiä makeiden vesien eliöyhteisöjen rakenteessa ja niihin perustuvien indeksien arvoissa. Tutkimussysteemien spatiaalinen konteksti (alueen laajuus ja paikkojen väliset spatiaaliset suhteet) selvästi vaikutti luonnon monimuotoisuutta kuvastavien indeksien arvojen vaihteluun. Lisäksi selvisi, että eri eliöryhmät ja indeksit olivat useimmiten liitoksissa hyvin erilaisiin selittäviin muuttujiin, osoittaen, että nämä mittarit kuvastavat eri asioita. Väitöskirjassa esitetyt havainnot on tärkeää huomioida vesistöjen ekologisen tilan ja luonnon monimuotoisuuden arviointi- ja seurantamenetelmiä kehitettäessä. Spatiaalisen kontekstin merkitys olisi hyvä huomioida myös nykyisten arviointi- ja seurantamenetelmien tuottamien tulosten tulkinnassa

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Ouhdouch, Yedir. "Bacteries actinomycetales rares productrices d'antifongiques : criblage, selection et etude taxonomique d'une souche active ; purification de l'antifongique elabore." Nancy 1, 1989. http://www.theses.fr/1989NAN10077.

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Miñana, i. Galbis David. "Diversitat fenotípica i genotípica del gènere "Aeromonas"." Doctoral thesis, Universitat de Barcelona, 2002. http://hdl.handle.net/10803/2416.

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En aquest estudi es van aïllar un total de 199 soques mesòfiles del gènere Aeromonas a partir de mostres de mol·luscs bivalves i d'aigües dolces. El medi agar dextrina ampicil·lina (ADA) fou el medi de cultiu més eficient en l'aïllament d'Aeromonas. La selecció de 16 proves fenotípiques clau va permetre la identificació a nivell d'espècie del 91 % de les soques estudiades. Es va realitzar un estudi de taxonomia numèrica amb 64 proves fenotípiques i 220 soques que, al 89 % de S[sub SM], va definir huit phena (I-VIII). Totes les soques d'una mateixa espècie o de diverses espècies d'un mateix complex fenotípic o fenoespècie es van agrupar en un únic phenon, excepte les soques tipus d'A. salmonicida i d'A. media que no s'agruparen en cap dels phena definits. Els phena V, VI i VII agruparen soques aïllades de mol·luscs bivalves no identificades a nivell d'espècie, la qual cosa suggereix l'existència de noves espècies del gènere Aeromonas. Per una altra banda, mentre la majoria de les espècies mostraren activitat beta-hemolítica, únicamente les espècies A. hydrophila, A. bestiarum i A. salmonicida van presentar activitat elastolítica. La presència d'espècies d'Aeromonas patògenes oportunistes i d'altres espècies amb factors de virulència fa recomanable la monitorització d'Aeromonas en aigües (potables, recreatives i de piscifactories) i en aliments que, com les ostres, es consumeixen crus o poc cuits.
Es va aplicar la tècnica d'electroforesi d'enzims multilocus (MLEE) a 122 soques de les espècies A. hydrophila, A. bestiarum, A. salmonicida, A. popoffii i A. trota. Mitjançant l'anàlisi de 15 enzims, s'obtingueren 79 perfils al·lèlics o tipus electroforètics (ETs). La diversitat genètica mitjana (H) de la mostra completa fou 0,64. Les subpoblacions A. hydrophila i A. salmonicida van presentar major diversitat genètica que les subpoblacions A. popoffii i A. bestiarum. Per una altra banda, l'anàlisi del desequilibri de lligament suggereix que l'estructura poblacional d'Aeromonas és clonal, ja què l'índex d'associació (I-subA) fou significativament diferent de 0 (I-subA=2,38, P menor que 0,0001). A una distància genètica menor que o igual a 0,7 el dendrograma de la relació genètica entre ETs va separar clarament les espècies A. salmonicida (grup II), A. trota (grup III) i A. hydrophila (grup IV), en canvi, les espècies A. bestiarum (subgrup Ib) i A. popoffii (subgrup Ic) es van separar a una distància genètica memor que o igual a 0,6. Les soques mesòfiles i psicròfiles de l'espècie A. salmonicida s'agruparen conjuntament. El dendrograma de la relació genètica entre ETs també va mostrar una bona correlació amb l'origen de les soques.
Finalment, la comparació entre la identificació fenotípica de les soques i les freqüències al·lèliques obtingudes en la técnica MLEE va mostrar que cinc loci, EST1 (esterasa 1), HEX (hexoquinasa), IDH (isocitrat deshidrogenasa), LDH1 (lactat deshidrogenasa 1) i MDH (malat deshidrogenasa), identifiquen correctament el 94 % de les soques estudiades.

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Sohier-Pérennes, Danièle. "Systématique des espèces Lactobacillus hilgardii et Lactobacillus brevis : Application à la détection des bactéries lactiques d'altération des vins." Bordeaux 2, 1998. http://www.theses.fr/1998BOR20612.

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En vinification, les bactéries lactiques conduisent la fermentation malolactique, processus de désacidification du vin. Cependant, certaines d’entre elles peuvent être à l’origine d’altérations. Le contrôle de la flore microbienne est donc souhaitable à toutes les étapes de la vinification, grâce à la mise en œuvre de méthodes d’identification de plus en plus efficaces. L’identification moléculaire des bactéries lactiques est désormais réalisée par une méthode d’hybridation ADN/ADN. Mais, des hybridations croisées sont observées entre plusieurs souches L. Hilgardii et L. Brevis, différenciées au préalable d’après leur profils API. Les souches fermentant ce pentose sont classées au sein de l’espèce L. Brevis, les autres au sein de l’espèce L. Hilgardii. La caractérisation moléculaire des espèces L. Hilgardii et L. Brevis constitue donc l’essentiel de ce travail. Des sondes et tests PCR spécifiques de l’espèce L. Hilgardii ont été élaborés. Par contre, dans le cas de L. Brevis, les polymorphismes génomiques observés laissent supposer que le regroupement de souches effectué sur la base de profil fermentaire ne correspond pas véritablement à une espèce. Ainsi, trois souches fermentant l’arabinose, mais possédant toutes les caractéristiques génomiques requises, ont été reclassés au sein de l’espèce L. Hilgardii, remettant ainsi en cause la validité du test biochimique. Une étude métabolique et génétique de l’assimilation de l’arabinose a donc été abordée chez différentes souches L. Hilgardii et L. Brevis. Les différences phénotyques observées entre les souches L. Hilgardii ne porteraient pas forcément sur la capacité ou non à fermenter l’arabinose. Enfin, dans le but de réaliser un contrôle de qualité efficace des vins, une méthode d’hybridation in situ a été adaptée au contrôle de la flore lactique avec les sondes d’ores et déjà utilisées pour des méthodes d’hybridation en tache ou sur colonie.

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Bernardet, Jean-François. "Etude phenotypique et genomique des bacteries appartenant aux genres cytophaga et flexibacter (ordre des cytophagales) et comparaison avec le genre flavobacterium : application a l'identification et a la taxonomie des especes ichtyopathogenes." Paris 7, 1989. http://www.theses.fr/1989PA077133.

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Les caracteres morphologiques et biochimiques ainsi que les adn d'une collection de bacteries appartenant a l'ordre des cytophagales et isolees en france a partir de poissons malades ont ete compares a ceux des souches-type de toutes les especes valides des genres cytophaga, flexibacter et flavobacterium ainsi qu'a ceux de plusieurs souches de flexibacter maritinus, flexibacter columnaris et cytophaga psychrophila isolees dans d'autres pays

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Lemmel, Florian. "Diversités taxonomique et fonctionnelle des communautés microbiennes en lien avec le cycle du carbone dans un gradient de sols multi-contaminés." Thesis, Université de Lorraine, 2019. http://www.theses.fr/2019LORR0004.

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Les activités sidérurgiques du siècle dernier ont laissé derrière elles des sols de friches multi-contaminés. Cette multi-pollution a dû conduire à une adaptation des communautés microbiennes, pouvant impacter leurs diversités et in fine le fonctionnement des sols. Dans ce contexte, les objectifs de mes travaux de thèse étaient : i) d’étudier la diversité taxonomique des communautés microbiennes mais aussi leur diversité fonctionnelle en lien avec le cycle du carbone, ii) d’identifier les éventuels liens qui unissent ces deux diversités et iii) de comprendre comment les caractéristiques des sols et leur pollution pouvaient modifier ces liens. Une collection de sols présentant un gradient de pollution par des hydrocarbures aromatiques polycycliques (HAP) et des éléments traces métalliques (ETM) a été étudiée. La diversité taxonomique des communautés bactériennes et fongiques a été obtenue par séquençage Illumina MiSeq et la diversité fonctionnelle métabolique a été estimée à l’aide des outils Biolog® et MicroResp™. La dégradation de deux substrats carbonés modèles, le phénanthrène (PHE) et la cellulose (CEL) marqués au 13C, a également été analysée par la technique de Stable Isotope Probing, qui en identifiant les microorganismes impliqués dans la dégradation de ces composés, permet de lier la diversité taxonomique à une fonction. Globalement, en sélectionnant les microorganismes, le niveau de contamination a modulé positivement ou négativement l’abondance relative de différents taxons bactériens et fongiques. Contrairement aux HAP, les ETM ont induit une diminution de la diversité fonctionnelle métabolique, mais aussi une tolérance accrue au zinc. Le potentiel fonctionnel de dégradation des HAP était positivement corrélé à la teneur en HAP des sols alors que les fonctions de dégradation du PHE et de la CEL étaient présentes dans tous les sols, quel que soit leur niveau de contamination. Les taux de dégradation de ces composés étaient positivement corrélés à l’abondance et la richesse microbienne, mais sans lien avec la pollution des sols. En outre, le taux de dégradation du PHE était expliqué par les abondances relatives des genres Massilia et Mycobacterium identifiés parmi les bactéries dégradantes. En conclusion, nous avons observé une diminution de l’intensité de dégradation de plusieurs composés carbonés, voire la disparition totale de la fonction, suggérant un possible dysfonctionnement du cycle du carbone dans certains des sols les plus pollués
The iron and steel activities of the last century have left behind multi-contaminated brownfields. This multi-pollution must have led to an adaptation of microbial communities, potentially impacting their diversities and ultimately the soil functioning. In this context, the objectives of my PhD thesis were: i) to study the taxonomic diversity of microbial communities, but also their functional diversity in relation to the carbon cycle, ii) to identify the possible relationships between these two diversities and (iii) to understand the impact of soil characteristics and pollution on communities. In this way, a collection of ten multi-contaminated soils, with both polycyclic aromatic hydrocarbons (PAH) and metallic trace elements (MTE) gradients, was studied. The bacterial and fungal taxonomic diversities were obtained using Illumina MiSeq sequencing and the metabolic functional diversity was estimated through Biolog® and MicroResp™ assays. The degradation of two model carbon substrates, namely 13C-labeled phenanthrene (PHE) and 13C-labeled cellulose (CEL), was also analyzed using Stable Isotope Probing technique, which, by identifying the microorganisms involved in the substrate degradation, allows to link function with taxonomic diversity. Overall, by selecting microorganisms, the contamination level positively and negatively modulated the relative abundance of different bacterial and fungal taxa. Unlike PAH, MTE induced a decrease of metabolic functional diversity, but also a greater zinc tolerance. The functional potential of PAH degradation was positively correlated with the PAH concentration in soils, while the PHE and CEL degradation functions were present in all soils, irrespective of their contamination level. Degradation rates of these compounds were positively correlated with microbial abundance and richness, but not linked to soil pollution. In addition, the PHE degradation rate was explained by the relative abundances of the Massilia and Mycobacterium genera, identified among the active PHE-degrading bacteria. In conclusion, we observed a decrease in the degradation intensity of several carbon compounds, or even the total disappearance of various functions, suggesting a potential dysfunction of carbon cycle in some of the most polluted soils

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Hamza, Abdou Azali. "Taxonomie et diagnostic des espèces de Xanthomonas associées à la gale bactérienne de la tomate et des Capsicum spp. : situation dans les Îles du Sud Ouest de l'océan Indien." Phd thesis, Université de la Réunion, 2010. http://tel.archives-ouvertes.fr/tel-00819814.

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La gale bactérienne des Solanées à graines est une maladie répandue dans la plupart des aires de production de tomate et des Capsicum spp. (piment, poivron) du monde. Elle est très sévère dans les régions tropicales et subtropicales et sa présence est récurrente dans la région Sud-Ouest de l'océan Indien. Cette maladie est complexe car cinq taxons sont actuellement reconnus comme agents causaux, X. vesicatoria , X. perforans , X. gardneri , X. euvesicatoria et X. campestris pv. raphani . Néanmoins certaines études récentes suggèrent des synonymies de certaines de ces espèces entre elles et également avec d'autres Xanthomonas. Les objectifs principaux de la thèse étaient (1) l'analyse de la diversité sur une collection mondiale à l'aide des deux techniques moléculaires à haut débit, AFLP et MLSA, avec un accent particulier sur la diversité génétique et pathologique régionale (2) la description des relations phylogénétiques entre ces taxons et les autres Xanthomonas (3) la mise au point d'un outil d'identification rapide qui tienne compte de la diversité de l'agent pathogène et basé sur des marqueurs SCAR identifiés par AFLP. Une absence de congruence entre les topologies d'arbres dérivées des séquences de 4 gènes de ménage étudiés a été mise en évidence, de même que plusieurs évènements de recombinaison sur trois d'entre eux. Un inventaire des espèces trouvées dans les îles SWIO a pu être dressé, mettant à jour une grande diversité dans cette région. Nos données ont confirmé de fortes similarités génétiques entre X. alfalfae , X. euvesicatoria et X. perforans d'une part et de X. cynarae et X. gardneri d'autre part, qui ont probablement le statut d'espèces-synonyme.

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Bourgeois, Emilie. "Contribution au développement de bioindicateurs microbiens pour l'évaluation de l'impact de pratiques agricoles sur les sols." Thesis, Dijon, 2015. http://www.theses.fr/2015DIJOS063/document.

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Le sol représente le support de la production agricole. A l’interface avec les autres compartiments de la biosphère, il remplit de nombreuses fonctions essentielles à la fourniture de services écosystémiques nécessaires au bien-être de nos sociétés. C’est aussi une ressource non renouvelable dont les propriétés physicochimiques et biologiques ont été altérées par le développement de l’agriculture intensive. La prise de conscience actuelle de cet état de fait a révélé la nécessité de définir de nouveaux modes de gestion adaptés à la préservation et à l’utilisation durable des sols. Elle a ainsi marqué l’entrée dans l’ère de l’agroécologie qui prône un modèle de production optimisant notamment les services rendus par la biodiversité afin de réduire le recours aux intrants et à l’utilisation d’énergie. Pour atteindre cet objectif, le développement d’une gamme d’indicateurs permettant d’évaluer les pratiques/systèmes agricoles en rendant compte de la qualité biologique du sol est donc indispensable. Cette thèse, dont l’objectif est de contribuer au développement de bioindicateurs microbiens de la qualité du sol, s’inscrit dans ce contexte agroécologique. Le choix de travailler sur les communautés microbiennes se justifie pleinement dans cette problématique car elles sont (i) présentes avec une forte densité et diversité dans tous les environnements, (ii) fortement impliquées dans le fonctionnement biologique et les services rendus par le sol, et (iii) elles répondent de façon très sensible aux changements des conditions environnementales en termes de modification de biomasse, de structure/diversité et d’activité. Elles offrent donc un potentiel important en termes de développement de bioindicateurs. Ce travail a porté plus précisément sur l’évaluation de deux indicateurs complémentaires : (i) la biomasse moléculaire microbienne et (ii) la diversité taxonomique microbienne. Dans une première partie nous avons éprouvé la robustesse de ces deux indicateurs en évaluant les biais associés à chacune des étapes techniques des procédures mises en œuvre pour leur mesure. Nous avons ensuite utilisé ces deux indicateurs dans différents contextes agronomiques pour évaluer leur pertinence. Un premier travail a ainsi consisté à suivre la réhabilitation du patrimoine microbien, par l’implantation d’une culture à vocation énergétique, d’un sol pollué irrigué pendant une centaine d’années par des eaux usées. Une seconde application a porté sur l’étude de l’impact de différentes pratiques agricoles sur les communautés microbiennes selon l’intensité du travail du sol (labour vs. travail réduit), la gestion des résidus de culture (export vs. restitution), et le type de culture (annuelle vs. pérenne).Les résultats montrent que la biomasse moléculaire microbienne et la diversité taxonomique obtenue par séquençage massif sont deux bioindicateurs robustes et sensibles pour décrire la qualité microbiologique des sols agricoles dans des contextes très variés. Ces deux indicateurs permettent de mettre en évidence aussi bien des perturbations des sols que l’impact positif de pratiques innovantes. Ils peuvent donc représenter des outils performants pour l’évaluation des systèmes agricoles, aidant à une amélioration de leur mode de gestion et, à long terme, permettant une utilisation durable des ressources fournies par ces sols
Soil is the support of agricultural production. It performs many functions essential to the provision of ecosystem services necessary for the well-being of our societies. Soil physicochemical and biological properties have been altered by the development of intensive agriculture while it is a non-renewable resource, revealing the need to develop new management practices suitable for the sustainability of soil quality. This also marked the entry into the “Agroecology” era, which promotes the development of new agricultural systems optimizing services provided by biodiversity to reduce the use of inputs and energy use. To achieve this aim, the development of a range of indicators to assess the impact of agricultural practices on the biological quality of the soil is essential. This thesis, which aims to contribute to the development of microbial bio-indicators of soil quality, is a part of this agroecological context. The choice to work on microbial communities is fully justified because they are (i) present with a high abundance and diversity in all environments, (ii) heavily involved in biological functioning and the soil ecosystem services, (iii) they respond very sensitive to changes in environmental conditions in terms of biomass, diversity and activity. They therefore have significant potential in terms of bio-indicators of development. This work has focused specifically on the evaluation of two complementary bioindicators: (i) the microbial molecular biomass and (ii) the microbial taxonomic diversity. In a first part we tested the robustness of these two bioindicators by assessing the biases associated with each of the procedure technical steps used for their measurement. We then used these bioindicators in different agricultural contexts to assess their sensitivity. A first work has followed the rehabilitation of microbial patrimony of a polluted soil irrigated for a hundred years by sewage, by implanting a bioenergy crop. A second application has focused on the impact of different agricultural practices on microbial communities depending on the intensity of tillage (tillage vs. reduced tillage), management of crop residues (export vs. restitution), and the crop type (annual vs. perennial). Results highlighted that microbial molecular biomass and microbial taxonomic diversity achieved by high throughput sequencing are both robust and sensitive bioindicators to describe the microbiological quality of agricultural soils in very different contexts. Both bioindicators allow evidencing soil disturbances but also the positive impact of innovative practices. They may therefore represent powerful tools for the assessment of agricultural systems, helping to improve their long term management, allowing a sustainable use of resources provided by soils

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Dissertations / Theses on the topic 'Bacterial taxonomy'

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