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Al-Zereini, Wael. "Natural products from marine bacteria." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=982197985.
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Cox, Michael J. "Marine methyl halide-utilising bacteria." Thesis, University of Warwick, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.426740.
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Simmons, Sheri Lynn. "Geobiology of marine magnetotactic bacteria." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/34276.
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Thesis (Ph. D.)--Joint Program in Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2006.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Includes bibliographical references.
Magnetotactic bacteria (MTB) biomineralize intracellular membrane-bound crystals of magnetite (Fe3O4) or greigite (Fe3S4), and are abundant in the suboxic to anoxic zones of stratified marine environments worldwide. Their population densities (up to 105 cells ml-1) and high intracellular iron content suggest a potentially significant role in iron cycling, but very little is known about their population dynamics and regulation by environmental geochemistry. The MTB community in Salt Pond (Falmouth, MA), a small stratified marine basin, was used as a model system for quantitative community studies. Magnetiteproducing MTB predominate slightly above the oxic-anoxic interface and greigiteproducing MTB predominate in sulfidic waters. A quantitative PCR (QPCR) assay was developed and applied to enumerate four major groups of MTB in Salt Pond: magnetite-producing cocci, barbells, the greigite-producing many-celled magnetotactic prokaryote (MMP), and a greigite-producing rod. The barbells were identified as [delta]-Proteobacteria while the rod was identified as the first MTB in the [gamma]-Proteobacteria.
(cont.) The previously thought to be a single species, consists of at least five clades with greater than 5% divergence in their 16s rRNA. Fluorescent in situ hybridization probes showed significant variation in clade abundances across a seasonal cycle in salt marsh productivity. FISH also showed that aggregates consist of genetically identical cells. QPCR data indicated that populations are finely layered around the oxic-anoxic interface: cocci immediately above the dissolved Fe(II) peak, barbells immediately below, the MMP in microsulfidic waters, and the greigite-producing rod in low numbers (100 cells ml-1) below the gradient region. The barbell reached 1-10% of total eubacteria in the late season, and abundances of cocci and barbells appeared to vary inversely. Calculations based on qPCR data suggest that MTB are significant unrecognized contributors to iron flux in stratified environments. Barbells can respond to high oxygen levels by swimming toward geomagneticsouth, the opposite of all previously reported magnetotactic behavior. This behavior is at least partially dependent on environmental oxidation-reduction potential. The co-existence of MTB with opposing polarities in the same redox environment conflicts with current models of the adaptive value of magnetotaxis.
by Sheri Lynn Simmons.
Ph.D.
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Chin, Jason. "Aminophosphonate metabolism by marine bacteria." Thesis, Queen's University Belfast, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.676275.
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Phosphorus plays a crucial role in biology, and so microorganisms have developed many ways of obtaining phosphorus including the catabolism of aminoalkylphosphonates. Previous studies have led to a model of phosphonate use only as a phosphorus source by phosphorus starved marine microorganisms. However, a small number of terrestrial bacteria can use specific phosphonates as a carbon or nitrogen source when not phosphorus starved, but this possibility has not been investigated in marine organisms. Enrichment cultures confirmed that phosphonates are bioavailable phosphorus sources for marine bacteria and also that AMPA, 2AEP, OH2AEP and PnAI can support growth as nitrogen sources even in the presence of phosphate. Twelve isolates from these cultures grew using 2AEP as the sole nitrogen source despite exogenous phosphate addition. Cell-free extracts showed that four isolates catabolised PnAcHyde to produce Pi and an aldehyde, characteristic of a PhnX enzyme. The remaining isolates catabolised PnAc to release Pi and acetate, characteristic of a PhnA enzyme. While these enzymes are known to be involved the degradation of 2AEP under phosphorus starvation this is the first demonstration of marine bacteria capable of phosphate-insensitive 2AEP catabolism by these enzymes. Another isolate used OH2AEP and 2AEP as nitrogen sources even with exogenous phosphate addition. OH2AEP degradation enzymes, induced by OH2AEP, produce an aldehyde, Pi and ammonium, consistent with the proposed HpnWX pathway. The aldehyde could not be identified. A collection of inhibition, product and cofactor studies showed that 2AEP catabolism is carried out by an unusual PhnWA pathway. Therefore marine microorganisms can use some aminoalkylphosphonates as nitrogen sources regardless of Pi concentrations, despite the current model of marine phosphonate catabolism excluding this possibility. This is achieved using a mixture of characterised and previously undescribed C-P cleavage pathways. As such we need to reconsider the importance of aminoalkylphosphonates to microbial nutrition and marine biogeochemistry.
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Granger, Julie. "Iron acquisition by heterotrophic marine bacteria." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape10/PQDD_0002/MQ44173.pdf.
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Villarreal-Chiu, J. F. "Organic phosphonate metabolism by marine bacteria." Thesis, Queen's University Belfast, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.557849.
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Phosphonates are a family of organophosphorus compounds characterized by the presence of a carbon- phosphorus bond. This bond provides greater chemical stability compared with analogous compounds containing the more reactive carbon-oxygen-phosphorus linkage (Quinn et al., 2007). Hence, it is important to consider their accumulation in the environment and possible toxic threat to ecosystems. This study explored the distribution ofphosphonate metabolic pathways among sequenced microorganisms and their prevalence and occurrence in the environmental metagenomic database using bioinformatic tools. Experiments carried out on a number of marine representative strains confirmed the capacity of their predicted phosphonate catabolic enzymes to utilize phosphonates for bacterial growth when supplied as phosphorus and to some extent, as nitrogen sources. The bacterium Roseovarius nubinhibens ISM was able to . produce methane through the aerobic degradation of methylphosphonate even in the presence of Pi concentrations up to 7.5mM. Also, this strain exhibited the unique characteristic of producing both polyhydroxybutyrate and polyphosphate concurrently as result of nutritional stress through either phosphorus or nitrogen limitation. Haloquadratum walsbyi was confirmed to be the only known archaeon to possess a phosphonate degradation pathway, and experiments confirmed the capability of this strain to consume phosphonates 2AEP, MPn and glyphosate as phosphorus sources.
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Long, Richard A. "Bacteria-bacteria antagonism on marine organic particles and its biogeochemical implications /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3035420.
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Longford, Sharon Rae Faculty of Science UNSW. "The ecology of epiphytic bacteria on the marine red alga Delisea pulchra." Awarded by:University of New South Wales, 2007. http://handle.unsw.edu.au/1959.4/36783.
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Bacteria are ubiquitous to marine living surfaces, taking on a broad spectrum of roles from mutualistic to pathogenic. Despite their universality, much remains unknown about their basic ecology and interactions with higher organisms. To address this gap, this thesis firstly examines the bacterial communities associated with three co-occurring marine eukaryote hosts from temperate Australia: the demosponge Cymbastela concentrica, the subtidal red macroalga Delisea pulchra and the intertidal green macroalga Ulva australis. Molecular characterisation of the bacterial communities was undertaken using 16S rRNA gene library analysis to compare within-host (alpha) and between-host (beta) diversity for the three microbial communities. This study highlights the potentially substantial contribution host-associated microorganisms could have on marine microbial diversity. The remaining focus for this thesis was on the bacterial community associated with D. pulchra. This alga produces a suite of biologically active secondary metabolites (furanones) that non-toxically inhibit acyl homoserine lactone (AHL)-driven quorum sensing in bacteria, affecting a range of phenotypes including colonisation and virulence traits. The ecology of D. pulchra???s epiphytic bacteria was investigated using a mechanistic approach to explain bacterial colonisation patterns. In particular, concepts and models of ecological succession founded in eukaryote ecology were investigated. The thesis concludes with a study investigating the effect of furanones and elevated temperature on bacteria-induced disease and thallus bleaching of D. pulchra. In the presence of furanones colonisation and infection of two Roseobacter isolates from D. pulchra???s epiphytic bacterial community were inhibited. Ruegeria strain R11 was demonstrated to have temperature regulated virulence, which caused thallus bleaching in furanone-free algae. The implications of elevated sea temperatures resulting from global warming for algal health are discussed.
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Stetter, Dennis. "Regulation of Beta-Glucosidase in Marine Bacteria." NSUWorks, 1996. http://nsuworks.nova.edu/occ_stuetd/46.
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The following is a study of the regulation of production of a catabolic enzyme, beta-glucosidase, by isolated strains of marine bacteria. Catabolic enzymes transform organic matter to monosaccharides which are utilized as an energy source for growth by bacteria. The bacterial strains were isolated from the Gulf Stream off the coast of Florida, as well as from particulate matter collected from waters adjacent to the Florida coast.
The first section describes the preparation of a liquid medium using sterile saltwater supplemented with inorganic nutrients and a carbohydrate component. This medium allowed growth of marine bacteria under carbohydrate-limiting conditions. A solid agar version of the media was also prepared, which allowed isolation of individual colonies of marine bacteria under carbohydrate-limiting conditions.
The second section describes analyses of the regulation of beta-glucosidase production by five isolated bacterial strains using methylumbelliferyl-glucopyranoside (MUF-glu) as a model substrate. The beta-glucosidase hydrolysis of MUF-glu to glucose and a highly fluorescing product, methylumbelliferon (MUF ), allowed a measurement of enzyme activity in laboratory cultures.
The experiments showed that four of the five bacterial strains isolated could regulate production of beta-glucosidase. When cellobiose, in particular, was the only carbohydrate present, the four strains showing regulatory ability produced elevated levels of enzyme activity. This elevated enzyme activity was not observed when glucose was provided as the only carbohydrate source. The fifth strain showed only low-level enzyme activity in the presence of cellobiose or glucose. This is the first evidence of the regulation of beta-glucosidase activity in particular strains of marine bacteria.
Authenticity of beta-glucosidase activity was confirmed with known inhibitors of beta-glucosidase, gluconic acid, and glucose. The enzyme activities of all the isolated strains, measured by hydrolysis of MUF-glu to fluorescent MUF, showed sensitivity to both enzyme inhibitors. The sensitivity was observed as lower MUF production compared to control assay samples with no inhibitor added.
The first isolated bacterial strain, from Gulf Stream waters, also showed an ability to repress the production of beta-glucosidase in the presence of glucose. This strain was tested with cylic AMP, known to neutralize glucose repression of beta-galactosidase in E.coli. Cyclic AMP, however, did not neutralize the effect· of glucose on repressing beta-glucosidase activity in the isolated marine bacterium.
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Green, Robert. "Iron and manganese homeostasis in marine bacteria." Thesis, University of East Anglia, 2012. https://ueaeprints.uea.ac.uk/47962/.
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Using a mixture of bioinformatic analyses, microarrays on cells that were grown in media that were either replete or depleted for manganese or for iron, and by making targeted mutations and reporter fusions, several important observations were made on the mechanisms of Mn and Fe homeostasis in the marine α‐proteobacterium Ruegeria pomeroyi (the main species studied here), and in other important marine bacteria. R. pomeroyi lacks most of the known Fe uptake systems, including TonB and outer‐membrane receptors, but has a predicted, but incomplete iron uptake ABC‐class transporter operon, whose expression is much enhanced in Fe‐depleted conditions, although a strain lacking these genes was unaffected in growth. The Fe‐specific regulatory network of R. pomeroyi was found to involve the Irr transcriptional regulator, which controlled the expression of several genes. Microarrays revealed many other genes whose expression was enhanced or diminished in Fe‐replete conditions, providing material for future work on the iron regulon of this bacterium, Turning to manganese, here too the expression of many genes was affected (up or down) by Mn availability. These included an operon corresponding to sitABCD, an effective ABC‐type Mn2+ transporter in many other bacteria. This was confirmed, directly, to be the case for Ruegeria. Bioinformatic analyses showed that some other Roseobacter strains lacked any previously known Mn2+ transporter, but instead, had a gene that likely encoded an inner membrane protein and was preceded by a motif (MRS box) that was known to be recognised by the Mn2+ ‐responsive transcriptional regulator Mur. It was confirmed that this gene, termed mntX, did indeed encode a manganese transporter and that MntX orthologues occurred in several other, unrelated marine bacteria, notably most strains of the pathogenic genus Vibrio (including V. cholerae) and some of the most abundant bacteria in the oceans, namely the SAR11 clade (Pelagibacter).
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Murray, Alexander Godfrey. "Modelling investigations of marine microplankton ecology." Thesis, University of Southampton, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239411.
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Hedlund, Brian P. "Diversity of marine polycyclic aromatic hydrocarbon degrading bacteria and their dioxygenases /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/11526.
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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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Bonin, Aly Hassan Marie-Claire. "Studies on the respiratory metabolism of the marine bacterium Alteromonas haloplanktis." Thesis, McGill University, 1985. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=72490.
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Vetter, Yves-Alain. "Bacterial foraging with cell-free enzymes /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/11033.
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Shao, Mingfei. "Autotrophic denitrification in nitrate-induced marine sediment remediation." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B44139226.
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Shao, Mingfei, and 邵明非. "Autotrophic denitrification in nitrate-induced marine sediment remediation." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B44139226.
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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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Muthusamy, Saraladevi. "Functional Profiling Of Metabolic Regulation In Marine Bacteria." Doctoral thesis, Linnéuniversitetet, Institutionen för biologi och miljö (BOM), 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-58257.
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Oceans are powered by active, metabolically diverse microorganisms, which are important in regulating biogeochemical cycles on Earth. Most of the ocean surface is often limited by nutrients, influencing bacterial growth and activities. Bacterial adaptation to fluctuating environmental conditions involves extensive reprogramming, and redirection of bacterial metabolism and physiology. In this thesis, I investigated the molecular mechanisms of bacterial adaptation strategies to sustain their growth and survival, focusing on the regulation of gene and protein expression in heterotrophic marine bacteria. Comparative proteomics analyses of the growth and non-growth conditions, uncovered central adaptations that marine bacteria employ to allow them to change their metabolism to support exponential growth in response to nutrients and to readjust to stationary phase under nutrient limitation. Our results highlight that during nutrient rich conditions three distinct bacteria lineages have great similarities in their proteome. On the other hand, we observed pronounced differences in behavior between taxa during stationary phase. Analyses of the proteorhodopsin containing bacterium Vibrio sp. AND4 during starvation showed that significantly improved survival in the light compared to darkness. Notably, proteins involved in promoting cell vitality and survival had higher relative abundance under light. In contrast, cells in the dark need to degrade their endogenous resources to support their basic cellular demands under starvation. Thus, light strongly influences how PR-containing bacteria organize their molecular composition in response to starvation. Study of alternative energy generation metabolisms in the Alphaproteobacteria Phaeobacter sp. MED193 showed that the addition of thiosulfate enhanced the bacterial growth yields. Concomitantly, inorganic sulfur oxidation gene expression increased with thiosulfate compared to controls. Moreover, thiosulfate stimulated protein synthesis and anaplerotic CO2 fixation. These findings imply that this bacterium could use their lithotrophic potential to gain additional energy from sulfur oxidation for both improving their growth and survival. This thesis concludes that analyses in model organisms under defined growth conditions gives invaluable knowledge about the regulatory networks and physiological strategies that ensure the growth and survival of heterotrophic bacteria. This is critically important for interpreting bacterial responses to dynamic environmental changes. Moreover, these analyses are crucial for understanding genetic and proteomic responses in microbial communities or uncultivated organisms in terms of defining ecological niches of planktonic bacteria
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França, Lucas Vagueiro de. "Macroalgae as feedstock for cultivation of marine bacteria." Master's thesis, Universidade de Aveiro, 2015. http://hdl.handle.net/10773/14921.
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Mestrado em Biotecnologia - Biotecnologia Industrial e AmbientalAlginate, laminarin and mannitol amount up to 60% of dry weight in brown macroalgae. The presence of alginate and laminarin-degrading enzymes and mannitol metabolic machinery have been confirmed by Matís, a partner in European BlueGenics project. Thus, in a biorefinery perspective, R. marinus can potentially perform the saccharification and fermentation of brown macroalgae carbohydrates to yield commercial valuable biocompounds, as thermostable enzymes and glycosidic carotenoids. Rhodothermus marinus is a moderate thermophilic (65ºC) and slight halophilic (1.0% NaCl) marine bacterium. Therefore, one of the objectives of this project was to decrease the NaCl concentration in the fermentation medium, since chloride leads to a lower equipment lifetime due to stainless steel corrosion of bioreactors. The main objective of this work was the study of the bacterium R. marinus pattern of growth when cultivated in the main brown macroalgal carbohydrates. This work was performed with five R. marinus strains, two of which were successfully acclimatized to cultivation in Medium 166, cryopreserved in glycerol and recultivated in liquid media, being subject of study in the assays with different carbon and sodium sources in shake flask. The growth studies with different carbon sources suggested that (i) strain 5 presented higher glucose consumption and growth, even though none of the strains consumed all the glucose available in the media; (ii) although none of strains consumed mannitol, strain 5 seemed to be more robust to its presence; and (iii) the growth differences between the controls and the assays with alginate and pretreated alginate were not significant enough to infer if any alginate consumption occurred. It was tested a partial and total substitution of NaCl by Na2SO4. The process was not successful, since Na2SO4 seem to represent a stress factor to both R. marinus strains. Interestingly, the strain 5, when cultivated in Medium 166 containing only a half of NaCl standard concentration, presented a similar growth pattern to control. In the operational conditions imposed in shake flask cultivations containing two tested brown macroalgae (orginial and pretreated) as feedstock for growth, mannitol was not consumed. It was not possible to monitor the alginate and laminarin saccharification and fermentation. Although, the results showed that brown macroalgae are a potential feedstock under the biorefinery concept, since some R. marinus growth was observed. The more promising result to BlueGenics project was obtained from shake flask cultivations of strain 5 in Medium 166 with 0.500% NaCl and 10.0 g.L-1 glucose, since the growth with low chloride content determinates the feasibility of the scale-up of the process to bioreactor . Because of that, the assay was validated in 3L controlled bioreactor. The process presented a μmax of 0.208 h-1, a maximum biomass concentration of 8.75 gX.L-1, a volumetric biomass production rate of 0.295 g.L-1.h-1 and a volumetric glucose uptake rate of 0.293 g.L-1.h-1. Some feeding strategies were tested but further assays have to be performed in order to optimize the bioprocess.
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Schmidt, Jill Lisa. "Spatial ecology of bacteria in surficial marine sediments /." Thesis, Connect to this title online; UW restricted, 2001. http://hdl.handle.net/1773/11058.
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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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Taylor, A. P. "Magnetotactic bacteria and their biominerals /." St. Lucia, Qld, 2002. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16108.pdf.
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Davidson, Seana Kelyn. "Biology of the bryostatins in the marine bryozoan Bugula neritina : symbiosis, cryptic speciation and chemical defense /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1999. http://wwwlib.umi.com/cr/ucsd/fullcit?p3035405.
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Lelchat, Florian. "Enzymes de dépolymérisation d'exopolysaccharides bactériens marins." Thesis, Brest, 2014. http://www.theses.fr/2014BRES0070/document.
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Les exopolysaccharides (EPS) sont des biopolymères pouvant être synthétisés par les Eucaryotes, lesArchées et les Procaryotes. Au niveau bactérien les EPS peuvent être impliqués dans la constitution du biofilm (phénomène de biofouling) lors de la colonisation de nouveaux milieux. Ces biopolymères ont des propriétés physico-chimiques et biologiques spécifiques et innovantes à haut potentiel biotechnologique (agroalimentaire, santé, cosmétique, ingénierie environnementale ...). A l'opposé, leurs rôles écologiques lors de l'établissement de biofilms de souches potentiellement pathogènes peuvent rendre leur éradication compliquée.Les processus de dépolymérisation par voie enzymatique sont nécessaires pour réaliser l'élucidation structurale fine des EPS complexes, pour la production de dérivés bio-actifs calibrés à faible poids moléculaire ou pour empêcher la formation de biofilm. La mise en évidence de ces phénomènes enzymatiques sur des microorganismes modèles peut également permettre de mieux cerner les flux de matière au sein de certains compartiments biologiques en particulier en milieu marin. Néanmoins la complexité et grande diversité de structures des EPS rendent la recherche d’enzymes de dépolymérisation spécifiques difficile.Deux stratégies ont été employées pour trouver des sources d'enzymes.1. La voie bactérienne via l’utilisation de bactéries marines productrices d’EPS.2. La voie virale par la recherche de polysaccharidases de bactériophages marins. En plus d’EPS marins déjà connus, de nouveaux substrats (EPS) originaux ont été produits et caractérisés à partir de batéries marines d’intérêts biotechnologiques et/ou écologiques pour les besoins du projet. Un criblage enzymatique sur 11 souches bactériennes du genre Alteromonas a permis de mettre en évidence que 7 d’entre elles présentaient une activité de dépolymérisation endogène vis-à-vis de leur propre EPS. Une bioprospection a été réalisée afin de constituer une virothèque à partir d’hôtes bactériens producteurs d’EPS dans le but de fournir une source de Cazymes virales potentielles. Sur 33 bactériophages, 10 ont été sélectionnés pour leur capacité à rester infectieux lorsque leurs hôtes synthétisent des EPS. Finalement un système hôte/virus a été sélectionné.Les 5 virus (appelés Carin-1 à 5) infectant Cobetia marina DSMZ 4741 ont été étudiés au niveau de leurs traits de vie. Les capacités de dépolymérisation de Carin-1 et Carin-5 sur l'EPS L6 ont été explorés plus en détail. En parallèle, la structure chimique de l'EPS L6 a été intégralement élucidéeExopolysaccharides (EPSs) are a class of biopolymer synthesized by Eukarya, Archea and Procarya.Bacterial EPSs are involved in biofilm establishment and biofouling phenomenon. These polymers have physicochemical and biological properties suitable with biotechnological valorization. At the opposite, their involvment in biofouling of pathogenic strains can be problematic.Enzymatic depolymerization process are necessary for EPSs structural elucidation, Bioactive oligosaccharides production or to disrupt polysaccharidic biofilms. The highlight of enzymatic phenomenon can help to understand biogeochimical process in the ocean. Nevertheless the important structural diversity as well as their complexity make the sourcing of specific enzymes difficult.Two strategies were used to find enzymes.1. The bacterial way by using EPS-producing marine strains2. The viral way, with marine bacteriophages.For the need of the study, several EPS-substrates were produced and characterized. The majority of them were totally new. An enzymatic screening on 11 marine Alteromonas strains shown that 6 were able to depolymerize their EPS in an endogenous way. A bioprospection was realized to isolates marine bacteriophages with potential viral Cazymes. 10 out of 33 phages were selectionned for their ability to be infectious with their hosts in EPS production induced. Finally, a host/virus system was chosen. The bacteriophages infecting Cobetia marina DSMZ 4741 (named Carin-1 to 5) were studied. The polysaccharidase activities of Carin-1 and Carin-5 on the L6 EPS were studied more deeply. In parallel, the complete structural elucidation of the L6 EPS was realized
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Staroscik, Andrew M. "Bacterioplankton seasonal dynamics in Narragansett Bay /." View online ; access limited to URI, 2003. http://0-wwwlib.umi.com.helin.uri.edu/dissertations/dlnow/3112130.
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Thi, Tuyen Do, Quyen Le Dinh, Thi Quyen Dinh, and Cuong Pham Van. "Isolation and identification of marine bacteria from marine mud in Vietnam with antimicrobial activity." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-99508.
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Seventeen bacterial strains were isolated from 9 marine mud samples from the inshore environments of the East Sea. Four bacterial strains showed an inhibition against all tested microorganisms Staphylococcus aureus ATCC10832, Escherichia coli JM109, and Fusarium oxysporum. 16S rRNA sequences of four bacterial strains were obtained by PCR using specific primers. PCR products were cloned into E. coli DH5a using pJET1.2 blunt vector. The recombinant plasmids were sequenced and the lengths of these 16S rRNA sequences were ~930bp. The 16S rRNA sequence from the four bacterial DB1.2, DB1.2.3, DB4.2 and DB5.2 strain showed a high identity of 97 to 99% with the 16S rRNA sequence from Photobacterium sp., Oceanisphaera sp., Shigella sp., Stenotrophomonas sp, respectivelyMười bảy chủng vi khuẩn đã được phân lập từ 9 mẫu bùn biển từ các vùng ven bờ biển Việt Nam. Bốn chủng vi khuẩn được ghi nhận có khả năng ức chế mạnh sự sinh trưởng và phát triển của các chủng vi khuẩn Staphylococcus aureus ATCC10832, Escherichia coli JM109, và thậm chí cả nấm Fusarium oxysporum. Trình tự gene 16S rRNA của bốn chủng vi khuẩn này đã được khuếch đại bằng PCR sử dụng cặp mồi đặc hiệu. Sản phẩm PCR được nối ghép vào vector pJET1.2 blunt sử dụng T4 ligase, hình thành plasmid tái tổ hợp và biến nạp vào E. coli DH5α. Khuẩn lạc có plasmid mang phân đoạn DNA chèn được nuôi cấy và tách plasmid. Trình tự 16S rRNA từ 4 chủng DB1.2, DB1.2.3, DB4.2 and DB5.2 chỉ ra có sự tương đồng 97 ÷ 99% so với trình tự 16S rRNA tương ứng của các chủng vi sinh vật biển trên ngân hàng gene thế giới là Photobacterium sp., Oceanisphaera sp., Shigella sp., và Stenotrophomonas sp
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李嵐 and Laam Li. "Effects of hypoxia on marine benthic communities : from bacteria to invertebrates." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/193402.
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Because of the eutrophication resulting from increasing anthropogenic activities, hypoxia (i.e. dissolved oxygen < 2.8 mg O2 L-1) is on the rise globally. The objective of this research was to understand more about the effects of hypoxia on the marine benthic communities. Particularly, it focused on the latent effects and indirect effects of hypoxia by investigating how early exposure to hypoxia affect the later life stage of a marine gastropod Crepidula onyx, and how hypoxia alter the bacterial composition of biofilms and the subsequent larval settlement of marine invertebrates.
In the first study, the larvae of C. onyx were exposed to 2, 3, and 6 mg O2 l-1. Under low food concentration (Isochrysis galbana at 1 × 105 cells l-1), larvae in both hypoxic treatments (2 and 3 mg O2 l-1) required a longer time to become competent to metamorphose. But when they did, they had a similar size and total lipid content to the control larvae. Moreover, the latent effects of early hypoxic exposure on the juvenile growth were evident. After 2 weeks development in field, the growth rate, mean dry weight and filtration rate of juveniles were significantly reduced in the hypoxic treatments. However, there was no discernible effect on larvae or juveniles when the food concentration during the larval stage was doubled (I. galbana at 2 × 105 cells l-1), suggesting that the latent effects of hypoxia can be offset by larval access to high algal concentration.
In the second study, the biofilms were exposed to hypoxia and normoxia in microcosms for up to 7 days, and their bacterial community composition was analysed by terminal-restriction fragment length polymorphism (T-RFLP). The results suggested that hypoxia altered the bacterial community structure within biofilms, and the difference between the hypoxia and normoxia treatments increased through the length of exposure period. The resulting changes in biofilms did not alter the larval settlement response of a model species (i.e. C. onyx) in laboratory assays. Nevertheless, when the biofilms were deployed in the field to allow natural larval settlement and recruitment, biofilms that had been exposed to hypoxia altered the overall larval settlement pattern of different marine invertebrates, potentially leading to a shift in the benthic invertebrate community.
This research suggested that periodic hypoxic events and the resulting exposure of organisms to hypoxia during their early development might have effects that persist across the life history. Moreover, it highlighted the possibility that the effects of hypoxia on species composition and structure of benthic invertebrate communities might be mediated through changes in biofilms and subsequently larval settlement and recruitment. To conclude, this research demonstrated that hypoxia could affect the growth in the later life stages of marine invertebrates and the recruitment of the benthic communities.published_or_final_version
Biological Sciences
Master
Master of Philosophy
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Salazar, Guiral Guillem. "Large-scale biogeography of marine pelagic bacteria and archaea." Doctoral thesis, Universitat Politècnica de Catalunya, 2019. http://hdl.handle.net/10803/665818.
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The dark ocean contains about 70% of the ocean’s microbial cells and 60% of its heterotrophic activity, which is mainly fueled by the flux of organic particles produced in the surface ocean and exported to the bathypelagic ocean (1,000 – 4,000 m depth). The bathypelagic ocean represents a nonhomogeneous environment and contains a variety of particles that are considered as the main supply of organic carbon to this environment. The microorganisms inhabiting this realm play a pivotal regulatory role in the biogeochemical cycles at a planetary scale. Accordingly, the study of these microorganisms is an essential step to decipher the ecological functioning of the deep ocean.
Chapters 1 to 3 in this Thesis are dedicated to the description of the prokaryotic community composition in the bathypelagic ocean at a global scale through the sequencing of ribosomal DNA and RNA fragments using data collected during the Malaspina 2010 expedition. Chapter 1 identifies the dominant prokaryotes in the deep ocean and reveals a high proportion (~50%) of previously undescribed prokaryotes. The water masses and the structure of the deep ocean’s floor, organized into basins, are identified as the main drivers of their biogeography. Chapter 2 addresses the differences between free-living and particle-attached bathypelagic prokaryotic communities. This is shown to be a phylogenetically conserved trait, indicating that the bathypelagic particles and the water surrounding them constitute two distinct niches and that transitions from one to the other have been rare at an evolutionary timescale. Finally, in Chapter 3 we identify a linear relationship between the 16S RNA/DNA ratio and particle attachment preference, suggesting a global relationship between the prokaryote’s preference for a particle-attached lifestyle and their growth rate.
While the deep ocean is a highly unexplored environment, a more complete knowledge exists for the epipelagic ocean (0 – 200 m depth). Steep gradients of light intensity and quality, temperature and nutrient availability characterize the oceans and impact on the distribution of species. However, different processes, such as the sinking of particles and the vertical movement of water masses, have been described as mechanisms capable of connecting the surface and deep layers of the ocean. These same processes could transport entire prokaryotic communities, a process theoretically proposed but never tested. In Chapter 4 we develop a tool (mtagger) for the extraction of short 16S ribosomal reads from metagenomes to describe the taxonomical composition of microbial communities. We propose and evaluate technical improvements compared to previous versions as a benchmark for its use in the last chapter. Chapter 5 is dedicated to the development of a modeling tool (disperflux) for the analysis of prokaryotic communities’ connectivity using data collected during the Tara Oceans expedition. We observe and describe a fast-decay relationship between community similarity and depth, which is consistently fitted by a power-law across the whole dataset, with the exception of 5 stations that are compatible with events of whole community export from the photic ocean to the mesopelagic.
In summary, this Thesis significantly contributes to the knowledge on the ecological functioning of marine prokaryotes by describing the structure of prokaryotic communities along the bathypelagic realm and the vertical gradient of the ocean and by the development of original methodological tools that may be applied to a variety of environments.El océano profundo contiene el 70% de las células microbianas del océano las cuales suponen el 60% de la actividad heterotrófica. Dicha actividad biológica está mantenida por un flujo de partículas orgánicas producidas en el océano superficial y exportadas al océano batipelágico (1,000 - 4,000 m de profundidad). Éste no es, por tanto, un ambiente homogéneo, sino que contiene una variedad de partículas consideradas el aporte dominante de carbono orgánico. Los microorganismos de este ambiente tienen, por tanto, un papel regulatorio central en los ciclos biogeoquímicos planetarios. Consecuentemente, el estudio de estos microorganismos supone un paso esencial para descifrar el funcionamiento ecológico del océano profundo. Los Capítulos 1 a 3 de esta Tesis están dedicados a la descripción a nivel global de la composición de las comunidades de procariotas en el océano batipelágico mediante la secuenciación de fragmentos del ADN y ARN ribosomal. En el Capítulo 1 se identifican los procariotas dominantes en el océano profundo y se revela la existencia de una alta proporción (~50%) de procariotas previamente no descritos. Se reconocen además las masas de agua y la orografía del fondo oceánico, organizado en cuencas, como factores claves en su biogeografía. En el Capítulo 2 se estudian las diferencias entre las comunidades de procariotas de vida libre y aquellos adheridos a partículas. Este rasgo se demuestra estar conservado filogenéticamente, indicando que las partículas del batipelágico y el agua que las rodea constituyen dos nichos claramente diferenciados y que las transiciones entre uno y otro por parte de los procariotas han sido eventos poco frecuentes a escalas evolutivas. Finalmente se identifica en el Capítulo 3 una relación lineal entre el cociente de 16S ARN/ADN ribosomal y la preferencia a un modo de vida adherido a partículas, lo que sugiere una relación a nivel global entre la adherencia a partículas y su tasa de crecimiento. Mientras el océano profundo es un ambiente ampliamente inexplorado, existe un mayor conocimiento del océano superficial o epipelágico (0 - 200 m de profundidad). Gradientes intensos en la cantidad y calidad de la luz, temperatura y concentración de nutrientes caracterizan a los océanos e influyen en la distribución vertical de las especies. Sin embargo, diferentes procesos, tales como la deposición de partículas o los movimientos verticales de masas de agua, se han descrito como mecanismos capaces de conectar las capas superficiales y profundas del océano. Estos mismos procesos podrían teóricamente exportar comunidades enteras de microorganismos, un proceso teóricamente propuesto pero no evaluado hasta la fecha. En el Capítulo 4 se desarrolla una herramienta informática (mtagger) para la utilización de fragmentos del gen 16S ribosomal extraídos de metagenomas y su utilización para la descripción taxonómica de comunidades de procariotas. En este capítulo se proponen y evalúan mejoras respecto a versiones anteriormente utilizadas, como paso previo a su uso en el último capítulo. El Capítulo 5 está dedicado al desarrollo de un modelo matemático (disperflux) para la descripción de la conectividad vertical entre comunidades de procariotas. Se observa y describe una disminución abrupta de la similitud de las comunidades de procariotas con la profundidad. Esta relación se ajusta a una ecuación potencial que resulta consistente a lo largo de todo el océano, a excepción de 5 localizaciones, que se demuestran compatibles con eventos de exportación masiva de comunidades desde la superficie al océano profundo. En resumen, esta tesis ha contribuido significativamente al conocimiento del funcionamiento ecológico de los procariotas marinos mediante la descripción a nivel global de estas comunidades en el océano profundo y en el gradiente vertical así como mediante el desarrollo de herramientas metodológicas novedosas aplicables a una amplia variedad de entornos
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Sapp, Melanie. "Interactions of marine bacteria in the pelagic food web." [S.l.] : [s.n.], 2006. http://e-diss.uni-kiel.de/diss_1783/d1783.pdf.
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Misciattelli, Natalia. "Control of pathogenic bacteria in marine larval culture systems." Thesis, Bangor University, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.311387.
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Jamal, Mamdoh Taha. "Studies on antibiotic-producing bacteria from the marine environment." Thesis, Heriot-Watt University, 2007. http://hdl.handle.net/10399/2044.
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Of >500 bacterial isolates from seaweed, namely Fucus serratus, algae (Halimeda sp, Sargassum sp), sponges (Siphonochalina sp, Leucetta 'chgosensis), sea cucumber, (Holothuria atra), star fish (Acanthaster planci), mangrove (Avecenia marina) roots, sea anemone, (Heteractis magnifica), ,jellyfish (Disambiguation), sediment and seawater from the Scottish and Saudi Arabian coasts, a culture of Bacillus licheniformis produced a novel protein with antibacterial activity against methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci and Listeria monocytogenes. The antibacterial activity was maximal in cultures prepared in Columbia broth -containing pieces of synthetic polyurethane sponge and shaken at 210-230 rpm. Antibacterial activity was not found in cultures grown statically or with different speeds of rotary shaking. Reduced activity was apparent in supernatants prepared from marine . 2216E broth and tryptone soya broth with or without 1% (w/v) sodium chloride. The antibacterial compound was sensitive to proteinase K, pronase and trypsin, but was not affected by Tween 20, 40, 60 or 80, or a- or ~-amylase. Activity was not adversely affected by heating to 40°C or treatment at pH 5-14. The bioactive compound was purified by gel filtration and ion exchange, and classified by using MALDI-TOF determined as a protein of 30.7 kDa, which had homology to the YbdN protein of B. licheniformis ATCC 14580. The gene encoding YbdN was isolated and transferred to Escherichia coli XL BLUE, and the product was purified by SDS-PAGE giving a single band with a molecular size 30.7 kDa.
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Novak, Halina. "Biochemical and structural characterisation of dehalogenases from marine bacteria." Thesis, University of Exeter, 2011. http://hdl.handle.net/10036/3577.
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An L-haloacid dehalohenase from the psychrophilic marine bacteria Psychromonas ingrahamii has been cloned, over-expressed in a bacterial expression system and biochemically characterised. The enzyme is stable at temperatures of up to 60ºC for 90 min and shows highest activity towards substrates with short carbon chains (≤C3). The enzyme is stable in up to 30% ethanol, methanol and DMSO when incubated for 1 h. The Km for the enzyme is 1.36 mM. The genome of AQP5750 from the Aquapharm Biodiscovery Ltd Microbial library was sequenced. An L-haloacid dehalohenase and a haloalkane dehalogenase gene were identified within the genome. The AQP5750 L-haloacid dehalohenase has been cloned, over-expressed in a bacterial expression system, biochemically characterised, crystallized and the native and crystal complex structure with chloropropionic acid (MCP) determined. The L-haloacid dehalohenase from AQP5750 shows highest activity at 55ºC towards brominated substrates with short carbon chains (≤C3). The enzyme shows increased activity of 150% in 40% DMSO and 123% in 30% methanol. The L-haloacid dehalohenase crystal complex structure with covalently bound MCP confirmed Asp 18 as the main catalytic residue. Residues His 183, Asp 186 and Glu 21 in the active site are proposed to be involved in activation of the catalytic water which attacks the ester intermediate in the second part of the SN2 dehalogenase mechanism. The AQP5750 haloalkane dehalogenase has been cloned, over-expressed in a bacterial expression system, crystallized and the native and complex structure with 1-hexanol has been determined. Substrate specificity experiments showed that the haloalkane dehalogenase from AQP5750 does not show high activity towards substrates used by other haloalkane dehalogenases with high amino acid sequence identity. The large active site cavity and the presence of Ser 176 and Arg 136 in the hydrophobic binding pocket may alter the binding of substrates tested which could account for the low activity observed.
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Cheung, Chin Wa Sunny. "Biofilms of marine sulphate-reducing bacteria on mild steel." Thesis, University of Portsmouth, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.241657.
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Clarke, Sean Aidan. "Hypermutation and adaptation of experimentally evolved marine Vibrio bacteria." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/81665.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2013.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 73-83).
Environmental bacteria display tremendous genetic diversity, but we are still learning how this diversity arises and relates to their wide range of habitats. Investigating how bacteria adapt helps us understand their contributions to environmental processes and informs forward engineering of bacteria for industrial applications. Experimental evolution is a powerful approach, with microbes especially, but it has mostly been applied to model organisms and metabolic functions. In the work here, we investigated the possibility, degree, and variability of adaptation of an environmental Vibrio strain by applying a little-used selection method appropriate to a relevant condition, salinity. We successfully isolated mutants with higher salt tolerance by selecting on salt gradient plates. Resequencing the genomes of the evolved strains revealed unprecedented hypermutation in three of nine parallel lineages. These mutator lines arose independently, and each of them accumulated more than 1500 single-base mutations. By comparison, there are only 302 single-base differences between the ancestor strain and another strain isolated in the wild. Hypermutation was associated with a deletion resulting from improper prophage excision. Members of this family of prophages are found in other proteobacteria, including well-studied human pathogens, from very different environments. Mutators are known to arise spontaneously in wild and clinical bacteria, but the extent of their adaptive contribution is unknown. We have preliminary evidence that this mechanism of evolution could be relevant in the environment, where horizontal gene transfer and mobile elements play known, significant roles in bacterial evolution.
by Sean Aidan Clarke.
Ph.D.
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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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McCaig, Allison E. "16S ribosomal DNA analysis of marine ammonia-oxidising bacteria." Thesis, University of Aberdeen, 1995. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU543307.
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Nitrification is central to the global cycling of nitrogen and is important for primary production and other processes in marine systems, where nitrogen is generally the limiting nutrient. The majority of studies on nitrification, however, have focused on terrestrial systems, where this process can cause significant losses of N-based fertilisers from agricultural land. Comparatively little is known of nitrification in marine systems and the organisms involved. In addition, technical difficulties in isolation of pure cultures of ammonia-oxidising bacteria have severely restricted studies of species diversity and community structure of these organisms. In this study, molecular technology, based on the 16S ribosomal RNA (rRNA) molecule was applied to the characterisation of marine communities of ammonia-oxidising bacteria. PCR primers were designed for specific amplification of the rRNA gene (rDNA) from ammonia-oxidisers belonging to the beta-subdivision of the Proteobacteria. These primers were used to characterise both enrichment cultures and communities within polluted and unpolluted sediment samples. These studies indicated considerable diversity of beta-subgroup ammonia-oxidisers within marine systems which has not previously been detected. It was also shown that enrichment and isolation techniques select for strains belonging to the genus Nitrosomonas while the majority of sequences obtained by direct analysis of rDNA amplified from total genomic extracts belonged to the genus Nitrosospira. In addition, novel isolation methods were developed which considerably reduced the level of heterotrophic contamination and greatly facilitated isolation of pure cultures. In situ probing, using fluorescently labelled rRNA oligonucleotide probes, indicated that CCD microscopy is less sensitive than UV microscopy alone due to quenching of the signal.
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Cuschieri, Katie Sarah. "Species diversity of aggregate-associated marine ammonia-oxidising bacteria." Thesis, University of Aberdeen, 2000. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU602054.
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Two broad communities can be distinguished in marine systems, those attached to amorphous aggregate material dispersed throughout the water column and those that are freely suspended in the water column (planktonic). It has been suggested that two distinct microbial populations are associated with each habitat due to phenotypic adaptation to the different conditions in aggregates and the surrounding water. The aim of this study was to investigate the diversity of aggregate-associated and planktonic marine ammonia oxidisers (AOBs - the organisms responsible for the rate limiting step in nitrification) in both natural environments and laboratory-reared systems and to determine whether aggregate material selected for particular groups of AOBs. Detection of AOBs relied heavily on the use of molecular analysis of extracted DNA. Thus, a preliminary study was performed to assess whether preferential lysis occurred when representatives of both genera within the B-subgroup AOBs {Nitrosospira multiformis and Nitrosomonas europaea) were exposed to lysis procedures commonly applied to marine samples. Minimal bias existed, with Nitrosomonas europaea proving to be less susceptible to lysis only when the lytic agents (sodium dodecyl sulphate and lysozyme) were absent or at concentrations 100-fold less than those applied in routine environmental extraction. Environmental populations of aggregate-associated and planktonic AOBs in the NW Mediterranean Sea were assessed in summer and winter at stations both within and beyond regions of fresh water inflow (the plume). Molecular analysis involved amplification, by the polymerase chain reaction, of 16S rRNA genes from extracted DNA using AOB-specific primers. Analysis of 16S rDNA sequences coupled with DGGE and specific probing revealed temporal and spatial effects in community structure of AOBs. In the summer, genus level selection of AOBs was observed with Nitrosospira dominating in the aggregate population and Nitrosomonas dominating in the planktonic phase. This was found in the surface waters of geographically distant sites within and outside the plume. Between-site differences were evident in the deeper waters with Nitrosospira-like sequences more abundant in plume diluted waters and Nitrosomonas like sequences more abundant outside this zone, while genus level selection between aggregate-associated and planktonic communities was not detected. In winter, a uniform pattern of AOB distribution emerged with an even distribution of two Nitrosospira sequences at each site on all aggregate and planktonic samples. The AOB community structure of sediment samples was not wholly resolved by application of direct molecular techniques and the culturable diversity was later examined by an enrichment-based approach. A laboratory-reared aggregate system was developed to assess the distribution and selection of inoculated pure and enrichment cultures of AOBs and to assess the effect of sampling technique on the observed community structure. Enclosed vessels containing North Sea water were rotated until aggregation of autochthonous particulate material formed discrete aggregates. No genus level selection of AOBs was observed in aggregate-associated and planktonic communities in North Sea water yet differences in the distribution of closely related sequences within cluster 1 Nitrosospira were observed between the two communities. Observed aggregate and planktonic community structure was affected by the method used to separate the two fractions. Active bacterial production was not necessary for aggregate formation if a pooled suspension of aggregates was sterilised and added to a medium of cell-free filtered sea water. Thus, the successful inoculation and retrieval of an N. multiformis culture within the cell free system suggested that it was appropriate for investigation of the colonisation dynamics of inoculated AOBs.
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Fandino, Laura B. "Molecular ecology of bacteria associated with marine phytoplankton blooms /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2002. http://wwwlib.umi.com/cr/ucsd/fullcit?p3064445.
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Raccagni, Monica. "Organic nitrogen uptake by marine algae : consequences for marine ecosystem functioning and biodiversity." Thesis, University of Plymouth, 2018. http://hdl.handle.net/10026.1/12816.
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Dissolved organic nitrogen (DON) represents a major pool of fixed, reactive nitrogen in marine systems. It is now recognized that this pool can support primary production and the ability of some algal species to exploit DON compounds as sources of Nitrogen (N) may indicate that specific DON components can exert selective pressure on the composition of the phytoplankton community. In this study the ability of monocultures of ecologically-relevant algal species from the English Channel (Emiliania huxleyi, Micromonas pusilla, Alexandrium minutum and Chaetoceros peruvianus) to grow with DON as the only N source was examined using different artificial media. Among the two tested artificial seawater recipes, Aquil* was preferred as it contained lower micronutrient concentrations, and gave better growth results for all used species. In order to constrain the DON uptake to algae alone, a method for bacterial removal was tested using antibiotic additions. Both Slocombe antibiotic mixture (Cefotaxime-Carbenicillin-Kanamycin-AugmentinTM) and Penicillin-Streptomycin-Neomycin used were effective and not toxic to the algae. Incubation with the antibiotic up to 48 hours and a transfer period into antibiotic-free medium after 72 hours proved to be effective. However, the treatment removed bacteria in A. minutum cultures only; further treatment would be required for the other species to be cultured axenically. The ability to use DON was tested for the above mentioned species using the amino acid L-Arginine (ARG) as the sole N source, and growth was compared with nitrate-containing cultures of the same species. All the selected species grew in both NOᴈ‾ and in ARG, reaching lower final densities when incubated with ARG, although these were not significant. This study has shown that E. huxleyi, A. minutum, M. pusilla and C. peruvianus can grow on organic N, either by direct or indirect uptake, and develop comparable biomasses to species using inorganic N. Both C. peruvianus and M. pusilla cultures contained dissolved ammonium at the end of the experimental period, indicating potential indirect use by the algae of organic N converted to inorganic N by bacteria. A. minutum grew in the presence of ARG along with the cosmopolitan E. huxleyi; N-demand estimates, based on the molar concentration of N-ARG consumed, correlated with the final cell density, indicating that the species did not develop on inorganic N produced from ARG mineralisation, but directly on the ON substrate. Since A. minimum has been linked to harmful algal blooms, and E. huxleyi contributes significantly to oceanic CaCOᴈ deposition, their ability to utilise DON has environmental consequences in addition to the oceanic N-budget. Climate change scenarios predict both episodic conditions of elevated rainfall and extended periods of dry conditions leading to variable riverine inputs to coastal areas, altered nitrogen to phosphorus (N:P) ratios, and changes in the inorganic to organic balance of the nutrient pools. Organic N can constitute up to 69 % of the total N pools, respectively, making it crucial, to understand the cycling of this fraction in coastal waters, and how changes in the composition of nutrient pools could impact on marine ecosystem function and health.
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Turon, Rodrigo Marta. "Macro- and micro -symbioses involving sponges: Ecological roles in the marine benthos." Doctoral thesis, Universitat de Barcelona, 2020. http://hdl.handle.net/10803/668685.
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The symbiotic lifestyle represents a fundamental contribution to the diversity of marine ecosystems. Sponges are ideal models to study symbiotic relationships from evolutionary and ecological points of view since they are the most ancient metazoans on Earth, are ubiquitous in the marine benthos, and establish complex symbiosis with both prokaryotes and animals, which in turn harbour their own bacterial communities.
In this thesis, we aim to go deeper into the mechanisms by which sponges establish symbiotic associations with members of the three domains of life, combining taxonomical, ecological, and molecular approaches. We study how sponges acquire their symbiotic microbes and whether these microbes contribute to shape the ecological distribution of their hosts. Moreover, we use the sponge-polychaete relationship as an example of multi-partner symbiosis and study the eukaryotic association from the microbial perspective. Finally, we focus on the less studied domain of life, the archaea, to gain insights into the composition and stability of these symbionts in sponges.
To assess these goals, we characterized the sponge assemblages in two contrasting environments (well-preserved and impacted) of Nha Trang Bay (Vietnam) and selected the most abundant species for the study of their microbiomes. Additionally, four sponge species harbouring thousands of polychaetes were sampled to analyse the relationships sponge-microbes-polychaetes. Sponges and polychaetes were identified and their respective microbiones and the seawater bacterial communities were analysed by high-throughput sequencing of the 16S rRNA gene (V4 region).
We first describe and illustrate the sponges collected to facilitate further taxonomic and faunistic studies in the area. Our samples belonged to 60 species (9 orders, 22 families, and 36 genera) of demosponges. A total of 24 species were added to the already known sponge fauna of Vietnam, from which, 11 species likely represent new species to science. The described species represent an increase of 8 % in the already known sponge list of Vietnam. Our results show that sponge assemblages were more diverse and rich in the well-preserved environments, being dominated by Neofibularia sp. and Aaptos suberitoides in the reefs, and by Monanchora unguiculata, Antho (Antho) sp., and Amphimedon sulcata in rocky habitats. On the other hand, impacted coral reefs were mainly dominated by two abundant species: Clathria reinwardti and Amphimedon paraviridis.
Similar ecological metrics were shown by the sponge microbiomes according to the type of habitat, being more diverse in the well-preserved environments. Morever, the sponge microbiomes of the sponge assemblages from the impacted habitats showed higher intra-species dispersion and lower core size (shared ZOTUs across species replicates) than microbiomes of sponges from the well-preserved environments. In this sense, we propose that the Anna Karenina concept, which states that intraspecific variability is higher in dysbiotic than in healthy individuals, can also be applied at the community level for the study sponge assemblages.
In our study sponges, bacterial communities were highly stable regardless of the environment, whereas some of their associated polychaetes varied depending on the sampling location. Environmental resilience to different habitat conditions was certainly true for bacterial communities of A. sulcata, the solely species that was found abundant in the two contrasting habitats explored.
Moreover, the high overlap in bacteria composition between sponges and seawater suggest microsymbiont acquisition from the environment. In a similar manner, polychaetes were also able to specifically select and enrich some bacteria from their food sponge. Overall, most sequences were shared between biotypes, but at differential abundances, leading to highly specific and stable invertebrate microbiomes, acquired from the environment. Our results support the tenet “Everything is everywhere, but the environment selects”.La vida en simbiosi representa una contribució fonamental a la diversitat dels ecosistemes marins. Les esponges són models ideals per l’estudi de les relacions simbiòtiques des del punt de vista evolutiu i ecològic, ja que són els metazous més antics de la Terra, són ubiqüistes al bentos marí, i estableixen simbiosis complexes amb procariotes i animals, que al seu torn, contenen les seves pròpies comunitats bacterianes. En aquesta tesis, volem aprofundir en els mecanismes pels quals les esponges estableixen associacions amb membres dels tres dominis de vida, combinant eines taxonòmiques, ecològiques i moleculars. Estudiem com les esponges adquireixen els seus microbis simbionts i com aquests microbis contribueixen a modelar la distribució ecològica de les esponges. A més, utilitzem la relació esponja-poliquet com a exemple de simbiosis multi-organisme i estudiem les associacions eucariotes des de un punt de vista microbià. Finalment, ens centrem en el domini de vida menys estudiat, les arqueas, per aprofundir en la composició i estabilitat d’aquests simbionts en esponges. Per assolir aquests objectius, vam caracteritzar els grups d’esponges de dos ambients diferenciats (impactat i ben preservat) de la badia de Nha Trang (Vietnam), i vam seleccionar les espècies més abundants per l’estudi del seu microbioma. Addicionalment, vam mostrejar quatre espècies d’esponges que contenien milers de poliquets per l’anàlisi de les relacions esponja-microbis-poliquets. Els nostres resultats mostren que les comunitats d’esponges eren més riques i diverses en els ambients ben preservats, i els seus microbiomes mostraven variables ecològiques similars, en els dos tipus d’ambients. La majoria de simbiosis estudiades mostraven una gran especificitat i estabilitat, independentment de l’ambient on vivia l’esponja. El gran solapament entre els bacteris de l’aigua i de l’esponja suggereix que hi ha adquisició microbiana de l’ambient. De forma similar, els poliquets també eren capaços d’adquirir específicament bacteris de les esponges de les quals s’alimentaven. En resum, la majoria de seqüències microbianes eren compartides entre els tres habitats estudiats (aigua/esponge/poliquet), però a diferents abundàncies, donant lloc a microbiomes específics i estables adquirits de l’ambient en els dos grups d’invertebrats estudiats .
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Lau, Winnie W. Y. "Understanding interactions between marine bacteria and phytoplankton : the influence of phytoplankton photorespiration on diversity and succession of glycolate-utilizing bacteria /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/11011.
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Coble, Paula G. "Marine bacteria as a source of dissolved fluorescence in the ocean." Woods Hole, Mass. : Woods Hole Oceanographic Institution, 1990. http://catalog.hathitrust.org/api/volumes/oclc/29442088.html.
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Zhang, Rui. "Bacterioplankton in Hong Kong waters : diversity, dynamics, and mortality /." View abstract or full-text, 2007. http://library.ust.hk/cgi/db/thesis.pl?BIOL%202007%20ZHANGR.
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Fjellheim, Anders Jon. "Selection and administration of probiotic bacteria to marine fish larvae." Doctoral thesis, Norwegian University of Science and Technology, Department of Biology, 2006. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-2217.
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Gerard, Jeffery M. "Antibiotic secondary metabolites of bacteria isolated from the marine environment." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/nq25055.pdf.
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Fowler, Emily. "On the molecular diversity of dimethylsulphoniopropionate catabolism by marine bacteria." Thesis, University of East Anglia, 2015. https://ueaeprints.uea.ac.uk/53453/.
Full textAbstract:
Dimethylsulphoniopropionate (DMSP) is the most abundant organic sulphur molecule in the oceans. Its breakdown by marine organisms is important for the global cycling of sulphur, and as a nutrient source for microbial life. In recent years, the molecular basis of DMSP catabolism by marine bacteria has begun to be unravelled, through the discovery of six different DMSP lyases and a DMSP demethylase, as well as downstream pathways. From these studies, it is becoming evident that there is great diversity in the way bacteria breakdown this important molecule. The work presented here further explores and expands our knowledge of this diversity. I have identified a novel DMSP lyase (DddK), which catalyses the cleavage of DMSP into acrylate and dimethyl sulphide (DMS) in the DMS-producing Candidatus Pelgaibacter ubique HTCC1062 - one of the most prolific bacteria on this planet. I have also shown that the γ-proteobacterium Oceanimonas doudoroffii, which has long been a study species for DMSP catabolism, has no fewer than three functional DMSP lyases - DddD, DddP1 and DddP2 - this being the first example of a species outside of the α-proteobacteria having multiple lyases. Additionally, I have presented a thorough bioinformatics analysis of the occurrence and synteny of genes associated with DMSP catabolism within sequenced members of the abundant Roseobacter clade, revealing some interesting patterns which warrant further experimental investigation. Finally, I have shown that the model marine Roseobacter species Ruegeria pomeroyi DSS-3 is able to use DMSP-derived acrylate as a sole carbon source via a fatty acid biosynthesis route, linked to propionate catabolism.
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Segopa, Ellen Kelebogile. "Marine bacteria as a potential source for novel antimicrobial compounds." University of the Western Cape, 2020. http://hdl.handle.net/11394/7828.
Full textAbstract:
>Magister Scientiae - MScThe high rate of rediscovery of known compounds has led to a decline in the discovery of novel natural products. The high biodiversity of organisms growing in extreme conditions such as oceans has led to the increased interest by researchers for their use as a source of novel natural products. Marine bacteria are known for their extensive biosynthetic capacity to produce diverse natural products, which are suitable for various biotechnology applications such as in agriculture, for treatment of fungal plant pathogens, and as antibiotics, for treatment of bacterial infections. This study aimed at discovering novel secondary metabolites from marine bacteria previously associated with novel marine invertebrate species endemic to the South African coast. The methodologies used in this study included a bioassay guided fractionation coupled to genome sequencing and mining. For the bioassay guided fractionation approach, the study first focused on screening marine bacteria for antimicrobial activity when cultured on 4 different media, against fungal strains previously shown to be virulent olive trunk pathogens. In parallel, the bacterial isolates with the most inhibitory activity against the fungal pathogens were also screened for antimicrobial activity against 4 indicator strains including Gram-negative Escherichia coli 1699 (E. coli), Pseudomonas putida, and Gram-positive Staphylococcus epidermidis ATCC14990, and Bacillus cereus ATCC10702. One of the marine bacterial isolates, PE6-126, showed diverse antimicrobial activity including antibacterial and antifungal activity against the tested strains. The genome sequencing data revealed that this isolate was B. cereus based on the average nucleotide identity (ANI) (>99%) to reference strains. antiSMASH analysis of the genome revealed nine predicted secondary metabolite clusters including bacteriocins (2), non-ribosomal peptide synthetase (NRPS) (2), siderophore (1), sactipeptide (1), betalactone (1), linear azol(in)e-containing peptides (LAP) - bacteriocin (1) and a terpene (1). Some of these pathways had low to no sequence similarity to known pathways, indicating the potential of these pathways to produce novel compounds. One of the pathways showed very high sequence similarity to the thuricin CD pathway in Bacillus thuringiensis. Considering that thuricin CD has been reported to have antimicrobial activity against B. cereus (ATCC1072), it was hypothesised that it could also be produced by PE6-126. However, the antimicrobial extract from PE6-126 was tested for sensitivity to proteinase K and heat treatment, which thuricin CD is known to be sensitive to. The results revealed that the antimicrobial activity was not lost after treatment, implying that a different metabolite could be responsible for the anti-B. cereus activity. In addition, PE6-126 initially displayed antimicrobial activity against a multi-drug resistant E. coli 1699, suggesting some of the antimicrobial compound/(s) produced by this strain could potentially be novel. The bioassay-guided fractionation approach coupled to Liquid Chromatography Mass Spectrometry (LC-MS) did not lead to identification of the antimicrobial compound/(s), therefore it remains a question whether the secondary metabolite pathways predicted by antiSMASH lead to the production of the active compound/(s). The results from this study showed that even well studied species have the potential to synthesize as yet undescribed compounds, based on the novelty of some of the pathways. This study highlights the importance of employing a genome-guided approach in drug discovery, as there may be many novel compounds to discover from biosynthetic pathways that have not yet been characterised. Further research is needed to identify the antimicrobial compound/(s) produced by PE6-126.
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Segopa, Ellen Kelebogile. "Marine bacteria as a potential source for novel antimicrobial compounds." University of the Western Cape, 2021. http://hdl.handle.net/11394/7918.
Full textAbstract:
>Magister Scientiae - MScThe high rate of rediscovery of known compounds has led to a decline in the discovery of novel natural products. The high biodiversity of organisms growing in extreme conditions such as oceans has led to the increased interest by researchers for their use as a source of novel natural products. Marine bacteria are known for their extensive biosynthetic capacity to produce diverse natural products, which are suitable for various biotechnology applications such as in agriculture, for treatment of fungal plant pathogens, and as antibiotics, for treatment of bacterial infections. This study aimed at discovering novel secondary metabolites from marine bacteria previously associated with novel marine invertebrate species endemic to the South African coast. The methodologies used in this study included a bioassay guided fractionation coupled to genome sequencing and mining. For the bioassay guided fractionation approach, the study first focused on screening marine bacteria for antimicrobial activity when cultured on 4 different media, against fungal strains previously shown to be virulent olive trunk pathogens. In parallel, the bacterial isolates with the most inhibitory activity against the fungal pathogens were also screened for antimicrobial activity against 4 indicator strains including Gram-negative Escherichia coli 1699 (E. coli), Pseudomonas putida, and Gram-positive Staphylococcus epidermidis ATCC14990, and Bacillus cereus ATCC10702. One of the marine bacterial isolates, PE6-126, showed diverse antimicrobial activity including antibacterial and antifungal activity against the tested strains. The genome sequencing data revealed that this isolate was B. cereus based on the average nucleotide identity (ANI) (>99%) to reference strains. antiSMASH analysis of the genome revealed nine predicted secondary metabolite clusters including bacteriocins (2), non-ribosomal peptide synthetase (NRPS) (2), siderophore (1), sactipeptide (1), betalactone (1), linear azol(in)e-containing peptides (LAP) - bacteriocin (1) and a terpene (1). Some of these pathways had low to no sequence similarity to known pathways, indicating the potential of these pathways to produce novel compounds. One of the pathways showed very high sequence similarity to the thuricin CD pathway in Bacillus thuringiensis. Considering that thuricin CD has been reported to have antimicrobial activity against B. cereus (ATCC1072), it was hypothesised that it could also be produced by PE6-126. However, the antimicrobial extract from PE6-126 was tested for sensitivity to proteinase K and heat treatment, which thuricin CD is known to be sensitive to. The results revealed that the antimicrobial activity was not lost after treatment, implying that a different metabolite could be responsible for the anti-B. cereusactivity. In addition, PE6-126 initially displayed antimicrobial activity against a multi-drug resistant E. coli 1699, suggesting some of the antimicrobial compound/(s) produced by this strain could potentially be novel. The bioassay-guided fractionation approach coupled to Liquid Chromatography Mass Spectrometry (LC-MS) did not lead to identification of the antimicrobial compound/(s), therefore it remains a question whether the secondary metabolite pathways predicted by antiSMASH lead to the production of the active compound/(s).The results from this study showed that even well studied species have the potential to synthesize as yet undescribed compounds, based on the novelty of some of the pathways. This study highlights the importance of employing a genome-guided approach in drug discovery, as there may be many novel compounds to discover from biosynthetic pathways that have not yet been characterised. Further research is needed to identify the antimicrobial compound/(s) produced by PE6-126.
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Harris, Jean Mary. "Relationships between invertebrate detritivores and gut bacteria in marine systems." Doctoral thesis, University of Cape Town, 1992. http://hdl.handle.net/11427/18326.
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Aspects of the feeding strategies and digestive invertebrate-microbial interactions of two saltmarsh thalassinid detritivores, the mudprawn Upogebia africana (Ortmann) and the sandprawn Callianassa kraussi Stebbing were examined. Resources available in their respective habitats were investigated together with the feeding apparatus, diet and digestive enzymes necessary for hydrolysis of refractory compounds of detritus. U. africana inhabits the upper reaches of Langebaan lagoon (Geelbek),. while C. kraussi was sampled near the mouth (Oesterwal). Both species occur intertidally. Physical characteristics of sediment and water fluctuate more widely at Geelbek than at Oesterwal. Geelbek also has higher mud and clay content in the sediment, and greater particulate load in the water. The resources available in both sediment and water from Geelbek were of greater quality (assessed by proportion of living component, C:N ratio) and quantity. In terms of distribution ofthe resource, quality was highest in surface sediments, while quality was greatest at burrow linings. The mode of feeding, gut structure and diet of the two prawn species differ, although gut throughput rates are similar (ca. 6h). U. africana is a filter feeder which non-selectively ingests small particles which are further sorted in the modified filtertype gastric mill into larger particles which enter the midgut, and smaller particles which are channeled into the hepatopancreas. U. africana has a relatively large throughput gut (fore, mid, hind) allowing large meals to be taken. This may be related to its reliance on vascular plant detritus for both carbon and nitrogen requirements, as shown by stable isotope analyses. By contrast, C. kraussi feeds by a combination of deposit feeding and filter feeding.