Microbial mats are natural heterotrophic and autotrophic communities dominated by cyanobacteria (blue-green algae). These constructed mats are durable, tolerant to a variety of toxins and resilient under changing environmental conditions. This research demonstrates that microbial mats provide an effective remediation treatment for 2,4,6 Trinitrotoluene (TNT) in water and soil. It showed that TNT is removed to undetectable limits after 5 days of treatment under any of the following conditions: light/dark; total light; total dark. This work also shows that in the presence of an inorganic material (lead), mats were able to remove both contaminants efficiently, thus making the microbial mat a good choice for mixed waste remediation. Kinetic studies performed during the first five hours of microbial treatment showed a pseudo first order reaction indicating that TNT removal is initially proportional to the concentration of TNT. The major metabolites detected after 24 hour of treatment were 4-amino-2,6- dinitrotoluene, 2-amino-4,6-dinitrotoluene, and 2,4-diamine-6-nitrotoluene. These metabolites have a toxicity level similar to TNT. However, mat extracts and growth medium concentrates taken after 24 hours treatment of TNT showed little or no toxicity. The lack of toxicity demonstrated by treated mat extracts and media concentrates suggest that these metabolites are not the final metabolic products. The chemical nature of these metabolites suggests that the chemical mechanism of biotransformation involves reduction of the nitro groups at the ortho and para position of the TNT structure. Results obtained from light and dark experiment suggest that photooxidation or photodegradation is not an important mechanism for degradation of TNT by mats. Results show that live mats likely degrade TNT via a biotransformation process. In comparison, heat killed mats show a much slower removal of TNT than live mats. TNT was the only species found in the water column and extracts of heat killed mats, which indicates that TNT is removed by a passive absorption process, but no evidence of biodegradation was observed.

Endosymbiosis is a pervasive phenomenon that has been a powerful force in insect evolution. In many well studied insect-bacterial associations, the bacteria can serve as reproductive manipulators, nutritional mutualists or defenders of their hosts. Fungi are also frequently associated with insects, and initial estimates suggest that these fungi are hyperdiverse. Saving a handful of examples, however, the functions of these fungi within insect hosts are largely unknown. This dissertation begins with a review that lays the conceptual groundwork for understanding bacterial and fungal endosymbiosis in insects. I make predictions about why one versus the other microbe might serve the insect, given any unique physiological, ecological or evolutionary conditions. I then aim to derive insights about microbial symbiosis by focusing on a particular system, that of brownbanded cockroaches, Supella longipalpa (Blattaria: Blattellidae) and their specialist wasp parasitoids, Comperia merceti (Hymenoptera: Encyrtidae). Here, I identify the symbiotic community of these two insects by using both culture-dependent and independent methods to characterize the vertically transmitted bacterial and fungal associates. Finally, I show that a heritable fungus in C. merceti, long presumed to be a mutualist, is parasitic under laboratory conditions: infected wasps incur fitness costs for housing the fungal symbiont relative to uninfected wasps. Additionally, although the fungus is not horizontally transmitted sexually, it is readily horizontally transmitted from the offspring of infected females to those of uninfected females that are using the same host.

Current prices and demand for petroleum hydrocabons have generated an increase of oil spills around the country and the world. Health and environmental impacts associated to these organic pollutants represent a huge concern for the general public, leading the public and private sector to develop new technologies and methods to minimize or eliminate those risks. Ex-Situ bioremediation through biopiles, as a main remediation technique to treat a wide range of hydrocarbons, has been a topic of considerable research interest over the last years. It provides an economical and environmental solution to restore the environment to background levels. Nevertheless, successful bioremediation under cold climate conditions is of considerable concern in countries like Canada, as low temperatures can delay the rate of bioremediation of oil hydrocarbons, thus limiting the operation of soil treatment facilities to certain times of the year. Recent research has found out that bioremediation could be conducted even at low or cold temperatures with larger periods of times. And even more, the addition of petroleum degrading microorganisms (bioaugmentation) and nutrients or biosurfactants (biostimulation) could enhance the process in some cases. In the present study, a comprehensive assessment of bioaugmentation and biostimulation strategies for ex-situ bioremediation of petroleum contaminated soil under cold climate conditions is proposed. Field scale biopiles were constructed and subjected to different concentrations of commercial microbial consortia and mature compost, as bioaugmentation and biostimulation strategies, in a soil treatment facility at Moose Creek, Ontario over a period of 94 days (November 2012 to February 2013). Assessment and comparison of the biodegradation rates of total petroleum hydrocarbons (TPH) and their fractions were investigated. Furthermore, a response surface methodology (RSM) based on a factorial design to investigate and optimize the effects of the microbial consortia application rate and amount of compost on the TPH removal was also assessed. Results showed that biopiles inoculated with microbial consortia and amended with 10:1 soil to compost ratio under aerobic conditions performed the best, degrading 82% of total petroleum hydrocarbons (TPHs) with a first-order kinetic degradation rate of 0.016 d_1, under cold temperature conditions. The average removal efficiencies for TPHs after 94 days for control biopiles, with no amendments or with microbial consortia or compost only treatments were 48%, 55%, and 52%, respectively. Statistical analyses indicated a significant difference (p < 0.05) within and between the final measurements for TPHs and a significant difference between the treatment with combined effect, and the control biopiles. On the other hand, the modeling and optimization statistical analysis of the results showed that the microbial consortia application rate, compost amendment and their interactions have a significant effect on TPHs removal with a coefficient of determination (R2) of 0.88, indicating a high correlation between the observed and the predicted values for the model obtained. The optimum concentrations predicted via RSM were 4.1 ml m-3 for microbial consortia application rate, and 7% for compost amendment to obtain a maximum TPH removal of 90.7%. This research contributes to provide valuable knowledge to practitioners about cost-effective and existing strategies for ex-situ bioremediation under cold weather conditions.

Current prices and demand for petroleum hydrocabons have generated an increase of oil spills around the country and the world. Health and environmental impacts associated to these organic pollutants represent a huge concern for the general public, leading the public and private sector to develop new technologies and methods to minimize or eliminate those risks. Ex-Situ bioremediation through biopiles, as a main remediation technique to treat a wide range of hydrocarbons, has been a topic of considerable research interest over the last years. It provides an economical and environmental solution to restore the environment to background levels. Nevertheless, successful bioremediation under cold climate conditions is of considerable concern in countries like Canada, as low temperatures can delay the rate of bioremediation of oil hydrocarbons, thus limiting the operation of soil treatment facilities to certain times of the year. Recent research has found out that bioremediation could be conducted even at low or cold temperatures with larger periods of times. And even more, the addition of petroleum degrading microorganisms (bioaugmentation) and nutrients or biosurfactants (biostimulation) could enhance the process in some cases. In the present study, a comprehensive assessment of bioaugmentation and biostimulation strategies for ex-situ bioremediation of petroleum contaminated soil under cold climate conditions is proposed. Field scale biopiles were constructed and subjected to different concentrations of commercial microbial consortia and mature compost, as bioaugmentation and biostimulation strategies, in a soil treatment facility at Moose Creek, Ontario over a period of 94 days (November 2012 to February 2013). Assessment and comparison of the biodegradation rates of total petroleum hydrocarbons (TPH) and their fractions were investigated. Furthermore, a response surface methodology (RSM) based on a factorial design to investigate and optimize the effects of the microbial consortia application rate and amount of compost on the TPH removal was also assessed. Results showed that biopiles inoculated with microbial consortia and amended with 10:1 soil to compost ratio under aerobic conditions performed the best, degrading 82% of total petroleum hydrocarbons (TPHs) with a first-order kinetic degradation rate of 0.016 d_1, under cold temperature conditions. The average removal efficiencies for TPHs after 94 days for control biopiles, with no amendments or with microbial consortia or compost only treatments were 48%, 55%, and 52%, respectively. Statistical analyses indicated a significant difference (p < 0.05) within and between the final measurements for TPHs and a significant difference between the treatment with combined effect, and the control biopiles. On the other hand, the modeling and optimization statistical analysis of the results showed that the microbial consortia application rate, compost amendment and their interactions have a significant effect on TPHs removal with a coefficient of determination (R2) of 0.88, indicating a high correlation between the observed and the predicted values for the model obtained. The optimum concentrations predicted via RSM were 4.1 ml m-3 for microbial consortia application rate, and 7% for compost amendment to obtain a maximum TPH removal of 90.7%. This research contributes to provide valuable knowledge to practitioners about cost-effective and existing strategies for ex-situ bioremediation under cold weather conditions.

Orientador: Lucia Regina Durrant, Matthew James Grossman / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-22T02:43:16Z (GMT). No. of bitstreams: 1 Santos_LigiaGibinidos_M.pdf: 3848321 bytes, checksum: 46f91a01a783f6fd7d5153ba73c6e8a0 (MD5) Previous issue date: 2013 / Resumo: Dentre os contaminantes ambientais mais abundantes, destacam-se os Hidrocarbonetos aromáticos policíclicos (HAPs), que apresentam elevado potencial tóxico, sendo imprescindível sua remoção do ambiente. O objetivo deste trabalho foi analisar, em microcosmos, a biodegradação de HAPs por um consórcio bacteriano e identificar fatores que influenciam nesta degradação e na análise dos dados. A degradação dos HAPs no solo sem histórico de contaminação foi muito semelhante em todos os microcosmos, apresentando uma porcentagem de aproximadamente 85%. Para analisar a toxicidade do solo antes e depois da biorremediação, realizou-se um testes de germinação de sementes de Lactuca sativa (alface). O teste mostrou baixa toxicidade do solo após 80 dias da contaminação, com ou sem a adição do consórcio. Durante estudos de remediação biológica, é necessário utilizar um marcador interno para minimizar a dispersão e extração irregulares dos contaminantes. Neste estudo foi utilizado o hexaclorobenzeno, que mostrou excelente, uma vez que não sofreu nenhum tipo de degradação. Análises moleculares mostram que a adição de HAPs alterou significativamente a comunidade microbiana, favorecendo os membros degradadores de tais poluentes. O consórcio adicionado inibiu o crescimento de alguns micro-organismos autóctones. Além disso, não houveram evidências de que os micro-organismos degradadores de HAPs adicionados persistiram, sugerindo que eles podem não competir eficientemente com a população microbiana autóctone. Não houve efeito claramente identificado do hexaclorobenzeno sobre o crescimento de micro-organismos, com exceção de um aumento no número de organismos pertencentes da classe Alphaproteobacteria / Abstract: Polycyclic aromatic hydrocarbons (PAHs) stand out as among the most abundant and toxic of environmental contaminants, and their removal from contaminated sites is indispensable for a healthy environment. The objective of this study was to analyze, in soil microcosms, the biodegradation of PAHs by a bacterial PAH degrading consortium and identify factors that influence this degradation and data analysis. Degradation of PAHs in soil with no history of contamination was very similar in microcosms with or without bioaugmentation, with the extent of PAH removal of about 85% in all cases. The germination of Lactuca sativa (lettuce) in soils taken from the microcosms was used to examine the toxicity of the soil before and after bioremediation. The test showed a low toxicity of the soil 80 days after PAH contamination, with or without the addition of the consortium. During studies of biological remediation it is necessary to use an internal non-biodegradable marker to minimize the effect of uneven dispersion and irregular extraction of pollutants. This study used hexachlorobenzene as the nonbiodegradable marker and it proved to be an excellent marker as it did not suffer any significant degradation in the soil microcosms. Molecular analyzes showed that the addition of PAHs significantly altered the microbial community by encouraging the growth of PAH degraders. In addition, the added microbial consortium was found to inhibit the growth of some of the indigenous microorganisms. Furthermore, there was no evidence that the added PAH degraders persisted, suggesting that they might not compete effectively with the native microbial population. There was little effect of hexachlorobenzene on the microbial community or on the removal of the PAH contaminants, with the exception of an increase in the number of organisms belonging to the class Alphaproteobacteria / Mestrado / Ciência de Alimentos / Mestra em Ciência de Alimentos

Les systèmes alimentaires occidentaux ne sont pas durables en termes d‘impacts environnementaux et d‘effet sur la santé. Une solution est de revisiter les modes de consommation en favorisant les produits à base de protéines végétales. Cependant, un des verrous à l‘introduction des protéines végétales dans notre alimentation est leurs défauts sensoriels qui sont un frein à l‘acceptabilité des produits par les consommateurs. La fermentation est un procédé ancien qui pourrait être un levier à ce verrou sensoriel. Dans ce contexte, l‘objectif de ce projet de thèse est d‘étudier les bénéfices sensoriels apportés par la fermentation de gels enrichis en protéines végétales à l‘aide de consortia microbiens sélectionnés. Pour cela, une stratégie alliant analyses sensorielles, microbiologie et physicochimie a été mise en œuvre. Deux types de matrices contenant 10% de protéines et 10% d‘huile de colza ont été étudiés : la première est constituée de 100% de protéines de pois et la deuxième est constituée d‘un mélange de protéines de lait (50%) et de pois (50%). Sur la base des connaissances de la matrice et des propriétés fonctionnelles des micro-organismes, 56 souches microbiennes ont été sélectionnées. Une stratégie raisonnée d‘assemblage de ces souches a été mise en place, basée sur la répartition équilibrée selon leur groupe phylogénétique, mais aussi sur la connaissance experte des fonctions cibles aromatiques recherchées. En parallèle, plusieurs procédés de gélification ont été étudiés pour structurer les gels. Dans un premier temps, la fermentation a été étudiée sur des émulsions non gélifiées pour permettre la sélection des communautés microbiennes spécifiques pour chaque matrice. Dans un second temps, le potentiel d‘adaptation et de fonctionnement des écosystèmes sélectionnés ont été étudiés sur les émulsions gélifiées. La croissance et l‘abondance des microorganismes dans les gels après trois et sept jours de fermentation ont été évaluées sur milieu spécifique et le potentiel aromatique des consortia a été cartographié par un panel sensoriel.Dans une dernière partie du travail, les défauts/bénéfices sensoriels de la fermentation ont été étudiés de point de vue sensoriel et analytique. Les résultats montrent un fort potentiel d‘implantation des bactéries lactiques (principalement Lactobacillus plantarum, Lactobacillus rhamnosus, Lactococcus lactis et Lactobacillus casei) et de la majorité des eucaryotes (en particulier Mucor et Geotrichum) pour l‘émulsion mixte comme pour l‘émulsion végétale. Même si les souches appartenant aux groupes Actinobacteria et Proteobacteria ne soient pas compétitives vis-à-vis de la flore endogène (Bacillus), certaines espèces comme Hafnia alvei, Acinetobacter johnsonii et Glutamicibacter arilaitensis, ont montré une forte croissance quand elles sont inoculées en associations. Des notes aromatiques spécifiques pour chaque émulsion ont été générées permettant de masquer la note végétale « verte » caractéristique du pois. Ainsi, deux consortia ont pu être sélectionnés sur la base de notes lactiques et fruitées pour l‘émulsion végétale (VEGAN), et de notes fruitées pour l‘émulsion mixte (MEGAN). Le potentiel d‘adaptation de ces deux consortia dépendait de la composition et de la structure des gels. Ainsi, le consortium VEGAN semble bien adapté pour le gel végétal et génère des notes torréfiées/grillées, alors qu‘il génère des notes laitières (crème fraiche/caillé frais) dans le gel mixte. Le consortium MEGAN s‘implante très bien dans les deux types de gels, générant des notes fromagères et fruitées dans le gel mixte, mais ne permet pas de masquer les notes vertes dans le gel végétal. Les défauts sensoriels attribués aux notes vertes et à l‘amertume sont liés principalement à la présence des aldéhydes et des acides aminés hydrophobes respectivement, mais restent encore à approfondir. (suite et fin du résumé dans la thèse) / Western food systems are not sustainable in terms of environmental impacts and health effects. One solution is to revisit consumption patterns by favoring products based on plant proteins. However, one of the barriers to the introduction plant proteins in our diet is their sensory defects which can be obstacles for the acceptability of products by consumers. Fermentation is an ancient process that could be a solution to this sensory issue. In this context, the aim of this PhD thesis is to study the sensory benefits provided by the fermentation of plant protein-based gels using selected microbial consortia. In order to accomplish this, a strategy combining sensory analyzes, microbiology and physicochemistry was implemented. Two types of matrices containing 10% protein and 10% rapeseed oil were studied: the first consists of 100% pea protein and the second consists of a mixture of milk proteins (50%) and pea proteins (50%).Based on knowledge of the matrix and the functional properties of microorganisms, 56 microbial strains were selected. A reasoned strategy of assembly of these strains was put in place, based on the balanced distribution according to their phylogenetic group, but also on the expert knowledge of the desired aromatic functions. In parallel, several gelling processes were studied to structure the gels. In the first step, the fermentation was studied on non-gelled emulsions to allow the selection of specific microbial communities for each matrix. In the second step, the adaptation and functioning potential of the selected ecosystems were studied on gelled emulsions. The growth and abundance of microorganisms in the gels after three and seven days of fermentation were evaluated on a specific growing medium and the aromatic potential of the consortia was mapped by a sensory panel. In the final section of this study, the sensory defects / benefits of fermentation were studied from a sensorial and analytical point of view. The results show a highpotential for implantation of lactic acid bacteria and the majority of eukaryotes (in particular Mucor and Geotrichum) for the mixed emulsion and for the vegetable emulsion. Although strains belonging to the Actinobacteria and Proteobacteria groups are not competitive with endogenous flora (Bacillus), certain species such as Hafnia alvei, Acinetobacter johnsonii and Glutamicibacter arilaitensis, have shown strong growth when inoculated into associations. Specific aromatic notes for each emulsion were generated to mask the green note characteristic of peas. Thus, two consortia were selected on the basis of lactic and fruity notes for the vegetable emulsion (VEGAN), and fruity notes for the mixed emulsion (MEGAN). The adaptation potential of these two consortia depended on the composition and structure of the gel. Thus, the VEGAN consortium seems well suited for vegetable gels and generates roasted / grilled notes, while it generates dairy notes (fresh cream / fresh curd) in the mixed gels. The MEGAN consortium implements itself very well in both types of gels, generating cheesy and fruity notes in the mixed gel, but does not mask the green notes in the vegetable gels. The sensory defects attributed to green notes and bitterness are mainly related to the presence of aldehydes and hydrophobic amino acids respectively, but still need to be deepened. This study validated a proof of concept of formulation of fermented food products and will create opportunities for innovation.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第20009号 / 農博第2193号 / 新制||農||1045(附属図書館) / 学位論文||H28||N5018(農学部図書室) / 33105 / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 小川 順, 教授 阪井 康能, 教授 栗原 達夫 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Nostoc é um gênero cianobacteriano com distribuição ubíqua que tem importância em diversos ecossistemas. Contudo, poucos genomas estão atualmente disponíveis para esse gênero. Enquanto Nostoc spp. são as cianobactérias mais comumente relatadas em relações simbióticas com fungos, animais, plantas e outros organismos, associações com outros micro organismos não receberam atenção similar. Como consequência das fortes interações entre cianobactérias e heterótrofos, culturas não axênicas são geralmente obtidas no isolamento dessas bactérias, o que proporciona uma oportunidade interessante para o desenvolvimento tanto de estudos genômicos quanto metagenômicos. Este trabalho teve como objetivo investigar as características genômicas e funcionais da linhagem Nostoc sp. CENA67, isolada de terra preta antropogênica, bem como estudar sua comunidade associada. Para esse fim, células de uma cultura não axênica de Nostoc sp. CENA67 foram sequenciadas com as plataformas MiSeq e Ion PGM e analisados com ferramentas genômicas e metagenômicas. A linhagem CENA67 de fato pertence à família Nostocaceae e possui algumas características em comum com cianobactérias do gênero Nostoc, porém diverge em certos aspectos morfológicos e filogenéticos do grupo típico de Nostoc, sugerindo que seja representante de um novo táxon. Além disso, seu genoma apresenta diferenças em relação aos genomas atualmente disponíveis para cianobactérias relacionadas ao gênero. A mineração desse genoma revelou 31 agrupamentos gênicos hipoteticamente relacionados à síntese de metabólitos secundários, a maioria dos quais não mostrou similaridade significativa com agrupamentos conhecidos. A análise de um agrupamento gênico de microviridina desvendou uma maior diversidade de genes para precursores dessa molécula do que se acreditava anteriormente, sugerindo que um número considerável de variantes ainda está a ser descoberta. A análise taxonômica da comunidade associada confirmou a dominância de cianobactérias na cultura, mas também revelou a presença de grande número de gêneros microbianos que normalmente são capazes de fixar nitrogênio atmosférico e estabelecer simbiose com plantas, incluindo Mesorhizobium, Sinorhizobium e Starkeya, entre outros. Rascunhos genômicos foram obtidos para Bradyrhizobium diazoefficiens, Bradyrhizobium japonicum, Burkholderia lata e Hyphomicrobium nitrativorans. Todavia, genes para fixação de nitrogênio não foram detectados nesses genomas, apesar de serem encontrados no genoma da cianobactéria e no metagenoma da comunidade, o que sugere que algumas populações podem estar sob pressão de seleção para a perda da capacidade de fixação de nitrogênio, provavelmente devido a este nutriente estar sendo fornecido pelo organismo mais abundante nesta comunidade, a cianobactéria. A análise funcional indicou vias exclusivas tanto à cianobactéria quanto à comunidade associada, e sugeriu a complementariedade de certos metabolismos. Os resultados possibilitam o aumento do conhecimento sobre a diversidade molecular e química do filo Cyanobacteria e levantam possíveis interações com micro organismos simbiontes / Nostoc is a cyanobacterial genus with ubiquitous distribution that is important in several ecosystems. However, few genomes are currently available for this genus. While Nostoc spp. are the most commonly reported cyanobacteria in symbiotic relationship with fungi, animals, plants, and other organisms, associations with other microorganisms have not received similar attention. As a consequence of tight interactions between cyanobacteria and heterotrophs, non-axenic cultures are usually achieved in the isolation of these bacteria, which provides an interesting opportunity for carrying out both genomic as metagenomic studies. This work aimed to investigate the genomic and functional characteristics of the strain Nostoc sp. CENA67, isolated from anthropogenic dark earth, and to study its associated community. For this purpose, cells from a non-axenic culture of Nostoc sp. CENA67 were sequenced with the platforms MiSeq and Ion PGM and analyzed with genomic and metagenomic tools. The strain CENA67 indeed belongs to the family Nostocaceae and presents some characteristics in common with cyanobacteria of the genus Nostoc, but diverges in certain morphological and phylogenetic aspects of the typical Nostoc group, suggesting that it is a representative of a new taxon. In addition, its genome presents differences in relation to the genomes currently available for cyanobacteria related to this genus. Genome mining revealed 31 gene clusters hypothetically related to the synthesis of secondary metabolites, most of which did not show significant similarity to known clusters. The analysis of a microviridin gene cluster unveiled a larger diversity of precursor genes for this molecule than was previously believed, suggesting that a considerable number of variants is still to be found. The taxonomic analysis of the associated community confirmed the dominance of cyanobacteria in the culture, but also revealed the presence of a great number of microbial genera that are usually capable of fixing atmospheric nitrogen and establishing symbiosis with plants, including Mesorhizobium, Sinorhizobium, and Starkeya, among others. Genomic drafts were obtained for Bradyrhizobium diazoefficiens, Bradyrhizobium japonicum, Burkholderia lata, and Hyphomicrobium nitrativorans. Nevertheless, genes for nitrogen fixation were not detected in these genomes, despite being found in the cyanobacterial genome and the community metagenome, suggesting that some populations might be under selection pressure for the loss of the ability to fix nitrogen, probably due to this nutrient being provided for the most abundant organism in this culture, the cyanobacterium. Functional analysis indicated pathways exclusive both to the cyanobacterium as to the associated community, and suggested the complementarity of certain metabolisms. The results allow the increase of the knowledge about the molecular and chemical diversity of the phylum Cyanobacteria and raise possible interactions with symbiotic microorganisms

Les réserves de pétrole sont sur le déclin, les prix des ressources fossiles fluctuent et le CO 2 dégagé par leur consommation contribue inéluctablement au réchauffement climatique. Ce phénomène, conduit notre société vers l'utilisation accrue de biomasse pour la génération d'énergie, de composés chimiques et de matériaux. La réduction des déchets est considérée comme indissociable de cette transition énergétique et en opposition aux préjugés, l’accroissement des déchets organiques peut être bénéfique dans cette recherche de solutions alternatives. En effet, cela conduit à la génération de grandes quantités de matières qui peuvent représenter de potentielles ressources. De plus, changer le statut des déchets en coproduits pour la production de bioénergies n’entre pas en concurrence avec les filières alimentaires et cela constitue un des principaux enjeux des biotechnologies. Sous certaines conditions, les bioconversions anaérobies représentent des procédés d’ingénierie prometteurs pour accomplir le double enjeu de la valorisation des coproduits et de la production de molécules d’intérêt énergétique et chimique (biocarburants, chimie verte...). En revanche, l’innovation dans les biotechnologies blanches est nécessaire pour la production robuste, performante, rentable et environnementalement acceptable de biomolécules à partir de ressources renouvelables. Dans ce contexte, la société AFYREN a été pensée et créée pour répondre à ce défi mondial via sa technologie « tout en un », AFYNERIE, qui s’inspire de la nature et des sciences. L’objectif premier de ce travail de thèse, cœur du procédé AFYNERIE, était d’étudier les performances de microorganismes anaérobies, sous forme de souches pures ou de consortia pour la valorisation de substrats plus ou moins complexes via un processus de méthanogenèse avortée. Pour cela, il était nécessaire de considérer, déjà à l’échelle du laboratoire, une projection dans le monde industriel. Nous avons alors démontré les capacités de la diversité microbienne à produire des molécules plateformes à partir de coproduits agro-industriels réels en mode stérile puis non stérile. Cette étude s’est appuyée en parallèle sur la caractérisation et la dynamique des populations microbiennes mises en jeu. Ensuite, l’accumulation des métabolites, à la fois inhibiteurs et d’intérêt, dans les milieux fermentaires en mode discontinu et avec des rendements compétitifs, a débouché sur la nécessité de surpasser ces limitations par le passage à un mode continu. Pour ce faire, un procédé d’extraction biocompatible des synthons issus de l’opération de fermentation a été mise en œuvre selon différents mode de réalisations. Ce couplage des opérations unitaires, sous forme de fermentation extractive, a livré des résultats prometteurs tout en étant bâtit dans un cadre de bioraffinerie et d’écologie industrielle qui tend vers le « zéro déchet ». Enfin, à l’inverse des autres technologies émergentes, pour se placer dans une approche de drop-in, la biologie et la chimie ont été associées. Le but a été d’illustrer la multipotence des acides gras volatils (AGVs) en termes d’applications industrielles et de réaliser la preuve de concept de la transformation de la biomasse non alimentaire en biomolécules d’intérêt énergétique et chimique. Ces travaux ont permis de soulever les points clés du changement d’échelle du procédé AFYNERIE et d’entrevoir des perspectives tant fondamentales qu’appliquées. Cette brique technologique, de par sa philosophie multi-intrants/multi-produits, couplant fermentation-extraction-synthèse, permet d’initier la transition au stade pilote d’un procédé innovant compatible avec une future économie biosourcée. / Fossil oil reserves are decreasing, oil prices are fluctuating, and the CO 2 released by oil consumption contributes to global warming. These are driving our society towards increased use of biomass for energy, chemical compounds and other materials. Minimizing waste has been seen as a concern associated with alternative energy efforts. Contrary to expectation, increasing organic waste can be beneficial for alternative energy efforts, because it would result in large amounts of organic resources that can be potential raw materials. Moreover, using waste as a resource for bioenergy production does not compete with human or animal food or agricultural surfaces, and that is one of the greatest challenges facing biotechnology. Using waste as a resource for biomolecule production would thus be an interesting approach to reducing waste in the environment and producing renewable materials. Under specific conditions, detrital biomass can be converted into biomolecules of interest by microorganisms. Anaerobic fermentation techniques represent promising engineering processes for accomplishing the dual goals of waste reduction and renewable biomolecule production for biofuel and green chemistry markets. On the other hand, innovative fermentation processes are necessary for the strong, successful, cost-effective and eco-friendly production of bulk chemicals from renewable resources. In this context, AFYREN company was thought and founded to answer this world challenge through its “all in one” technology, AFYNERIE, which is inspired from the nature and sciences. The first objective of this thesis, heart of the AFYNERIE process, was to study the performances of anaerobic microorganisms, in the form of pure strains or of consortia for the valorization of more or less complex substrata via a process of failed methanogenesis. For that purpose, it was necessary to consider, already at the laboratory scale, a projection in the industrial world. Then, we demonstrated the capacities of the microbial diversity to produce platform molecules from real agro-industrial by-products in sterile and then non sterile mode. This study leaned in parallel on the characterization and the dynamics of involved microbial populations. Then, the accumulation of metabolites, which are at the same time inhibitory and of interest, in fermentative media in batch mode and with competitive yields, resulted in the necessity of surpassing these limitations by the passage in a continuous mode. To do this, a process consisted of a biocompatible extraction of synthons stemming from the operation of fermentation was implemented according to different mode of realizations. This coupling of single operations, in the form of extractive fermentation, delivered promising results while builds in a frame of biorefinery and industrial ecology which tightens towards a “zero waste”. Finally, contrary to the other emergent technologies, to take place in a drop-in approach, biology and chemistry were associated. The purpose was to illustrate the versatility of volatile fatty acids (VFAs) in terms of industrial applications and to realize the proof of concept of the transformation of the non-food biomass in biomolecules of energy and chemical interest. These works allowed to underline key points of the scale-up of AFYNERIE process and to glimpse perspectives fundamental as well as applied perspectives. This technological brick, due to its multi-inputs / multi-products philosophy, coupling fermentation-extraction-synthesis, allows to introduce the transition to the pilot stage of an innovative process compatible with a future biobased economy.

Nostoc é um gênero cianobacteriano com distribuição ubíqua que tem importância em diversos ecossistemas. Contudo, poucos genomas estão atualmente disponíveis para esse gênero. Enquanto Nostoc spp. são as cianobactérias mais comumente relatadas em relações simbióticas com fungos, animais, plantas e outros organismos, associações com outros micro organismos não receberam atenção similar. Como consequência das fortes interações entre cianobactérias e heterótrofos, culturas não axênicas são geralmente obtidas no isolamento dessas bactérias, o que proporciona uma oportunidade interessante para o desenvolvimento tanto de estudos genômicos quanto metagenômicos. Este trabalho teve como objetivo investigar as características genômicas e funcionais da linhagem Nostoc sp. CENA67, isolada de terra preta antropogênica, bem como estudar sua comunidade associada. Para esse fim, células de uma cultura não axênica de Nostoc sp. CENA67 foram sequenciadas com as plataformas MiSeq e Ion PGM e analisados com ferramentas genômicas e metagenômicas. A linhagem CENA67 de fato pertence à família Nostocaceae e possui algumas características em comum com cianobactérias do gênero Nostoc, porém diverge em certos aspectos morfológicos e filogenéticos do grupo típico de Nostoc, sugerindo que seja representante de um novo táxon. Além disso, seu genoma apresenta diferenças em relação aos genomas atualmente disponíveis para cianobactérias relacionadas ao gênero. A mineração desse genoma revelou 31 agrupamentos gênicos hipoteticamente relacionados à síntese de metabólitos secundários, a maioria dos quais não mostrou similaridade significativa com agrupamentos conhecidos. A análise de um agrupamento gênico de microviridina desvendou uma maior diversidade de genes para precursores dessa molécula do que se acreditava anteriormente, sugerindo que um número considerável de variantes ainda está a ser descoberta. A análise taxonômica da comunidade associada confirmou a dominância de cianobactérias na cultura, mas também revelou a presença de grande número de gêneros microbianos que normalmente são capazes de fixar nitrogênio atmosférico e estabelecer simbiose com plantas, incluindo Mesorhizobium, Sinorhizobium e Starkeya, entre outros. Rascunhos genômicos foram obtidos para Bradyrhizobium diazoefficiens, Bradyrhizobium japonicum, Burkholderia lata e Hyphomicrobium nitrativorans. Todavia, genes para fixação de nitrogênio não foram detectados nesses genomas, apesar de serem encontrados no genoma da cianobactéria e no metagenoma da comunidade, o que sugere que algumas populações podem estar sob pressão de seleção para a perda da capacidade de fixação de nitrogênio, provavelmente devido a este nutriente estar sendo fornecido pelo organismo mais abundante nesta comunidade, a cianobactéria. A análise funcional indicou vias exclusivas tanto à cianobactéria quanto à comunidade associada, e sugeriu a complementariedade de certos metabolismos. Os resultados possibilitam o aumento do conhecimento sobre a diversidade molecular e química do filo Cyanobacteria e levantam possíveis interações com micro organismos simbiontes / Nostoc is a cyanobacterial genus with ubiquitous distribution that is important in several ecosystems. However, few genomes are currently available for this genus. While Nostoc spp. are the most commonly reported cyanobacteria in symbiotic relationship with fungi, animals, plants, and other organisms, associations with other microorganisms have not received similar attention. As a consequence of tight interactions between cyanobacteria and heterotrophs, non-axenic cultures are usually achieved in the isolation of these bacteria, which provides an interesting opportunity for carrying out both genomic as metagenomic studies. This work aimed to investigate the genomic and functional characteristics of the strain Nostoc sp. CENA67, isolated from anthropogenic dark earth, and to study its associated community. For this purpose, cells from a non-axenic culture of Nostoc sp. CENA67 were sequenced with the platforms MiSeq and Ion PGM and analyzed with genomic and metagenomic tools. The strain CENA67 indeed belongs to the family Nostocaceae and presents some characteristics in common with cyanobacteria of the genus Nostoc, but diverges in certain morphological and phylogenetic aspects of the typical Nostoc group, suggesting that it is a representative of a new taxon. In addition, its genome presents differences in relation to the genomes currently available for cyanobacteria related to this genus. Genome mining revealed 31 gene clusters hypothetically related to the synthesis of secondary metabolites, most of which did not show significant similarity to known clusters. The analysis of a microviridin gene cluster unveiled a larger diversity of precursor genes for this molecule than was previously believed, suggesting that a considerable number of variants is still to be found. The taxonomic analysis of the associated community confirmed the dominance of cyanobacteria in the culture, but also revealed the presence of a great number of microbial genera that are usually capable of fixing atmospheric nitrogen and establishing symbiosis with plants, including Mesorhizobium, Sinorhizobium, and Starkeya, among others. Genomic drafts were obtained for Bradyrhizobium diazoefficiens, Bradyrhizobium japonicum, Burkholderia lata, and Hyphomicrobium nitrativorans. Nevertheless, genes for nitrogen fixation were not detected in these genomes, despite being found in the cyanobacterial genome and the community metagenome, suggesting that some populations might be under selection pressure for the loss of the ability to fix nitrogen, probably due to this nutrient being provided for the most abundant organism in this culture, the cyanobacterium. Functional analysis indicated pathways exclusive both to the cyanobacterium as to the associated community, and suggested the complementarity of certain metabolisms. The results allow the increase of the knowledge about the molecular and chemical diversity of the phylum Cyanobacteria and raise possible interactions with symbiotic microorganisms