No description available.

No description available.

Methanogenesis is the predominant terminal process of polymer degradation in anaerobic marine sediments depleted of sulfate; however, characterization of a marine consortium has not been previously reported. A marine methanogenic consortium consisting of fermentative, hydrogen-producing acetogenic and methanogenic bacteria is described. An acetotrophic methane-producing strain of bacteria was isolated. This isolate expresses three distinct morphovars: individual cocci, cell aggregates and communal cysts. Individual cocci are 1.9 µm in diameter and are nonmotile, but have fimbria-like structures. Cells have a thin protein cell wall. Acetate, methanol, methylamine, dimethylamine and trimethylamine are substrates for growth; formate and hydrogen are not. Sodium chloride and magnesium concentrations found in seawater are required for optimum growth. RNA homology values indicated that this isolate is a new species. Methanosarcina acetivorans is the proposed specific epithet. This is the first report of an acetotrophic methane-producing species indigenous to marine sediments. A method is described for mass culturing this and other acetotrophic methanogens using a pH auxostat. A strictly methylotrophic methane-producing strain was also isolated and is described. Only trimethylamine, dimethylamine, methylamine and methanol were substrates for growth. Cells were nonmotile, irregular cocci 1 µm in diameter and had a thin protein cell wall. Sodium chloride and magnesium concentrations found in seawater were required for optimum growth. Biotin was the only organic supplement required for growth in mineral medium. Fe was required for growth; Ni and Co were stimulatory. This isolate is a new genus based on RNA homology. Methanococcoides is the proposed genus and Methanococcoides methylutens is the specific epithet. Population studies suggest that this species is uniquely adapted for methylated amine degradation in marine sediments. The phylogenetic relationships of M. acetivorans, M. methylutens and other acetotrophic and methylotrophic species were determined by RNA and DNA homology techniques. Phylogenetic and physiological results in this study indicated that the population of methanogenic bacteria in marine sediments is both unique and equally diverse as the population of freshwater methanogenic species. / Ph. D.

Natural product drug discovery has traditionally been the corner stone of medicine having provided cures to many of today's most common diseases. In particular, antibiotics have revolutionised healthcare and extended human lifespan. However, since their introduction into the clinic, resistance to these drugs has arisen. With the number of new antibiotics being discovered in recent years declining, and fewer drugs making it past clinical trials, we have reached the point where antibiotic resistant infections have become common place and a serious threat to health and society. There is now an urgent requirement for the discovery of new antibiotics and in particular those with unexploited mode of action. This thesis details the different areas of natural product drug development from discovery through to analogue generation. In Chapter one, the history of natural products as therapeutics is explored with a particular focus on antibiotics and how resistance arises against these agents. It outlines why the discovery of new antibiotics is so important and new methods used to facilitate this search. Chapter two follows with the development of a screening platform for antibiotic induction, using the model Streptomyces; Streptomyces coleiolor M145. A variety of culture additives are explored for their ability to induce secondary metabolism production. Chapter three then details the sampling and identification of microbes from a pseudo-marine environment and their screening for their ability to produce secondary metabolites with antibiotic properties. The second half of this thesis centres on the non-ribosomal peptide echinomycin. Collaborators Aquapharm supplied the marine derived strain AQP-4895, capable of producing echinomycin. Chapter four details the establishment of AQP-4895 culturing conditions and the shift observed in production profile. Next Chapter five looks at producing echinomycin analogues through precursor directed biosynthesis. A range of halogenated quinoxaline carboxylic acids are synthesised and fed to AQP-4895, and the respective echinomycin analogues monitored by LC-MS. Chapter Six then aims to direct biosynthesis of the halogenated analogues, using mutasynthesis. Due to the lack of genetic data available surrounding the strain, an unusual approach was taken, using iPCR to create a template for homologous recombination.

The phylogenetic diversity of two continental shelf picoplankton communities was examined by analyzing SSU (16S) ribosomal RNA (rRNA) genes amplified from environmental DNA with bacterial-specific primers and the polymerase chain reaction (PCR). Picoplankton populations collected from the pycnocline (10 m) over the eastern continental shelf of the United States near Cape Hatteras, North Carolina, and surface seawater (10 m) from the western continental shelf of the United States 8 km west of Yaquina Head, Oregon, served as sources of bulk nucleic acids used in this study. A total of 285 SSU rRNA gene clones were analyzed in the two libraries, more than doubling the number previously available from seawater samples. In contrast to previous studies of bacterioplankton diversity from the open-ocean, a large proportion of the rDNA clones recovered in this study (38%) were related to plastid SSU rRNA genes, including plastids from bacillariophyte, prymnesiophyte, cryptophyte, chrysophyte, and prasinophyte algae, as well as a number of unique plastid rRNA gene clones for which no close phylogenetic relatives were discovered. A majority of the bacterial gene clones recovered (72% of bacterial clones) were closely related to rRNA gene lineages discovered previously in clone libraries from open-ocean marine habitats, including the SAR86 cluster (�� Proteobacteria), SAR83, SAR11, and SAR116 clusters (all �� Proteobacteria), the marine Gram-positive cluster (Actinomycetes), the marine group A/SAR406 cluster, and a cluster of environmental clones within the flexibacter-cytophaga-bacteroides phylum. A majority of the remaining bacterial clones were phylogenetically related to the �� and �� subclasses of the Proteobacteria, including an rDNA lineage within the Type I methylotroph Glade of the �� subclass. The abundance of plastid rDNAs and the lack of cyanobacterial-related clones, as well as the presence of �� Proteobacteria, are features of these coastal picoplankton gene clone libraries which distinguish them from similar studies of oligotrophic open-ocean sites. Overall, however, these data indicate that a limited number of as yet uncultured bacterioplankton lineages, related to those previously observed in the open-ocean, can account for the majority of cells in these coastal marine bacterioplankton assemblages. / Graduation date: 1998

No description available.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 147-160). / Predatory bacteria are ubiquitous in aquatic environments and may be important players in the ecology and biogeochemistry of microbial communities. Three novel strains belonging to two genera of marine flavobacteria, Olleya and Tenacibaculum, were cultured from coastal sediments and found to be predatory on other bacteria on surfaces. Two published species of the genus Tenacibaculum were also observed to grow by lysis of prey bacteria, raising the possibility that predation may be a widespread lifestyle amongst marine flavobacteria, which are diverse and abundant in a variety of marine environments. The marine flavobacterial clade is known to include species capable of photoheterotrophy, scavenging of polymeric organic substances, pathogenesis on animals, the degradation and lysis of phytoplankton blooms and, now, predation on bacterial communities. Strains from the two genera were found to exhibit divergent prey specificities and growth yields when growing predatorily. Olleya sp. predatory cells accumulated to an order of magnitude greater cell densities than Tenacibaculum sp. cells on equivalent prey cell densities. Experiments were conducted to constrain the potential of the novel isolates to affect prey communities under more environmentally relevant conditions. An investigation of the minimum number of predatory cells needed to generate clearings of prey cells found that the inoculation of individual predatory flavobacteria cells can ultimately result in dense lytic swarms. In some cases, the susceptibility of particular prey species to lysis by a flavobacterial predator was found to vary based on the growth state of the prey cells or the presence of their spent growth media. A novel methodology for the experimental study of biofilms was used to assess the impact of exposure to predatory marine flavobacteria on the release of macronutrients from prey biofilms. The Olleya sp. predator had a stimulative effect on macronutrient release while the Tenacibaculum sp. did not, further suggesting the two groups of predators are adapted to different ecological niches. / by Erin C. Banning. / Ph.D.

Thesis (Ph. D.)--University of Hawaii at Manoa, 1995. / Includes bibliographical references (leaves 125-127). / Microfiche. / xii, 151 leaves, bound ill. 29 cm

A variety of aquatic bacteria were isolated and tested for their ability to degrade humic substances and their aromatic residues/monomers which serve as precursors of the trihalomethanes (THMs) found in chlorinated drinking waters. The majority of them were Gram-negative, oxidative types dominated by pseudomonads. Most of the 146 isolates were found to utilize as their sole source of carbon several or more of ten aromatic compounds known to be products of degradation of humus and also to be precursors of THMs. The aromatics tested, with percent of the isolates utilizing the compound in parentheses, were: p-hydroxybenzoate (49), vanillic acid (48), 3,5-dihydroxybenzoic acid (16), syringic acid (19), vanillin (30), benzoic acid (27), ferulic acid (34), resorcinol (9), catechol (8) and protocatechuic acid (27).

En environnement marin, la colonisation des surfaces solides par les microorganismes est progressive et suit une logique taxonomique et/ou fonctionnelle des espèces. Les biofilms ainsi formés représentent des systèmes multi-cellulaires entourés d’une matrice de substances polymériques extracellulaires (SPE). L’objectif de ce travail était de comprendre comment des acteurs microbiens (bactéries et diatomées) interagissent dans deux types de biofilms marins (biofilm benthique et biofilm sur structures métalliques portuaires). Dans cette étude, des modèles bactériens isolés de ces biofilms ont été identifiés et caractérisés. Dans un premier volet, leur capacité à former des biofilms stables a été évaluée dans différentes conditions. Quatre souches ont été ainsi sélectionnées : Flavobacterium sp. II2003, Roseobacter sp. IV3009, Roseovarius sp. VA014 et Shewanella sp. IV3014. Dans un deuxième volet, les effets des sécrétomes des bactéries marines issues du même habitat ont été évalués sur ces modèles. Deux souches se distinguent par leur capacité à produire des molécules influençant négativement la formation de biofilms : Pseudoalteromonas sp. IIIA004 produit un peptide de 2224 Da présentant une activité antibiofilm vis-à-vis de Roseovarius sp. VA014 et Pseudomonas sp. IV2006 inhibe la formation de biofilm de Flavobacterium sp. II2003. Dans les deux cas, les antibiofilms sont actifs contre un large spectre de bactéries suggérant ainsi plusieurs applications potentielles dans les domaines marin et médical. Dans le dernier volet, les effets des sécrétomes de la diatomée Navicula phyllepta ont été évalués sur les modèles de bactéries benthiques. Cette diatomée s’est distinguée par sa capacité à sécréter des polysaccharides inhibant ou stimulant la formation de biofilms selon les souches cibles. / In the marine environment, solid surface colonization by microorganisms is progressive and follows a taxonomic and/or functional logic. Biofilms formed are multi-cellular systems surrounded by a matrix of extracellular polymeric substances (EPS). The objective of this work was to understand how microbial actors (bacteria and diatoms) interact in two types of marine biofilms (benthic biofilm and biofilm on metallic structures of a harbor). In this study, bacterial models isolated from these biofilms have been identified and characterized. In a first part, their ability to form stable biofilms was evaluated under various conditions. Four strains were selected: Flavobacterium sp. II2003, Roseobacter sp. IV3009, Roseovarius sp. VA014 and Shewanella sp. IV3014. In a second part, the effects of secretomes of the marine bacteria from the same habitat were evaluated on these models. Two strains are distinguished by their ability to produce molecules negatively influencing biofilm formation: Pseudoalteromonas sp. IIIA004 produces a 2224 Da peptide with an antibiofilm activity toward Roseovarius sp. VA014 and Pseudomonas sp. IV2006 inhibits the biofilm formation of Flavobacterium sp . II2003. In both cases, the antibiofilms are active against a broad spectrum of bacteria suggesting several potential applications in marine and medical fields. In the last part, the effects of secretomes of the Navicula phyllepta diatom were evaluated on benthic bacteria models. This diatom was distinguished by its ability to secrete polysaccharides stimulating or inhibiting biofilm formation by target strains.