No description available.

Epiphytic bacterial communities on the surfaces of marine algae are poorly characterised. Most information available on marine bacterial epiphytes is derived from culture-based studies. With the rapid development of molecular community analysis technologies, it is now possible to obtain a more comprehensive picture of marine microbial populations on living surfaces. The intertidal macroalga Ulva australis, belongs to the cosmopolitan group of green marine algae (Ulvales) known to require the presence of bacteria for normal growth and has been suggested to employ specific bacteria for the defence against fouling by micro- and macro-organisms. This thesis has examined the composition and structure of the surface associated bacterial community on Ulva australis using 16S rRNA gene clone library, denaturing gradient gel electrophoresis (DGGE), and catalysed reporter deposition ??? fluorescence in situ hybridisation (CARD-FISH) analysis. The 16S rRNA gene clone library revealed that the five main bacterial groups present in the surface associated community were Bacteriodetes, Planctomycetes, Alpha-, Gamma-, and Delta-Proteobacteria. Twenty-two sequence phylotypes were identified, suggesting that the epiphytic community was of relatively low diversity. A clone similar to an algal morphogenesis inducing Cytophaga strain was identified, indicating that U. australis harbours bacteria important for thallus structural maintenance. DGGE analysis showed that while the bacterial community varied over spatial and temporal (seasons) scales it also included a stable subpopulation consistently associated with the seaweed surface. Sequencing of selected DGGE bands suggested that members of the Alphaproteobacteria and the Bacteriodetes belonged to the stable subpopulation. Using CARD-FISH with different phylogenetic probes demonstrated that Alphaproteobacteria (~ 70%) and Cytophaga-Flavobacteria (~13%) constituted the majority of bacterial cells on the surface of U. australis. A comparison of the results provided by the molecular community analysis methods, employed in this thesis, and those of culturing of epiphytic bacteria from U. australis revealed that each approach provides different patterns of phylogeny and extent of diversity. For example, the culture collection and the clone library detected a relatively high amount of Gammaproteobacteria, however, DGGE and CARD-FISH did not. Also, low species diversity clone sequences and isolates of Alphaproteobacteria contrasted with the high numbers detected by the DGGE analysis. In addition to the phylogentic determination of the epiphytic bacterial community, CARDFISH was also used to assess the organisation and distribution of bacterial cells across different zonal regions on seaweed surface. It was found that approximately 40% of bacterial cells clustered in aggregates, or microcolonies. These aggregations were considered to be heterogeneous in composition and were mainly comprised of multiply species. The occurrence of more non-viable solitary single rather than aggregated cells suggests that aggregates might offer greater protection to bacterial cells from the harsh conditions in the intertidal zone. More broadly, CARD-FISH was found to be a useful tool for studying microcolonies and was also successfully applied to detect slow growing soil microcolonies cultivated using a novel soil substrate membrane system culturing technique without the need to perform an rRNA enrichment incubation. The findings in this thesis, as described from the application of a number of molecular community analysis techniques such as clone library, DGGE and CARD-FISH, have improved our understanding of the diversity and structure of the epiphytic bacterial community associated with U. australis. Morevover, the information provided may to design future studies in the ecology of bacteria-seaweed interactions, including symbiotic interactions, and aid in marine biotechnology applications such as identifying bacteria which produce bioactive secondary metabolites.

Thesis (M.E.S.)--The Evergreen State College, 2009. / Title from title screen (viewed 2/24/2010). Includes bibliographical references (leaves 98-107).

No description available.

Epiphytic bacterial communities on the surfaces of marine algae are poorly characterised. Most information available on marine bacterial epiphytes is derived from culture-based studies. With the rapid development of molecular community analysis technologies, it is now possible to obtain a more comprehensive picture of marine microbial populations on living surfaces. The intertidal macroalga Ulva australis, belongs to the cosmopolitan group of green marine algae (Ulvales) known to require the presence of bacteria for normal growth and has been suggested to employ specific bacteria for the defence against fouling by micro- and macro-organisms. This thesis has examined the composition and structure of the surface associated bacterial community on Ulva australis using 16S rRNA gene clone library, denaturing gradient gel electrophoresis (DGGE), and catalysed reporter deposition ??? fluorescence in situ hybridisation (CARD-FISH) analysis. The 16S rRNA gene clone library revealed that the five main bacterial groups present in the surface associated community were Bacteriodetes, Planctomycetes, Alpha-, Gamma-, and Delta-Proteobacteria. Twenty-two sequence phylotypes were identified, suggesting that the epiphytic community was of relatively low diversity. A clone similar to an algal morphogenesis inducing Cytophaga strain was identified, indicating that U. australis harbours bacteria important for thallus structural maintenance. DGGE analysis showed that while the bacterial community varied over spatial and temporal (seasons) scales it also included a stable subpopulation consistently associated with the seaweed surface. Sequencing of selected DGGE bands suggested that members of the Alphaproteobacteria and the Bacteriodetes belonged to the stable subpopulation. Using CARD-FISH with different phylogenetic probes demonstrated that Alphaproteobacteria (~ 70%) and Cytophaga-Flavobacteria (~13%) constituted the majority of bacterial cells on the surface of U. australis. A comparison of the results provided by the molecular community analysis methods, employed in this thesis, and those of culturing of epiphytic bacteria from U. australis revealed that each approach provides different patterns of phylogeny and extent of diversity. For example, the culture collection and the clone library detected a relatively high amount of Gammaproteobacteria, however, DGGE and CARD-FISH did not. Also, low species diversity clone sequences and isolates of Alphaproteobacteria contrasted with the high numbers detected by the DGGE analysis. In addition to the phylogentic determination of the epiphytic bacterial community, CARDFISH was also used to assess the organisation and distribution of bacterial cells across different zonal regions on seaweed surface. It was found that approximately 40% of bacterial cells clustered in aggregates, or microcolonies. These aggregations were considered to be heterogeneous in composition and were mainly comprised of multiply species. The occurrence of more non-viable solitary single rather than aggregated cells suggests that aggregates might offer greater protection to bacterial cells from the harsh conditions in the intertidal zone. More broadly, CARD-FISH was found to be a useful tool for studying microcolonies and was also successfully applied to detect slow growing soil microcolonies cultivated using a novel soil substrate membrane system culturing technique without the need to perform an rRNA enrichment incubation. The findings in this thesis, as described from the application of a number of molecular community analysis techniques such as clone library, DGGE and CARD-FISH, have improved our understanding of the diversity and structure of the epiphytic bacterial community associated with U. australis. Morevover, the information provided may to design future studies in the ecology of bacteria-seaweed interactions, including symbiotic interactions, and aid in marine biotechnology applications such as identifying bacteria which produce bioactive secondary metabolites.

Thesis (Ph. D.) -- Lincoln University, 2008. / Also available via the World Wide Web.

Thesis (M.S.) in Ecology and Environmental Science--University of Maine, 2006. / Includes vita. Includes bibliographical references (leaves 55-60).

No description available.

Orientador: João Semir / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-04T11:21:58Z (GMT). No. of bitstreams: 1 Breier_TiagoBoer_D.pdf: 1087652 bytes, checksum: e8ab6c859380cf07d34a73fde28e3149 (MD5) Previous issue date: 2005 / Resumo: O presente estudo aborda quatro comunidades de epífitos vasculares em diferentes formações florestais do Estado de São Paulo, comparando composição florística, formas de vida, síndromes de polinização e dispersão, com base nos dados coletados em uma amostragem padronizada realizada em áreas de 10,24ha em cada formação: Floresta de Restinga (Parque Estadual Ilha do Cardoso), Floresta Ombrófila Densa Submontana (Parque Estadual Carlos Botelho), Floresta Estacional Semidecidual (Estação Ecológica Caetetus) e Cerradão (Estação Ecológica Assis). Foram registradas respectivamente 178, 161, 25 e 16 espécies de epífitos vasculares, ou seja, plantas que crescem sem contato caule-solo, incluindo plantas com estruturas haustoriais. Ao todo, nas quatro parcelas, foram registradas 277 espécies de epífitos vasculares pertencentes 109 gêneros e a 37 famílias. As maiores similaridades, no nível de espécie, foram encontradas comparando a flora das florestas mesófilas entre si e a flora das florestas higrófilas entre si, as demais comparações par a par, entre uma floresta mesófila e uma higrófila apresentaram baixos valores de similaridade. A única espécie presente nas quatro formações foi Pleopeltis angusta (Polypodiaceae). Em todas as áreas, holoepífitos verdadeiros foram à forma de vida com maior número de espécies. Entomofilia e anemocoria foram respectivamente às síndromes de polinização e dispersão com maior número de espécies. Estudos detalhados sobre estrutura e distribuição espacial das comunidades de epífitos indicam grandes diferenças na ocupação do espaço, de acordo com o tipo de floresta. A riqueza de epífitos apresentou diferentes respostas, de acorco com o tipo florestal, a parâmetros quantitativos dos forófitos e a parâmetros quantitativos das parcelas. Palavras-chaves: epífitos vasculares, comunidades, síndromes de polinização, síndromes de dispersão, formas de vida, biogeografia, ecologia / Abstract: This work presents four communities of vascular epiphytes in different forest formations in the State of São Paulo, and it compares the floristic composition, life forms, pollination and dispersal syndromes, using data collected through standardized samplings, performed in 10,24ha areas in each formation: Coastal Plain Forest (Ilha do Cardoso State Park), Submontane Rain Forest (Carlos Botelho State Park), Seasonal Semideciduous Forest (Caetetus Ecological Station) and Woody Savanna Forest (Assis Ecological Station). I sampled respectively 178, 161, 25 and 16 species of vascular epiphytes (plants that grow without stem-soil contact, including plants with haustorial structures. Altogether, in the four plots studied, there were 277 species of vascular epiphytes belonging to 109 genera and 37 families. The highest similarity values, in the species level, were found in the comparison among the flora of mesophilous forests and among the flora of hygrophilous forests; the other paired comparisons, between one mesophilous and one hygrophilous forest, presented the lowest similarities values. The only species common to all four forest formations, in the plot sampling, was Pleopeltis angusta (Polypodiaceae). In all areas, the life form of true holoepiphyte was the richer. Entomophily and anemocory were, respectively, the most diverse syndromes. Detailed studies on the spatial distribution of epiphyte communities suggest large differences in space occupation, according to forest type. Epiphyte richness presented different types of relationship, according to forest formation, to quantitative parameters of phorophytes and to quantitative parameters measured in the plots. Keywords: vascular epiphytes, community, pollination syndromes, dispersal syndromes, life forms, biogeography, ecology / Doutorado / Biologia Vegetal / Doutor em Biologia Vegetal

Submitted in fulfillment for the Degree of Masters of Applied Sciences (Biotechnology), Durban University of Technology, Durban, South Africa, 2016. / Activated sludge (AS) flocs are paramount in biological treatment of wastewater, are comprised of microbial consortia with organic and inorganic material bound together by extra polymeric substances (EPS). The filamentous bacteria play a vital role in the floc formation process by providing the necessary structural support. Presence of epiphytic attachment on selected filamentous bacteria is a commonly occurring phenomenon in activated sludge samples. Different theories have been proposed to describe this phenomenon; however, not much research has been carried out to explore the profundity of the attachment. In this study, an attempt has been made to elucidate the intrinsic nature of the epiphytic attachment between the bacterial rods and filamentous bacteria based on microscopic (morphological and structural) analysis. Characterization of these epiphytes were performed using fluorescence in situ hybridization (FISH) at group level using Alpha, Beta and Gamma Proteo-bacterial probes. Morphological characteristics of filament hosts and the bacterial rods at the interface region was assessed using scanning electron microscopy (SEM). The SEM micrographs indicated that the attachment was facilitated by more than the EPS layer. Further ultrastructural examination using transmission electron microscopy (TEM) indicated a possible cell-to-cell interaction between epiphytes and the selected filaments. Fibrillar structures resembling amyloid-like proteins were observed within the filament cell targeted by the epiphytes. An interaction was apparent between the amyloid like proteins and the epiphytes as exhibited by the direction of fibrillar structures pointing towards the approaching epiphytes. Common bacterial appendages such as pili and fimbria were absent at the interface and further noted was the presence of cell membrane extensions on the epiphytic bacteria protruding towards the targeted filamentous cell. The sheath of host filaments however, remained intact and unpenetrated, during colonization. Amyloid-like fibrils at interface may potentially play the role of attachment sites for the attaching epiphytes, as attachment facilitating appendages were not visualized. / M