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Dissertations / Theses on the topic 'Marine microbiology'
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Prüße, Elmar Alexander [Verfasser]. "Scalable bioinformatic methods and resources for ribosomal RNA gene based studies / Elmar Alexander Prüße. Max Planck Institute for Marine Microbiology. International Max PlanckResearch School of Marine Microbiology." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2012. http://d-nb.info/1035218291/34.
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Lane, Eileen. "Bacterial associations with commercially important marine bivalves." Thesis, University of Glasgow, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.388539.
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Davis, Claire Louise. "Physiological and ecological studies of mannitol utilizing marine bacteria." Doctoral thesis, University of Cape Town, 1985. http://hdl.handle.net/11427/7595.
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Bibliography: leaves 166-191Bacteria were isolated from the kelp beds on the West Coast of South Africa. Strains isolated from the water column and kelp fronds were classified as Pseudomonas, Vibrio, Acinetobacter and Flavobacterium species. Bacterial diversity in adjacent kelp dominated habitats was examined using numerical analysis, and it was found that nearshore and offshore isolates were similar, whereas bacteria isolated from beached kelp and interstitial waters were dissimilar from them and from each other. Changes in numbers of bacteria able to form colonies on plates were monitored during upwelling and downwelling conditions.
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Duhaime, Melissa Beth [Verfasser]. "Exploring the Marine Virosphere: From Genome Context to Content / Melissa Beth Duhaime. Max Planck Institute for Marine Microbiology." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2012. http://d-nb.info/1035020165/34.
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Miller, Lorna. "Interaction of copper and organotin with marine bacteria." Thesis, University of Edinburgh, 1985. http://hdl.handle.net/1842/15387.
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McGowan, Veronica. "Detection, isolation and characterization of marine methanotrophs." Thesis, University of Warwick, 1992. http://wrap.warwick.ac.uk/73519/.
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In order to investigate the occurrence of methanotrophs in the marine environment, representative organisms have been isolated from seawater. As traditional methods for isolating and cultivating methanotrophs were found to be unsuccessful when applied to the marine environment, new techniques for methanotroph isolation were developed. These were used to enrich for methanotrophs in several marine areas. Two bacteria isolated from marine areas have been extensively characterized. Both isolates appear to be typical of Type I methanotrophs and have an absolute requirement for sodium chloride. The nitrogen assimilation of the isolates was studied in detail. Both isolates appear to have unusual nitrogen assimilation pathways. A method for detecting methylotrophs and methanotrophs without cultivation has also been developed. The polymerase chain reaction has been adapted to amplify DNA sequences specific to methylotro~ls and methanotrophs. This has been used to detect amplify DNA sequences in DNA extracted from water samples from a range of fresh water and marine environments. The methods has been demonstrated to be specific for methylotrophic and methanotrophic DNA. DNA from non-methylotrophic bacteria was not amplified. Initial studies on the application of this method for enumeration has also been studied. An investigation into the occurrence of methanotrophs in the Southern Ocean was also carried out. Methanotrophic activity was examined in two areas of the Southem Ocean. This was compared with the methane concentration in the water and total bacterial activity.
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Sepulveda, Blanca Perez. "Molecular basis of cyanphage resistance in marine Synechococcus." Thesis, University of Warwick, 2015. http://wrap.warwick.ac.uk/77568/.
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Marine phytoplankton are responsible for ~50 % of global primary production and encompass a wide range of microorganisms characterized by being phototrophs. Within this group are the marine picocyanobacteria encompassing the phylogenetically closely related genera Synechococcus and Prochlorococcus. Bacteriophage lysis, as well as grazing by eukaryotic protists, play central roles as the major biotic causes of Synechococcus mortality in pelagic systems. However, Synechococcus populations show no extinction, suggesting high rates of production counteract this mortality, or that specific bacteriophage resistance and prey-selectivity mechanisms exist. This thesis set out to determine the molecular basis of cyanophage resistance in marine Synechococcus, using previously isolated cyanophage resistant Synechococcus sp. WH7803 mutants. Whole genome sequencing (WGS) analysis revealed that these cyanophage-resistant Synechococcus sp. WH7803 mutants, as well as a re-sequenced wild type strain, possessed a distinctive mutation profile, with a high number of mutations present in each mutant and with mutations present at a variable frequency. Such a profile is in stark contrast to what was recently found in Prochlorococcus where specific mutations could be identified at 100 % frequency (Avrani et al., 2011). The mutation profile of Synechococcus sp. WH7803 prevented the precise identification of specific genes involved in cyanophage resistance in this strain. This profile was hypothesised to be related to Synechococcus sp. WH7803 being an oligoploid organism, i.e. possessing more than one chromosome copy. Indeed, a qPCR assay that was optimised showed this strain possesses on average four chromosome copies. Subsequent isolation and WGS characterisation of cyanophage resistant mutants from the monoploid strain Synechococcus sp. WH7805 revealed a completely different mutation profile, most similar to that previously described for Prochlorococcus. This identified mutations in a single gene, encoding a possible glycosyltransferase, that were confirmed by Sanger sequencing, as being potentially responsible for cyanophage resistance in this strain.
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Pearman, John K. "Molecular ecology and transcriptomics of marine photosynthetic picoeukaryotes." Thesis, University of Warwick, 2012. http://wrap.warwick.ac.uk/45785/.
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Photosynthetic picoeukaroytes (PPEs), defined here as single celled organisms <3 μm in diameter, are significant contributors to primary production. Until recently, marine PPEs had received relatively little research attention in contrast to the more numerous picocyanobacteria. Molecular studies have now started to reveal the diversity of this group, using both the nuclear 18S rRNA gene and the plastidtargeted 16S rRNA gene as taxonomic markers. The latter marker has the advantage of directly targeting the PPE community, counteracting the problem of heterotrophic sequences dominating clone libraries. As well as PCR based molecular approaches, genomic studies of PPEs are starting to reveal the metabolic capabilities of these organisms. In this thesis, taxonomic information obtained on two flow-sorted PPE populations (Euk-A and Euk-B) showed that pico-prymnesiophytes, largely representing lineages with no close cultured counterpart, dominated the Euk-A and Euk-B libraries (54 and 58%, respectively) in tropical and sub-tropical waters of the Atlantic Ocean. Radiotracer work performed elsewhere had shown these PPE groups contribute up to 19% and 38% (Euk-A and Euk-B, respectively) to total CO2 fixation, demonstrating the importance of these PPE groups in marine carbon cycling. To further assess the taxonomic composition and distribution of these Euk-A and Euk-B PPE populations at the ocean-basin scale, clone libraries were constructed along an Atlantic Meridional Transect (AMT18). Major components of these flow cytometry sorted PPE populations were Prymnesiophyceae and Chrysophyceae using plastid markers, or Prasinophyceae and Dinophyceae (nuclear markers) including several lineages with no cultured counterparts. In surface waters a latitudinal diversity gradient was observed with a peak in PPE diversity found in the equatorial region. Distribution patterns of specific PPE groups and OTUs were subsequently correlated with measured environmental parameters, although most of the variation in PPE diversity was not explained by the measured variables. Attempts were undertaken to obtain into culture novel PPEs, especially those representative of oligotropic regions. However, the majority of isolates obtained were related to Prasinoderma or Chlorella which are cosmopolitan, fast-growing genera. Even so, some isolates more relevant of open ocean environments were obtained, including a clade VIIA prasinophyte and a Pelagomonas sp. Trancriptomics was used to further assess the functional potential of specific PPE populations, firstly in cultures using both an Ochromonas sp. and a prasinophyte as being representative of organisms present along AMT18. This approach revealed a C4 carbon concentrating mechanism in the clade VIIA prasinophyte and enzymes required for a functioning urea cycle in the Ochromonas sp. A pipeline was also developed to undertake a metatranscriptomic approach on a flow cytometrically sorted PPE population from the south Atlantic gyre. This approach revealed a diatom-like C4 carbon concentrating system in the metatranscriptome. Overall, this thesis has given new insights into the diversity of specific PPE groups at the ocean basin-scale, developed a new pipeline for the transcriptomic analysis of PPEs both in culture and in the environment, and in so doing has provided new information on the functional potential of these important photosynthetic organisms.
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Fuller, Nicholas Jonathon. "Molecular approaches to the study of marine cyanophages." Thesis, University of Warwick, 1998. http://wrap.warwick.ac.uk/81090/.
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Cyanophages are thought to play an important role in the mortality and clonal composition of marine Synechococcus spp., and have been shown to be widespread throughout the world's oceans. However, relatively little research has been made into the molecular analysis of marine cyanophages. This study continued previous research to develop molecular probes (PCR primers) which would specifically detect cyanophages which infect marine Synechococcus spp., and be used to interrogate natural marine cyanophage populations. An attempt was made to develop a rapid technique for quantifying marine cyanophages, using competitive PCR (cPCR). For the development of cyanophage-specific PCR primers, several cyanophages which infected Synechococcus sp. strains WH7803 and WH80 18 were isolated from coastal Bermuda and the Sargasso Sea. A region of DNA had previously been found which showed homology amongst several marine cyanophages, and to T4 gene 20, which encodes a minor capsid protein. Homologues from three cyanophages were completely sequenced, and two, potentially cyanophage-specific, PCR primers were designed. The primers detected only marine cyanophages which belonged to the family Myoviridae, regardless of the geographical location of their isolation. They also detected cyanophages which infected different marine Synechococcus spp. strains, and therefore provide a more comprehensive tool than infective methods. The primers were able to detect as few as 190 cyanophages Ilr1, which would correspond to an in situ concentration of 103 PFU mH. The PCR should therefore detect most natural concentrations of marine cyanophages in surface waters, especially with prior concentration from seawater. Preliminary experiments showed that PCR products could be obtained from as little as I III of un concentrated seawater. PCR therefore provides a sensitive method for the detection of marine cyanophages, which is far more rapid than traditional infection techniques. Quantification by cPCR was attempted. An internal competitor was constructed, and a calibration curve was drawn for three cyanophages, with a loglinear relationship over ca. three orders of magnitude of cyanophage numbers. This demonstrates that rapid quantification of a known marine cyanophage is possible. However, cPCR of the three different cyanophages resulted in three different calibration curves. Hence, quantification of a marine sample containing a mixture of cyanophages was not yet possible. The cyanophage-specific primers were then applied to marine samples which were collected whilst on the AMT-2 cruise, from Port Stanley (Falkland Islands) to Plymouth (UK). Cyanophages were concentrated by tangential flow filtration, and PCR products were obtained from most of the surface samples throughout the Atlantic Ocean. Products from some of the stations were sequenced, providing novel genetic information of natural marine cyanophage populations. The results showed that cyanophage populations were highly diverse, with at least twelve genetically different cyanomyoviruses in one sample. Some sequences obtained from the same sample were clearly very similar to each other, whilst others within a sample could be as diverse as those isolated from different oceans. However, very similar sequences were obtained from some samples separated by thousands of miles, in different hemispheres, or even in different oceans.
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Schuster, Ute. "Microbial methane oxidation in marine sediment around intertidal gas seeps." Thesis, University of Essex, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.241218.
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Castillo, de la Peña Yaiza M. "Interactions between marine picoeukaryotes and their viruses one cell at a time = Interacciones entre picoeucariotas marinos y sus virus célula a célula." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/668341.
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Marine viruses are key components of marine microbial communities, as they influence the cellular abundances and the community structure of microbes, participate in their genetic exchange, and intervene in the ocean biogeochemical cycles. Most studies dealing with the role of viruses in the marine environment have been done from a bulk community point of view, but going from the bulk community perspective to specific virus─host relationships is essential in order to understand the role of viruses in shaping a determined host community, in modifying host genomes, and ultimately in the release of organic compounds from the lysed cells. For this reason, in this thesis we implemented and applied different methodologies that are able to detect, visualize and quantify virus─host interactions in marine eukaryotes at the single cell level. We focused on picoeukaryotes (cells <3 µm) because they play crucial roles in marine food webs and biogeochemical cycles, and virus─host interactions in natural populations of these minute eukaryotes are largely unknown.
In the first chapter we combined previously developed techniques, used to assess prokaryotic host─phage interactions, to implement VirusFISH for detecting specific virus─host dynamics, using as a model system the photosynthetic picoeukaryote Ostreoccocus tauri and its virus OtV5. With the VirusFISH technique, we could also monitor the infection, as well as quantify the free viruses produced during the lysis of the host in a non-axenic culture, which allowed the calculation of the burst size. This study set the ground for the application of the VirusFISH technique to natural samples.
In the second chapter of this thesis, we applied VirusFISH to seawater samples from the Bay of Biscay (Cantabrian Sea) to study the dynamics of viral infection in natural populations of Ostreococcus along a seasonal cycle. We were able to quantify the percentage of cells infected over time, and compared these results with the transcriptional viral and host activities derived from metatranscriptomic data. This constitutes the first study where a specific viral─host interaction has been visualized and monitored over time in a natural system.
Picoeukaryotes in the ocean are prevalently uncultured, and thus, in the third chapter of this thesis we went an step further to unveil novel viral─host relationships in eukaryotic uncultured hosts. For this purpose, we mined single amplified genomes (SAGs) of picoeukaryotes obtained during the Tara Oceans expedition for viral signatures. We found that almost 60% of the cells analyzed presented an associated virus with narrow host specificity. Some of the viral sequences were widely distributed and some geographically constrained, and they were preferentially found at the deep chlorophyll maximum. Moreover, we found a mavirus virophage potentially integrated in four SAGs of two different lineages, suggesting the presence of virophages is more common than previously thought.
In summary, in this thesis we have implemented and used techniques that allow us to detect and monitor specific virus─host interactions, which is one of the major challenges in marine viral ecology. On the one hand, VirusFISH arises as a powerful technique that can be easily adapted to any host─virus system that has been genome-sequenced. On the other hand, the results obtained with the single cell genomics offer the opportunity to formulate hypothesis based on detected viral─host interactions in uncultured prevalent marine picoeukaryotes, which can be later tested using experimental approaches.Se han realizado muchos estudios sobre el rol de los virus en ambientes marinos desde el punto de vista de comunidad global, pero es esencial que vayamos hacía una visión más específica de relación virus─hospedador. Por ello, en esta tesis implementamos y aplicamos diferentes metodologías para estudiar interacciones virus─hospedador, centrándonos en picoeucariotas marinos ya que se conoce muy poco de ellos en poblaciones naturales. En el primer capítulo implementamos la técnica VirusFISH, permitiendo detectar dinámicas específicas virus─hospedador eucarióticos, usando como modelo Ostreococcus tauri y su virus OtV5. VirusFISH permitió monitorizar la infección, cuantificar en un cultivo no axénico los virus libres producidos durante la lisis y calcular el tamaño de explosión. Este estudio estableció la base para la aplicación de VirusFISH en muestras naturales. En el segundo capítulo aplicamos VirusFISH en muestras de agua natural para estudiar las dinámicas de infección en Ostreococcus. Cuantificamos el porcentaje de células infectadas durante un ciclo estacional y lo comparamos con las actividades transcripcionales de virus y Ostreococcus spp. Este constituye el primer estudio donde se visualiza y monitoriza una interacción específica virus─hospedador en el tiempo en un sistema natural. En el tercer capítulo descubrimos nuevas relaciones virus─hospedador en células no cultivadas, analizando genomas amplificados individuales de picoeucariotas, encontrando que la mayoría de las células presentaron al menos un virus. Estas secuencias víricas se encontraron preferentemente en el máximo profundo de clorofila, algunas de ellas ampliamente distribuidas por los océanos y otras constreñidas geográficamente. Además, encontramos un virofago mavirus potencialmente integrado en dos linajes distintos, sugiriendo que los virofagos son más comunes de lo que se pensaba. En resumen, hemos implementado y usado técnicas que nos han permitido detectar y monitorizar interacciones específicas virus─hospedador, uno de los mayores retos en la ecología microbiana marina. Por un lado, VirusFISH surge como una técnica potente que puede ser fácilmente adaptada a cualquier sistema virus─hospedador del cual tengamos el genoma secuenciado. Por otro lado, los resultados obtenidos con la genómica de célula individual muestran la oportunidad de formular hipótesis basadas en interacciones virus─hospedador detectadas en picoeucariotas marinos no cultivados, que pueden ser posteriormente testadas mediante aproximaciones experimentales.
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Fuller, Andrew Kenneth Radburne. "The grazing and growth rates of some marine protozoa measured in batch and continuous culture with particular reference to the heterotrophic dinoflagellate Oxyrrhis marina." Thesis, Royal Holloway, University of London, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325771.
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Montero, Rocha Ana Bertha. "Studies on bacterial infections in marine crustaceans, with emphasis on Vibrio harveyi." Thesis, Heriot-Watt University, 1998. http://hdl.handle.net/10399/1189.
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Grébert, Théophile. "Pigment diversity in marine Synechococcus sp. : molecular basis, evolution and ecological role." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066614/document.
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Les picocyanobactéries marines Synechococcus sont les seconds organismes photosynthétiques les plus abondants sur Terre. Elles présentent une grande diversité pigmentaire du fait de différences dans la composition de leur antenne collectrice de lumière (phycobilisome), ce qui leur permet d'utiliser efficacement une grande partie du spectre lumineux. Cependant, l'évolution, l'écologie et les bases moléculaires de cette diversité restent mal comprises. La comparaison d'une région génomique impliquée dans la synthèse des phycobilisomes de 54 souches et de populations naturelles m'a permis de proposer un scénario pour l'évolution des différents types pigmentaires et de montrer que cette diversité pigmentaire précède la diversification des Synechococcus marins. J'ai ensuite développé une procédure bioinformatique pour quantifier l'abondance relative de tous les types pigmentaires connus à partir de métagénomes. Appliquée aux données de Tara Oceans, cela m'a permis de décrire leur répartition à l'échelle mondiale, révélant que l'acclimatation chromatique de type IV, qui permet aux cellules de modifier leur spectre d'absorption en fonction de la couleur de la lumière, domine les populations naturelles de Synechococcus, et que des mutants naturels de l'acclimatation chromatique prévalent dans les étendues oligotrophes de l'océan Pacifique sud. Enfin, la caractérisation génétique de deux membres d'une famille d'enzymes liant les pigments à la phycoérythrine II, constituant majeur des phycobilisomes, a apporté de nouvelles perspectives sur les bases moléculaires de l'acclimatation chromatique et révélé l'importance des variations alléliques dans la diversité des types pigmentairesMarine Synechococcus are the second most abundant photosynthetic organisms on the planet. These picocyanobacteria present very diverse pigmentations due to differences in the composition of their light-harvesting antenna (phycobilisome), allowing them to efficiently exploit a wide range of spectral niches. Yet, the evolution, ecology and molecular bases of the different Synechococcus pigment types are not well understood. By comparing the genomic regions involved in the synthesis of phycobilisome rods from 54 sequenced isolates spanning all cultured pigment types and from natural Synechococcus populations, I proposed a scenario for the evolution of the different pigment types and showed that the pigment diversity of marine Synechococcus predates the diversification of this genus. Then, I developed a bioinformatic pipeline for reliably quantifying all known Synechococcus pigment types from metagenomes. Applying it to the Tara Oceans dataset allowed me to describe for the first time their distribution in the global ocean and revealed that type IV chromatic acclimation, a process by which cells can match their absorption properties to the ambient light colour, is widespread and constitutes the dominant pigmentation in Synechococcus populations. It also showed that natural chromatic acclimation mutants prevail in wide oligotrophic areas of the southern Pacific Ocean. Finally, I genetically characterized two members of an enzyme family binding chromophores to phycoerythrin-II, a major component of phycobilisomes. This provided new insights into the molecular bases of chromatic acclimation and revealed the importance of allelic variation for the diversity of pigment types
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Smith, Alastair F. "How do marine bacteria respond to nutrient limitation? : a lipidomics approach." Thesis, University of Warwick, 2017. http://wrap.warwick.ac.uk/95214/.
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Microbes inhabiting surface waters of the Earth’s oceans are exquisitely adapted to their nutrient-poor environment. Marine phytoplankton, for example, are able to reduce their requirements for phosphorus by replacing membrane phospholipids with alternative non-phosphorus lipids. Heterotrophic bacteria, which can also thrive when phosphorus is scarce, had not, however, been shown to carry out this process – seemingly placing these organisms at a competitive disadvantage. In this thesis, I show that substitution of membrane phospholipids for a variety of non-phosphorus lipids is a conserved response to phosphorus deficiency amongst phylogenetically diverse marine heterotrophic bacteria. By deletion mutagenesis and complementation in the model marine bacterium Phaeobacter sp. MED193 and heterologous expression in recombinant Escherichia coli, I confirmed the roles of a phospholipase C (PlcP) and a glycosyltransferase in lipid remodelling. Analyses of two large collections of marine metagenomes, the Global Ocean Sampling (GOS) and Tara datasets, demonstrate that PlcP is particularly abundant in areas characterised by low phosphate concentrations. To better understand the lipids that potentially replace phospholipids during this remodeling process, I investigated a number of poorly-characterised aminolipids that are prevalent in the globally important marine Roseobacter group. I was able to identify two genes involved in the synthesis of one of these lipids, a glutamine lipid. Subsequent phylogenetic analysis of one of these genes revealed that the capacity to synthesise glutamine lipid appears to be virtually ubiquitous within the Roseobacter group. A further class of aminolipids was present in many Roseobacter strains, which I identified as a novel class of homotaurine-containing lipids using high-resolution, accurate mass spectrometry. These homotaurine lipids were detected in a battery of Roseobacter strains, enabling me to employ a comparative genomics approach to identify genes potentially involved in their biosynthesis. Surprisingly, neither of these aminolipids appeared to play an important role in the response to phosphorus limitation in the Roseobacter strains tested. Together, these results point to a key role for lipid substitution as an adaptive strategy enabling heterotrophic bacteria to thrive in vast, phosphorus-depleted areas of the ocean. Although phosphorus-free lipids play a crucial role in this process of adaptation, my work emphasises that many of these lipids are not simply substitutes for phospholipids but rather appear to have important roles in the cell in their own right.
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H, Boström Kjärstin. "Nitrogen fixation among marine bacterioplankton." Doctoral thesis, Högskolan i Kalmar, Naturvetenskapliga institutionen, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:hik:diva-24.
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While bacterioplankton indisputably control vital biogeochemical paths in the cycling of carbon and nutrients in the world’s oceans, our knowledge about the functional and genetic diversity of bacterioplankton communities is negligible. In this thesis, molecular and more traditional microbiological methods were used to study the specific function of N2-fixation and in a general sense diversity of marine bacterioplankton species. Most oceans are nitrogen limited and, therefore, adaptive to bacterioplankton capable of N2-fixation. Recent studies have found nifH genes (coding for the nitrogenase enzyme) related to diverse heterotrophic bacteria in oceanic seawater samples indicating that, along with cyanobacteria, also heterotrophic bacteria benefit from N2-fixation. Here, molecular and cultivation methods were used to examine diazotrophic bacterioplankton in the Baltic Sea. We successfully isolated heterotrophic N2-fixing bacteria belonging to the γ-proteobacterial class by means of low-nitrogen plates and semi-solid diazotrophic medium tubes. The isolates required low-O2 conditions for N2-fixation. Using Real-time PCR it was found that heterotrophic bacterioplankton carrying the nifH gene was abundant (3 x 104 nifH gene copies L seawater-1) at locations in the Southwest Baltic proper. With the aim to identify the main N2-fixing organisms in Baltic Proper surface waters, a clone library of nifH gene transcripts (RNA) was generated. Clone inserts were exclusively related to Aphanizomenon sp. and Nodularia sp. Using quantitative real-time PCR it was found that the nifH gene expression from Nodularia sp. was highly variable between stations in the Baltic Proper but was 10-fold higher during mid summer relative to early summer and fall. A diel study showed a 4-fold increase in Nodularia transcript concentrations at early to mid day relative to rest of the day. Real-time PCR was found to be a powerful and highly sensitive method for measuring gene expression. Since nucleic acids are a prerequisite for molecular analyses of bacterioplankton dynamics a protocol to extract DNA from seawater samples was developed with the aim to maximize the yield of high-quality DNA. Each step in the protocol was important for the efficiency of extraction. The obtained extraction efficiencies were up to 92% for seawater samples and up to 96% for isolates. The protocol provides a guideline for DNA extraction from seawater samples for other studies. In a global sampling campaign (9 locations from polar, tropical and temperate regions) we sampled DNA from surface water and constructed 16S rRNA gene libraries to investigate diversity and biogeography of bacterioplankton. Approx. 80% of the sequences found were similar to sequences already deposited in GenBank, indicating that a large fraction of the marine bacterioplankton already has been sampled, which in turn suggests a limited global bacterioplankton diversity. This thesis have improved our knowledge about the composition and nifH gene expression of the diazotrophic bacterioplankton community in the Baltic Sea and contribute significantly to the discussion on global marine bacterioplankton diversity and biogeography.Östersjön är ett av världens största brackvattensystem. Den ekologiska balansen i detta hav är hotad på grund av övergödning. Mycket arbete har därför fokuserats på att reducera utsläppen av näringsämnen, speciellt kväve. Dessa ansträngningar kan dock motverkas av bakterier som har förmåga att omvandla luftens kväve till metaboliskt användbart ammonium (kvävefixering). På sommaren är Östersjöns primärproduktion begränsad av kväve, med följden att det årligen uppstår massiva blomningar av kvävefixerande bakterier, framför allt cyanobakterier. Dessa är främst Aphanizomenon och Nodularia, men inte endast de fototrofa cyanobakterierna har förutsättningar att fixera N2. NifH gener (genen som kodar för nitrogenas) bärs också av heterotrofa bakterioplankton, vilket har visats i studier i främst Atlanten och Stilla havet. Med hjälp av två olika odlingsmetoder lyckades vi isolera heterotrofa kvävefixerande bakterier tillhörande klassen γ-proteobakteria från Östersjön. Svårigheten med att finna dessa bakterier ligger i att de kräver en miljö med mycket låg syrehalt för att kunna fixera kväve. Resultaten från denna studie ledde oss vidare till att undersöka vilka organismer som uttrycker nifH genen (och då troligen även fixerar kväve) i Östersjön. En av de bakterier som isolerats kunde påvisas med Realtids PCR i ett relativt stort antal (3 x 104 nifH genkopior per liter) vid en av de ursprungliga provtagningsstationerna. För att söka rätt på de olika organismtyper som uttrycker nifH skapades ett klonbibliotek baserat på mRNA extraherat från havsvatten. Det visade sig då att alla de närmare 100 kloner som sekvenserades tillhörde antingen Aphanizominon eller Nodularia. De heterotrofa bakteriernas nifH genuttryck var troligen i jämförelse med dessa cyanobakterier alltför lågt för att kunna detekteras. Realtids PCR mätningar av Nodularias nifH genuttryck visade på en stor variation mellan de olika provtagningsstationerna samt mellan de olika provtagningstillfällena. Vi fann dock en kraftig ökning under juli med en nedgång igen i augusti. En dygnscykelstudie visade att Nodularia nifH genuttrycket ökade under förmiddagen med en topp mitt på dagen för att sedan minska igen. Detta troligen med anledning av att den energikrävande kvävefixeringsprocessen sker under de ljusa timmarna då cellen får energi från fotosyntesen. I de molekylärbiologiska metoderna som används för att få information om identitet och aktivitet hos skilda organismer krävs att DNA och RNA kan extraheras från prover tagna i naturliga vattenmiljöer. Även om antalet bakterier tillsynes är högt, så är mängden DNA och RNA per liter havsvatten relativt låg, därför krävs ett väl fungerande protokoll för denna extraktion. I en inledande studie i denna avhandling optimerades en metod för att utvinna DNA. Ett antal sådana protokoll finns publicerade men dessa har ofta lågt utbyte. Det nya protokollet har hög effektivitet, vilket gör att små provvolymer kan användas (2 ml jämfört med tidigare flera liter) och därmed ökar hanterbarheten. Vi visar i denna studie att varje steg 7 i DNA-extraktionsprotokollet är viktigt för att ge en hög effektivitet. Detta protokoll kan med fördel användas som vägledning för många olika typer av studier. På grund av att många havsbakterier inte kan bilda kolonier och alltså inte växa på traditionella medier har det varit svårt att få en klar bild av artrikedomen. Molekylärbiologin har dock gjort det möjligt att identifiera bakterier med hjälp av 16S rRNA genen, en enorm mängd gensekvenser från världens alla hav har inkommit till den gemensamma databanken (GenBank). År 2002 gjordes en studie där man sammanställde informationen i denna databank, för att få en bild av artrikedomen i världshaven. Resultatet av denna studie var att det i världshaven fanns färre bakterietyper än vad många forskare har spekulerat i. I denna avhandlig har vi utfört en studie där vi gjorde en stor global provtagning för att se om denna undersökning överensstämde med den datainformativa. Provtagning från nio lokaliteter gjordes i de tempererade, tropiska och polarhaven. Ett genbibliotek från varje lokal gjordes och kloner sekvenserades. Resultatet visar i likhet med den datainformativa undersökningen på en begränsad artrikedom. 80% av gensekvenserna fanns redan i databanken, vilket tyder på att de flesta arter redan har blivit funna. Dessutom visade det sig att få av bakterierna återfanns på alla ställen och många återfanns endast på ett ställe. Utöver detta visade det sig att det fanns en ökad artrikedom ju närmare ekvatorn man kom, vilket tidigare har visats för större organismer. Studierna i denna avhandling har ökat förståelsen för hur sammansättningen av det kvävefixerande bakteriesamhället i Östersjön ser ut samt bidragit till diskussionen om den globala artrikedomen bland bakterioplakton och dess utbredning.
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Gobet, Angélique [Verfasser]. "Microbial Community Ecology of Temperate Coastal Sands / Angélique Gobet. Max Planck Institute for Marine Microbiology." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2012. http://d-nb.info/1035019701/34.
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Goldsmith, Dawn. "Marine Viral Diversity and Spatiotemporal Variability." Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/5227.
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Marine viruses are the most numerous biological entities in the ocean, with an estimated abundance of 4 x 1030. They merit study not only because of their sheer abundance, but also because of the role they play in the Earth's biogeochemical cycles. Viral lysis of bacteria redirects the flow of nutrients among marine microbes, which ultimately affects the efficiency of the biological pump. Viral diversity is important because most viruses are host-specific. In preying on a certain type of bacteria, viruses affect the diversity and structure of the bacterial community, leading to changes in carbon and nutrient flows. In turn, such variations can alter the amount of carbon dioxide in the Earth's atmosphere. However, studying viral diversity presents challenges. Morphological similarities among many types of viruses make it preferable to use genetic methods of investigation, but the absence of a single gene common to all families of viruses hampers the identification of viruses in environmental samples. Nonetheless, some genes are shared within phage families, and those shared ("signature") genes can be used as markers to identify members of a family. In addition, community profiling methods can fingerprint the diversity of a viral community.
Most previous studies of marine viral communities consist of a single glimpse—a representation of the community at a single time and place, or at a few depths sampled at one time. While the resources required to collect marine samples often make broader or repeated sampling impracticable, without studies conducted over greater time and spatial ranges, our knowledge of marine viral dynamics will remain limited. To gain strides in understanding spatial and temporal variability in marine viral diversity, this dissertation focused on a detailed examination of viral diversity at a single site in the Sargasso Sea. Time and depth intervals for sampling were kept as uniform as possible in order to strengthen the conclusions to be drawn from the research.
The Sargasso Sea is a seasonally oligotrophic portion of the North Atlantic Ocean, characterized by deep convective winter mixing and summer stratification of the water column. A tremendous amount of oceanographic research has been conducted in the Sargasso Sea because it is home to the Bermuda Atlantic Time-series Study (BATS), one of the world's longest-running ocean time series studies. Because of the core monthly measurements made at the BATS site and the vast amount of ancillary research that uses BATS as a platform, the site is an excellent place to study viral diversity. Using a variety of techniques, this research aimed to expand our knowledge of viral dynamics by analyzing the viral community of the Sargasso Sea over a several-year period, through different seasons, and at different depths.
The first chapter developed phoH as a new signature gene for assessing marine viral diversity. The phoH gene is disproportionately present in fully-sequenced marine phage, as opposed to phage isolated from non-marine environments, and is widespread in the marine environment. Diversity of the phoH gene was high, and most of the sequences recovered belonged to phylogenetic groups that did not contain any cultured representatives, indicating that cultured phage isolates do not adequately represent the diversity found in marine environments. Composition of the phoH communities at each sampled location and depth was distinguishable according to phylogenetic clustering, although most phoH clusters were recovered from multiple sites. These factors demonstrate that phoH will be useful for studying marine phage diversity worldwide.
Chapter 2 analyzed the viral diversity of a depth profile at BATS by amplifying and deep sequencing the phoH gene. This comprehensive study of the gene's diversity over three different years, several seasons, and a range of depths from the surface to 1000 m revealed that the viruses at BATS contain a large pool of phoH sequences, but that most of those sequences are rare. The phoH sequences were dominated by just a few operational taxonomic units (OTUs). Rarefaction analysis showed that the sequencing was sufficient to capture the diversity of the gene at BATS, and in fact no new phylogenetic clusters were identified that were not seen in the small amount of Sanger sequencing performed for the initial phoH study in Chapter 1. Some of the more abundant phoH OTUs recurred every season and every year, in varying degrees, although similar depths and seasons clustered together. Overall, the phoH gene revealed depth-based, seasonal, and interannual differences in the diversity of the viral community at BATS.
Chapter 3 continued the extensive examination of viral diversity at BATS by using several signature genes and a fingerprinting technique to assess changes between winter and summer viral communities over two depths in three different years. This chapter investigated whether the annually recurring subsurface peak in viral abundance corresponded to recurring changes in composition of the viral community in the vicinity of the peak. Clustering analysis was used to determine which samples were most similar. The results demonstrated that the viral communities at the surface and at 100 m depth were more similar to each other in winter (March), regardless of the year, than they were in summer (September), when the water column is stratified as opposed to well-mixed. These findings may stem from physical factors such as UV irradiation of viral particles during stratification, as well as seasonal and depth-related differences in host communities associated with the depth of the mixed layer.
This dissertation provides substantial advances to the field of microbial ecology. First, the development of phoH as a signature gene is an important addition to the limited set of tools available for studying marine viral diversity. This research also constitutes the first deep sequencing of a signature gene for marine viruses, providing a guide for the depth of sequencing needed to capture the diversity of a marine viral community and a benchmark for the level of viral diversity to expect in an oligotrophic marine system. Finally, the dissertation expands our knowledge of the viral community at BATS by examining the community based on four different measures of composition, rather than abundance. The research presented here also suggests several avenues of future investigation, including redesigning the phoH primers to expand their scope, sampling the viral community at BATS at the precise depth of the peak in abundance, working to identify the hosts of aquatic gokushoviruses, and culturing and sequencing additional marine viruses in order to improve the reflection of natural environmental communities in genomic databases.
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Yilmaz, Pelin [Verfasser]. "Improving the Usage of ribosomal RNA Gene in Microbiology and Microbial Ecology: Importance of Standardization and Biocuration / Pelin Yilmaz. Max Planck Institute for Marine Microbiology." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2012. http://d-nb.info/1035211068/34.
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Woo, Edward Samuel. "Nucleotide sequence and phylogeny of a plastocyanin gene in the marine diatom, «Thalassiosira oceanica»." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=32418.
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Diatoms are thought to have acquired an Fe-containing cytochrome (cyt) c6 to transfer electrons between cyt b6f and photosystem (PS) I of the photosynthetic apparatus like other chlorophyll a/c-containing phytoplankton. Here we report the isolation and cloning of a plastocyanin gene from Thalassiosira oceanica (CCMP 1005). The gene encoded a Cu-containing protein that is known in other organisms to functionally replace the Fe-containing cyt c6. The inferred protein sequence had the highest identity with the green haptophyte, Emiliania huxleyi, and possessed many of the globular properties necessary for function and interaction with upstream and downstream partners. Eleven strains of oceanic and coastal diatoms were screened for the presence of the plastocyanin gene using degenerate primers: one other species was observed to contain the gene; T. oceanica (CCMP 1006). Phylogenetic analysis of the 5.8 rRNA gene of these species showed that both T. oceanica strains with plastocyanin were closely related to each other. The cloned sequence of T. oceanica (CCMP 1006) contained greater than 80% of the protein-coding region and shared 99% nucleotide identity and 100% conserved unique intronic region. The inferred protein sequence of this species had 100% identity with the inferred protein sequence of T. oceanica (CCMP 1005).Durant l'évolution de la photosynthèse, il est pensé que les diatomées ont acquis cytochrome (cyt) c6, une protéine contenant un atome de Fe, pour le transfert des électrons entre le complexe cyt b6f et le photosystème (PS) I de l'appareil photosynthetique, comme d'autres phytoplanctons ayant les chlorophyll a/c. Ici, nous rapportons l'isolement et clonage du gène de plastocyanin du diatomée Thalassiosira oceanica (CCMP 1005). Le gene codait une protéine contenant un atome de Cu qui est connue de remplacer fonctionellement cyt c6 (contenant un atome de Fe). La sequence inférée de la proteine montrait la plus grande identité avec Emiliania huxleyi, un haptophyte vert (green haptophyte), et possèdait de nombreuses propriétés globulaires nécessaires aux fonctions et intérections avec les protéines partenaires en amont et en aval. Onze espèces de diatomées océanique et côtières ont été examinées pour la présence du gène codant pour plastocyanin en utilisant les amorces dégénérées (degenerate primers): une autre espèce a révélé la présence du gène de plastocyanin; T. ocenica (CCMP 1006). L'analyse phylogénétique des gènes 5.8 rRNA de cet espèce a démontré que la souche de T. oceanica possèdant le plastocyanin sont étroitement reliées entre elles. Les séquences clônées de T. oceanica (CCMP 1006) recelaient plus de 80% de la région cryptant la protéine et partageaient 99% des nucléotides et 100% des régions introniques uniques. La séquence de protéine inférée de ces espèces de phytoplanctons ont démontré 100% d'identité avec celle inférée pour T. oceanica (CCMP 1005).
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Yam, Emily M. "The Role of Bacteria-Particle Interactions in Marine Snow Dynamics." W&M ScholarWorks, 2007. http://www.vims.edu/library/Theses/Yam07.pdf.
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Lindh, Markus. "Role of Different Carbon Sources for Growth, Production and Community Composition of Bacterioplankton." Thesis, University of Kalmar, School of Pure and Applied Natural Sciences, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:hik:diva-149.
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It has been suggested that growth, production and community structure of bacterioplankton are dependent on resource availability. However, previous studies have only investigated the effect of either organic substrate mixtures or a few single organic substrates on the bacterioplankton community. The aims of this study were to investigate the impact of five different relevant carbon sources on the bacterioplankton community. This impact was evaluated comparing treatments on samples taken from Skagerrak and the Baltic Sea, in whole seawater cultures. Analysis of bacterial abundance, bacterial production (as leucine incorporation), bacterioplankton DNA community structure and colony-forming bacteria growing on agar plates were evaluated. Differences between carbon sources in terms of bacterial numbers were relatively small, with strong growth responses for L-amino acids, glucose, acetate and pyruvate with the only exception of glycolate where growth was lower. Bacterial production, on the other hand, presented marked differences, different patterns for each carbon source, especially in the Baltic Seawater. Furthermore, differences in colony size and number of colony forming bacteria in the different treatments were important. The analysis of DNA community from each experiment, by denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rDNA, allowed a visualization of the microbial community structure. Sequencing of the stronger bands on the gel revealed the identity of the dominant bacterial species. In terms of bacterioplankton community structure, differences between carbon sources and between environments were important. One unknown species belonging to gamma-proteobacteria was both unique and dominant for glucose treatment in the Baltic experiment. Another gamma-proteobacteria , a Vibrio was found to specialize in glucose in the Skagerrak experiment. One uncultured bacterium belonging to a alpha-proteobacteria, both unique and dominant was found in glycolate, also this in Skagerrak, another uncultured alpha-proteobacteria was clearly dominant for glucose treatment in Skagerrak. Some bands were also present in most treatments, e.g. uncultured species belonging to bacteroidetes in Skagerrak and beta-proteobacteria in Baltic, suggesting that those species are not specialized in consuming a single carbon source. As a conclusion different carbon sources clearly had an individual but important role for bacterioplankton properties. The properties also showed to be dependent on the environment.
Nr:6355
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Dabrowska, Alicja. "Opening up the black box of marine phototroph-heterotroph interactions." Thesis, University of Warwick, 2017. http://wrap.warwick.ac.uk/102039/.
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Although marine microorganisms drive the major biogeochemical cycles in marine ecosystems, there is a dearth of information on interactions between phototrophic and heterotrophic organisms co-occurring in oceanic waters. The aim of this project was to study these interactions using Synechococcus sp. as the model phototroph – a cosmopolitan and highly abundant member of the picophytoplankton. Heterotrophic bacteria most-frequently present in non-axenic Synechococcus sp. cultures, were identified by PCR screening using primers targeting the 16S rRNA gene. Members of the Nitratireductor, Rhodobacteraceae, Muricauda and Phyllobacteriacae genera were present in more than half of all the cultures tested (Chapter 3). Using a member of the Rhodobacteraceae as the model heterotroph, specific metabolites present in axenic cultures and co-cultures were analysed (Chapter 4). Much lower concentrations of these specific metabolites were present in the milieu of Synechococcus – Roseobacter co-cultures compared to axenic Synechococcus cultures as discovered by LC-MS. Natural product database searches suggest that these may be a group of novel compounds. A Synechococcus sp. WH7803 null mutant in the gene encoding a type III polyketide synthase was constructed (Chapter 5). A targeted exometabolomic analysis showed a decreased production of the metabolites identified above in the mutant strain compared to the wild type. Growth was considerably affected in the T3 PKS mutant and T3 PKS mutant culture supernatants had a stronger negative growth effect on a range of picocyanobacteria and green algal species than the wild type extract. Further research is required to establish the precise biological function of the observed molecules, their biosynthetic pathway and their function in the natural environment. Improving our understanding of interactions between environmentally important microorganisms not only helps us to learn more about how biogeochemical cycles in the ocean function, but can also provide new natural products for use in the pharmaceutical industry.
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Church, Matthew J. "Microbial dynamics and biogeochemistry in the North Pacific Subtropical Gyre." W&M ScholarWorks, 2003. https://scholarworks.wm.edu/etd/1539616610.
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The research presented in this dissertation describes the influence of planktonic bacterial growth on upper ocean organic matter dynamics in the North Pacific Subtropical Gyre (NPSG). Examination of the temporal dynamics in dissolved organic matter (DOM) was coupled with investigations that targeted the influence of heterotrophic bacterial production (HBP) on organic matter fluxes in the NPSG. Nine cruises to the Hawaii Ocean Time-series field site Station ALOHA revealed that HBP accounted for a large flux of organic carbon in the upper ocean of the NPSG. HBP was significantly enhanced by sunlight, with photoenhancement of HBP accounting for 3.2 mol C m-2 yr-1, equivalent to 21% of the annual photoautotrophic production in this ecosystem. These observations suggest that HBP in the upper ocean of the oligotrophic NPSG exerts a large influence over organic matter fluxes in this ecosystem, and that a large fraction of HBP depends on sunlight. Several experiments were conducted to asses the response of heterotrophic protein production to irradiance at Station ALOHA. The results of these experiments revealed that HBP responded to irradiance similar to the response of photosynthesis to irradiance in this ecosystem. Upper ocean HBP increased with light intensity at low light fluxes (<200 mumol quanta m-2 s -1), but saturated or declined with increasing irradiance. Experiments conducted in the upper and lower photic zone revealed significant photoinhibition of bacterial production in the lower photic zone. Overall, the heterotrophic response was similar to the photosynthetic response, suggesting light-driven HBP could result from mixotrophic growth by the photoautotrophic unicellular cyanobacteria Prochlorococcus. Analyses of dissolved organic matter (DOM) inventories from 1988 to 1999 revealed multiyear increases in the inventories of dissolved organic carbon, nitrogen, and phosphorous (DOC, DON, and DOP) in the upper ocean of the NPSG. During the latter half of the observation period, rates of DOP accumulation declined, coincident with significant DOC and DON accumulation. Analyses of bacterial population dynamics between 1992 and 1999 revealed an apparent shift in the abundance of Prochlorococcus during the period of observation. These results suggest that prokaryote population structure directly influences the cycling of organic matter in this ecosystem.
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Church, Matthew J. "Limitation of Bacterial Growth by Dissolved Organic Matter and Iron in the Southern Ocean." W&M ScholarWorks, 1999. https://scholarworks.wm.edu/etd/1539617971.
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Falkenhayn, Carol J. "Growth Rate and Grazing Dynamics of Coccoid Cyanobacteria in the Lower Chesapeake Bay." W&M ScholarWorks, 1990. https://scholarworks.wm.edu/etd/1539617613.
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Muller, Terri A. "Effects of Sunlight and Seasonal Temperature on Persistence of Four Bacteriophages in an Estuarine Environment." W&M ScholarWorks, 1995. https://scholarworks.wm.edu/etd/1539617680.
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Collumb, Christopher J. "Effects of Simulated Sediment Resuspension Events on the Abundance of Water Column Bacteria of Tomales Bay, California." W&M ScholarWorks, 1995. https://scholarworks.wm.edu/etd/1539617681.
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Countway, Peter Dylan. "Carbon Production and Growth Physiology of Heterotrophic Bacteria in a Subtropical Coral Reef Ecosystem." W&M ScholarWorks, 1999. https://scholarworks.wm.edu/etd/1539617745.
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Morgan, Jessica A. "Bacterial Properties and Dissolved Organic Matter Distributions in the Black Sea." W&M ScholarWorks, 2003. https://scholarworks.wm.edu/etd/1539617804.
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Oliver, Jacques L. "Iron and carbon limitation of prokaryotic growth in the ocean." W&M ScholarWorks, 2005. https://scholarworks.wm.edu/etd/1539616797.
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Studies were undertaken to examine the roles of iron and carbon in modulating prokaryotic growth in the ocean. The context of the first study was an open-open iron fertilization experiment in the high nutrient, low chlorophyll (HNLC) regime in the Southern Ocean. The context of the second study was the oligotrophic, iron-replete, and organic carbon-limited northwest Sargasso Sea. Experimental sea water cultures were amended with an iron chelator, desferrioxamine B (DFOB), and other nutrients to examine the effects of iron and carbon limitation on growth. In the first study prokaryotic abundance, carbon production, and growth rate increased in response to iron in two experimental locations north and south of the Antarctic Polar Front Zone (North Patch and South Patch, respectively). However, prokaryotes responded indirectly to iron-induced phytoplankton production. Prokaryotic production was highly correlated to particulate primary production (r2 = 0.80). Prokaryotes comprised a larger percentage of particulate organic carbon (POC) in the North versus the South Patch relative to non-fertilized waters. Analysis of prokaryotic community structure was also examined. Results showed unique prokaryotic communities existed in the North and South Patch for both iron-fertilized and non-fertilized waters. Additionally, community composition shifted over time in the South Patch and was distinct from non-fertilized waters. Measures of community diversity indicated an increase in taxonomic richness and diversity in iron-fertilized waters over time. Specific taxonomic groups monitored over time in the South Patch exhibited a differential response to the iron-induced phytoplankton bloom. at the domain level, the biomass response was greater for Eubacteria compared to Archaea. at the clade level, Cytophaga-Flavobacteria net biomass yields outpaced SAR11, although both exhibited significant increases (p < 0.05) in net growth rate over time in the South Patch. In the second study DFOB did not limit utilization of organic carbon (glucose). Conversely, DFOB stimulated prokaryotic growth in a dose-dependent manner. The trend of the response to DFOB was similar to glucose; however, the magnitude of the response (i.e. growth rate and biomass yield) at higher equivalent carbon doses was greater than that of glucose. Additionally, DFOB and glucose elicited a differential taxonomic response.
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Howard, Katharine Mary. "Carbon metabolism and growth of marine unicellular cyanobacteria belonging to the genus Synechococcus." Thesis, University of Warwick, 1990. http://wrap.warwick.ac.uk/107984/.
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An investigation was made into the carbon metabolism of the marine unicellular cyanobacterium, Synechococcus sp., strain WH7803, in laboratory cultures and natural populations. Synechococcus WH7803 grown in continuous culture, was used to study the effect of different irradiances (10 - 90/iEm‘2s"1) on the growth and photosynthetic characteristics of the organism. Growth saturated at relatively low irradiances (@55/iEm'2s'r). Parameters were measured for photosynthetic relationships, pigment concentrations and total quantities of DNA, RNA and protein present in the cells. Although the photosynthetic maximum was highest in cultures grown at high irradiances, alpha (initial slope) was steeper in low light-grown cultures indicating a higher photosynthetic efficiency in these cultures. The assays for DNA, RNA and protein were used to establish a general pattern of response under the different light conditions. Respiratory rates of batch cultures were measured at different irradiances and the heterotrophic potential of these cultures was tested using an oxygen electrode. No significant alteration in the respiratory rate was observed for a range of organic compounds added to growing cultures in the dark. Trials with two inhibitors to remove heterotrophic microbial activity from natural populations proved insufficiently sensitive for further use. Three studies of natural populations from the North Sea and Celtic Sea were carried out to determine the abundance and distribution of Synechococcus species, and to measure their rates of photosynthesis and other physiological/ ecological properties compared to other phytoplankton. As with laboratory cultures the data indicate that natural populations utilise low irradiances efficiently; however Synechococcus sp., have been found to be equally abundant and productive in the surface mixed layer where they experience high irradiances (1700/iEm*2s‘1). Cellular fractionation of ^C labelled samples was used to determine the physiological consequences of growth at high irradiances. In laboratory cultures the percentage 14C incorporated into protein remains high (@50%), at high and low irradiances, whereas incorporation into the polysaccharide and nucleic acids was typically higher at high irradiances. In natural assemblages the percentage incorporation into protein remained high (@55%) and into polysaccharide and nucleic acids relatively low at @17%. In natural assemblages significantly more label was detected in the lipid fraction.
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Mohammad, Hadi Hussein. "Studies on biosynthesis and activity of antibiotics thiomarinol from marine bacteria." Thesis, University of Birmingham, 2017. http://etheses.bham.ac.uk//id/eprint/7278/.
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Mupirocin (Pseudomonic acid A) has long been used against Methicillin Resistant Staphylococcus aureus MRSA, yet bacteria have developed resistance, threatening future use. Structurally similar to mupirocin is thiomarinol A, a natural compound produced by the marine bacterium Pseudoalteromonas spp, which possesses stronger antibacterial activities. However, it differs from mupirocin by four distinct differences and among these are extra 4-hydroxylation and joining to pyrrothine. Studying these differences should enhance our understanding of the molecular assembly and biosynthesis machinery. Complementation and mutagenesis studies identified the tmuB gene to be responsible for the 4-hydroxylation as a final tailoring step. In vivo and in vitro studies on purified TmuB revealed that it can hydroxylate diverse pseudomonic acids but is inhibited by molecules with an 8-hydroxyl group, which primarily affects catalysis rather than binding. Molecular modelling plus docking and mutagenesis provides increased understanding of both TmuB potential to modify other substrates and how mupirocin activity can be modulated by 4-hydroxylation. This study also expressed holA, purified its gene product, a non-ribosomal polypeptide synthetase (NRPS), and assayed its activity by pyrophosphate release. It presents a proposed pathway for pyrrothine biosynthesis catalysed by HolA, which exhibits the unusual ability to join two cysteine molecules by a single NRPS module.
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Rubelmann, Haydn III. "A Functional Approach to Resolving the Biogeocomplexity of Two Extreme Environments." Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/5432.
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The biodiversity of two distinct marine environments was observed to describe the biogeocomplexity of these extreme ecological systems. A shallow-water hydrothermal vent in Papua New Guinea served as a study of a thermophilic ecosystem influenced by arsenic rich vent fluids while a 60 m deep offshore primarily anoxic karst sink served as a study of an anaerobic sulfur-influenced habitat. Both environments support unique biological communities that are influenced by the physical and chemical pressures imposed on them by the harsh conditions of these systems. In Tutum Bay, Ambitle Isle, Papua New Guinea, a transect was created from a shallow hydrothermal vent that extended 120 m away from the vent. Previous studies have shown that the geochemistry of the system is heavily influenced by arsenic which is toxic to most organisms. In this study, macro- and meiofauna were collected and scored and combined with bacterial sequence data collected along the length of the transect. It was found that near vent sites harbored biological communities more similar than sites further from the vent. Many species were found only at sites near the hydrothermal vent. Near-vent communities were less diverse than those away from the vent, and biodiversity generally increased as distance from the vent increased. Distinct correlations between thermophilic organisms and temperature were observed. The metabolic repertoire of the microbial communities suggests that many strategies are used to obtain energy and carbon. The relative abundance of bacteria containing genes to reduce arsenic was comparable to those able to reduce sulfur compounds. Primary production appeared to be a mix of chemo- and phototrophy. Food webs and association analysis suggest a complex interplay between macrofaunal, meiofaunal and bacterial communities. While the system is heavily influenced by arsenic, no specific correlation between the relative abundance of arsenic metabolizing organisms and the amount of arsenic in the system could be drawn. This is likely due to the fact that most of the arsenic produced by the system is readily adsorbed onto iron oxyhydroxides, reducing the arsenic's bioavailability.
The anoxic conditions at Jewfish sink provide a different hurdle than the hot arsenic conditions found in Papua New Guinea. The anoxic conditions are shared by other pit features found in karst geography, but the metabolic processes between Jewfish sink and these other karst habitats are different. The blue holes and black holes of the Bahamas are some of the most well-studied of these karstic pits. In these features, which are large circular pits with diameters of over 300 m, light and sulfur are used as a means of energy acquisition. Jewfish sink, having an opening only 6 m in diameter, is light restricted compared to these systems. As a result, the strategy of organisms dwelling in the anoxic conditions of the sink is different than those found at the well-studied holes in the Bahamas. Geochemical measurements were recorded over two time periods spanning a combined total of 6 years. The anoxic bottom waters of Jewfish sink remain stable and contained high levels of sulfide throughout most of the seasons studies. Sequence analysis of prokaryotes within the sink showed that sulfur reducers had the highest relative abundance compared to other functional guilds. To monitor the changes of the microbial communities within the sink, bacterial communities were examined at 4 depths within the sink at 9 different intervals over a period of 685 days. Denaturing Gradient Gel Electrophoresis (DGGE) was used to fingerprint 16s rRNA bacterial communities and dissimilatory sulfite reducing communities by targeting the 16s rRNA bacterial gene and the dsr gene associated with dissimilatory sulfite reducing bacteria and archaea. The lowest depth studied within the sink (40 m) remained stable chemically and biologically until a turnover event occurred within the second winter of the study. This turnover event disrupted the biological communities at 40 m and led to a reestablished community comprised of different species that those found prior to the event. Upper waters within the sink show that clines establish themselves seasonally and partition zones that confine bacterial communities that are more similar to each other within these zones while excluding bacterial communities that are outside of these zones. Oxygenated water was shown to not contain prokaryotes containing the dsr gene. As the oxycline changed seasonally, dissimilatory sulfite reducing prokaryotes containing the dsr gene remained in the anoxic zone and required time to reestablish themselves whenever oxygenated water displaced them.
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Rihtman, Branko. "Viral infection of marine picoplankton under nutrient depletion conditions : pseudolysogeny and magic spot nucleotides." Thesis, University of Warwick, 2016. http://wrap.warwick.ac.uk/89873/.
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Cyanobacteria are major players in marine biogeochemical processes, primarily CO2 fixation via oxygenic photosynthesis, and nitrogen cycling. These phototrophs occupy a variety of oceanic niches, with their distribution and abundance being shaped by a range of abiotic (e.g. temperature, light, nutrients) and biotic factors (e.g. grazing and virus infection). Viruses infecting cyanobacteria are termed cyanophage. During evolution these cyanophages have acquired an arsenal of ‘auxilliary metabolic genes’ (AMGs), often horizontally acquired, which can influence the metabolism of the infected host thereby optimising viral production. Cyanophage infection of their host under sub-optimal growth conditions can lead to deleterious effects on infection success. For example, cyanophage S-PM2 infection of Synechococcus under P-deplete conditions causes a delayed latent phase and decreased burst size – a process termed pseudolysogeny. In this thesis I set out to provide a molecular understanding of pseudolysogeny, at the same time hypothesising that specific cyanophage AMGs help to avoid the negative effects of sub-optimal host growth conditions on the infection process. In support of this, infection by cyanophages that possess putative P-stress related AMGs do not show signs of delay (Chapter 3), and the presence of these genes in cyanophage genomes correlates well with the prevailing P conditions in the temporal and spatial niches from which these cyanophages were isolated (Chapter 4). Meanwhile, in a cyanophage lacking such nutrient stress genes, and thus entering pseudolysogeny during infection under P-deplete conditions, transcriptional profiling showed retardation in the timing of known cyanophage temporal gene expression clusters (Chapter 6). Moreover, a significant increase in expression of several cyanophage early genes involved in DNA replication was also observed under these P stress conditions compared to infection of a P-replete host. Quantitation of intracellular cyanophage DNA showed that while levels were generally lower under P-deplete conditions, the rate of DNA replication between P-replete/deplete conditions was similar. The observed increased expression of cyanophage genes involved in DNA replication during the early stages of infection may thus be an evolved response to compensate for decreased levels of intracellular phosphate experienced under these conditions (Chapter 6). Overlaid on top of specific bacterial nutrient stress responses is the ‘stringent’ response, mediated by the alarmone molecule (p)ppGpp, a process which occurs under prolonged nutrient stress and in late stationary phase. A bacterial gene mazG, encodes a pyrophosphatase which participates in (p)ppGpp homeostasis. Interestingly, a mazG orthologue is found as part of the cyanomyovirus core genome, suggesting that cyanophages attempt to alter intracellular signalling during the course of infection. The stringent response has been shown to have a particularly negative effect on phage replication, with (p)ppGpp levels in a cyanobacterial host being previously shown to be dramatically reduced under phage infection. In this thesis I show that the Synechococcus host mazG is dispensable for growth under normal laboratory conditions. However, this Synechococcus mazG mutant shows a modified cyanophage infection profile, slower and less productive, compared to the WT, under P-deplete conditions (Chapter 5). Furthermore, comparison of enzymatic activity of host and cyanophage MazG showed that the viral orthologue exhibits an increased affinity towards GTP, compared to the host protein and a general preference towards G and C nucleotides (Chapter 5), possibly reflecting the low GC content of cyanophage genomes. Thus, the cyanophage and host MazG may have additional functions in phosphate metabolism and controlling DNA integrity, a hypothesis strengthened by experimental evidence for the cyanophage mazG being over-expressed under P-deplete conditions (Chapter 6). Taken together, data presented in this thesis demonstrates a general strategy by cyanophages to acquire host genes involved in modification of central metabolism or that regulate host signalling. Furthermore, once acquired, cyanophage genes appear to have evolved divergent functions to suit specific differences in genome content, compared with their host, as well as mechanisms to regulate transcription of these genes in response to external nutrient stimuli. Thus, this study expands our view of lytic phages, and suggests sophisticated mechanisms occur for overpowering their hosts under a range of infection conditions. This new information provides a mechanistic understanding of viral infection in a ubiquitious primary producer under environmetally relevant conditions, and will undoubtedly improve our ability to understand and model biogeochemical cycling performed by these key marine phototrophs in a more accurate manner.
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Route-Stephens, Margaret Gail Joan. "A study of the chemical and microbiological nature of the sea surface film across a marine discontinuity." Thesis, Bangor University, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.317310.
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Ilikchyan, Irina N. "Phosphonates Utilization in Marine and Freshwater Picocyanobacteria." Bowling Green State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1229969527.
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Sislak, Christine Demko. "Novel Thermophilic Bacteria Isolated from Marine Hydrothermal Vents." PDXScholar, 2013. https://pdxscholar.library.pdx.edu/open_access_etds/1486.
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As part of a large study aimed at searching for patterns of diversity in the genus Persephonella along the north to south geochemical gradient of the ELSC, ten novel strains of Alphaproteobacteria were isolated unexpectedly. Using defined media under microaerophilic conditions to enrich for Persephonella from chimney samples collected at the seven vent fields on the ELSC and the dilution to extinction by serial dilution method to purify cultures, a total of ten strains belonging to the Alphaproteobacteria were isolated. Two of these isolates, designate MN-5 and TC-2 were chosen for further characterization and are proposed as two new species of a novel genus to be namedThermopetrobacter. Both strains are aerobic, capable of chemoautotrophic growth on hydrogen and grow best at 55°C, pH 6 and 3.0% NaCl. Strain MN-5 is capable of heterotrophic growth on pyruvate and malate and TC-2 is only able to grow heterotrophically with pyruvate. The GC content of MN-5 is 69.1 and TC-2 is 67 mol%. GenBank BLAST results from the 16S rRNA gene reveal the most closely related sequence to MN-5 is 90% similar and the most closely related sequence to strain TC-2 is 89% similar.
Sampling at a shallow marine vent on the coast of Vulcano Island, Italy in 2007 led to the isolation of a novel species of Hydrogenothermus, a genus within the Hydrogenothermaceae family. This isolate, designated NV1, represents the secondHydrogenothermusisolated from a shallow marine vent. NV1 cells are rod-shaped, approximately 1.5μm long and 0.7μm wide, motile by means of a polar flagellum and grow singularly or in short chains. Cells grow chemoautotrophically using hydrogen or thiosulfate as electron donors and oxygen as the sole electron acceptor. Growth was observed between 45 and 75°C with an optimum of 65°C (doubling time 140 min), pH 4.0-6.5 and requires NaCl (0.5-6.0% w/v). The G+C content of total DNA is 32 mol%.
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Ostrowski, Martin Biotechnology & Biomolecular Sciences Faculty of Science UNSW. "Physiological adaptation to nutrient limitation in a marine oligotrophic ultramicrobacterium Sphingopyxis alaskensis." Awarded by:University of New South Wales. School of Biotechnology and Biomolecular Sciences, 2006. http://handle.unsw.edu.au/1959.4/27422.
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Sphingopyxis (formerly Sphingomonas) alaskensis, a numerically abundant species isolated from Alaskan waters and the North Sea represents one of the only pure cultures of a typical oligotrophic ultramicrobacterium isolated from the marine environment. In this study, physiological and molecular characterization of an extinction dilution isolate from the North Pacific indicate that it is a strain of Sphingopyxis alaskenis, extending the known geographical distribution of this strain and affirming its importance as a model marine oligotroph. Given the importance of open ocean systems in climatic processes, it is clearly important to understand the physiology and underlying molecular biology of abundant species, such as S. alaskensis, and to define their role in biogeochemical processes. S. alaskensis is thought to proliferate by growing slowly on limited concentrations of substrates thereby avoiding outright starvation. In order to mimic environmental conditions chemostat culture was used to study the physiology of this model oligotroph in response to slow growth and nutrient limitation. It was found that the extent of nutrient limitation and starvation has fundamentally different consequences for the physiology of oligotrophic ultramicrobacteria compared with well-studied copiotrophic bacteria (Vibrio angustum S14 and Escherichia coli). For example, growth rate played a critical role in hydrogen peroxide resistance of S. alaskensis with slowly growing cells being 10, 000 times more resistant than fast growing cells. In contrast, the responses of V. angustum and E. coli to nutrient availability differed in that starved cells were more resistant than growing cells, regardless of growth rate. In order to examine molecular basis of the response to general nutrient limitation, starvation and oxidative stress in S. alaskensis we used proteomics to define differences in protein profiles of chemostat-grown cultures at various levels of nutrient limitation. High-resolution two-dimensional electrophoresis (2DE) methods were developed and 2DE protein maps were used to define proteins regulated by the level of nutrient limitation. A number of these proteins were identified with the aid of mass spectrometry and cross-species database matching. The identified proteins are involved in fundamental cellular processes including protein synthesis, protein folding, energy generation and electron transport, providing an important step in discovering the molecular basis of oligotrophy in this model organism.
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Hopkins, Max Stephen. "Investigating the Diversity of Single-Stranded DNA Bacteriophages in Marine Environments." Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/5243.
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There are estimated to be 1030 virus-like particles in the world's oceans. Most are viruses that infect bacteria, called `bacteriophages' or simply `phages'. Phages exert tremendous influence on marine biogeochemical cycling because they are responsible for about half of all bacterial death in the oceans, causing nutrient release into the dissolved and particulate organic matter pools. Traditional paradigms of phage biology held that most of these ocean phages belonged to the Caudovirales group: phages that contain a double-stranded DNA genome within a geometric capsid `head' to which a `tail' is joined, in one of several morphological variants, that is the main structure allowing the phage to interact and infect a host bacterium. Compared to tailed phages, small, non- tailed, single-stranded DNA-containing phages have been an historical afterthought; believed to exist only in specialized, niche environments. However, recent studies harnessing advances in technology have revealed that single-stranded DNA phages are ubiquitous to nearly every marine environment yet tested.
Small, icosahedral, single-stranded DNA bacteriophages of the subfamily Gokushovirinae (family Microviridae) exemplify the difficulty that viruses can present as study subjects. They are difficult to visualize by epifluorescence microscopy and contain a paucity of genetic and protein material. As a result, recognition of their importance in marine environments has lagged behind that of tailed, double-stranded DNA bacteriophages. This thesis seeks to redress this knowledge gap.
The first chapter expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from ten diverse environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. The data was aggregated in several informative ways. Multiple alignments were combined with a predicted 3D-structure to reveal regions of both high and low conservation. Viewed in a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different sample types. Some environments, particularly pelagic sediments, appear as hotbeds of gokushovirus diversity, while freshwater springs were the least diverse.
The second chapter used the same primer set to detect gokushovirus communities at 0 m and 100 m depth in two seasons from three years at the Bermuda Atlantic Time- series Study (BATS) site. As a result of twenty-six years of constant sampling, the annual hydrodynamic cycling of BATS is very well understood. This wealth of knowledge allows us to hypothesize that the winter deep mixing layer will act to connect the viral communities between 0 m and 100 m. Conversely, in summer when stratification occurs, viral communities at the two depths will become divergent. We find compelling evidence to support this hypothesis.
The final chapter of this thesis details continuing efforts to characterize the first non-tailed, single-stranded DNA, temperate phage to infect a member of the globally important genus of marine autotroph, Synechococcus. Efforts undertaken have spanned genomic, metagenomic and proteomic methodologies. The lack of culturable, phage-host model systems for small, single-stranded DNA phages is today one of the most glaring impediments to increased understanding of these viruses. In combination with the data presented on environmental diversity, steps taken towards establishing this Synechococcus phage as a culturable model system makes this thesis a major contribution to the understanding of environmental ssDNA phages.
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Arfken, Ann. "The Eastern Oyster Microbiome and its Implications in the Marine Nitrogen Cycle." W&M ScholarWorks, 2017. https://scholarworks.wm.edu/etd/1516639592.
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Microbial communities associated with a particular space or habitat, or microbiomes, play significant roles in host health and the regulation of biogeochemical cycles. In oysters these microbiomes may be important contributors in the removal of biologically available nitrogen (N) from the coastal and marine environment through the process of denitrification. Denitrification is the microbially mediated step-wise reduction of nitrate (NO3-) or nitrite (NO2-) to N2 gas. Excess nitrogen in the Chesapeake Bay has been implicated in the increase of eutrophication and other detrimental effects including harmful algal blooms, hypoxia, and loss of benthic communities. Oyster reefs have been shown to enhance the rates of denitrification in nearby sediments, but little is known about the oyster microbiomes or associated microbes responsible for denitrification (denitrifiers). Furthermore, the identification of the oyster core microbiome, or set of resident microbes continually present in the oyster, is relatively unknown. Assessing the stable underlying core is necessary to evaluate and predict the effect of varying environmental conditions on the oyster microbiome and oyster denitrification. A combined 16S targeted metagenomic and metabolic inference approach was used in this study to investigate the gill, gut and shell microbiomes of the eastern oyster (Crassostrea virginica) and their associated denitrifiers in response to spatial and temporal changes. Denitrification activity was linked to community structure using methods such as quantitative PCR of nitrous oxide reductase genes (nosZ) and 15N isotope pairing technique with experimental flow-through design. The oyster gill, gut, and shell microbiomes all showed distinct and unique core microbiomes, suggesting an importance of the core to oyster function or health. Denitrifier abundance and activities were most consistent in the shell microbiomes indicating a stable, pool of potential denitrifiers for oyster denitrification. In comparison, oyster gill and gut denitrifier abundances and activities were highly variable and likely related to transient denitrifiers ingested with food particles. Additionally, denitrifiers demonstrated niche differentiation between the different oyster microbiomes, indicating different groups of denitrifiers are responsible for performing denitrification in the oyster. Assessing the stability and variability of the oyster microbiome and associated denitrifiers provides a greater understanding of the oyster’s role in denitrification and the mitigation of excess N in marine and coastal environments.
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Ramond, Pierre. "Diversité fonctionnelle des protistes marins de l'écosystème côtier." Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUS210.
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Les protistes sont les eucaryotes du compartiment microbien. Les rôles et adaptations de ces organismes dans leur milieu constituent leur diversité fonctionnelle. Parce que beaucoup ont été découvert récemment, la diversité fonctionnelle des protistes marins est peu connue. Dans cette thèse, la diversité fonctionnelle des protistes marins de l’écosystème côtier a été étudiée en couplant la taxonomie génétique (V4-ADNr 18S) et 13 traits. Dans un premier temps, à l’inverse des procaryotes, un fort lien entre taxonomie et fonctions est mis en évidence, impliquant que des changements de composition sont susceptibles de modifier le fonctionnement de l’écosystème. Les petits protistes soutiennent une plus grande diversité fonctionnelle, car influencés par une plus grande disponibilité en ressource. Dans une application associée à un front de marée, l’influence de l’environnement sur la diversité des protistes est étudiée. Les protistes phototrophes démontrent un maximum de diversité au niveau du front. Ce maximum est influencé par la dispersion (existence d’un écotone) ainsi que par des cycles de perturbations qui permettent de diminuer localement la compétition exclusive. La diversité des protistes hétérotrophes semble moins structurée par l’environnement, probablement parce que leur nutrition se fait par des interactions biotiques moins influencées par l’environnement. Finalement, nous observons que les protistes parasites sont spécialisés à leurs proies. Ces résultats soulignent que le rôle de prédation des communautés de protistes passe par l’intermédiaire d’interactions spécifiques entre les protistes hétérotrophes et leurs proiesProtists are the eukaryotic share of microbial communities. The distinct roles and adaptations of marine protists to their environment constitutes their functional diversity. Many marine protist have been discovered by DNA-based taxonomy, however the functional diversity of these organisms is unknown. In this project, the functional diversity of marine protist is studied by coupling a genetic survey (V4-18S rDNA) of various coastal ecosystems and a trait approach constituted of 13 traits. As a first step, in terms of functional redundancy, changes in the community of marine protists were tightly coupled with changes in functional diversity. These results contrasts with observations about prokaryotes and the distinct evolutionary process at stake are commented. The small size-fraction displayed a higher functional diversity probably influenced by a higher resource availability for this compartment. In a tidal front, the influence of the environment on marine protists is studied. The phototrophic protists presented a maximum of diversity at the front. The diversity maximum was influenced by dispersal (at an ecotone) but also by disturbance cycles which allowed to decrease competitive exclusion. Reversely, the diversity of heterotrophic protists was less structured by this environment, probably because their nutrition is related to biological interactions more than by the environment. In a last section, parasitism of a single dinoflagellate species was shown to be carried out by few specialized parasites. These results underline that the predation role of protistan communities might be dictated by specialized interactions involving heterotrophic protists and their prey
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Cicirelli, Elisha M. "Bacterial quorum-sensing in the marine sponge environment implications on motility and flagellar biosynthesis /." [Bloomington, Ind.] : Indiana University, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3297116.
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Thesis (Ph.D.)--Indiana University, Dept. of Biology, 2007.Title from dissertation home page (viewed Sept. 29, 2008). Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0818. Adviser: Clay Fuqua.
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Tsoi, Man Yee. "Dynamics of bacterial community in Hong Kong waters /." View Abstract or Full-Text, 2002. http://library.ust.hk/cgi/db/thesis.pl?BIOL%202002%20TSOI.
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Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2002.Includes bibliographical references (leaves 84-87). Also available in electronic version. Access restricted to campus users.
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Klindworth, Anna [Verfasser]. "RNA based research development, application and analysis within the MIMAS project / Anna Klindworth. Max Planck Institute for Marine Microbiology." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2013. http://d-nb.info/1035269147/34.
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Ince, Andrew Peter. "The cultivation of marine microalgae within a tubular photobioreactor as a source of polyunsaturated fatty acids." Thesis, Liverpool John Moores University, 2006. http://researchonline.ljmu.ac.uk/5805/.
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Woolven-Allen, John. "An investigation into the potential impacts of ocean acidification and ocean fertilisation on the genetic diversity of marine bacterial assemblages." Thesis, University of Warwick, 2008. http://wrap.warwick.ac.uk/2244/.
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Based on the increase of 16S rRNA gene sequences in databases it is possible to design improved oligonucleotide primers for this gene. Primers were designed in silico to specifically amplify fragments of the gene from the Alpha, Beta and Gamma subgroups of the Proteobacteria, as well as from Bacteroidetes, Firmicutes, Cyanobacteria and Planctomycetes and tested in silico and in vitro. The aim was to investigate bacterioplankton diversity and reveal greater fingerprint diversity within these groups than is possible using primers specific for the entire domain Bacteria, and also to reduce clone library redundancy. It was then aimed to investigate the potential impacts of increased pCO2 and ocean fertilisation with iron (Fe) and phosphorus (P), on bacterioplankton diversity. Group-specific clone libraries representing contrasting marine regions were analysed, and the usefulness and specificity of the primers validated. The clone libraries showed members of the oligotrophic marine group (OMG) to be present in an in situ coastal mesocosm supplemented with nutrients. The newly-developed group-specific primers were used in combination with an improved method of denaturing gradient gel electrophoresis (DGGE) to profile in detail bacterial communities in mesocosms, which were maintained at 750 ppm of pCO2, the level projected for the global surface ocean in the year 3000, and 380 ppm of CO2, the present level. Increased pCO2 correlated with a decrease in abundance of some members of the Gammaproteobacteria. Otherwise there was little impact on diversity due to raised pCO2. The same DGGE protocol was applied to samples from an ocean Fe and P fertilisation experiment. Diversity change due to Fe was not evident. However in seawater amended with P there was an explosive growth of some cells with 16S rRNA genes similar to those of the SAR86 clade, and others with similarity to Gammaproteobacteria with large genomes such as Oceanospirillum sp. and Psychromonas sp.
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Schöttner, Sandra Iris [Verfasser]. "Bacterial habitat differentiation in cold- and warm-water coral reef ecosystems / Sandra Iris Schöttner. Max Planck Institute for Marine Microbiology." Bremen : IRC-Library, Information Resource Center der Jacobs University Bremen, 2012. http://d-nb.info/1035019795/34.
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Geiselbrecht, Allison D. "The distribution and PAH-degradative potential of Cycloclasticus spp. in the marine environment /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/11493.
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Lau, Ken Wan Keung. "The identification of novel marine bacteria, and the construction of single chain fragment variable antibodies for the control of a viral pathogen /." View abstract or full-text, 2006. http://library.ust.hk/cgi/db/thesis.pl?AMCE%202006%20LAU.
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