Dissertations / Theses: 'Microorganismes marins'

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Coll, Lladó Montserrat. "Expressió gènica en microorganismes marins." Doctoral thesis, Universitat Politècnica de Catalunya, 2013. http://hdl.handle.net/10803/129684.

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Ara que es comença a treure l’entrellat -o si més no a tenir una nova perspectiva- de la diversitat de microorganismes present als oceans gràcies a la biologia molecular i a la metagenòmica, el següent pas és esbrinar quines són les noves funcions que aquesta amaga i com són utilitzades i per qui a l’oceà. La regulació de l’expressió gènica és la base de la versatilitat i l’adaptabilitat de qualsevol organisme al medi on viu. De l’estudi dels gens expressats d’un organisme es poden deduir correctament moltes de les característiques del medi on la seva vida es desenvolupa habitualment. En cada situació els organismes expressen solament una part del seus gens, responent tant a factors interns (per exemple el cicle cel·lular) com a factors externs (temperatura, llum, aport de nutrients...). Les tecnologies de seqüenciació massiva també s’han aplicat en l’estudi de l’expressió de les comunitats microbianes marines (metatranscriptòmica). Tanmateix, aquestes tecnologies encara no estan prou optimitzades i sovint proporcionen seqüències que no poden ser assignades a cap gen conegut. En aquesta tesi ens hem plantejat l’estudi de l’expressió gènica dels microorganismes marins a tres escales diferents: a escala de comunitat, de genoma, i de gen. L’esforç més gran ha estat estudiar l’expressió gènica a escala de comunitat, on el nostre repte ha estat desenvolupar una tècnica equivalent als mètodes “d’empremta dactilar” (fingerprinting) del DNA que s’usen de forma rutinària –com la DGGE o l’ARISA- per tal d’explorar la dinàmica dels patrons d’expressió gènica de les comunitats de microbis marins, permetent la comparació d’un gran nombre de mostres a un preu assequible i sense la necessitat prèvia de saber les seqüències dels RNA missatgers. Aquesta tècnica, batejada com a TFA (de “Transcriptome Fingerprinting Analysis”), ens ha permès estudiar I) les variacions estacionals en els patrons d’expressió gènica dels picoeucariotes marins de l’Observatori Microbià de la Badia de Blanes durant 4 anys, i II) les variacions dels patrons d’expressió al llarg d’un gradient espacial horitzontal i vertical i d’un gradient temporal. En ambdós casos, els canvis d’expressió s’han comparat amb els canvis en l’estructura de la comunitat (mitjançant l’ARISA). A escala genòmica hem estudiat la resposta transcripcional global d’un microorganisme heteròtrof a la llum. La llum és responsable d’una gran quantitat de respostes fisiològiques. Una gran part dels microorganismes del mar que utilitzen la llum ho fan mitjançant la fotosíntesis, però existeixen d’altres microorganismes que utilitzen la llum de manera diferent, com els fotoheteròtrofs, que la utilitzen per generar energia però no fixen CO2. En un dels estudis de genòmica ambiental es va descobrir la presència d’una proteïna fotoactiva, la proteorodopsina, associada a un grup de bacteris marins no cultivats. Les proteorodopsines són responsables d’un nou mecanisme de fototrofia als oceans; funcionen com a bombes de protons accionades per la llum que generen un gradient de protons a la membrana per tal de sintetitzar ATP. A escala de gen, en aquesta tesi hem estudiat mitjançant RT-PCR l’expressió del gen de la proteorodopsina en un cultiu d’una flavobacteria marina i hem vist que la llum augmentava els seus nivells d’expressió.
Recent advances have been crucial to understand, or at least to have a new perspective, on the diversity of microorganisms present in the oceans through molecular biology and metagenomics. The next step is to find out what functions are hidden within this diversity and how and when are they used. The regulation of gene expression is the basis of the versatility and adaptability of any living organism to the environment. The study of the genes expressed in an organism can help to deduce many of the characteristics of the environment. Usually, organisms express only a portion of their genes in response to both internal factors (e.g. cell cycle) and external factors (temperature, light, nutrients, etc.). Massive sequencing technologies have also been applied to the study of the expression of genes in marine microbial communities (metatranscriptomics). However, these technologies are not yet sufficiently optimized and often provide sequences that cannot be assigned to known genes. In this PhD thesis I have studied gene expression of marine organisms at three different levels: at the community level, at the genome level, and at the gene level. The major effort was dedicated to gene expression at the community level, where the challenge was to develop a technique equivalent to DNA fingerprinting methods that are routinely used -such as ARISA or DGGE- in order to explore the dynamics of gene expression patterns in marine microbial communities, allowing the comparison of a large number of samples at an affordable price and without the need for prior knowledge of the messenger RNA sequences. This technique, called TFA (from “Transcriptome Fingerprinting Analysis”), has then been used to study I) seasonal variations in gene expression patterns of marine picoeukaryotes at the Blanes Bay Microbial Observatory during 4 years, and II) changes in expression patterns along spatial horizontal and vertical gradients and diel cycles. In both cases, expression changes were compared with changes in community structure (by ARISA). At the genomic level I have studied the global transcriptional response to light of a heterotrophic microorganism. Light is responsible for a large number of physiological responses. A large fraction of marine microorganisms that use light perform photosynthesis, but there are other organisms as photo-heterotrophs, who use light to generate energy but do not fix CO2. At the gene level, we have studied the proteorhodopsin gene expression by RT-PCR in a culture of a marine flavobacterium. In a study of environmental genomics, the presence of this photoactive protein was found to be associated with a group of uncultivated marine bacteria. Proteorhodopsins are responsible of a new mechanism of phototrophy in the oceans; they act as proton pumps powered by light that generate a membrane proton gradient in order to synthesize ATP. In the present study it was found that light increased the expression levels of the proteorhodopsin gene.

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Le, Loarer Alexandre. "Production et caractérisation de métabolites bioactifs issus de microorganismes isolés d'une éponge de la zone océan Indien, Scopalina hapalia." Electronic Thesis or Diss., La Réunion, 2024. https://elgebar.univ-reunion.fr/login?url=http://thesesenligne.univ.run/24_10_A_LELOARER.pdf.

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Ce projet de thèse porte sur la production et la caractérisation de métabolites bioactifs issus de micro-organismes isolés d'une éponge de la zone océan Indien, Scopalina hapalia. Cette éponge, collectée en 2013 à Mayotte a fait l'objet de travaux antérieurs au sein du LCSNSA. Les micro-organismes qui en ont été isolés, ont été cultivés et ont démontrés une ou plusieurs activités anti-âge, activités ciblées durant le projet de recherche européen TASCMAR, auquel a participé le LCSNSA. Ce doctorat s'intègre dans le cadre du nouveau projet de recherche PHAR (Financement FEDER) porté par le LCSNSA et consacré à la valorisation des molécules bioactives issues de la biodiversité de la zone Sud-Ouest de l'Océan Indien. Au cours de ce projet, les bio-activités ciblées seront des activités anti-cancéreuse, anti-âge, anti-malarique et anti-diabétique. Le travail de recherche proposé s'intègre au défi majeur de la stratégie de “croissance bleue” de l'Union Européenne et pourrait permettre de répondre aux priorités de santé publique en lien avec le vieillissement de la population. Pour ce travail de thèse, plusieurs micro-organismes isolés de Scopalina hapalia seront sélectionnés selon leurs activités biologiques démontrées antérieurement. Différentes conditions de cultures seront testées afin de trouver des paramètres favorables à la synthèse des métabolites recherchés. Les productions microbiennes seront analysées chimiquement afin de caractériser les profils métaboliques des microorganismes. Les extraits seront ensuite testés afin de déceler de nouvelles activités biologiques ciblées dans le projet PHAR. Le micro-organisme le plus prometteur sera consécutivement produit à grande échelle afin d'isoler et d'identifier la ou les molécules bioactives. La culture de cette souche microbienne sera ensuite optimisée en utilisant des plans d'expériences ce qui permettra d'explorer plus précisément le potentiel du micro-organisme marin sélectionné
This thesis project focuses on the production and characterization of bioactive metabolites from microorganisms isolated from a sponge from the Indian Ocean zone, Scopalina hapalia. This sponge collected in 2013 in Mayotte has been the subject of previous work within the LCSNSA. The microorganisms that have been isolated have been cultured and have demonstrated one or more anti-aging activities, targeted activities during the European TASCMAR research project, in which the LCSNSA participated. This PhD is part of the new PHAR research project funded by the LCSNSA and dedicated to the valorization of bioactive molecules from the biodiversity of the South West Indian Ocean area. During this project, targeted bio-activities will be anti-cancer, anti-aging, anti-malaric and anti-diabetic activities. The proposed research work is part of the major challenge of the European Union's "blue growth" strategy and could help address public health priorities related to the aging of the population. For this thesis work, several microorganisms isolated from Scopalina hapalia will be selected according to their biological activities previously demonstrated. Different culture conditions will be tested in order to find favorable parameters for the synthesis of the desired metabolites. Microbial production will be analyzed chemically to characterize the metabolic profiles of microorganisms. The extracts will then be tested for new targeted biological activities in the PHAR project. The most promising micro-organism will consecutively be produced on a large scale in order to isolate and identify the bioactive molecule (s). The culture of this microbial strain will then be optimized using experimental designs which will allow more precise exploration of the potential of the selected marine microorganism

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Bensaker, Bachir. "Contribution à la modélisation et à l'identification d'un processus de croissance de micro-organismes marins (Dinophysis acuminata)." Le Havre, 1988. http://www.theses.fr/1988LEHA0002.

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Ce travail présente une contribution à la modélisation et à l'identification d'un processus biologique complexe à l'évolution mal connue. Le processus considéré est l'apparition et le développement des micro-organismes marins toxiques Dionophysis acuminata, ce qui implique d'importantes conséquences économiques et sanitaires. Un premier modèle du type "boîte noire" est construit à partir de l'exploitation de données physiques, chimiques et biologiques prélevées périodiquement sur site. Ce modèle nous a permis de mettre en évidence les principaux facteurs influençant le phénomène et permettra, à l'avenir, de prédire l'évolution du processus et de détecter une prolifération trop importante de ces micro-organismes. En se basant sur la modélisation des mécanismes physiques, chimiques et biologiques élémentaires des principaux facteurs nous avons construit un second modèle dit "de connaissance" afin d'améliorer la compréhension du processus. Ce travail apporte une contribution très importante au projet de réalisation d'un système automatique de prévision des phénomènes d'eaux colorées sur le site d'Antifer.

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Pham, Giang Nam. "Développement de nouveaux antibiotiques dirigés contre des bactéries multirésistantes à partir de microorganismes marins inexploités." Electronic Thesis or Diss., Université Côte d'Azur, 2024. http://www.theses.fr/2024COAZ5028.

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La vaste diversité biologique et chimique dans l'environnement marin en fait une ressource précieuse pour la découverte de nouveaux antibiotiques, en réponse à l'émergence de la crise des antibiotiques à l'échelle mondiale. Cependant, le taux de découverte de nouveaux médicaments d'origine marine semble insuffisant par rapport à son potentiel. Dans un effort pour contribuer à la recherche de composés prometteurs pour le développement de nouveaux antibiotiques, nous avons étudié les métabolites secondaires et l'activité biologique de quatre souches de champignons : Fusarium equiseti, Anthracocystis flocculosa, Scedosporium dehoogii et Amesia nigricolor.En ce qui concerne les composants chimiques, 45 composés ont été isolés, appartenant principalement aux classes des chromones, des alcaloïdes, des polykétides cycliques, des glycolipides, des sesquiterpènes et des naphtalènes. 18 composés (représentant 40 %) ont été identifiés comme nouveaux composés. Les structures de ces composés ont été élucidées en utilisant une combinaison de HRMS, de RMN, de diffraction des rayons X, de méthode de Mosher modifiée et de calculs chimiques quantiques (de ECD et analyse de probabilité ML-J-DP4 et DP4+). Parmi eux, les déhoogiikétones A-B (C3.1-2) isolées du champignon S. dehoogii possédaient des squelettes de bergamotène réarrangés, décrits pour la première fois dans la nature.En ce qui concerne l'activité biologique, six dérivés de fusarochromanone (C2.1-6) isolés de F. equiseti (dont deux sont nouveaux : C2.2, C2.6) ont montré une cytotoxicité allant de forte à modérée sur trois lignées cellulaires testées (RPE1, HCT-116, U2OS). Seuls deux de ces composés ont présenté une activité d'inhibition contre trois (ABL1, JAK3, EphB1) des seize kinases protéiques testées. Seuls trois flocculosines A-C (C3.1-3) sur huit dérivés isolés d'A. flocculosa ont montré une activité antibactérienne contre S. aureus S25. Ces résultats ont révélé la relation structure-activité des dérivés de fusarochromanone et de flocculosine.La equisetin (C2.8) isolée de F. equiseti a présenté une forte activité antibactérienne contre S. aureus S25 mais n'a montré aucune cytotoxicité sur trois lignées cellulaires testées (RPE1, HCT-116, U2OS). Les chaetochromines A et B (C5.7-8) ont présenté une forte activité antibactérienne mais ont montré une toxicité cellulaire allant de faible à modérée sur la lignée cellulaire (THP-1) et les cellules primaires testées (RBC, PBMC), indiquant une possible fenêtre thérapeutique. Ces trois composés méritent d'être étudiés davantage dans les étapes de développement des antibiotiques
The enormous biological and chemical diversity in the marine environment is making it a valuable resource for the discovery of new antibiotics, in response to the emergence of antibiotic crisis worldwide. However, the rate of discovery of new marine-derived drugs seems insufficient compared to its potential. In an effort to contribute to the search for hit compounds for the development of new antibiotics, we investigated the secondảy metabolites and biological activity of four fungi strains: Fusarium equiseti, Anthracocystis flocculosa, Scedosporium dehoogii, and Amesia nigricolor.Regarding chemical components, 45 compounds were isolated, mainly belonging to chromones, alkaloids, cyclic polyketides, glycolipids, sesquiterpenes, and naphthalenes classes. 18 compounds (accounting for 40%) were identified as new compounds. The structures of these compounds were elucidated using a combination of HRMS, NMR, X-ray diffraction, modified Mosher's method, and quantum chemical calculations (ECD, ML-J-DP4, and DP4+ probability analysis). Among them, dehoogiiketones A-B (C3.1-2) isolated from the fungus S. dehoogii possessed rearranged bergamotene skeletons, described for the first time in nature.Regarding biological activity, six fusarochromanone derivatives (C2.1-6) isolated from F. equiseti (two of which are new: C2.2, C2.6) showed cytotoxicity ranging from strong to moderate on three tested cell lines (RPE1, HCT-116, U2OS). Only two of these compounds exhibited inhibition activity against three (ABL1, JAK3, EphB1) out of sixteen tested protein kinases. Only three flocculosins A-C (C3.1-3) out of eight derivatives isolated from A. flocculosa showed antibacterial activity against S. aureus S25. These findings revealed the structure-activity relationship of fusarochromanone and flocculosin derivatives.Equisetin (C2.8) isolated from F. equiseti exhibited strong antibacterial activity against S. aureus S25 but showed no cytotoxicity on three tested cell lines (RPE1, HCT-116, U2OS). Chaetochromins A and B (C5.7-8) exhibited strong antibacterial activity but showed cell toxicity ranging from weak to moderate on tested cell line (THP-1) and primary cells (RBC, PBMC) isolated from the blood of healthy donors, indicating a possible therapeutic window. These three compounds are worthy of further research stages in antibiotic development

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Landreau, Matthieu. "Immobilisation et culture continue en bioréacteur gas-lift de microorganismes marins thermophiles et hyperthermophiles anaérobies." Thesis, Brest, 2016. http://www.theses.fr/2016BRES0015/document.

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Depuis la découverte des cheminées hydrothermales, de multiples travaux ont été menés afin d’en étudier la diversité microbienne. Les inventaires moléculaires réalisés ont ainsi mis en évidence une grande diversité d’espèces qui contraste avec la faible proportion (1 %) d’espèces isolées par approche culturale. Une nouvelle approche d’immobilisation cellulaire par inclusion dans une matrice de polymères (gellane et xanthane) a ainsi été développée pour permettre l’étude de ces communautés thermophiles anaérobies marines. Le système, basé sur la formation d’une émulsion entre une solution de polymères inoculée et de l’huile, permet le piégeage de cellules dans des billes de gel de 1 à 2 mm de diamètre. Les conditions optimales d’immobilisation ont été obtenues pour une émulsion réalisée à 80 °C sous agitation (150 tr/min) à partir d’une solution de gellane (2,5 %) et de xanthane (0,25 %) avec 12 g/L de NaCl et 4 g/L de citrate de sodium, bullée à l’azote et réduit au Na2S avant inoculation. Les billes ont montré une bonne résistance mécanique après 5 semaines d’incubation à des pH compris entre 5,4 et 8, des températures allant jusqu’à 90 °C et des concentrations en NaCl et soufre allant jusqu’à respectivement 80 et 5 g/L. Des cultures en batch de Thermosipho sp. AT1272 et Thermococcus kodakarensis KOD1 immobilisées ont permis d’obtenir des concentrations allant jusqu’à 107 cellules/g de billes et 108 cellules/mL de fraction liquide. Une culture en continu réalisée en bioréacteur gas-lift pendant 41 jours à partir d’une communauté synthétique immobilisée composée de 8 souches (hyper)thermophiles a démontré la capacité de l’immobilisation cellulaire à protéger les cellules face à un stress oxique et à les maintenir (3 des 8 souches) dans le bioréacteur jusqu’à ce que les conditions de culture soient propices à leur croissance. La réactivité de la communauté immobilisée face aux changements environnementaux (température) a également été démontrée. Enfin, la culture en continu réalisée pendant 64 jours d’un échantillon immobilisé de diffuseur du site Rainbow a permis la croissance de plusieurs espèces bactériennes et archéennes (Oceanithermus sp., Thermococcus sp.) dont une partie n’a été détectée que dans les billes (Sulfurimonas sp., Nitratifractor sp., Vibrio sp.) par clonage-séquençage. L’ensemble de ces résultats ont permis de valider l’utilisation d’un protocole d’immobilisation par inclusion dans une matrice de polymères pour l’étude des communautés hydrothermales, de leur diversité et de leur dynamique
Since the discovery of hydrothermal vents, multiple studies have been conducted in order to study microbial diversity. Molecular inventories realized have thus demonstrated a great diversity of species that contrasts with the low proportion (1%) of species isolated by culture approach. A new cell immobilization approach by inclusion in a polymer matrix (gellan and xanthan) has been developed for the study of these thermophilic anaerobic marine communities. The system, based on the formation of an emulsion between an inoculated polymer solution and oil, allows the entrapment of cells in gel beads with a diameter between 1 and 2 mm. The optimal immobilization conditions were obtained for emulsion performed at 80 °C with stirring (150 rpm) with a polymer solution composed of gellan (2.5%) and xanthan (0.25%) with 12 g/L of NaCl and 4 g/L of sodium citrate, bubbled with nitrogen and reduced with Na2S before inoculation. The beads showed a good mechanical stability after a 5-week incubation at pH between 5.4 and 8, temperatures up to 90 °C and NaCl and sulfur concentrations up to respectively 80 and 5 g/L. Batch cultures of immobilized Thermosipho sp. AT1272 and Thermococcus kodakarensis KOD1 yielded concentrations up to 107 cells/g of beads and 108 cells/mL of liquid fraction. A continuous culture performed in a gas-lift bioreactor for 41 days of an immobilized synthetic community composed of 8 (hyper)thermophilic strains demonstrated the capacity of cell immobilization to protect cells from oxique stress and to maintain them (3 of 8 strains) in the bioreactor until having suitable culture conditions for their growth. The reactivity of the immobilized community to environmental change (temperature) was also demonstrated. Finally, the continuous culture performed for 64 days of an immobilized diffuser sample from Rainbow site allowed the growth of several bacterial and archaeal species (Oceanithermus sp., Thermococcus sp.), part of which was detected only in the beads (Sulfurimonas sp., Nitratifractor sp., Vibrio sp.) by cloning-sequencing. All these results have validated the use of an immobilization protocol by inclusion in a polymer matrix for the study of hydrothermal communities, of their diversity and their dynamics

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Bontemps, Nathalie. "Noyau pyridoacridine : structure et synthèse d'alcaloi͏̈des cytotoxiques isolés d'Invertébrés marins." Perpignan, 1996. http://www.theses.fr/1996PERP0240.

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Ce memoire est consacre a la recherche et a l'etude de nouveaux metabolites secondaires a potentialites pharmacologiques isoles d'invertebres marins. La purification biodirigee d'extraits de l'ascidie cystodytes dellechiajei, orientee par un test d'interaction avec l'adn en clhp, a conduit a l'isolement d'un nouvel alcaloide cytotoxique de la famille des pyridoacridines: la cystodamine. Sa structure a ete etablie par des methodes d'analyses spectroscopiques: uv, ir, sm et rmn 1d (#1h et #1#3c) et 2d (dqfcosy, hmbc, hmqc). Afin de confirmer la structure proposee et d'evaluer les potentialites pharmacologiques de cette molecule, sa synthese a ete entreprise. La strategie envisagee passe par la meridine, son analogue hydroxyle isole par f. J. Schmitz de l'ascidie amphicarpa meridiana, et comporte deux types de reactions cles: une addition d'un derive de l'acide de meldrum au niveau d'une fonction amine suivie d'une cyclisation thermique et une reaction de couplage organometallique catalysee par du palladium. La synthese totale de la meridine a pu etre mise au point en 12 etapes avec un rendement global de 9%, ce qui represente une nette amelioration par rapport a la seule synthese publiee a ce jour (0,2%). Le passage de la meridine (oh) a la cystodamine (nh#2) n'a pu aboutir mais l'etude spectroscopique des derives obtenus lors de cette synthese a pu fournir des arguments en faveur de la structure proposee

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Boulanger, Anna. "Recherche de métabolites secondaires marins, d'intêret pharmacologique : étude structurale de cyclodepsipeptides naturels." Perpignan, 1994. http://www.theses.fr/1994PERP0179.

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Cette thèse est consacrée a la recherche et a l'étude de metabolites secondaires cytotoxiques et inhibiteurs enzymatiques des trois ascidies polysyncraton bilobatum, stomozoa murrayi et trididemnum cyanophorum, selon un criblage biodirige ou chimiodirige. Diverses techniques chromatographiques ont permis notamment de purifier les didemnines h et i cyclodepsipeptides antitumoraux dont les structures ont ete determinees par les methodes d'analyse spectrale u. V, i. R. , s. M. , et essentiellement r. M. N. (#1h et #1#3c/1 et 2d).

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Dezaire, Ambre. "Caractérisation de molécules issues de microorganismes associés aux organismes marins, capables d'agir sur les cellules métastatiques du cancer du sein." Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUS010.

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Au stade de carcinome in situ, la tumeur mammaire peut être retirée chirurgicalement. mais, à des stades plus avancés, les cellules tumorales peuvent subir une transition épithélio-mésenchymateuse, devenir invasive et chimioresistante. Les produits naturels représentent la majorité de nos médicaments et La biodiversité marine, dont les micro-organismes, est à l'origine de plusieurs médicaments sur le marché, en oncologie. Notre stratégie consiste en la caractérisation de molécules extraites de 70 souches fongiques associées aux algues brunes. Les extraits bruts et les molécules sont selectionnées sur leur capacité à inhiber la prolifération et la migration des cellules tumorales. Un test de viabilité a mis en évidence un extrait issu d'une souche de Paradendryphiella arenaria, très actif sur la lignée épithéliale MCF7 (IC50 de 0.37 µg / mL) et la lignée invasive MCF7-Sh-WISP2 (0.19 µg /mL). La purification de son extrait a permis l'isolement de la hyalodendrine, très cytotoxique (IC50 de 0.07 µg / mL sur les mcf7 et 0.046 µg / mL sur les MCF7-Sh-WISP2), ainsi qu'un nouveau dérivé de pentanorlanostane et du methoxycarbonyl methyl cholate. L'étude du mécanisme d'action de la hyalodendrine a montre des modifications des protéines p53, HSP60, HSP70 et PRAS40. Parallèlement, un test de migration des cellules MCF7-Sh-WISP2 simplifié en plaque 96 puits, a identifié un extrait brut très actif mais non cytotoxique, de Penicillium echinatum. Les molecules de l'extrait one été etudiee de manière déréplicative par élaboration d'un réseau moléculaire. L'ensemble de ces résultats ont montré le fort potentiel thérapeutique de champignons marins par leurs activités anti-metastatiques
At the in situ carcinoma stage, the breast tumor can be surgically removed. But at later stages, tumor cells can undergo an epithalial-mesenchymal transition, become invasive and chemoresistant. Natural products represent the vast majority of our drugs on the market, especially in oncotherapy. Our experimental strategy consists in isolating and characterizing molecules extracted from 70 fungal strains associated to brown algae. Crude extracts and molecules are then selected for their capacity to inhibit cancer cell proliferation and migration. A first viability assay highlited a crude extract derived from the fungus Paradendryphiella arenaria, very active against the epithelial cancer cell line MCF7 (IC50 of 0.37 µg / mL) and its invasive counterpart MCF7-Sh-WISP2 (0.19 µg / mL). The purification of its extract allowed the isolation of the very cytotoxic hyalodendrin (IC50 of 0.07 µg / mL on MCF7 and 0.046 µg / mL on MCF7-Sh-WISP2), as well as a new pentanorlanostan derivative and the methoxycarbonyl methyl cholate. The mechansim of action of the hyalodendrin revealed p53, HSP60, HSP70 and PRAS40 protein modifications. In parallel, a simplified 96 well plate migration assay let identify a very active but non cytotoxic crude extract, from Penicillium echinatum. The molecules of this extract were studied by dereplication using a molecular network. Together, these results showed the strong therapeutic potential of marine fungi trhough their anti-metastatic activities

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Aigle, Axel. "Connexion entre les cycles de l'azote et du manganèse chez shewanella algae C6G3, isolée de sédiments marins côtiers." Aix-Marseille, 2015. http://www.theses.fr/2015AIXM4092.

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Cornec, Laurence. "Mise en évidence et étude de deux enzymes thermostables : lipase et estérase, de micro-organismes thermophiles isolés d'écosystèmes hydrothermaux sous-marins." Compiègne, 1995. http://www.theses.fr/1995COMPD859.

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Deux activités enzymatiques thermostables -lipase et estérase-, ont été recherchées chez 160 isolats thermophiles, ainsi que sur 133 cultures d'enrichissement dans le cas des lipases, obtenus à partir d'échantillons prélevés au niveau de sources hydrothermales profondes. Le caractère archaeaen et thermophile de la majorité des isolats étudiés a rendu nécessaire un travail d'adaptation des protocoles aux spécificités de ces micro-organismes. Les méthodes ainsi mises au point ont permis de mettre en évidence deux cultures d'enrichissements productrices de lipases, obtenues à 75°C et 95°C. 47 isolats de la collection ainsi que 8 souches de référence ont montré une activité estérase intracellulaire. Trois profils différents d'activité estérasique ont été mis en évidence sur gel d’électrophorèse après révélation colorée spécifiques : simple, double et multi-bandes, respectivement pour 36, 10 et 1 isolats. Il a également été montré que la fréquence de production des estérases s'accroit chez les archaea isolées à haute température et pH acide. L'estérase produite par P. Abyssi souche GE5, archaea isolée à 2000 m de profondeur, et croissant de façon optimale à 96°C, a alors été étudiée de façon plus approfondie. La caractérisation de l'enzyme dans l'extrait brut ainsi que de l'enzyme purifiée a montré une thermostabilité très élevée, supérieure à celle montrée par l'estérase produite par une autre archaea, Sulfolobus acidocaldarius (Sobek et Görisch, 1988). L'estérase de P. Abyssi a été purifiée 187 fois avec un rendement de 11,4% : c'est un monomère de 205-264 kDa, de point isoélectrique égal à 3,6. Elle montre une large spécificité de substrat (aliphatique, aromatique) mais hydrolyse préférentiellement les esters d'acides à courte chaîne. Son comportement est de type michaelien vis-à-vis des esters de para-nitrophénol. L'inhibition par le PMSF suggère la présence de résidu sérine dans le site actif et corrobore l'hypothèse de l'appartenance de l'estérase de P. Abyssi à la classe des carboxylestérases (EC 3. 1. 1. 1), comme le suggérait le profil de spécificité de substrats.

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Ladrat, Christine. "Mise en évidence et étude de deux enzymes thermostables de micro-organismes thermophiles isolés d'écosystèmes hydrothermaux sous-marins." Compiègne, 1993. http://www.theses.fr/1993COMPD586.

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La présence de deux activités enzymatiques thermostables : la beta-glucosidase et l'alcool déshydrogénase (ADH) a été recherchée sur 190 isolats thermophiles obtenus à partir d'échantillons prélevés sur sept sites hydrothermaux (deux dans le bassin de Lau, deux dans le bassin Nord-Fidjien et trois sur la ride du Pacifique oriental). 83 isolats possèdent l'activité beta-glucosidase et seulement 10 l'ADH. L'étude de la thermostabilité de ces enzymes a orienté le travail de caractérisation enzymatique vers deux isolats archaebactériens ultra-thermophiles : l'isolat ST549 pour la beta-glucosidase et l'isolat AL662 pour l'ADH. Une production maximale de beta-glucosidase par l'isolat ST549 a été obtenue avec le milieu BHIS contenant du cellobiose à 5 g1. La caractérisation de l'enzyme dans l'extrait brut ainsi que de l'enzyme purifiée a montré une thermostabilité élevée et une activité optimale à 100°C et à pH 6. La protéine est dimérique, a un poids moléculaire de 130000 daltons et un point isoélectrique de 4,3. L'hydrolyse des substrats ne correspond pas à un comportement michaélien et est activée par le glucose et les polyols tels que le sorbitol et le glycérol. L'étude de la spécificité vis-à-vis des substrats a montré que d'autres activités beta-glycosidases sont associées à l'activité beta-glucosidase. L'alcool-déshydrogénase de l'isolat AL662 est thermostable, présente une activité optimale à 75°C, à pH 8,3 et en présence de NaCl. La protéine n'a pas été totalement purifiée mais montre une spécificité de substrats large et une énantiosélectivité élevée. Le développement d'applications industrielles potentielles passe par une étude plus approfondie des deux enzymes.

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Morineau-Thomas, Odile. "Mise en oeuvre d'un module d'ultrafiltration à écoulement tourbillonnaire non entretenu : application à la séparation de suspensions modèles de bentonite et de plusieurs cultures de microorganismes marins." Nantes, 2001. http://www.theses.fr/2001NANT2072.

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Ce travail est consacré à l'application d'un écoulement tourbillonnaire non entretenu pour la conception d'un module d'ultrafiltration. Ce type d'hydrodynamique est obtenu dans un module annulaire muni d'une entrée tangentielle unique à sa base. Dans un premier temps, une étude comparative a été réalisée entre ce module à écoulement tourbillonnaire et deux autres modules générant des écoulements tangentiels classiques, plan et axial annulaire, lors de l'ultrafiltration de suspensions modèles de bentonite. Le module à écoulement tourbillonnaire permet d'atteindre des flux de perméation augmentés de 70% par rapport à ceux obtenus avec un module tangentiel plan classique pour un gradient pariétal de vitesse moyen à la surface de la membrane égal à 800 s-1. Cette augmentation est fortement liée au caractère tridimensionnel de l'écoulement tourbillonnaire qui induit une érosion supplémentaire du dépôt de particules formé à la surface de la membrane. De plus, la consommation énergétique est diminuée de 10 à 30% par rapport à un procédé comportant une cellule plane dans les mêmes conditions
The present work is devoted to the study of a swirling decaying flow generated by a unique tangential inlet at the bottom of an annular ultrafiltration unit. In a first time, a comparative study has been realized between this swirling module and two other units generating classical tangential flows, plane and axial annular, during the ultrafiltration of model suspensions of bentonite

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Ben, Aissa Fatma. "Ecologie microbienne des systèmes hydrothermaux marins alcalins de la baie de Prony (Nouvelle-Calédonie)." Thesis, Aix-Marseille, 2015. http://www.theses.fr/2015AIXM4760.

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Nous avons étudié l’écologie microbienne d’un site hydrothermal alcalin sous-marin peu profond (0-50 m) localisé dans la baie de Prony (PHF) dans le sud de Nouvelle-Calédonie (Pacifique Sud-Ouest) comparable par son fonctionnement au site hydrothermal alcalin profond (800m) de Lost City (LCHF) (Dorsale médio-atlantique). PHF au même titre que LCHF est un système hydrothermal ultramafique associé à des réactions de serpentinisation des roches du manteau terrestre, libérant des fluides anoxiques très alcalins (jusqu'à pH 11) riche en calcium, en hydrogène et en méthane dissous. Le site hydrothermal de Prony (PHF) est caractérisé par de grandes cheminées de carbonate émettant des fluides dont la température n’excède pas 40°C. Les approches moléculaires ont démontré une prédominance des bactéries (Firmicutes, Deltaproteobacteria …) sur les archées (Methanosarcinales). En ce qui concerne les mises en culture, elles sont restées vaines pour la plupart des grands groupes trophiques recherchés (bactéries sulfato-réductrices, archées méthanogènes) excepté pour les fermentaires relevant du phylum des Firmicutes. Deux nouvelles bactéries appartenant à ce phylum ont été isolées. Il s’agit (i) de Vallitalea pronyensis vraisemblablement associée aux cheminées hydrothermales et (ii) d’Alkaliphilus hydrothermalis qui serait plutôt indigène aux fluides alcalins émis par les cheminées si l’on en juge par ses conditions physico-chimiques optimales de croissance en adéquation avec celles des fluides. Ces deux microorganismes représentent les premiers anaérobies stricts isolés de systèmes hydrothermaux alcalins serpentinisés à ce jour
We studied the microbial ecology of an alkaline hydrothermal submarine shallow field (0-50 m) located in Prony Bay (PHF) in the south of New Caledonia (SW Pacific) similar to the deep alkaline hydrothermal site (800m) of Lost City (LCHF) (Mid-Atlantic Ridge). Similarly to LCHF, PHF is an ultramafic hydrothermal system functioning on the basis of serpentinization reactions of the mantle rocks, releasing anoxic, highly alkaline fluids (to pH 11) rich in calcium, and in dissolved hydrogen and methane. The Prony hydrothermal field (PHF) is characterized by large carbonate chimneys emitting fluids with temperatures not exceeding 40 °C. Molecular approaches revealed a prevalence of Bacteria (Firmicutes, Deltaproteobacteria…) over Archaea (Methanosarcinales). Regarding microbial cultures, they were unsuccessful for most major trophic groups (sulfate-reducing bacteria, methanogens) with the exception of fermentative representatives of the phylum Firmicutes. Two novel bacteria belonging to this phylum were isolated. They include (i) Vallitalea pronyensis which is likely associated with hydrothermal vents and (ii) Alkaliphilus hydrothermalis which should be indigenous to alkaline fluids emitted from chimneys since its growth optimal physicochemical conditions match those of fluids. These two bacteria represent the first anaerobic microorganisms isolated from alkaline hydrothermal serpentinized systems so far

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Bruno, Renato. "Identification, caractérisation et fonctions des peptides antimicrobiens chez les vers extrémophiles." Thesis, Lille 1, 2020. http://www.theses.fr/2020LIL1R036.

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L'intérêt et la demande de nouveaux composés tels que les peptides antimicrobiens (PAMs) se sont accrus au cours des dernières décennies en raison de l'émergence de bactéries multi-drogues résistantes.Les PAMs sont en première ligne de la défense immunitaire innée de tous les organismes: elles apportent une réponse rapide à un large spectre de micro-organismes envahissants (bactéries, champignons, virus et parasites) et un moyen alternatif de les éliminer avec un développement lent de la résistance bactérienne, représentant des nouveaux médicaments potentiels. Ils contribuent également à la symbiose chez les vertébrés et les invertébrés en contrôlant, modelant et confinant la microflore symbiotique dans compartiments anatomiques spécifiques (intestin, bactériomes, peau).La majorité des PAMs ont été trouvées chez les animaux (environ 75%) dont seulement 2% appartiennent à des organismes marins.Dans ce contexte, l'objectif de cette thèse était d'élargir les connaissances actuelles sur les PAMs chez les vers marins extrémophiles, en analysant comment les facteurs externes de l'habitat des vers affectent la structure et la bioactivité des peptides.Le premier chapitre donne un panorama de l'état de l'art sur les différentes structures et fonctions des PAMs chez les vers (annélides et nématodes), afin de souligner la grande diversité et l'originalité de leurs structures primaires, qui imitent les styles de vie et l'écologie très variés des vers.Le deuxième chapitre décrit la recherche de nouveaux groupes de PAMs provenant de trois espèces de nématodes méiobenthiques marins vivant dans sédiments anoxiques. La purification biochimique et l'identification de nouvelles PAMs produites par ces minuscules espèces ont été étudiées, fournissant des preuves que sont des sources intéressantes d'antibiotiques. Les limites de l'application de la méthode biochimique à des animaux aussi petits, non élevés en laboratoire avec une répartition géographique imprévue, ont également été discutées.Le troisième chapitre examine le cas unique de trois membres de la famille BRICHOS-PAM, la polaricine, l'arénicine et l'alvinellacine, issus de polychètes vivant dans des habitats très distincts (respectivement polaire, tempérée et hydrothermales). Nous avons étudié leur adaptation à divers facteurs abiotiques et biotiques, ce qui a permis de mettre en évidence l'adaptation des activités biologiques aux bactéries environnementales et l'influence des températures et du pH sur la sélection naturelle des PAMs. Comme le nombre de ponts disulfure augmente avec la sévérité de l'habitat du ver, nous avons réalisé la même étude sur les analogues PAMs sans ponts disulfure, montrant leur implication dans la stabilité des peptides.Enfin, les rôles du domaine BRICHOS du précurseur de l'alvinellacine ont été étudiés. Nous l’avons produit par recombinaison et avons mis en évidence une fonction de type chaperon dans l'immunité externe des vers, les aidant à affronter des habitats extrêmes.Cette thèse nous permet de conclure que les vers marins extrêmes constituent des sources précieuses de substances bioactives prometteuses, possédant des caractéristiques particulières (structure uniques, pH et thermotolérance). De plus, ils représentent un modèle intéressant pour étudier l'évolution des PAMs, en tant qu'acteurs de la défense immunitaire des vers dans des conditions environnementales extrêmes et fluctuantes
There is a growing interest and demand of new compounds such as antimicrobial peptides (AMPs) during the last decades because of emerging Multi Drugs Resistant bacteria.AMPs are in the first line of innate immune defence of all organisms: they provide a rapid response to a broad spectrum of invading microorganisms (bacteria, fungi, viruses and parasites) and an alternative way to eliminate them (mostly by bacterial membrane disruption) with slow development of bacterial resistance, representing a potential class of new drugs. They also contribute to symbiostasis in vertebrates and invertebrates by controlling, shaping, and confining the symbiotic microflora in specific anatomical compartments (gut, bacteriomes, skin).Most of them (about 75%) come from animals among which only 2% of them belong to marine organisms. Marine AMPs are unique and structurally diverse presumably because they have evolved under the pressure of highly varying physicochemical conditions and high density of bacteria notably proteobacteria, the bacterial family generating the most problematic drug resistances in human at the present time.The recent discovery of abundant and well-adapted worms in several extreme marine environments (polar, hydrothermal, abyssal, polluted, etc.), in co-occurrence with a large number and variety of bacteria, provided the opportunity to study an interesting source of unknown molecules with high antimicrobial potential.In this context, the goal of this PhD was to expand the current knowledge on marine worms AMPs from extreme environments, analyzing how the external factors of worms habitat affect the structure and bioactivity of the peptides. The first chapter gives an overview on the state of the art about the different structures and functions of AMPs in worms (annelids and nematodes), to highlight the wide diversity and originality of their primary structures, that presumably mimics the highly diverse life styles and ecology of worms.The second chapter of this thesis describes the search of new groups of AMPs from three species of marine meiobenthic nematodes inhabiting the anoxic sediments. Biochemical purification and identification of novel AMPs produced by these tiny species were investigated, providing evidences that two of the three Oncholaimidae nematodes sp. constitute interesting sources of small sized antibiotics. The limitations of applying biochemical method to such small animals, not raised in the lab with an unexpectedly random distribution were also discussed. The third chapter examines the unique case of three members of BRICHOS-AMP family, polaricin, arenicin and alvinellacin from polychaetes living highly distinct habitats (polar, temperate and hot chimneys of hydrothermal vents respectively). We studied their adaptation to varying abiotic (thermal and pH variations) and biotic factors (environmental bacterial communities), providing a clear evidence of the adaptation of the biological activities to the environmental bacteria and the influence of the temperatures and the pH on the natural selection of AMPs. Because the number of disulfide bridges of the AMPs increases with the harshness of the worm habitat, we performed the same study with the AMPs devoid of disulfide bonds, showing their involvement in the thermal and pH stability of the peptides. Finally, roles of BRICHOS domain from alvinellacin precursor were investigated. We recombinantly produced it and provide evidences of a chaperone-like function in the external immunity of worms, helping them to face extreme habitats.From this thesis, we can conclude that extreme marine nematodes and annelids constitute valuable sources of promising bioactive substances, possessing peculiar characteristics (such as uncommon structure, pH- and thermo-tolerance). Moreover, they represent a remarkably attractive model to study AMPs evolution, as actors of worm’s immune defence in extreme and fluctuating environmental conditions

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15

Bruno, Renato. "Identification, caractérisation et fonctions des peptides antimicrobiens chez les vers extrémophiles." Electronic Thesis or Diss., Université de Lille (2018-2021), 2020. http://www.theses.fr/2020LILUR036.

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L'intérêt et la demande de nouveaux composés tels que les peptides antimicrobiens (PAMs) se sont accrus au cours des dernières décennies en raison de l'émergence de bactéries multi-drogues résistantes.Les PAMs sont en première ligne de la défense immunitaire innée de tous les organismes: elles apportent une réponse rapide à un large spectre de micro-organismes envahissants (bactéries, champignons, virus et parasites) et un moyen alternatif de les éliminer avec un développement lent de la résistance bactérienne, représentant des nouveaux médicaments potentiels. Ils contribuent également à la symbiose chez les vertébrés et les invertébrés en contrôlant, modelant et confinant la microflore symbiotique dans compartiments anatomiques spécifiques (intestin, bactériomes, peau).La majorité des PAMs ont été trouvées chez les animaux (environ 75%) dont seulement 2% appartiennent à des organismes marins.Dans ce contexte, l'objectif de cette thèse était d'élargir les connaissances actuelles sur les PAMs chez les vers marins extrémophiles, en analysant comment les facteurs externes de l'habitat des vers affectent la structure et la bioactivité des peptides.Le premier chapitre donne un panorama de l'état de l'art sur les différentes structures et fonctions des PAMs chez les vers (annélides et nématodes), afin de souligner la grande diversité et l'originalité de leurs structures primaires, qui imitent les styles de vie et l'écologie très variés des vers.Le deuxième chapitre décrit la recherche de nouveaux groupes de PAMs provenant de trois espèces de nématodes méiobenthiques marins vivant dans sédiments anoxiques. La purification biochimique et l'identification de nouvelles PAMs produites par ces minuscules espèces ont été étudiées, fournissant des preuves que sont des sources intéressantes d'antibiotiques. Les limites de l'application de la méthode biochimique à des animaux aussi petits, non élevés en laboratoire avec une répartition géographique imprévue, ont également été discutées.Le troisième chapitre examine le cas unique de trois membres de la famille BRICHOS-PAM, la polaricine, l'arénicine et l'alvinellacine, issus de polychètes vivant dans des habitats très distincts (respectivement polaire, tempérée et hydrothermales). Nous avons étudié leur adaptation à divers facteurs abiotiques et biotiques, ce qui a permis de mettre en évidence l'adaptation des activités biologiques aux bactéries environnementales et l'influence des températures et du pH sur la sélection naturelle des PAMs. Comme le nombre de ponts disulfure augmente avec la sévérité de l'habitat du ver, nous avons réalisé la même étude sur les analogues PAMs sans ponts disulfure, montrant leur implication dans la stabilité des peptides.Enfin, les rôles du domaine BRICHOS du précurseur de l'alvinellacine ont été étudiés. Nous l’avons produit par recombinaison et avons mis en évidence une fonction de type chaperon dans l'immunité externe des vers, les aidant à affronter des habitats extrêmes.Cette thèse nous permet de conclure que les vers marins extrêmes constituent des sources précieuses de substances bioactives prometteuses, possédant des caractéristiques particulières (structure uniques, pH et thermotolérance). De plus, ils représentent un modèle intéressant pour étudier l'évolution des PAMs, en tant qu'acteurs de la défense immunitaire des vers dans des conditions environnementales extrêmes et fluctuantes
There is a growing interest and demand of new compounds such as antimicrobial peptides (AMPs) during the last decades because of emerging Multi Drugs Resistant bacteria.AMPs are in the first line of innate immune defence of all organisms: they provide a rapid response to a broad spectrum of invading microorganisms (bacteria, fungi, viruses and parasites) and an alternative way to eliminate them (mostly by bacterial membrane disruption) with slow development of bacterial resistance, representing a potential class of new drugs. They also contribute to symbiostasis in vertebrates and invertebrates by controlling, shaping, and confining the symbiotic microflora in specific anatomical compartments (gut, bacteriomes, skin).Most of them (about 75%) come from animals among which only 2% of them belong to marine organisms. Marine AMPs are unique and structurally diverse presumably because they have evolved under the pressure of highly varying physicochemical conditions and high density of bacteria notably proteobacteria, the bacterial family generating the most problematic drug resistances in human at the present time.The recent discovery of abundant and well-adapted worms in several extreme marine environments (polar, hydrothermal, abyssal, polluted, etc.), in co-occurrence with a large number and variety of bacteria, provided the opportunity to study an interesting source of unknown molecules with high antimicrobial potential.In this context, the goal of this PhD was to expand the current knowledge on marine worms AMPs from extreme environments, analyzing how the external factors of worms habitat affect the structure and bioactivity of the peptides. The first chapter gives an overview on the state of the art about the different structures and functions of AMPs in worms (annelids and nematodes), to highlight the wide diversity and originality of their primary structures, that presumably mimics the highly diverse life styles and ecology of worms.The second chapter of this thesis describes the search of new groups of AMPs from three species of marine meiobenthic nematodes inhabiting the anoxic sediments. Biochemical purification and identification of novel AMPs produced by these tiny species were investigated, providing evidences that two of the three Oncholaimidae nematodes sp. constitute interesting sources of small sized antibiotics. The limitations of applying biochemical method to such small animals, not raised in the lab with an unexpectedly random distribution were also discussed. The third chapter examines the unique case of three members of BRICHOS-AMP family, polaricin, arenicin and alvinellacin from polychaetes living highly distinct habitats (polar, temperate and hot chimneys of hydrothermal vents respectively). We studied their adaptation to varying abiotic (thermal and pH variations) and biotic factors (environmental bacterial communities), providing a clear evidence of the adaptation of the biological activities to the environmental bacteria and the influence of the temperatures and the pH on the natural selection of AMPs. Because the number of disulfide bridges of the AMPs increases with the harshness of the worm habitat, we performed the same study with the AMPs devoid of disulfide bonds, showing their involvement in the thermal and pH stability of the peptides. Finally, roles of BRICHOS domain from alvinellacin precursor were investigated. We recombinantly produced it and provide evidences of a chaperone-like function in the external immunity of worms, helping them to face extreme habitats.From this thesis, we can conclude that extreme marine nematodes and annelids constitute valuable sources of promising bioactive substances, possessing peculiar characteristics (such as uncommon structure, pH- and thermo-tolerance). Moreover, they represent a remarkably attractive model to study AMPs evolution, as actors of worm’s immune defence in extreme and fluctuating environmental conditions

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Navarri, Marion. "Métabolites secondaires de champignons de sédiments marins profonds : criblages génétique et fonctionnel et caractérisation structurale de molécules antimicrobiennes." Thesis, Brest, 2016. http://www.theses.fr/2016BRES0127/document.

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La propagation des micro-organismes résistants aux antibiotiques menace le système mondial de santé publique. Pour lutter contre ce phénomène, le renouvellement des molécules utilisées en antibiothérapie est devenu une priorité mondiale. Les antibiotiques étant principalement d’origine microbienne, l’étude des micro-organismes et de leurs métabolites s’est donc renforcée et s’oriente vers des écosystèmes peu explorés comme les biotopes marins.Nous avons exploré les activités antimicrobiennes d’une collection de 183 champignons isoles de sédiments marins profonds et collectés entre 4 et 1884 mètres sous le plancher océanique. Le potentiel de production de métabolites de cette collection a été révélé par un criblage génétique ciblant les PolyKetide synthase (PKS), les Non-Ribosomal Peptide Synthetase (NPRS), les TerPene Synthase (TPS) et les hybrides PKS-NRPS. Après avoir regroupé les isolats en fonction de leur profil MSP PCR, 110 ont été sélectionnés pour un criblage fonctionnel, montrant une forte proportion de champignons filamenteux antimicrobiens (32%).Après extraction et fractionnement, les composés bioactifs de 3 souches ont été caractérisés aux niveaux structural et fonctionnel. Ainsi, O. griseum UBOCC-A-114129 produit la fuscine, la dihydrofuscine, la secofuscine et la dihydrosecofuscine, P. bialowiezense UBOCC-A-114097 produit l’acide mycophénolique et Penicillium sp. produit UBOCC-A-114109 la rugulosine.Parallèlement, des analyses en LC-HRMS, réalisées sur des extraits fongiques, ont révélé un grand nombre de métabolites non décrits dans les bases de données. Les champignons des sédiments marins constituent donc un réservoir de structures originales à explorer
The spreading of antimicrobial resistant microorganisms jeopardizes global health caresystem. To counteract this threat the renewal of antibiotic molecules is a global priority. Antibioticcompounds are mainly originated from microorganisms, so microorganisms and their secondarymetabolites received an increasing interest. The search for new natural antimicrobial compoundsfrom microorganisms gained untapped ecosystems as marine biosphere.We investigated the antimicrobial properties of a fungal collection. The 183 fungal isolateswere collected from deep subseafloor sediment and isolated between 4 and 1,884 meters belowthe seafloor. Secondary metabolites production potential was studied for all isolates in thecollection by screening genes coding PolyKetide Synthase (PKS), Non-Ribosomal Peptide Synthetase(NRPS), TerPene Synthase (TPS) and hybrid PKS-NRPS. After isolates dereplication according to theirMSP-PCR fingerprinting, an antimicrobial screening was performed for 110 isolates, highlighting ahigh proportion of filamentous fungi with antimicrobial properties (32%).After extraction and bio-guided fractionation bioactive metabolites isolated from 3 strains,were characterized in a structural and functional manner: O. griseum UBOCC-A-114129 producedfuscin, dihydrofuscin, secofuscin and dihydrosecofuscine, P. bialowiezense UBOCC-A-114097synthetized mycophenolic acid and Penicillium sp. UBOCC-A-114109 produced rugulosin.In the meantime, LC-HRMS analysis, performed on fungal extracts, showed a great proportionof metabolites not detected in interrogated databases. So, deep subseafloor fungi, represent anuntapped reservoir of original structures to explore

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Noël, Cyril. "Réseaux microbiens de dégradation des hydrocarbures aux interfaces oxie/anoxie des sédiments marins côtiers." Thesis, Pau, 2017. http://www.theses.fr/2017PAUU3038/document.

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Les écosystèmes marins côtiers sont constament soumis à des pollutions, notamment aux hydrocarbures, du fait de leur localisation et de leurs caractéristiques environnementales. Le rôle clé des microorganismes dans la dégradation de ces polluants est aujourd’hui très bien décrit. Toutefois, les conditions d’oxygénation fluctuantes dans ces environnements côtiers, dues aux marées et aux activités de bioturbation de la macrofaune, influencent les communautés microbiennes.Ainsi, ce travail de thèse a eu pour objectif de caractériser, l’assemblage de communautés microbiennes hydrocarbonoclastes de sédiments marins côtiers soumises à des oscillations oxie/anoxie en présence de pétrole lors d’une expérience en bioréacteurs. L’adaptation des bactéries marines hydrocarbonoclastes notamment des genres Alcanivorax et Cycloclasticus vis-à-vis de ces variations d’oxygène a pu être investiguée par oligotypage. Des écotypes ont été identifiés en fonction des conditions d’oxygénation démontrant ainsi les capacités d’adaptation aux conditions oscillantes d’oxygène de ces deux genres. La structure des communautés archéennes (séquençage des transcrits du gène de l’ARNr 16S) n’a pas montré de modification évidente liée aux conditions d’oxygénation démontrant ainsi des capacités d’adaptation et/ou de résistance plus importantes chez ces microorganismes comparées aux communautés bactériennes. Enfin, les analyses métagénomiques ont mis en évidence une réponse fonctionnelle spécifique aux oscillations oxie/anoxie. Ainsi, ces travaux de thèse apportent de nouvelles connaissances sur l’influence des variations d’oxygénation sur les communautés microbiennes et par conséquent sur la dégradation des hydrocarbures au sein des écosystèmes marins côtiers
Coastal marine ecosystems are constantly subject to pollution, particularly hydrocarbons, because of their location and their environmental characteristics. The key role of microorganisms in the degradation of these pollutants is now well described. However, fluctuating oxygenation conditions in these coastal environments, due to tides and macrofauna bioturbation activities influence microbial communities.Thus, this thesis work aimed to characterize the assembly of microbial hydrocarbonoclastic communities of coastal marine sediments subjected to oxic/anoxic oscillations in the presence of oil during a bioreactor experiment. The adaptation of MOHCB, particularly of Alcanivorax and Cycloclasticus genera, to these oxygen variations has been investigated by oligotyping. Ecotypes were identified according to the oxygenation conditions demonstrating adaptation capacities of these two genera to the oscillating oxygen conditions. The structure of archaeal communities (16S rRNA transcript sequencing) did not show any modification related to the oxygenation conditions thus demonstrating greater adaptation and/or resistance capacities in these microorganisms compared to the bacterial communities. Finally, metagenomics analyses revealed a specific functional response to oxic/anoxic oscillations. Thus, this thesis provides new insights into the influence of oxygenation variations on microbial communities and consequently on the degradation of hydrocarbons in coastal marine ecosystems

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Lassudrie, Malwenn. "Effets combinés des dinoflagellés toxiques du genre Alexandrium et d'agents pathogènes sur la physiologie des bivalves." Thesis, Brest, 2014. http://www.theses.fr/2014BRES0113/document.

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Les populations de bivalves exploités subissent régulièrement des épizooties qui affaiblissent voire déciment les stocks, et qui peuvent avoir des conséquences majeures pour l’aquaculture. Ces maladies, dues à des virus, bactéries, ou parasites, se développent particulièrement au printemps et en été. Ces périodes de l’année offrent également des conditions propices aux efflorescences de micro-algues toxiques, dont des dinoflagellés du genre Alexandrium. Ainsi, le risque de co-occurrence d’efflorescences d’Alexandrium sp. et de maladies infectieuses chez les bivalves est élevé. Or, ces micro-algues synthétisent et excrètent des neurotoxines et des composés cytotoxiques responsables d’altérations physiologiques chez les bivalves. L’objectif de cette thèse est d’évaluer les effets combinés d’une exposition à Alexandrium sp. et d’une infection par des agents pathogènes sur la physiologie des bivalves, à travers l’étude de différentes interactions tripartites bivalve – pathogène – Alexandrium sp. Les résultats de ce travail indiquent que différents profils de réponse existent en fonction des espèces impliquées dans ces interactions. Ainsi, une exposition à Alexandrium sp. peut augmenter le taux d’infection par des agents pathogènes chez des bivalves ou au contraire le diminuer. Les réponses hémocytaires associées peuvent traduire l’implication des défenses immunitaires dans ces modulations hôte-pathogène. De plus, l’exposition à des agents pathogènes peut interférer avec le processus d’accumulation de toxines algales dans les tissus des bivalves, illustrant la complexité de ces interactions. Ces résultats, associés à l’observation de lésions tissulaires chez les bivalves peuvent traduire l’altération des activités de nutrition (filtration, digestion…). Ce travail de thèse apporte une meilleure compréhension de l’implication des efflorescences toxiques dans le développement des maladies touchant les bivalves d’intérêt commercial, mais également de l’implication de l’environnement biotique des bivalves sur l’accumulation de phycotoxines réglementées
Bivalve populations undergo regular epidemics that weaken or decimate exploited stocks and thus limit aquaculture. These diseases are caused mainly by viruses, bacteria or parasites, and occur primarily during spring and summer. This period of the year also provides favorable conditions for toxic dinoflagellate blooms, including species of the genus Alexandrium. Thus, the risk of Alexandrium sp. blooms and infectious diseases co-occurring in bivalves is high. However, these micro-algae synthesize and excrete toxins and cytotoxic compounds responsible for physiological changes in bivalves and could lead to an immuno-compromised status.The objective of this thesis is to evaluate the combined effects on bivalve physiology of exposure to the toxic dinoflagellate, Alexandrium sp., and infection by pathogens, through the study of different bivalve - pathogen - Alexandrium sp. tripartite interactions. The results of this work highlight the species-specific nature of these impacts.Thus, exposure to Alexandrium catenella reduces the herpesviruses infection in oyster Crassostrea gigas, whereas the dinoflagellate A. fundyense increases the susceptibility of C. virginica oyster to the parasite Perkinsus marinus, probably via immuno-suppression, as suggested by the partial inhibition of hemocyte responses. Additionally, the effect of a toxic algal bloom on oyster susceptibility to opportunistic diseases when exposed to a new microbial environment (simulating a transfer) was evaluated. Hemocyte responses to a changing microbial environment were suppressed by exposure to A. catenella, although no new bacterial infection was detected.Finally, exposure to pathogens or to a new microbial environment interferes with the processes by which oysters exposed to A. catenella accumulate algal toxins, illustrating the complexity of these interactions. These results provide a better understanding of the involvement of toxic algal blooms in the development of diseases affecting commercial bivalve species, but also of the involvement of the bivalve biotic environment in the accumulation of regulated toxins

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Legentil, Laurent. "Etude d'aza-analogues des alcaloïdes marins de type pyrroloquinoline, wakayine et tsitsikammamines à activité antitumoral potentielle : approche vers la synthèse totale des produits naturels." Toulouse 3, 2004. http://www.theses.fr/2004TOU30283.

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Les alcaloïdes marins wakayine et tsitsikammamines A et B appartiennent à la famille des 1,3,4,5-tetrahydropyrrolo[4,3,2-de]quinolines. Ces molécules présentent des propriétés cytotoxiques qui pourraient être liées à l'inhibition des topoisomérases I et II. La synthèse de deux types d'aza-analogues de ces alcaloïdes a été réalisée (analogues pyrazoloquinolines et pyrroloquinolines). Le noyau pyrazole est obtenu via une réaction de cycloaddition dipolaire [3+2] entre des quinones variées et des espèces diazo-alkyles ou -aryles. Le noyau iminoquinone est ensuite formé par cyclisation intramoléculaire. Les différents intermédiaires de synthèse ont été évalués vis-à-vis de leurs propriétés cytotoxiques in vitro sur 5 lignées cellulaires différentes, ainsi que vis-à-vis de l'inhibition des topoisomérases I et II. De nombreuses molécules inhibent l'une ou les deux topoisomérases alors que peu de composés présentent une activité cytotoxique (de l'ordre du micromolaire). La synthèse totale de ces alcaloïdes a été étudiée. Le schéma de rétrosynthèse est basé sur une réaction d'addition de Michael entre une 3-éthylamine-indole-dione et des β-cétoamines diversement protégées. Un analogue ouvert des tsitsikammamines à ainsi été obtenu
The marine alkaloids wakayin and tsitsikammamines A and B belong to the 1,3,4,5-tetrahydropyrrolo[4,3,2-de]quinolines family. They both possess cytotoxic properties which seem related to inhibition of topoisomérases I and II. Two series of aza-analogues of these compounds (pyrazoloquinolines and pyrroloquinolines analogues) have been investigated. The pyrazole ring was obtained on the basis of a [3+2] dipolar cycloaddition reaction between various quinones and diazo species (alkyls or aryls). The iminoquinone moiety was then formed through an intramolecular cyclisation. The different compounds have been evaluated for both in vitro cytotoxic activity against 5 dictinct cancer cell lines and topoisomérases I and II inhibition. Most of the compounds inhibit one or the two enzymes whereas only few of them exhibit cytotoxic activity with IC50 values of micromolar order. The total synthesis of the natural alkaloids has also been studied. The retrosynthetic pathway was based on a Michael addition between 3-éthylamine-indoledione and different protected β-cétoamines. An original analogue of tsitsikammamines has been obtained

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Bahrou, Andrew S. "Polonium volatilization by tellurite resistant marine microorganisms." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 85 p, 2009. http://proquest.umi.com/pqdweb?did=1885462311&sid=5&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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Doghri, Ibtissem. "Interactions moléculaires entre microorganismes au sein de biofilms en milieu marin : mise en évidence de biomolécules antibiofilm." Thesis, La Rochelle, 2015. http://www.theses.fr/2015LAROS016/document.

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

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Cornejo, Castillo Francisco Miquel. "Diversity, ecology and evolution of marine diazotrophic microorganisms." Doctoral thesis, Universitat Politècnica de Catalunya, 2017. http://hdl.handle.net/10803/461801.

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Biological N2 fixation, the reduction of dinitrogen (N2) gas to biologically available nitrogen, is a fundamental process since it represents a source of new nitrogen for marine life in areas where this important element can be limiting, supporting primary productivity and thus biological carbon export to the deep ocean. This process is performed by the nitrogen-fixing prokaryotic microorganisms (the so-called diazotrophs). However, very little is still known about the identity and ecology of diazotrophs, which largely limits our capacity to understand the global significance of this process, and to predict potential variations in nitrogen fixation upon changes in environmental conditions. In this thesis, we aimed at improving the knowledge on the diversity, ecology and evolution of the marine nitrogen-fixing microorganisms in the open ocean. Most current knowledge on diazotrophic diversity has been obtained using the nifH marker gene, which encodes for a structural protein of the enzymatic complex that performs the N2 fixation reaction. Thus, in Chapter 1 we first conducted a global exploration of the nifH gene extracted from metagenomic data derived from 68 globally distributed stations collected during the Tara Oceans expedition. This approach differs from previous studies in that it does not rely on primers to detect the nifH genes, and thus allows a more quantitative estimation of the contribution of these microorganisms and a more realistic view of their diversity. This study provides a first `primer-free¿ global map of the distribution of open ocean diazotrophic communities across ocean basins and throughout the water column, showing that diazotrophs often occurred at very low abundances, and that in general they were significantly more abundant in the mesopelagic than in photic waters. Likewise, we uncovered novel diversity that had remained unnoticed in all previous primer-based studies, since we demonstrate that more than half of the detected nifH variants cannot be captured by the primers used. This suggests that most diazotroph diversity studies may be disregarding an important fraction of the nitrogen-fixing community members. Among the diazotrophs detected in Chapter 1, the most abundant was the unicellular cyanobacterium C. Atelocyanobacterium thalassa (UCYN-A), which lives in symbiosis with a prymnesiophyte alga and has been shown to be a relevant player in nitrogen fixation. Thus, in Chapter 2 and Chapter 3, we explored aspects related to the ecology, diversity and evolution of this remarkable microorganism. We detected UCYN-A in the South Atlantic Ocean using not only metagenomic approaches but also microscopic visualization techniques (CARD-FISH). This allowed us to unveil that different UCYN-A lineages, UCYN-A1 and UCYN-A2, live in symbiosis with two distinct prymnesiophyte partners of different sizes. Both UCYN-A lineages showed a streamlined genome expression towards nitrogen fixation. We estimated that these two lineages diverged almost 100 Mya under a strong purifying selection process. Finally, in Chapter 3 we focused on the study of UCYN-A3, another lineage of which very little was known, to gain insight into its ecology. Using an array of methods (PCR, qPCR, CARD-FISH and metagenomes) we could visualize and identify for the first time UCYN-A3 and its association with an alga of different size, which suggests that different UCYN-A lineages occupy different planktonic compartments that are not always considered when nitrogen fixation of nifH diversity are studied. Finally, we manage to reconstruct a significant fraction of its genome, establishing that this lineage constitutes a new UCYN-A genomic species. Overall, this thesis has significantly contributed to expand the knowledge on marine diazotrophic organisms, unveiling new diversity and new planktonic compartments that could potentially lead to a better understanding of the marine nitrogen cycle.
La fijación biológica de nitrógeno, es decir, la reducción del nitrógeno (N2) a amonio, es un proceso fundamental ya que representa una fuente de nitrógeno para la vida marina en áreas donde este elemento es limitante, posibilitando la producción primaria y por tanto la exportación de carbono al océano profundo. Este proceso se lleva a cabo por microorganismos procariotas, los llamados diazotrofos. Sin embargo, aún sabemos muy poco sobre la identidad y la ecología de estos microorganismos, lo que limita enormemente nuestra comprensión de la importancia global de este proceso, y nuestra capacidad de predecir cambios en la fijación de N2 ligados a cambios en el ambiente. El objetivo de esta tesis, por tanto, fue ahondar en el conocimiento de la diversidad, ecología y evolución de los microorganismos diazotrofos en el océano. La mayoría del conocimiento actual sobre la diversidad de diazotrofos se deriva del gen marcador nifH, que codifica una proteína estructural del complejo enzimático responsable de la fijación de nitrógeno. Por tanto, en el Capítulo 1 realizamos una exploración global del gen nifH usando datos metagenómicos de 68 estaciones muestreadas durante la campaña oceanográfica Tara Oceans. Nuestra aproximación se diferencia de los estudios anteriores ya que no se basa en el uso de cebadores para detectar el nifH y posibilita por tanto una cuantificación más precisa de la diversidad real. Este estudio representa el primer mapa global (no basado en cebadores) de la distribución de diazotrofos en el océano desde superficie hasta el mesopelágico. Aunque la abundancia de diazotrofos fue muy baja en general, era significativamente mayor en el océano profundo. Asimismo, descubrimos nuevos diazotrofos que habían pasado desapercibidos en los estudios basados en cebadores: más de la mitad de los diazotrofos detectados no se capturan por los cebadores para el nifH. Esto sugiere que la mayoría de estudios previos pueden haber obviado una fracción importante de las comunidades de fijadores de nitrógeno. Entre los diazotrofos detectados en el Capítulo 1, el más abundante fue la cianobacteria unicelular C. Atelocyanobacterium thalassa (UCYN-A), que vive en simbiosis con un alga primnesiofita y que juega un papel importante en la fijación de nitrógeno. En los capítulos 2 y 3 nos dedicamos a estudiar en detalle los aspectos relacionados con la ecología, diversidad y evolución de este diazotrofo. Mediante el análisis de metagenomas y de técnicas de visualización microscópicas como el CARD-FISH pudimos detectar UCYN-A en el atlántico sur, revelando que UCYN-A1 y UCYN-A2, dos linajes diferentes de UCYN-A, viven en simbiosis con dos hospedadores diferentes, dos primnesiofitas de tamaños distintos. Además, el análisis del perfil de expresión del genoma de ambos linajes mostró una dedicación optimizada a la fijación de nitrógeno. La edad de divergencia de UCYN-A se estimó en unos 100 millones de años, y presumiblemente ocurrió bajo presiones evolutivas de tipo estabilizadora. Por último, en el Capítulo 3, nos centramos en el estudio de UCYN-A3, otro linaje del que se sabe muy poco. Mediante el uso de varios métodos (PCR, qPCR, CARD-FISH y metagenomas) se logró visualizar e identificar por primera vez el linaje UCYN-A3 asociado con una alga de tamaño diferente, lo que sugiere que los distintos linajes de UCYN-A ocupan diferentes compartimentos planctónicos que no siempre se consideran en estudios de diversidad de nifH o de fijación de nitrógeno. Finalmente, pudimos reconstruir una fracción importante del genoma de UCYN-A3, estableciendo que representa una especie genómica diferente a las anteriores. En definitiva, esta tesis ha contribuido significativamente al conocimiento de los diazotrofos en el océano mediante el descubrimiento de nueva diversidad como de nuevos compartimentos del plancton donde puede darse la fijación de nitrógeno y que podrían ayudar a entender mejor el ciclo marino del nitrógeno.

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Abd, Elrazak Ahmed Abdo Ahmed. "Production of polyunsaturated fatty acids from marine microorganisms." Thesis, University of Newcastle Upon Tyne, 2012. http://hdl.handle.net/10443/1786.

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Polyunsaturated Fatty Acids (PUFAs), especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are increasingly attracting scientific attention due to their significant health promoting role in the human body. However, the human body lacks the ability to produce them in vivo. The limitations associated with the current sources of ω-3 fatty acids and ω-6 fatty acids from animal and plant sources have led to increased interest in microbial production. Marine bacteria provide a suitable alternative, although the isolation of production strains and the identification of operating conditions must be addressed before manufacturing processes become economically viable. Sea sediment samples were collected from three different environments including Mid Atlantic Ridge, Red Sea and Mediterranean Sea. The isolates were screened for PUFA production using a fast colourimetric method and verified by gas chromatography/mass spectroscopy. The isolated PUFA producers were characterised and identified on the basis of 16S rRNA gene sequencing and analysis. Three different isolates were chosen for this study. These were labelled as 717, 66 and Hus-27. The chosen isolates were subjected to an optimisation study to maximise their productivity. This optimisation strategy included identifying a suitable production medium by applying a statistical design of experiment methodology (Plackett-Burman and Central Composite Design). A chemically defined media was identified for isolates 717 and 66 in order to determine the limiting media components and to study the effect of carbon/nitrogen ratio on the productivity of isolates. As an important step in the process development of the microbial PUFA production, the culture conditions at the bioreactor scale were optimised for isolate 717 using a Response Surface Methodology (RSM) revealing the significant effect of temperature, dissolved oxygen and the interaction between them on the EPA production. Two sets of continuous stirred-tank reactor (CSTR) experiments were also performed to test the effect of growth rates on EPA production and the effect of temperature at constant growth rate as this was identified as the most significant factor affecting EPA production. This optimisation strategy led to a significant increase in the amount of EPA produced by isolates under investigation, where the amount of EPA increased from 9 mg/g biomass, 33 mg/l representing 7.6% of the total fatty acids to 45 mg/g, 350 mg/l representing 25% of the total fatty acids using isolate 717. A significant increase was also achieved using isolate 66 with the amount of EPA increased from 5.5 mg/g, 14 mg/l representing 3.5% of the total fatty acids to 32 mg/g, 285 mg/l representing 15% of the total fatty acids. For isolate Hus-27 the amount of EPA increased from 0.6 mg/g, 3 mg/l representing 2.2% of the total fatty acids to 8 mg/g, 36 mg/l representing 8% of the total fatty acids. The stability of the produced oil and the complete absence of heavy metals in bacterial biomass are considered as an additional benefit of bacterial EPA compared to other sources of PUFA. To our knowledge this is the first report of a bacterial isolate producing EPA with such high yields making large scale manufacture much more economically viable.

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Benazzi, Giuseppe. "Micro fluidic cytometry for analysis of marine microorganisms." Thesis, University of Southampton, 2010. https://eprints.soton.ac.uk/141969/.

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Knowledge of the distribution and concentration of phytoplankton (microscopic algae that live in the oceans) is important, as this reflects and may modify environmentally important events such as pollution, climate change and carbon dioxide sequestration. Optical based flow cytometry has proved to be strategically important for the study of marine environments in general and of phytoplankton in particular because it enables rapid, simultaneous quantitative analysis of multiple optical properties of particles. Unfortunately, cost, complexity and size limit the widespread use of this technique for the study and monitoring of phytoplankton. The objective of this research was to solve some of the above mentioned problems by developing a small device for deployment on remote underwater vehicles (RUV) for in situ flow cytometric analysis of marine organisms. The core of the system was a lab-on-a-chip (LOC) device with a microfluidic channel with integrated optics and electrodes for the detection of the optical and electrical characteristics of phytoplankton. The work describes the design, fabrication, characterisation and testing of various LOC devices, together with data and analysis of results. The devices were able to clearly distinguish different populations of phytoplankton and other micro-particles on the basis of their optical and electrical properties. The systems had performance comparable with commercial instruments. Research also included bio-physical measurements (electro rotation and dielectrophoresis) of marine organisms to allow further modelling of the information obtained from the LOC cytometer.

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Sharma, S. L. "Hydrocarbon degradation by microorganisms from the marine environment." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 1999. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/2938.

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Heindl, Herwig [Verfasser]. "Antimicrobially active microorganisms associated with marine bryozoans / Herwig Heindl." Kiel : Universitätsbibliothek Kiel, 2011. http://d-nb.info/1033824429/34.

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Edwards, Jennifer Lynne. "Genes and proteins involved in polysaccharide colonisation by marine microorganisms." Thesis, University of Liverpool, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.526977.

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Romas, Lisa. "Functional identification of microorganisms that transform mercury in marine sediments." Wright State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=wright1278616625.

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Albakosh, Mouna Abdalhamed. "Identification and characterization of microorganisms associated with marine macroalgae Splachnidium rugosum." University of the Western Cape, 2014. http://hdl.handle.net/11394/4711.

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>Magister Scientiae - MSc
Marine macroalgae are known to carry diverse bacterial communities which interact with their hosts in both harmful and beneficial ways. Algae hosts provide the bacteria with a rich source of carbon in the form of carbohydrate polysaccharides such as fucoidan, agar and alginate, which the bacteria enzymatically degrade. Splachnidium rugosum is a brown alga (Phylum: Phaeophyta) that grows exclusively in the Southern Hemisphere along the temperate shores of South Africa, New Zealand and Australia. While several studies have investigated S. rugosum distribution and fucoidan production, the microbiome of S. rugosum remains largely uncharacterized. Thus, the major objective of the present study was to isolate, identify and characterize epiphytic bacterial communities associated with S. rugosum. Algae were sourced from Rooi Els (Western Cape, South Africa) during winter 2012. Culture based methods relied on a range of selective marine media including marine agar, nutrient sea water agar, nutrient agar and thiosulfate-citrate-bile-salts-sucrose agar to determine the composition and uniqueness of bacterial communities associated with S. rugosum. Epiphytic isolates were identified to species level by 16S rRNA gene sequence analysis and encompassed 39 Gram-negative and 2 Grampositive bacterial taxa. Isolates were classified into four phylogenetic groups, Gamma - Proteobacteria, Alpha-Proteobacteria, Firmicutes and Bacteriodetes. Bacteria belonging to the phylum Gamma-Proteobacteria were the most abundant, with Vibrio and Pseudoalteromonas being the dominant genera. Three isolates with low sequence identity (˂97%) to their closest relatives could possibly represent novel species. These isolates were grouped into the genera Shewanella, Sphingomonas and Sulfitobacter. All bacterial isolates (41) were screened for antimicrobial activity against the following test strains: Escherichia coli, Bacillus cereus, Staphylococcus epidermidis, Mycobacterium smegmatis Micrococcus luteus and Pseudomonas putida. Fifteen isolates (36%) displayed antimicrobial activity against one or more of the test strains, while one isolate (Pseudomonas species) showed broad spectrum antimicrobial activity against all the test strains except for E. coli. This study provides the first account of the diversity and composition of bacterial populations on the surface of S. rugosum, and demonstrates the ability of these bacteria to produce antimicrobial compounds. Despite recent advances in metagenomics, this study highlights the fact that traditional culturing technologies remain a valuable tool for the discovery of novel bioactive compounds of bacterial origin.

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Guidi, B. "ENZYMES FROM MARINE MICROORGANISMS FOR THE PREPARATION OF BIOLOGICALLY ACTIVE MOLECULES." Doctoral thesis, Università degli Studi di Milano, 2018. http://hdl.handle.net/2434/541057.

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This PhD project focuses on the identification, isolation and characterization of new biocatalysts able to generate biologically active molecules with significant enantioselectivity. Through screening, we identified marine strains, from MaCuMBA (Marine Culturable Microorganism for Biotechnological Applications) and BIODEEP (Biotechnologies form the deep) European project collections, which show a marked enantioselectivity on intermediates of molecules of biological interest. Biotransformation substrate range included pramipexole, as main target, but it also embraces other common building blocks for synthetic industrial preparation. The stereoselective reduction of structurally different ketones using halotolerant marine yeasts (Meyerozyma guilliermondii and Rhodotorula mucilaginosa) was studied using cells grown and bio-converted in seawater. The preparation of valuable chemicals through water-saving (bio)processes based on the direct exploitation of seawater is a significant step towards sustainable biocatalysis. By choosing a suitable strain, high yields and stereoselectivity could be achieved in most cases. Notably, high chemoselectivity and enantioselectivity were observed using R. mucilaginosa in the reduction of aromatic β-ketonitriles, which allowed the recovery of the optically pure corresponding alcohols; notably, reduction with whole cells of yeasts generally give a mixture of undesired products, as observed with M. guilliermondii. Keto-reduction potential of thirty-three marine bacterium species was checked and afterwards the possibility to convert this substrate directly into the optically pure amine was investigated: marine bacteria were screened to identify transaminase activity. Based on the previous results in terms of halotolerance and transaminase activity, the marine bacterium strain Virgibacillus pantothenticus 21D was selected for the genome sequencing in order to clone and express an ω-transaminase enzyme. A recombinant non-marine ketoreductase from Pichia glucozyma (KRED1-Pglu) was used for the enantioselective reduction of various cyclic ketones including pramipexole ketone intermediate. Thanks to co-factor recycling system, the purified enzyme showed very promising results. The soluble expression of a novel omega transaminase from a newly isolated halotolerant marine bacterium Virgibacillus pantothenticus was attained. Despite of several standard methodologies applied, the marine wild-type enzyme was total insoluble in E. coli host and it was satisfactorily solubilized by one single-point mutation, allowing the characterization of the new omega transaminase. The enzyme shows an interesting salt and solvent tolerance, in accordance to its origin and it results particularly active on some interesting building blocks molecules.

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Ferreira, Ana Catarina Morouço. "The key enzyme for mannosylglyceramide synthesis in Rhodothermus marinus." Master's thesis, Universidade de Aveiro, 2010. http://hdl.handle.net/10773/904.

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Mestrado em Biologia Aplicada
Na presença de elevadas concentrações de sal no meio de cultura a bactéria halotermofílica Rhodothermus marinus acumula no interior das células compostos orgânicos de baixo peso molecular designados solutos compatíveis. Nestas condições e à temperatura de 65 ºC, este organismo acumula elevados níveis de manosilgliceramida (MGA) e manosilglicerato (MG) e níveis mais baixos de trealose, glutamato e glucose. O soluto manosilgliceramida é um derivado de manosilglicerato no qual o OH do grupo carboxílico é substituído por um grupo amino. Este soluto com carga neutra foi detectado pela primeira vez por RMN na bactéria R. marinus e, até ao momento, não há registo da sua presença ou acumulação em nenhum outro microorganismo. A forma como a bactéria R. marinus gere o seu metabolismo por forma a sintetizar este soluto permanece uma incógnita. Em R. marinus, os dois genes localizados imediatamente a seguir aos dois genes envolvidos na biossíntese de MG codificam duas enzimas, uma identificada como uma “hypothetical protein” com um domínio pertencente à família Acetil transferases e a outra identificada como uma aminoácido desidrogenase. No presente trabalho estudou-se a possibilidade de a enzima aminoácido desidrogenase ser responsável pela libertação de um grupo amino a partir de um aminoácido e a possibilidade da “hypothetical protein” ser responsável pela transferência desse grupo amino para a molécula de manosilglicerato (molécula carregada negativamente) ou para o intermediário fosforilado, o manosil-3-fosfoglicerato (MPG), percursor de manosilglicerato. Realizaram-se ensaios enzimáticos usando extractos celulares de R. marinus e testaram-se diferentes substratos com o objectivo de detectar a síntese de MGA. O produto das reacções foi separado e analisado por cromatografia de camada fina (TLC). O gene que codifica a “hypothetical protein” foi clonado e expresso na estirpe E. coli BL21. Simultaneamente, estudou-se a viabilidade de a estirpe CC-16 de T. thermophilus, uma estirpe naturalmente competente, ser um hospedeiro termofílico adequado para expressão dos genes responsáveis pela síntese de MG e, desta forma perspectivar também a sua utilização como hospedeiro para a sobreprodução do soluto raro, manosilgliceramida. ABSTRACT: The halothermophilic bacterium Rhodothermus marinus has been described to accumulate intracellular solutes at high salt concentrations in the growth medium. In this condition at a temperature of 65ºC this organism accumulates high levels of mannosylglyceramide (MGA) and mannosylglycerate (MG) and low levels of trehalose, glutamate and glucose. Mannosylglyceramide, an ammonia derivative of mannosylglycerate (MG), is an uncharged compatible solute first detected by NMR and, thus far, was only found to accumulate in R. marinus. However, the orchestration of the metabolism of R. marinus for the biosynthesis of this solute remains unknown. In R. marinus, the two genes immediately downstream the genes involved in MG biosynthesis encode two enzymes, one identified as a hypothetical protein with a motif belonging to acetyl transferases family and the other identified as an amino acid dehydrogenase. We investigated the possibility of the later enzyme be the responsible for the release of an amino group from an amino acid donor and the former for the transfer of amino group for MG (negative charge molecule)r for the mannosyl-3-phosphoglycerate (MPG) the phosphorylated precursor of MG. The enzyme assays to detect the production of MGA were carried out using cell extracts of R. marinus. Products were separated and analysed by thin layer chromatography (TLC). Moreover the gene encoding the hypothetical protein was cloned and expressed in E. coli BL21. In parallel, we studied the viability of the genetic amenable T. thermophilus strain CC-16 be a suitable thermophilic host to express genes for the synthesis of MG, prospecting its utilization as a host for the overproduction of the rare solute mannosylglyceramide.

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Mabande, Edmund Rufaro. "Antimicrobial discovery from South African marine algae." University of the Western Cape, 2018. http://hdl.handle.net/11394/6592.

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>Magister Scientiae - MSc
Antimicrobials are chemical compounds that destroy or inhibit the growth of microorganisms. The majority of these antimicrobials are actually natural products or natural product derived with key examples being the pioneer antibiotics penicillin and cephalosporin. Antimicrobials are an extremely important class of therapeutic agents; however, the development of drug resistance and slow pace of new antibiotic discovery is one of the major health issues facing the world today. There is therefore a crucial need to discover and develop new antibacterial agents. In this study, the potential of marine algae as a source of new antibiotics was explored. Crude organic extracts and chromatographic fractions obtained from small-scale extraction of 17 different marine algae were used to prepare a pre-fractionated library that would be tested against several disease causing microorganisms. The activity of the pre-fractionated library and purified compounds was determined against a panel of drug resistant microorganisms namely Acinetobacter baumannii ATCCBAA®-1605™, Enterococcus faecalis ATCC® 51299™, Escherichia coli ATCC® 25922™, Staphylococcus aureus subsp. aureus ATCC® 33591™ and Candida albicans ATCC® 24433™. Finally, cytotoxicity tests of 50 selected library extracts and isolated compounds were done against two cell lines namely MCF-7 (breast cancer) and HEK-293 (kidney embryonic). Based on their antimicrobial activity and interesting chemical profiles, the seaweeds Plocamium sp. and Stypopodium multipartitum were selected for further study. Three new and unusual halogenated monoterpenes (4.16, 4.17 and 4.18) were isolated from Plocamium sp., and an unusual meroditerpenoid (5.8) was isolated from Stypopodium multipartitum. The metabolites were purified using preparative (silica gel) chromatography as well as semipreparative normal phase HPLC. The structures of purified compounds were determined from spectroscopic data, including nuclear magnetic resonance (NMR) spectroscopy. A small library of 153 fractions was generated from collections of South African marine algae. Pre-fractionated crude extracts showed excellent antimicrobial activity against all microbes but particularly against Staphylococcus aureus. The compounds were generally active against the Gram positive bacteria and the yeast. In conclusion, three antimicrobial halogenated monoterpenes and an unusual monoterpene were isolated from a Plocamium sp. and Stypopodium multipartitum respectively. Antimicrobial activity of crude fractions was excellent but that of isolated compounds was not as great as anticipated.

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Krzysiak, Amanda J. "The isolation and characterization of natural products from marine plants and microorganisms /." Electronic version (PDF), 2006. http://dl.uncw.edu/etd/2006/krzysiaka/amandakrzysiak.pdf.

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ZEAITER, ZAHRAA. "TOWARDS THE BIOTECHNOLOGICAL EXPLOITATION OF MARINE MICROORGANISMS: INVESTIGATION ON CULTIVATION, PRESERVATION AND GENETIC MANIPULATION." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2017. http://hdl.handle.net/10281/170815.

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Capaci di colonizzare habitat variegati ed eterogenei e di stabilire interazioni con piante e animali, i microrganismi rappresentano la forma di vita più abbondante e diversa presente sul nostro pianeta. In particolare, i microrganismi marini sono considerati un interessante reservoir di diversità genetica e funzionale, i cui prodotti potrebbero essere sfruttati in molti settori industriali, come, ad esempio, la produzione di composti naturali bioattivi, agenti farmaceutici o enzimi. Tuttavia, a causa della mancanza di efficienti metodi di isolamento e/o di coltivazione, la maggior parte di essi risulta ancora largamente incoltivabile e, di conseguenza, non sfruttabile. Recentemente, la consapevolezza che i microrganismi marini rappresentano una fonte interessante di molecole bioattive sta spingendo l’interesse della comunità scientifica verso questo filone di ricerca, come documentato dagli ultimi bandi pubblicati nei programmi EU e dai relativi progetti finanziati. Un ulteriore ed importante argomento di interesse riguarda l’utilizzo di sistemi di manipolazione genetica applicabili ai microrganismi marini. Generalmente, i sistemi di manipolazione genetica hanno lo scopo di ottenere ceppi che esprimono determinanti genetici desiderati o di inserire, in ceppi selezionati, delle varianti genetiche che codificano per specifici cambiamenti fenotipici. In particolare, una delle applicazioni più interessanti nel campo della microbiologia ambientale è quello di sfruttare i metodi della manipolazione genetica per esplorare l’enorme e sconosciuta risorsa di informazione genetica associata ai campioni ambientali (ad esempio, attraverso la costruzione di librerie metagenomiche nella metagenomica funzionale) e di studiare il potenziale biotecnologico dei microrganismi coltivati (ad esempio per indagare le funzioni geniche). In seguito ad un crescente interesse nei riguardi di questo argomento, la parte iniziale della tesi di dottorato è stata dedicata ad un’accurata analisi della letteratura per poter presentare in una review le metodologie fino ad oggi utilizzate nella manipolazione genetica di ceppi batterici di origine marina. In particolare, l’attenzione è stata rivolta alla trasformazione naturale ed artificiale (specialmente al metodo dell’elettroporazione) e alla coniugazione, poiché applicate con successo su ceppi marini. Il mio progetto di dottorato si è focalizzato sullo studio di alcuni degli aspetti in grado di influenzare lo sfruttamento biotecnologico dei batteri marini, con particolare riferimento alla loro coltivazione, crioconservazione e manipolazione genetica. In primo luogo, ho valutato la capacità di diversi ceppi batterici marini di entrare ed uscire dallo stato definito “vitale ma non coltivabile” (in inglese viable but non culturable, VBNC), dal momento che questa condizione è stata proposta come uno dei motivi responsabili dell’incoltivabilità dei microrganismi ambientali. Una seconda parte del lavoro è stata dedicata al confronto della capacità di crioconservazione di ceppi marini da parte di diversi composti, convenzionali e non, in esperimenti di conservazione a lungo termine. Successivamente, ho valutato la capacità di determinati batteri marini, con interesse biotecnologico, di essere manipolati geneticamente. Infine, l’ultima parte del lavoro è stata dedicata al sequenziamento del genoma di un microrganismo marino isolato dall'interfaccia del bacino anossico ipersalino profondo Discovery, che si trova nel Mar Mediterraneo.
Microorganisms are the most diverse and abundant living organisms on Earth, inhabiting different and heterogeneous terrestrial and aquatic habitats and establishing interactions with plant, animal and human hosts. Particularly, marine microorganisms represent an intriguing reservoir of genetic and functional diversity, the products of which could be exploited in many different industrial sectors; for instance, they can produce bioactive natural compounds, pharmaceutical agents or enzymes useful in industrial applications. However, marine microorganisms are still largely uncultured, and thus unexploited, due to the lack of current efficient isolation and/or cultivation methods. Recently, the awareness that marine microorganisms represent a fascinating source of bioactive molecules is encouraging the interest from the scientific community, as also highlighted by last calls in the EU programs and related funded projects. In this scenario, understanding the genetic manipulation systems to be applied to marine microorganisms represents an important issue too. Genetic manipulation systems are generally aimed at obtaining new improved strains expressing desired genetic determinants or to insert genetic variants encoding for specific phenotypic changes. Particularly, one of the most interesting applications in the field of environmental microbiology is to exploit genetic manipulation methodologies to explore the enormous undiscovered source of genetic information associated to the environmental samples (e.g. by the construction of metagenomics libraries in functional metagenomics) and to study the biotechnological potential of cultured microorganisms (e.g. to investigate gene functions). Since the increasing interest on this topic, an initial part of this PhD thesis has been devoted to a thorough analysis of the literature in order to present in a review the genetic manipulation methodologies hitherto applied on marine strains. In particular, the attention has been directed to natural and artificial transformation (especially electroporation) and conjugation, since they have been successfully applied to marine strains. The aim of my PhD project was to investigate those aspects that could affect the biotechnological exploitation of marine bacteria, i.e. cultivation of novel strains, cryopreservation of isolated ones and their genetic manipulation. First, I evaluated the ability of several marine bacteria to enter and exit from the state defined as “viable but non culturable” (VBNC), since this state has been proposed as one of the putative reasons for the uncultivability of environmental microorganisms. A second part of the work has been dedicated to the comparison of the protection property of several compounds, conventional or not, used as bacterial cryo-protectants, in long-term conservation experiments and testing different marine strains. Then, I assessed the capability of selected strains with biotechnological interest to be genetically manipulated. Finally, last part of the work has been devoted to the genome sequencing of a marine bacterium isolated from the interface of the deep hypersaline anoxic basin Discovery, located in the Mediterranean Sea. In conclusion, a better comprehension of mechanisms driving the entrance of marine microorganisms in the VBNC state and the resuscitation from it, their criopreservation and genetic manipulation procedures would contribute to improve the different stages of the marine biodiscovery pipeline.

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35

Rufaro, Mabande Edmund. "Antimicrobial discovery from South African marine algae." University of the Western Cape, 2018. http://hdl.handle.net/11394/6529.

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>Magister Scientiae - MSc
Antimicrobials are chemical compounds that destroy or inhibit the growth of microorganisms. The majority of these antimicrobials are actually natural products or natural product derived with key examples being the pioneer antibiotics penicillin and cephalosporin. Antimicrobials are an extremely important class of therapeutic agents; however, the development of drug resistance and slow pace of new antibiotic discovery is one of the major health issues facing the world today. There is therefore a crucial need to discover and develop new antibacterial agents. In this study, the potential of marine algae as a source of new antibiotics was explored. Crude organic extracts and chromatographic fractions obtained from small-scale extraction of 17 different marine algae were used to prepare a pre-fractionated library that would be tested against several disease causing microorganisms. The activity of the pre-fractionated library and purified compounds was determined against a panel of drug resistant microorganisms namely Acinetobacter baumannii ATCCBAA®-1605™, Enterococcus faecalis ATCC® 51299™, Escherichia coli ATCC® 25922™, Staphylococcus aureus subsp. aureus ATCC® 33591™ and Candida albicans ATCC® 24433™. Finally, cytotoxicity tests of 50 selected library extracts and isolated compounds were done against two cell lines namely MCF-7 (breast cancer) and HEK-293 (kidney embryonic).

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36

Lowe, Kristine L. "Biogeochemical cycling of metals in redox-stratified marine environments : role of anaerobic microorganisms." Diss., Georgia Institute of Technology, 1999. http://hdl.handle.net/1853/25187.

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Sunkel, Vanessa Ann. "The investigation of novel marine microorganisms for the production of biologically active metabolites." Thesis, Rhodes University, 2009. http://hdl.handle.net/10962/d1004579.

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New drugs, particularly antibiotics, are urgently required to combat the increasing problem of antibiotic resistant human pathogens. Due to the scarcity of products available today, the pharmaceutical industry is now under pressure to reassess compounds derived from plants, soil and marine organisms. Pharmaceutical companies are showing renewed interest in marine biotechnology as the oceans represent a rich source of both biological and chemical diversity of novel molecular structures with anti-cancer, anti-inflammatory and antibiotic properties. Formerly unexplored locations, such as deep ocean sediments, show great potential as a source of genetically novel microorganisms producing structurally unique secondary metabolites. In this research, a metabolite producing marine Pseudoalteromonas strain, known as AP5, was initially used to develop methods for the detection, optimisation of production and extraction of bioactive metabolites from other potentially novel marine isolates. Two hundred and seventy six (276) marine isolates from water and sediment samples from the Antarctic Ocean and Marion Island were isolated. Ten visually different isolates were screened for bioactivity against Gram-positive and -negative bacteria, fungi and yeast. Three out of the 10 isolates, WL61 , WL 114 and WL 136, appeared to be novel Streptomyces spp. showing activity against different test organisms. Many of these marine microorganisms are difficult to culture in the laboratory, particularly when they are cultivated continuously in shake flasks as they can stop producing bioactive compounds. The cultivation of marine isolates in bioreactors may be a more beneficial process for the optimisation of metabolite production compared to conventional liquid fermentation techniques whereby the solid-liquid-air interface of membrane bioreactors can imitate the natural environment of microbes. The membrane bioreactor system is a stable growth environment with low shear that supports steady-state biofilm growth consisting of a high cell density due to a high mass transfer of nutrients and oxygen to the cells. This approach was employed and isolates WL61, WL114 and WL136 were immobilised onto ceramic membranes using Quorus single fibre bioreactors (SFR). The SFRs were used to establish the most suitable growth medium for continuous secondary metabolite production. The best growth conditions were applied to the Quorus multifibre bioreactor (MFR) for scale up of biologically active metabolites, highlighting the potential of bioreactor technology for use in bioprospecting for isolating and screening novel and known organisms for new and interesting natural products. Furthermore, the Quorus MFR was shown to be suitable for the production of high yields of antimicrobial metabolites and is an efficient new fermentation production system. Purification by HPLC fractionation was used to characterise four major compounds from isolate WL 114 extracts. NMR structure elucidation identified one of the two primary compounds as Bisphenol A. The complete chemical structure for the second potent bioactive compound could not be determined due to the low concentration and volume of material.
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Loukas, Christos-Moritz. "Lab-on-a-chip technology for in situ molecular analysis of marine microorganisms." Thesis, University of Southampton, 2016. https://eprints.soton.ac.uk/404272/.

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In situ monitoring of ocean biology is typically done in the form of sample collection during ship based cruises or other field expeditions, and sample analysis either on-board the ship or in a laboratory at a later time. However such expeditions can be expensive, labour intensive, and only follow pre-defined courses and locations. Alternative methods are used and in development in an effort to provide flexibility and reduced costs. Molecular methods are valuable tools in ecological studies, offering high specificity, reliability and excellent limits of detection. Techniques including polymerase chain reaction (PCR) and nucleic acid sequence based amplification (NASBA) are now routinely used for the monitoring of microorganisms in water (e.g. pathogens, biotoxins and viruses). The use of these techniques, however, is time consuming, costly, and requires substantial training and specially adapted laboratories, making them impractical in many field applications or where infrastructure is limited. Recent advances in microfluidic research have demonstrated that molecular techniques (e.g. qPCR, NASBA) can be applied on lab-on-a-chip (LOC) systems for the in situ detection of target organisms or biomarkers in natural waters. Microfluidic devices (i.e. LOC systems) can automatically perform multiple laboratory functions on a single integrated and compact chip. NASBA is particularly attractive for LOC applications targeting RNA, because it is an isothermal amplification assay and does not require complex microfluidic systems. A NASBA assay, targeting toxic microalgae Karenia brevis, has been successfully automated using a LOC-based, bench-top sensor “LabCardReader” here at the National Oceanography Centre of Southampton (NOCS). The purpose of this work has been to develop and optimise a fully automated molecular assay on a novel lab-on-a-chip system, which performs RNA-based amplification, for the detection and quantification of marine microorganisms. This PhD provides significant developments in the field of lab-on-chip technology, as well as in situ sample collection and processing for harmful algal bloom (HAB) monitoring. This thesis reports on (1) the optimisation of an internal control (IC) NASBA assay for the detection and quantification of microorganisms while examining the validity of the technique under varying physiological states and growth conditions; (2) the long-term preservation and storage of NASBA reaction components; (3) the development of a fully automated, fully preserved, lab-on-a-chip-based IC-NASBA protocol for real-time detection and quantification of microorganisms; (4) the development of a simple, rapid, and reliable sample collection and concentration method, aimed for in situ application and compatibility with nucleic acid analysis techniques.

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Cheung, Ka-hong. "Chromate toxicity assessment and detoxification by bacteria from the marine environment /." View the Table of Contents & Abstract, 2006. http://sunzi.lib.hku.hk/hkuto/record/B36249890.

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Matobole, Relebohile Matthew. "Matrix comparison of isolation conditions for secondary metabolite producing marine sponge associated bacteria." University of the Western Cape, 2015. http://hdl.handle.net/11394/4754.

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>Magister Scientiae - MSc
The discovery of novel secondary metabolites has declined significantly in recent years whereas there is a rise in the number of multi-drug resistant pathogens and other types of diseases. The decline in natural product discovery was due to high rediscovery of already known compounds and the costs in developing natural products. As a result pharmaceutical companies lost interest in investing in natural product discovery. However, there is a renewed interest in marine sponge associated microorganisms as a rich and untapped source of secondary metabolites. The objective of this study was to design a matrix to investigate the extent to which the One Strain-Many Compounds (OSMAC) approach applies to a collection of marine sponge isolates harvested from two South African marine sponge samples. Terminal restriction fragment length polymorphisms (T-RFLP) analysis was used to investigate and ascertain the two marine sponges which hosted the highest microbial diversities to be used for further culture-dependent studies. The culture-dependent studies, using 33 media which included liquid enrichment, heat treatments and antibiotic treatments, resulted in 400 sponge isolates from the two marine sponges Isodictya compressa and Higginsia bidentifera. Using antibacterial overlay assays, 31 dereplicated isolates showed antibacterial activity. Bioactivities were also exhibited against E. coli 1699 which is genetically engineered for resistance against 52 antibiotics which implies that some of the bioactive compounds could be novel. The 16S rRNA gene sequences revealed that the microbial phyla isolated from the marine sponges belonged to Actinobacteria, Firmicutes and Proteobacteria (Alphaproteobacteria and Gammaproteobacteria).Thirty isolates were selected for an OSMAC-based matrix study, 17 of which showed noantibacterial activities in preliminary screening. The application of the OSMAC approach using co-culture and 36 culture conditions resulted in 6 isolates showing antibacterial activities, three of which did not show activities in preliminary screening. One of these, a Bacillus pumilus isolated from I. compressa displayed antibacterial activity against 5 indicator strains whereas in preliminary screening it had not shown activity. The results show that marine sponges can host novel microbial species which may produce novel bioactive compounds. The results also confirm that traditional methods employing a single culture condition restricts the expression of some biosynthetic pathways of microorganisms and as a result many metabolites have yet to be identified.

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Berglund, Johnny. "Pelagic microorganisms in the northern Baltic Sea : Ecology, diversity and food web dynamics." Doctoral thesis, Umeå : Univ, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-618.

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Frouel, Stéphane. "Effets probiotiques de préparations bactériennes commerciales en aquaculture marine." Caen, 2007. http://www.theses.fr/2007CAEN2005.

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Le potentiel probiotique de préparations microbiennes commerciales basées sur 2 lactobacilles et leur milieu de culture a été testé sur les premiers stades d’animaux marins (bar Dicentrarchus labrax, crevettes Litopenaeus stylirostris, artémies Artemia salina et coquilles St Jacques Pecten maximus). In vitro, les 2 souches tolérent les conditions marines et exercent un antagonisme contre des bactéries pathogènes probablement par sécrétion d’acides organiques. In situ, cette activité a été très peu retrouvée mais ces préparations améliorent la survie de tous les animaux excepté Pecten maximus. Aussi la croissance chez les crustacés est corrélée à une augmentation des activités enzymatiques digestives (trypsine et alpha-amylase). Chez le bar, on a observé également une stimulation de la phosphatase acide et l’apparition de vésicules d’endocytose au niveau des entérocytes qui pourraient intervenir dans le système immunitaire car des effets positifs ont été notés sur quelques paramètres immuns du tissu sanguin. L’influence des produits sur la microflore n’est manifeste que chez les larves de crevettes avec une diminution des Vibrios. Les différents essais ont montré que l’activité des produits résultent plus du milieu modifié par les bactéries que des souches elles-mêmes. Aussi, un biotest développé avec Artemia salina (modèle réagissant de manière identique aux crevettes à ces produits microbiens) a permis d’initier la purification de molécules bioactives contenues dans ces produits. Deux protéines de poids moléculaires de 50 KDa et 68 KDa stimulant les activités enzymatiques digestives des artémies ont été partiellement purifiées. Leur caractérisation est en cours
The probiotic potential of commercial bacterial preparations based on 2 lactobacilli and their medium was tested on the early stages of several marine organisms (seabass Dicentrarchus labrax, shrimp Litopenaeus stylirostris, brine shrimp Artemia salina and french scallop Pecten maximus). In vitro, the 2 strains were resistant to the marine conditions and displayed a good antimicrobial activity, probably due to the secretion of organic acids. In situ, these preparations enhanced survival of all animals, except Pecten maximus. Moreover, growth of crustaceans was correlated with an increase of digestive activities (trypsin and alpha-amylase). In seabass, the acide phosphatase was also stimulated and endocytosis vesicles appeared in enterocytes. They might be involved in the stimulation of immune system because some positive effects were observed on immune parameters of blood. Bacterial microflora was changed by the products only in shrimp larvae with a decrease of vibrios. The different experiments have displayed that microbial product activity was due more to the culture media modified by lactobacilli than the strains themselves. Thus, a biotest developed with Artemia salina (which reacted of similar manner as larval shrimp to these microbial preparations), allowed to initiate the purification of the bioactive molecules contained in these products. Two proteins with respective molecular weight of 50 KDa and 68 KDa seemed to play a major role in stimulation of digestive enzymatic activity of these artemia. They were partially purified and their characterization is in progress

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43

Jackson, S. M. "An investigation of the biology of marine fouling microorganisms with special reference to biocide control." Thesis, University of Portsmouth, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.234694.

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Witowski, Chris G. "Investigation of Bioactive Metabolites from the Antarctic Sponge Dendrilla membranosa and Marine Microorganisms." Scholar Commons, 2015. https://scholarcommons.usf.edu/etd/5602.

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Natural products continue to be a valuable source of compounds in research involving chemical ecology and drug discovery. Secondary metabolites are biosynthesized to benefit the host organism in its environment (feeding deterrence from predators, antibiotic properties to avoid infection, etc.) but these compounds also serve as useful scaffolds in drug discovery applications. The research herein describes both aspects of these two branches of natural products chemistry. The Antarctic sponge Dendrilla membranosa produces diterpenes, of which membranolide A, deters feeding of the predatory amphipod Gondogenia antarctica. A metabolomic study of several sponges was undertaken to determine environmental factors that govern the metabolism of D. membranosa. Habitat specificity, above or below the algal canopy, was a significant factor for the chemical clustering of sponges as well as the abundance of potential amphipod predators that are prevalent within the canopy. Another D. membranosa diterpene, aplysulphurin, undergoes degradation upon methanolic treatment to form the methoxy membranolides B-H. An investigation of these artifacts reveals potent activity against the leishmaniasis-causing parasite Leishmania donovani. Microorganisms also generate a significant number of bioactive natural products. Biotic and abiotic culture stressors such as co-culturing and epigenetic modification, respectively, will be explored to turn on cryptic biosynthetic pathways. These techniques are shown to produce unique secondary metabolites from cultures and further reinforce the one strain many compounds approach to the versatile and formidable microbial domain.

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Cheung, Ka-hong, and 張嘉康. "Chromate toxicity assessment and detoxification by bacteria from the marine environment." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B45015351.

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Musat, Niculina. "Molecular characterization of symbiotic associations between chemoautotrophic sulfur-oxidizing microorganisms and nematodes in shallow marine sediments." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=983618240.

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Boudaud, Nicolas. "Apport de la spectroscopie IRTF dans la caractérisation polyphasique de microorganismes impliqués dans les phénomènes de corrosion marine." Caen, 2008. http://www.theses.fr/2008CAEN2017.

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Les processus de Corrosion Induite par les Microorganismes (CIM) dépendent de la nature et du métabolisme des communautés bactériennes colonisant le biofilm et des propriétés intrinsèques de celui-ci, se développant sur les surfaces métalliques sous l’influence des paramètres physico-chimiques régis par l’environnement marin. Les Bactéries Sulfato-Réductrices (BSR) et les Bactéries Thiosulfato-Réductrices (BTR) sont décrites comme particulièrement agressives vis-à-vis des matériaux métalliques immergés. Dans le but d’étudier cette flore particulière, une spectrothèque sulfurogène de référence a été créée selon des conditions de culture spécifiques et standardisées. L’analyse des spectres infrarouges de vingt-deux BSR et BTR de collection a démontré une claire discrimination de ces souches au niveau genre. Cette base de données spectrales a ensuite été utilisée à des fins phénotypiques et comparatives pour caractériser la biodiversité bactérienne anaérobie cultivable, potentiellement impliquée dans la corrosion localisée et accélérée de coupons métalliques en acier au carbone immergés douze mois dans trois sites portuaires différents. En parallèle, cette biodiversité a été évaluée par des méthodes de biologie moléculaire et chromatographiques. Les résultats obtenus à partir de ce système expérimental ont mis en évidence des profils de corrosion atypiques et fonction des zones d’immersion. L’analyse des complexes « dépôts-biofilms » a montré que selon les méthodes culturales employées, trois communautés bactériennes majeures se distinguent : le genre Vibrio (communauté dominante), le genre Desulfovibrio (groupe métabolique potentiellement corrosif) et le groupe des Clostridiales (communauté émergente). En prolongement, les potentialités de la spectroscopie IRTF pour la caractérisation de bactéries d’implication corrosive ont permis d’ouvrir des perspectives sur une étude industrielle appliquée. La mise en œuvre de ce projet a contribué à démontrer l’influence des communautés bactériennes sur le caractère « actif » ou « passif » de biofilms formés sur des matériaux métalliques en acier inoxydable
Microbiologically Induced Corrosion (MIC) depends on the nature and metabolism of the microbial communities constituting the biofilm and the intrinsic properties of biofilm, developing on metallic surfaces under the influence of the physical and chemical environmental parameters. Sulfate-Reducing Bacteria (SRB) and Thiosulfate-Reducing Bacteria (TRB) are described to be particularly aggressive against immersed metallic materials. In order to study this particular flora, a sulfurogen reference library was created according to specific culture conditions. The analysis of infrared spectra of twenty-two SRB and TRB collection strains prove a clearly discrimination at the genus level. This spectral database was then used for comparative and phenotypic purposes to characterize biodiversity of cultivable anaerobic bacteria, potentially involved in accelerated localized corrosion of carbon steel coupons These coupons have been immersed twelve months in three different harbour zones (Le Havre, Marseille et Saint Nazaire). In parallel, this biodiversity was also evaluated by molecular and chromatographic methods. The obtained results from this experimental system have shown various atypical corrosion profiles according to immersed zones. The analysis of “deposits-biofilms" complexes showed that according to the cultivate methods used, three leading bacterial communities can be distinguished: the Vibrio genus (dominant community), the Desulfovibrio genus (metabolic group potentially corrosive) and the Clostridiales group (emergent community). By extension, potentialities of FT-IR spectroscopy for characterization of corrosive bacteria have paved the way to an applied industrial study. The implementation of this project has contributed to demonstrate the influence of bacterial communities on the "active" or "passive" character of biofilms formed on stainless steel materials

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Flores, Gilberto Eugene. "Microbial Ecology of Active Marine Hydrothermal Vent Deposits: The Influence of Geologic Setting on Microbial Communities." PDXScholar, 2011. https://pdxscholar.library.pdx.edu/open_access_etds/250.

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The discovery of deep-sea hydrothermal vents in 1977 revealed an ecosystem supported by chemosynthesis with a rich diversity of invertebrates, Archaea and Bacteria. While the invertebrate vent communities are largely composed of endemic species and exist in different biogeographical provinces, the possible factors influencing the distribution patterns of free-living Archaea and Bacteria are still being explored. In particular, how differences in the geologic setting of vent fields influence microbial communities and populations associated with active vent deposits remains largely unknown. The overall goal of the studies presented in this dissertation was to examine the links between the geologic setting of hydrothermal vent fields and microorganisms associated with actively venting mineral deposits at two levels of biological organization. At the community level, bar-coded pyrosequencing of a segment of the archaeal and bacterial 16S rRNA gene was employed to characterize and compare the microbial communities associated with numerous deposits from several geochemically different vent fields. Results from these studies suggest that factors influencing end-member fluid chemistry, such as host-rock composition and degassing of magmatic volatiles, help to structure the microbial communities at the vent field scale. At the population level, targeted cultivation-dependent and -independent studies were conducted in order to expand our understanding of thermoacidophily in diverse hydrothermal environments. Results of these studies expanded the phylogenetic and physiological diversity of thermoacidophiles in deep-sea vent environments and provided clues to factors that are influencing the biogeography of an important thermoacidophilic archaeal lineage. Overall, these studies have increased our understanding of the interplay between geologic processes and microorganisms in deep-sea hydrothermal environments.

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Ouertani, Selmene. "Effet de l'ajout de biochar sur les microorganismes des marais filtrants artificiels traitant des effluents de serre." Doctoral thesis, Université Laval, 2019. http://hdl.handle.net/20.500.11794/66853.

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Les marais filtrants artificiels (MFA) forment un système biologique et passif de traitement des eaux usées constituant une alternative durable aux traitements conventionnels des effluents de cultures en serre. La performance des MFAs à réduire la charge polluante des effluents de culture et l’émission de gaz à effet de serre est étroitement liée aux communautés microbiennes. Afin d’optimiser l’activité biologique des MFAs et par conséquent leur performance, l’enrichissement en biochar des substrats filtrants pourrait constituer une avenue prometteuse. Le biochar, produit de la pyrolyse de la biomasse, est utilisé comme amendement pour les sols. Toutefois, les conséquences de son utilisation dans les systèmes d’épuration des eaux usées comme les MFAs sont peu connues jusqu’à nos jours. Les objectifs de cette thèse étaient donc de : (1) évaluer l’effet d’un biochar sur la diversité et l’activité des microorganismes dans les MFAs ; (2) évaluer l’effet du biochar sur l’efficacité des MFAs à réduire la charge en pesticides dans les effluents de cultures ; (3) évaluer l’effet du biochar sur les microorganismes des MFAs en présence de pesticides, et finalement (4) évaluer l’effet de l’utilisation de l’eau traitée par les MFAs comme eau d’irrigation sur la croissance des plantes et la diversité microbienne de la rhizosphère d’une culture de tomate. Les résultats obtenus ont démontré que le biochar n’a pas eu un effet majeur sur la composition des populations bactériennes dans les substrats et les effluents des marais. Toutefois, le biochar a affecté le taux d’expression de plusieurs gènes clés impliqués dans le fonctionnement des MFAs incluant ceux contrôlant le dégagement des gaz à effet de serre. Par ailleurs, l’utilisation des eaux traitées par les MFAs comme eau d’irrigation n’a pas affecté le développement des plantes de tomate. Au contraire, des bactéries connues pour leur stimulation de la croissance des plantes comme Flavobacterium, Rhizobium, Azospirillum et Pseudomonas ont été détectées en abondance. Finalement, en présence de pesticides, le biochar a exercé un effet protecteur sur les communautés microbiennes des MFAs permettant ainsi de maintenir leur performance à réduire les charges polluantes dans les effluents de serre. Toutefois, l’effet du biochar sur la capacité des marais à réduire la concentration des pesticides a été spécifique au type de pesticide. Ces travaux suggèrent que l’amendement des MFAs avec du biochar peut être une pratique utile pour améliorer et optimiser le fonctionnement des MFAs en atténuant certains de leurs inconvénients comme le dégagement des gaz à effet de serre. Ils ont démontré également la faisabilité et l’importance de la valorisation des eaux traitées par les MFAs.
Recently, the use of constructed wetlands (CWs), which form a biological and passive system of wastewater treatment, has been proposed as an alternative to conventional treatments of greenhouse effluents. The performance of CWs can be improved by the enrichment of their substrates with various products affecting their microbial communities, thus reducing the impact of some related problems such as the release of greenhouse gases. Biochar, which is the product of biomass pyrolysis, is used as an amendment in the soil. However, the consequences of its use with substrates in wastewater treatment systems such as CWs are little known until today. The objectives of this thesis were (1) to evaluate the effect of a biochar on the diversity and activity of microorganisms in CWs, (2) to evaluate the effect of biochar on the efficiency of CWs to reduce pesticides in greenhouse effluents, (3) to evaluate the effect of biochar on microorganisms in CWs in the presence of pesticides, and finally (4) to assess the effect of using water treated in CWs as irrigation water on tomato growth and rhizosphere microbial diversity. The obtained results demonstrated that biochar did not have a major effect on the composition of bacterial populations in CWs substrates and effluents. However, biochar affected the expression rate of several key genes in CWs functioning, including those involved in the release of greenhouse gases. Also, the use of CWs s treated waters to grow tomato plants in hydroponic crops did not present any physiological or microbiological risk to tomato plants. In fact, plant growth-promoting bacteria such as Flavobacterium, Rhizobium, Azospirillum and Pseudomonas were detected in abundance in the rhizosphere of tomato plants. Finally, in the presence of pesticides, biochar showed a protective effect on the microbial communities of CWs and thus makes it possible to maintain CWs performance in reducing pollutant loads in greenhouse effluents. However, the effect of biochar on CWs performance in reducing pesticides is specific to the type of pesticide. This work highlights the utility of biochar in improving the functioning of CWs and in circumventing some of their disadvantages such as the release of greenhouse gases. The feasibility and the importance of the valorization of water treated by CWs was also demonstrated.

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Chen, Ying 1975 Dec 19. "Sources and fate of atmospheric nutrients over the remote oceans and their role on controlling marine diazotrophic microorganisms." College Park, Md. : University of Maryland, 2004. http://hdl.handle.net/1903/1967.

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Thesis (Ph. D.) -- University of Maryland, College Park, 2004.
Thesis research directed by: Marine-Estuarine-Environmental Sciences. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

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Dissertations / Theses on the topic 'Microorganismes marins'

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