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Unbranched heterocytous cyanobacteria exhibit complex filament and colony architectures and variable life strategies from symbionts to free living planktic and non-planktic species. They are counted among microbial groups showing an extensive production of secondary metabolites, resulting in both pharmaceutically important and toxic compounds. The main focus of this thesis is to broaden our knowledge on bioactive secondary metabolite potential in this widespread group of cyanobacteria. An effective combination of methods including whole genome sequencing, bioinformatic analysis, and analytical chemistry techniques are applied to accomplish this task. The discrepancies in distribution of various classes of compounds among ecological groups defined by different life strategies are discussed. Additionally, the thesis endeavours to test multidisciplinary approaches to tackle taxonomic assignments of unresolved unbranched heterocytous cyanobacteria using morphological, phylogenetic and ecophysiological methods, including a meta-analysis of morphological traits.

Morphology and ultrastructure of 25 oscillatorian strains was examined and phylogenetic analysis of 16S rDNA oscillatorian sequences was conducted. Genera Phormidium and Oscillatoria were shown to be polyphyletic. Although morphologically similar strains are found in different branches of the phylogenetic tree, considerable correlation between molecular, ultrastructural and some morphological and ecological traits was detected in several lineages.

Submitted by (lucia.rodrigues@ufrpe.br) on 2017-03-22T12:38:56Z No. of bitstreams: 1 Mariote dos Santos Brito Netto.pdf: 2798345 bytes, checksum: 06d5992ae421bc76a692bd417a393470 (MD5) / Made available in DSpace on 2017-03-22T12:38:56Z (GMT). No. of bitstreams: 1 Mariote dos Santos Brito Netto.pdf: 2798345 bytes, checksum: 06d5992ae421bc76a692bd417a393470 (MD5) Previous issue date: 2012-07-31 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / The identity of Lasiodiplodia species in causing stem-end rot papaya is reveal. In the current study the Lasiodiplodia species isolated from papaya in Northeastern Brazil are described, as well as their distribution in seven different populations. Lasiodiplodia isolates are characterized through cultural, morphological, patogenicity and virulence data, and from phylogenetic analyses based on the complete sequence of the ITS region and partial sequence of the translation elongation factor-1α gene. Based on sequence data, three previously described species were identified (Lasiodiplodia theobromae, L. pseudotheobromae, L. hormozganensis) together with one unknown species. L. theobromae was the most prevalent species in all populations. All Lasiodiplodia species were pathogenic. / A identidade das espécies de Lasiodiplodia causando podridão peduncular em mamão é revelada. No presente estudo espécies de Lasiodiplodia isoladas de mamão no Nordeste do Brasil são descritas, bem como, a sua distribuição em sete diferentes populações. Os isolados de Lasiodiplodia foram caracterizados por inferência filogenética baseada na sequência completa da região ITS e na sequencia parcial do gene fator de alongamento, pelas características culturais e morfológicas, bem como pela patogenicidade e virulência. Três espécies previamente descritas foram identificadas (L. theobromae, L. pseudotheobromae, L. hormozganensis) juntamente com uma espécie desconhecida. Lasiodiplodia theobromae foi a espécie mais prevalente em todas as populações. Todas as espécies de Lasiodiplodia foram patogênicas.

Orientador: José Luiz Pereira / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-21T13:27:50Z (GMT). No. of bitstreams: 1 Lopes_AlinedeSouza_M.pdf: 1681631 bytes, checksum: f77820cebe02c8058ad8b01cc2f36a6e (MD5) Previous issue date: 2012 / Resumo: O gênero Aspergillus é um grupo de fungos que possui diversas espécies produtoras de micotoxinas, distribuídas principalmente em três seções denominadas de Nigri, Flavi e Circumdati. Estudos para isolamento destas espécies estão sendo executados para se conhecer a micobiota e atuar na prevenção e redução da contaminação dos alimentos, principalmente por micotoxinas, como também são úteis nas descobertas de novas espécies. A identificação de fungos, como o gênero Aspergillus sp foi, por muito tempo,realizada através de suas características morfológicas, sendo hoje amparadas por técnicas como a Biologia Molecular, fisiologia e detecção de metabólitos específicos produzidos pelos microrganismos. Com este objetivo, este trabalho apresenta o inicio do levantamento de dados relacionado à ocorrência, caracteres morfológicos, fisiológicos,bioquímicos e moleculares, assim como a distribuição geográfica. A partir do isolamento de 10.048 cepas potencialmente toxigênicos de amostras de café, cacau, castanha do Brasil e frutas secas (tâmaras, uvas passas, figos e ameixas), matérias-primas de projetos desenvolvidos no Laboratório de Microbiologia do Instituto de Tecnologia de Alimentos (ITAL), 5.069 destes isolados foram preservadas em sílica gel, exigindo a catalogação dos dados. Neste acervo, a section Flavi predominou com o número de 2.507 culturas (32% destas cepas foram produtoras de aflatoxinas), seguida da section Nigri com 2.078 e 463 da section Circumdati que, somando, contribuiram com 11% de fungos produtores de ocratoxina A. Os Aspergillus da section Nigri apareceram em número considerável em todos os substratos, confirmando a sua predominância destes como contaminantes de alimentos. As amostras de castanha do Brasil contribuíram com o maior número de isolados, principalmente pela biodiversidade da floresta e colheita extrativista. Fungos que apresentaram estruturas diferenciadas, representantes de grupos com mesmas características, toxicidade ou espécies novas foram encaminhados para outros tipos de identificação. Duzentos e setenta e seis culturas foram identificadas por análise molecular, 435 pela extração de seus metabólitos e 87 espécies foram classificadas através da identificação polifásica. A distribuição das culturas apresentou representantes do Norte, Nordeste, Sul e Sudeste do Brasil, sendo que o Pará e Amazonas contribuíram com 2.759, como também culturas originárias de amostras de outros países como Irã,Turquia, Tunísia, EUA, México, Espanha e Argentina. A rotina de uma coleção consiste em novos isolamentos, manutenção do acervo e atualização do banco de dados, um trabalho enriquecedor para a ciência e que nunca se encerra / Abstract: The genus Aspergillus is part of a fungi group with several species that produce mycotoxins, mainly distributed in three sections named Nigri, Flavi and Circumdati. Studies to isolate these microorganism types are being made to know the mycobiota and their function in prevention and reduction of food contamination, mainly by mycotoxins and also to discover new species. The Aspergillus fungi identification was for a long time made by morphological characteristics but now it is supported by techniques such as molecular biology, physiology and detection of microorganism metabolites. With the objective this work presents the beginning of data collection related to the occurrence, morphological, physiological, biochemical and molecular, as well as the geographic distribution. From the potentially toxigenic strains isolation of 10,048 samples of coffee, cocoa, Brazil nuts and dried fruit (dates, raisins, figs and prunes) raw materials for projects developed in the Laboratory of Microbiology, Institute of Food Technology (ITAL), 5069 of these isolates were preserved in silica gel, requiring cataloging data. In this collection section Flavi predominates with 2,507 cultures (32% of these strains are aflatoxin producers) followed by section Nigri with 2,078 and 463 of section Circumdati that together, contributes 11% of ochratoxin A fungi producing. The Aspergillus section Nigri showed a considerable number of all substrates, confirming its predominance and resistance as a food contaminant. Brazil nut samples contributed with the largest number of strains due to forest biodiversity and harvest extraction. Fungi that had differentiated structures, group representatives with similar characteristics, toxicity or new species were referred to other types of identification. Two hundred and seventy six isolates were identified by molecular analysis with 435 metabolites, 88 species of Aspergillus showed the two forms, being classified by polyphasic identification. The genus Aspergillus was identified widely from countries such as Iran, Turkey, Tunisia, USA, Mexico, Spain and Argentina. In Brazil there are representatives from the North, Northeast, South and Southeast, and Para and Amazonas states that contributed to 2,759 cultures. The collection routine consists of new insolation, collection maintenance and updating of the database, which is an undending task for the enrichment of science / Mestrado / Ciência de Alimentos / Mestra em Ciência de Alimentos

The modern taxonomic revision of cyanobacteria is a work in progress, with both theoretical and practical challenges to be addressed. This thesis investigated selected terrestrial cyanobacterial taxa using a polyphasic approach, based on molecular phylogenetic analysis and accompanied by phenotypic characterization and nomenclatural treatment. Diverse methodological approaches were used including optical and transmission electron microscopy, molecular analysis (DNA sequencing) of cyanobacterial strains, single cells and filaments, and phylogenetic analysis of multiple genomic loci. This study provided systematic revisions of individual cyanobacterial genera and the entire phylum, and suggestions for future study projects.

With an adoption of modern methods of polyphasic approach to the study of cyanobacteria, an increased demand for the revision of the traditional taxonomy has emerged. This thesis is devoted to the systematic revisions of selected terrestrial cyanobacteria at several taxonomic levels. The methodology included thorough morphological characterization of cultured cyanobacterial strains using light and electron microscopy complemented with analyses of the molecular data: DNA sequencing, phylogenetic analyses based on 16S rRNA gene and the adjacent 16S-23S ITS region, and comparison of the predicted secondary structures of this region. Descriptions of new species, genera, families and an in-depth characterization of a previously poorly known family were achieved.

Submitted by (lucia.rodrigues@ufrpe.br) on 2017-03-23T16:20:44Z No. of bitstreams: 1 Willie Anderson dos Santos Vieira.pdf: 939430 bytes, checksum: b3f788b1dafa1b55d7a74abaf64a9110 (MD5) / Made available in DSpace on 2017-03-23T16:20:44Z (GMT). No. of bitstreams: 1 Willie Anderson dos Santos Vieira.pdf: 939430 bytes, checksum: b3f788b1dafa1b55d7a74abaf64a9110 (MD5) Previous issue date: 2012-02-28 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / In the current study the Colletotrichum species isolated from mango in Pernambuco state in Brazil are described, as well as their distribution in different plant tissues. The Colletotrichum isolates are characterized through cultural, morphological, patogenicty and vivirulence data, and from phylogenetic analyses based on a partial sequence of the gene glyceraldehyde-3-phosphate dehydrogenase (GPDH). There was significant difference in isolament frequency among sites and plant tissues. In the locality of Aldeia (site III) it was observed the highest isolation frequency. The old limb was the part of plant most colonized in a higher number of sites. Colletotrichum asianum, C. fructicola, C. cliviae, C. boninense and two unidentified species were found as endophyte in mango, and C. asianum was prevalent over the other. All isolates were pathogenic in mango fruits. The phylogenetic analysis revealed groupings that were congruent with morphological characters, but did not group isolates according to phenotypic characters. There was no distribution pattern of species in different areas, neither in plant tissues. / No presente estudo são relatadas as espécies de isolados de Colletotrichum endofíticos associados a mangueiras no Estado de Pernambuco/Brasil, e sua distribuição nos diferentes tecidos da planta em cinco diferentes áreas. Isolados foram caracterizados cultural e morfologicamente, quanto à patogenicidade e virulência, e através de inferências filogenéticas baseadas na sequência parcial do gene gliceraldeído-3-fosfato desidrogenase (GPDH). Houve diferença significativa na freqüência de isolamento de Colletotrichum em função da área de coleta e do tecido da planta. Na localidade de Aldeia (área III) foi observada a maior freqüência de isolamento de Colletotrichum. O limbo maduro foi a parte da planta mais colonizada por Colletotrichum em um maior número de áreas. Colletotrichum asianum, C. fructicola, C. cliviae, C. boninense e duas espécies não identificadas ocorrem como endófitas em mangueira, e C. asianum foi prevalente sobre as demais. Todos os isolados foram patogênicos em frutos de manga. A análise filogenética revelou agrupamentos que foram congruentes com os caracteres morfológicos analisados, porém não agrupou isolados conforme características fenotípicas. Também não foi observado padrão de distribuição das espécies nas diferentes áreas, nem nos tecidos vegetais.

Orientadores: Gilson Paulo Manfio, Valeria Maia de Oliveira / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-04T23:38:45Z (GMT). No. of bitstreams: 1 AbreuFilho_BenicioAlvesde_D.pdf: 6208226 bytes, checksum: e8676e4b88ce9781e64eda102999921b (MD5) Previous issue date: 2005 / Resumo: Trinta linhagens de bactérias acidotermofílicas isoladas do processamento industrial de suco de laranja concentrado congelado (Frozen Concentrated Orange Juice, FCOJ) em diferentes regiões do estado de São Paulo foram estudadas, utilizando-se uma abordagem polifásica, a fim de se determinar a diversidade e potencial deteriogênico destas em processos de produção de FCOJ no país. A caracterização dos isolados envolveu a determinação da capacidade de crescimento e produção de odor em suco reconstituído, análises fenotípicas (padrão de utilização de carboidratos, sistema API 50 CH), quimiotaxonômicas (perfil de FAMES, sistema MIDI) e de caracterização molecular (ARDRA de região espaçadora DNAr 16S-23S com Hae III, Hha I e Msp I, e análise filogenética de DNAr 16S). Todos os isolados foram identificados como pertencentes ao gênero Alicyclobacillus pelos padrões característicos de ácidos graxos. Diferentemente de relatos de literatura, foi confirmada a presença de omega-ciclohexil-C17:0 e omega-ciclohexil-C19:0 em amostras identificadas como A. pomorum. Das 30 amostras ambientais de aliciclobacilos analisadas, 21 foram capazes de se multiplicar em suco de laranja reconstituído após 24 ou 48 h de incubação a 45 °C, mas apenas 10 produziram odor característico de biodeterioração. Seis ribotipos de ARDRA foram obtidos para os isolados, permitindo a alocação destes nas espécies A. acidocaldarius e A. acidoterrestris, e em grupos relacionados a espécies válidas designados como A. acidocaldarius-like e A. pomorum-like / Abstract: Thirty strains isolated from industrial processing of frozen concentrated orange juice (FCOJ) in different regions of the state of São Paulo were studied using a polyphasic approach with the goal of determining the diversity and deteriogenic potential of isolates from FCOJ production in Brazil. Characterization of isolates involved determining their ability to grow and produce odor in reconstituted orange juice, and phenotypic (carbohydrate utilization, API 50 CH), chemotaxonomic (FAMES, MIDI system) and molecular analyses (ARDRA of 16S-23S rDNA spacer region, Hae III, Hha I and Msp I, and 16S rDNA phylogenetic analysis). All isolates were identified as Alicyclobacillus spp. according to the characteristic fatty acid patterns. Contrary to literature data, omega-cyclohexyl-C17:0 and omega-cyclohexyl-C19:0 were confirmed in samples identified as A. pomorum. From the 30 environmental alicyclobacili samples analyzed, 21 were able to grow in reconstituted orange juice after 24 or 48 hs incubation at 45 °C, but only 10 isolates yielded a characteristic biodeterioration odor. Six ARDRA patterns were obtained for the isolates analyzed, enabling them to be assigned to A. acidocaldarius and A. acidoterrestris, and to groups related to valid species named A. acidocaldarius-like and A. pomorum-like / Doutorado / Doutor em Ciência de Alimentos

Our current knowledge of chrysophyte diversity is still generally based on traditional morphospecies descriptions. Accordingly, sequence data exist for the minority of all described species. Consequently, several common morphotypes (e.g. Ochromonas-like flagellate) are scattered across the phylogenetic tree of Chrysophytes. It is evident that the postulated taxonomic diversity certainly does not reflect the real species richness in Chrysophytes. Moreover, recent studies on silica scaled chrysophytes (Mallomonas, Paraphysomonas, Synura) clearly demasked common problematics of (pseudo)cryptic species even within this group possessing relatively good species concept based on the ultrastructure of silica scales and bristles. Contrary, most of chrysophytes are naked flagellates forming stomatocysts as the only solid structure in their life cycles. While single-celled Ochromonas and Spumella were recently revisited using molecular genetic techniques, Uroglena-like colonials remained untreated. Therefore, the main objective of this thesis was to provide a modern taxonomic revision of the widespread colonial chrysophytes causing conspicuous seasonal massive population booms, Synura s.l. and Uroglena s.l., by a polyphasic approach encompassing molecular phylogeny, morphology/ultrastructure and ecology....