Extreme environments provide a unique source of often highly adapted and tolerant organisms. Research on organisms in these habitats has led to the discovery of novel and useful compounds and may assist in understanding the impact of global change on biodiversity. The Dry Valleys of Eastern Antarctica are vast, ice-free regions believed to be the coldest, driest desert on Earth. Despite these harsh conditions, there is an increasing amount of evidence demonstrating that the soil ecosystems of the Dry Valleys sustain a wide diversity of microorganisms. The research presented is an inter-valley comparison study which aims to scrutinize microbial communities and environmental factors driving their distribution in the Dry Valleys. Automated ribosomal intergenic spacer analysis (ARISA) was used to provide a snapshot of bacterial and cyanobacterial communities living in the mineral sands in Miers Valley, Beacon Valley, Upper Wright Valley and at Battleship Promontory. Rigorous analysis of physico-chemical differences between the soils of these four valleys was undertaken in hope to understand the environmental parameters driving the distribution and biodiversity of microbial communities present. Multivariate statistical analysis and ordination of ARISA and physico-chemical data revealed that bacterial communities from each valley form distinctive clusters. Conversely, cyanobacterial communities showed less diversity and a more even distribution between valleys.

Produtos recalcitrantes como os bifenilos policlorados (PCBs) e hidrocarbonetos têm chamado a atenção de pesquisadores em diversas partes do mundo devido a sua persistência e efeitos nocivos ao meio ambiente e ao homem. O conhecimento da biodiversidade genotípica e fenotípica dos microrganismos degradadores de compostos xenobióticos é de grande importância para a compreensão dos aspectos ecológicos envolvidos na biodegradação microbiana; incluindo a dispersão geográfica das bactérias biodegradadoras que, pode também ser considerada e utilizada como modelo para a compreensão de padrões de distribuição geográfica de microrganismos autóctones do ambiente. Devido a presença destes compostos na Baía de Santos é de grande interesse o presente estudo da diversidade microbiana de isolados neste ambiente. Este trabalho visou investigar a ocorrência e diversidade de bactérias capazes de degradar PCBs e hidrocarbonetos nas amostras coletadas no estuário de Santos. Para o estudo destas amostras foram utilizadas técnicas tradicionais de cultivo e análise química de degradação de hidrocarbonetos e PCBs. Técnicas de biologia molecular também foram aplicadas para estudar os diferentes perfis genotípicos obtidos por BOX-PCR. Além disso, foi verificada a presença de genes catabólicos nestes microrganismos e também foi realizada a identificação dos mesmos através da técnica de seqüenciamento do gene 16SrRNA. Como resultado deste estudo, foram obtidos 61 isolados que foram submetidos à técnica de rep-PCR, empregando o iniciador BOX-A1R obtendo-se 30 amplificações com 28 padrões de bandas distintos. Esses isolados, foram então, testados para 6 genes catabólicos distintos, obtendo-se resultado positivo para os genes todC1 (tolueno), ndoB (naftaleno), xylE (xileno) e bphA (bifenilo). No entanto não foram observado genótipos distintos para as áreas afetadas. Nos testes de degradação foram obtidos 12 isolados degradadores de PCBs e 44 isolados degradadores de hidrocarbonetos. Nas análises de seqüenciamento do gene 16SrRNA, foram obtidos 11 gêneros distintos de bactérias, sendo que a maioria dos isolados se encontravam dentro do grupo filogenético de Proteobactéria na subdivisão Gama Proteobactéria. A partir dos resultados de degradação, da pesquisa dos genes catabólicos e dos parâmetros físico-químicos, foi possível observar que a área estudada apresenta um forte potencial para biorremediação com microrganismos autóctones degradadores de hidrocarbonetos e PCBs. / Recalcitrant compounds such as polychlorinated biphenyls (PCBs) and hydrocarbons have attracted researcher’s attention all over the world, because of their persistence and side effects to the environment and to the humanity. The knowledge of genotypic an phenotypic biodiversity of xenobiotic compound degrading-microorganisms is extremely important for the comprehension of ecological aspects involved in microbial biodegradation; including the biodegrading-bacteria geographic dispersion that may also consider and provide a model for the comprehension of the patterns of geographic distribution of autochthonous microorganisms in the environment. Because of the presence of these compounds in Santos Estuary, it is very important the present study of microbial diversity in this environment. The purpose of this work is to investigate the occurrence and the bacterial diversity that are able to degrade PCBs and hydrocarbons in samples of the Santos Estuary. For that, samples were collected and analyzed using traditional techniques of culturing and chemical analyses of PCBs and hydrocarbons biodegradation. Molecular Biology techniques were also used to determine the presence of catabolic genes, to study the different genotypic patterns of BOX-PCR and to identify the microorganisms. As a result, 61 isolates were obtained, and then they were amplified with the BOX-PCR primer resulting in 30 amplicons with 28 different band patterns. These isolates were then tested for 6 distinct catabolic genes with positive results for the todC1 (toluene), ndoB (naphthalene), xylE (xylene) and bphA (biphenyl) genes. In the degradation tests, 12 PCBs degrading-isolates and 44 hydrocarbons degrading-isolates were obtained. As a result of the identification, was obtained 11 different genera of bacteria. Besides, most of the microorganisms belonged to the Gamma Proteobacteria subdivision. As a conclusion of these results and from the chemical and physical parameters studied in this work, was possible to notice that the studied area presents a noticeable potential for bioremediation with hydrocarbons and PCBs autochthonous degrading-microorganisms.

La pollution des écosystèmes marins côtiers par les hydrocarbures, en particulier les HAPs, est un problème environnemental majeur. Le même constat est fait pour le littoral Sud de Sfax (Tunisie) dont la pollution presque généralisée menace sérieusement les ressources naturelles existantes dans la région. La caractérisation physico-chimique des échantillons marins prélevés à partir des trois ports (plaisance, commerce et pêche) de la ville de Sfax, prouve une contamination par des micropolluants organiques (hydrocarbures) et inorganiques (métaux) qui sont considérés comme des excellents traceurs de la pollution urbaine et industrielle et ils font partie des composés les plus toxiques étant donné leur faible biodégradation. La méthode d’empreinte moléculaire (PCR-SSCP) montre une dominance du domaine Bacteria suivie des Eucarya et des Archaea au sein des échantillons marins étudiés. Les analyses statistiques par le logiciel R ont montré l’absence de corrélation entre la communauté bactérienne identifiée par PCR-SSCP et les paramètres physico-chimiques étudiés.Dans une autre partie de travail, quatre souches bactériennes marines hydrocarbonoclastes ont été isolées et caractérisées sur les plans phénotypique et phylogénétique, après des enrichissements sur des HAPs et sur le pétrole brut: FLU5 de Bacillus stratosphericus, NAPH6 de Pseudomonas aeruginosa, PYR2 de Bacillus licheniformis isolées sur le fluoranthène, le naphtalène et le pyrène, respectivement, en présence de 30 g/l NaCl; et CO100 de Staphylococcus sp., isolée sur le pétrole brut, en présence de 100 g/l NaCl. Les analyses chromatographiques, GC-MS ou GC-FID, montrent les capacités biodégradatives intéressantes de ces composés récalcitrants par les bactéries isolées. En outre, ces quatre souches bactériennes, sont capables de produire des biosurfactants nommés BS-FLU5, BS-NAPH6, BS-PYR2 et BS-CO100, sur plusieurs sources de carbones, y compris l’huile de friture résiduelle, un substrat bon marché, minimisant ainsi le coût élevé de production de ces tensioactifs. Les analyses MALDI-TOF/MS, des biosurfactants BS-FLU5, BS-PYR2 et BS-CO100 purifiés, montrent qu’il s’agit des lipopeptides, les biosurfactants BS-NAPH6 sont de nature rhamnolipidique, sur la base des analyses FTIR. Ces quatre biosurfactants sont caractérisés par des propriétés tensiactives intéressantes : une faible CMC, une importante réduction de la tension de surface... Ils sont stables vis-à-vis d’une large gamme de pH, de température et de salinité. De plus, ces agents tensioactifs sont doués d’activité de remobilisation des hydrocarbures contenus dans des sols pollués par. Les biosurfactants BS-FLU5, BS-PYR2 et BS-CO100, présentent des activités anti-adhésives et anti-biofilms intéressantes contre des biofilms de certains microorganismes pathogènes. Par ailleurs, une propriété cicatrisante remarquable sur des plaies d’excision chez un modèle expérimental de rats de race Wistar, a été montrée par les quatre biosurfactants pour des concentrations de l’ordre de 5 et 10 mg/ml, en comparaison avec un cicatrisant de référence (CICAFLORA®). A noter que, l’évaluation de la cytotoxicité des biosurfactants étudiés, a montré qu’ils n’ont pas des effets toxiques sur des cellules rénales humaines HEK-239 à des concentrations jusqu’à 1000 µg/ml pour BS-FLU5 et BS-CO100 et jusqu’à 200 µg/ml pour BS-NAPH6 et BS-PYR2. La production des biosurfactants de la souche FLU5 à l’échelle pilote (deux fermenteurs de 20 et 100 litres, volume total), en présence d’un milieu économique, montre une augmentation des quantités des biosurfactants produits par rapport à l’échelle laboratoire (erlenmeyer, 1 litre). L’ensemble de ces résultats prometteurs, montrent que les souches marines isolées FLU5, NAPH6, PYR2 et CO100, ainsi que leurs biosurfactants demeurent d’intérêts biotechnologiques pour divers types d’applications, tels que la bioremédiation, l’agroalimentaire, la cosmétique... / Pollution of coastal marine ecosystems by hydrocarbons, in particular polycyclic aromatic hydrocarbons (PAHs), is a major environmental problem. The South coast of Sfax (Tunisia) is an example of a polluted ecosystem subject to both urbanization and industrialization including the outfall of untreated domestic sewage and wastewaters, fishery activities, as well as ship traffic and boat pollution. The physico-chemical characterization of the seawater taken from three harbours (pleasure, commercial and fishing) of the city of Sfax, showed a heavy contamination by organic and inorganic micropollutants. These are excellent tracers of urban and industrial pollution, and they are among the most toxic compounds due to their low biodegradation.The molecular fingerprinting technique (PCR-SSCP) showed the dominance of the Bacteria domain followed by Eucarya and Archaea within the studied marine samples. Statistical analysis using the R software, showed that no correlation was identified between the bacterial community identified by PCR-SSCP and the studied physico-chemical parameters.In another part, four marine, aerobic and hydrocarbonoclastic strains: Bacillus stratosphericus FLU5, Pseudomonas aeruginosa NAPH6, Bacillus licheniformis PYR2, isolated after enrichments on fluoranthene, naphthalene and pyrene, respectively, and in the presence of 30 g/l NaCl. Strain Staphylococcus sp. CO100 was isolated after enrichment on crude oil, in the presence of 100 g/l. Chromatographic analysis (GC-MS or GC-FID), showed the interesting biodegradative capacities of these recalcitrant compounds by the isolated bacteria.Besides, these strains showed their capacity to produce efficient surface active agents BS-FLU5, BS-NAPH6, BS-PYR2 and BS-CO100, on several substrates and in particular the residual frying oil, which is a cheap and renewable carbon source alternative, thus minimizing the high cost of producing surfactants. The MALDI-TOF/MS analysis of the purified BS-FLU5, BS-PYR2 and BS-CO100 biosurfactants revealed that they are belonging to lipopeptide family. FTIR analysis showed the glycolipid nature, more precisely the rhamnolipid type, of biosurfactant BS-NAPH6.These four biosurfactants are characterized by interesting tensioactive properties (low CMC, important surface tension reduction...). Furthermore, these surface active agents showed interest stability against a broad range of pH, temperature and salinity. The application of these biosurfactants, in oil recovery, from hydrocarbons-contaminated soil, showed that they were more effective on the hydrocarbon-remobilization than some tested synthetic surfactants. The biosurfactants BS-FLU5, BS-PYR2 and BS-CO100, were found to have notable anti-adhesif and anti-biofilm activities, being able to prevent and eliminate the biofilm formation by pathogenic microorganisms. Moreover, the four tested biosurfactants showed an interesting healing activity, on the wound site in a rat model. They increased significantly the percentage of wound closure when compared to the untreated and CICAFLORA® (a reference pharmaceutical product) treated groups, using two different concentrations (5 and 10 mg/l). Interestingly, the evaluation of the cytotoxicity of the studied biosurfactants, showed that they have no toxic effects on human HEK-239 cells at concentrations up to 1000 μg/ml for BS-FLU5 and BS-CO100 and up to 200 μg/ml for BS-NAPH6 and BS-PYR2. An attempt to produce biosurfactant produce by strain FLU5 on a pilot-scale (fermentors of 20 and 100 liter, as total volume), using a cost-effective medium, was also performed. Preliminary results showed an increase in the quantities of biosurfactantsBS-FLU5 produced on a pilot-scale compared to the lab-scale (Erlenmeyer of 1 liter).These results highlight the interest for potential use of strains FLU5, NAPH6, PYR2 and CO100, as well as their biosurfactants, in a wide variety of industrial, environmental and biotechnological applications.

To understand the soil microbial community structures of different locations and altitudes, as well as the fluctuation of microbial populations foward seasonal change, this study investigated the biodiversity of soil microbiota of eight sampling sites along the Lao-Nong River basin during 4/11/2003~3/21/2004. The results showed that the soil properties were different among these sampling sites. The soil temperatures were ranging in between 24~32¢J, except Tianchr, the highest altitude sampling site (7~19¢J) ; pH values were 4.00 (Tianchr) ~8.20 (Tauyuan) ; moisture contents were 2.31% (Liouguei) ~70.23% (Tianchr) ; total organic carbon contents were 0.38% (Linkou) ~36.21% (Tianchr) ; total organic nitrogen contents were 0.067% (Tauyuan) ~0.672% (Tianchr); the C/N ratio were 7.0~25.0, except Tianchr (42 in average) . In microbial community structures analysis, bacteria were the most abundant organisms among all soil samples (106~108 CFU per gram of soil) . The amount of other microbes were as follow: nitrogen-fixing microbes 105~107 CFU, actinomycetes 104~107 CFU, fungi 104~106 CFU, cellulolytic microbes 104~106 CFU, and the least one was phosphate- solubilizing microbes 103~105 CFU. For molecular biological microbiota analysis, the bead-beating DNA extraction method resulted the richest bacterial 16S rDNA DGGE profile. The16S rDNA DGGE profiles of various samples taken from different seasons showed somewhat seasonal variations that might relate to the specific climates of Taiwan, such as the plum rains and typhoons. Moreover, we also successfully cultured and preserved many microbes with specific biological functions. These microorganisms will provide a useful resource for further research and development in the biotechnology industries.

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2006. / Härtill 6 uppsatser.

Produtos recalcitrantes como os bifenilos policlorados (PCBs) e hidrocarbonetos têm chamado a atenção de pesquisadores em diversas partes do mundo devido a sua persistência e efeitos nocivos ao meio ambiente e ao homem. O conhecimento da biodiversidade genotípica e fenotípica dos microrganismos degradadores de compostos xenobióticos é de grande importância para a compreensão dos aspectos ecológicos envolvidos na biodegradação microbiana; incluindo a dispersão geográfica das bactérias biodegradadoras que, pode também ser considerada e utilizada como modelo para a compreensão de padrões de distribuição geográfica de microrganismos autóctones do ambiente. Devido a presença destes compostos na Baía de Santos é de grande interesse o presente estudo da diversidade microbiana de isolados neste ambiente. Este trabalho visou investigar a ocorrência e diversidade de bactérias capazes de degradar PCBs e hidrocarbonetos nas amostras coletadas no estuário de Santos. Para o estudo destas amostras foram utilizadas técnicas tradicionais de cultivo e análise química de degradação de hidrocarbonetos e PCBs. Técnicas de biologia molecular também foram aplicadas para estudar os diferentes perfis genotípicos obtidos por BOX-PCR. Além disso, foi verificada a presença de genes catabólicos nestes microrganismos e também foi realizada a identificação dos mesmos através da técnica de seqüenciamento do gene 16SrRNA. Como resultado deste estudo, foram obtidos 61 isolados que foram submetidos à técnica de rep-PCR, empregando o iniciador BOX-A1R obtendo-se 30 amplificações com 28 padrões de bandas distintos. Esses isolados, foram então, testados para 6 genes catabólicos distintos, obtendo-se resultado positivo para os genes todC1 (tolueno), ndoB (naftaleno), xylE (xileno) e bphA (bifenilo). No entanto não foram observado genótipos distintos para as áreas afetadas. Nos testes de degradação foram obtidos 12 isolados degradadores de PCBs e 44 isolados degradadores de hidrocarbonetos. Nas análises de seqüenciamento do gene 16SrRNA, foram obtidos 11 gêneros distintos de bactérias, sendo que a maioria dos isolados se encontravam dentro do grupo filogenético de Proteobactéria na subdivisão Gama Proteobactéria. A partir dos resultados de degradação, da pesquisa dos genes catabólicos e dos parâmetros físico-químicos, foi possível observar que a área estudada apresenta um forte potencial para biorremediação com microrganismos autóctones degradadores de hidrocarbonetos e PCBs. / Recalcitrant compounds such as polychlorinated biphenyls (PCBs) and hydrocarbons have attracted researcher’s attention all over the world, because of their persistence and side effects to the environment and to the humanity. The knowledge of genotypic an phenotypic biodiversity of xenobiotic compound degrading-microorganisms is extremely important for the comprehension of ecological aspects involved in microbial biodegradation; including the biodegrading-bacteria geographic dispersion that may also consider and provide a model for the comprehension of the patterns of geographic distribution of autochthonous microorganisms in the environment. Because of the presence of these compounds in Santos Estuary, it is very important the present study of microbial diversity in this environment. The purpose of this work is to investigate the occurrence and the bacterial diversity that are able to degrade PCBs and hydrocarbons in samples of the Santos Estuary. For that, samples were collected and analyzed using traditional techniques of culturing and chemical analyses of PCBs and hydrocarbons biodegradation. Molecular Biology techniques were also used to determine the presence of catabolic genes, to study the different genotypic patterns of BOX-PCR and to identify the microorganisms. As a result, 61 isolates were obtained, and then they were amplified with the BOX-PCR primer resulting in 30 amplicons with 28 different band patterns. These isolates were then tested for 6 distinct catabolic genes with positive results for the todC1 (toluene), ndoB (naphthalene), xylE (xylene) and bphA (biphenyl) genes. In the degradation tests, 12 PCBs degrading-isolates and 44 hydrocarbons degrading-isolates were obtained. As a result of the identification, was obtained 11 different genera of bacteria. Besides, most of the microorganisms belonged to the Gamma Proteobacteria subdivision. As a conclusion of these results and from the chemical and physical parameters studied in this work, was possible to notice that the studied area presents a noticeable potential for bioremediation with hydrocarbons and PCBs autochthonous degrading-microorganisms.

This study turns to what is for many an everyday item – yogurt – as a critical zone observatory, a synergistic, place-based laboratory which aims to integrate heterogenous representations of planetary phenomena as they are registered at a common surface. Yogurt has an impressive cultural endurance largely derived from its prominence in various paradigms of health. The product has culturally endured in another sense: as a common cultural medium where humans and microbes have met for generations. This study begins with a profile of yogurt as most encounter it today to consider how normative notions of health interface with the temporal and spatial imaginaries entailed in commodity geographies. Commoditized yogurt is characterized by a low and limited microbial biodiversity compared to yogurts produced outside of the commodity context. Yogurt is therefore presented as a micro case study to consider modes by which we sense and valuate ecological phenomena beyond the perceptible surface, how such sens-abilities intersect models of health, and to what effect. To trace a history of yogurt along these contours, I introduce it as a particular kind of artefact: a global object. As an object of environmental history, I define a global object as a global commodity with a high potential to be re-localized, and therefore with a high potential to re-shape commodity geographies. However, this trajectory is contingent upon framing yogurt as a critical zone observatory – a site where global phenomena like human-microbial interaction may become familiar and intimate. Guided by new materialist theory, I weave together historical and ethnographic case studies from the following consortium: resident yogurt bacteria, artisanal yogurt producers and home fermenters, a mystical immunologist, and an 11th century linguistic scholar. Through these perspectives, I both sketch and apply a framework for de-centered, interspecies histories of cultural (re)production through an extended metaphor of biofilm: the coagulative bacterial structure giving yogurt its characteristic texture. In so doing I provide a re-articulation of “the probiotic” as an integrative case of human and more-than-human health. The study concludes by directing these implications towards a consideration of aesthetic engagement by displaying how fermentation practice may enliven matters of re-diversification and re-localization.

Les sols représentent environ 63% des émissions de N2O et à eux seuls les sols tropicaux représentent 23% de ce budget soit une contribution bien plus élevé que les sols tempérés. Ces sols sont connus pour abriter une grande biodiversité d'invertébrés dominés par quatre types i.e. termites, vers de terre, fourmis et larves de scarabaeid. Ces groupes macrofaunal sont considérés comme des ingénieurs des sols via notamment leurs actions de régulation de la disponibilité des ressources chimiques, tels que l'azote minéral pour les micro-organismes. Cette régulation est due à leurs capacités de digestion spécifiques de la matière organique ainsi que la création et/ou la modification des habitats des sols. Cette étude est basée sur l'hypothèse suivante (i) l'environnement digestif et les structures biogéniques de ces ingénieurs du sol sont considérées comme des « hot spot » d' émissions de N2O (ii) les taux d'émission de N2O varient en fonction de leurs régimes alimentaires, cette macrofaune ingérant des substrats avec différents C:N (iii) le taux d'émission de N2O de chaque invertébré est corrélé à la densité des communautés bactériennes digestives impliquées dans l'émission de N2O (bactéries nitrifiantes et dénitrifiantes) et à leur teneur en azote minéral dans leur tube digestif. Pour évaluer ces différentes hypothèses, des mesures des taux d'émission de N2O ont été effectuées in vitro en aérobiose pour la macrofaune (30 espèces différentes en provenance d'Afrique, d'Amérique du Sud et d'Europe) et leurs matériels biogéniques associées (nids, turricules). L'abondance des gènes fonctionnelles des bactéries nitrifiantes (AOA et AOB) et dénitrifiantes (nirK, nirS, nosZ) ont été quantifiés par PCR quantitative. Les termites humivores et champignonnistes ainsi que les larves de scarabaeid émettent des quantités significatives de N2O alors que les fourmis n'en émettent pas. Quand aux termites xylophages et litièrivore, ils absorbent le N2O. Les structures biogéniques des vers de terre (turricules) et des fourmis (nid) émettent des quantités importantes de N2O ce qui n'est pas le cas des nids de termites. La faune du sol et leurs structures biogéniques associées, sont donc, dans la majorité des cas étudiés, un lieu d'émission de N2O, confirmant ainsi notre première hypothèse. Ce travail a également démontré qu'il y a avait une étroite corrélation entre régime alimentaire et intensité de l'émission de N2O au sein de chaque type de macrofaune étudié. En revanche, l'abondance des gènes des communautés digestive nitrifiantes et dénitrifiantes et le contenu en N minéral au sein du tube digestif ne semblent pas être des proxies pertinents des émissions de N2O. A partir de ces mesures, des calculs ont été effectuées pour déterminer l'importance de ces émissions à l'échelle des écosystèmes tropicaux étudiés (forêt et savane). Ces calculs suggèrent que la macrofaune du sol dans ces écosystèmes pourrait contribuer entre 0,1 à 11,7% et 0,1 à 8,8% du budget total des émissions de N2O, respectivement. Les résultats de ces travaux devraient contribuer à une meilleure prise en compte de la composante biotique dans la modélisation des émissions de gaz à effet de serre provenant des sols en milieu tropical. / Soils account for about 63% of N2O emissions. Tropical soils are estimated to emit 23% of global N2O emission budget which is much higher than temperate soil N2O emissions. These soils also harbor a huge biodiversity of invertebrates dominated by four types of macrofauna i.e. termites, earthworms, ants and scarabaeid grubs. These macrofaunal groups are considered as soil engineers because they regulate the availability of chemical resources, like mineral nitrogen, for the microorganisms via their specific digestion capabilities and/or by creating and modifying soil habitats. This study is based on the following hypothesis (i) the gut environment or biogenic structures of these soil engineers are considered as hotspots of N2O emission (ii) the N2O emission rates will vary according to their feeding behavior as these macrofauna thrive on diverse substrates with different C:N ratio (iii) the rate of N2O emission in each soil fauna will also depend on the gut density of the bacterial communities involved in the N2O emission (nitrifiers and denitrifiers) and on the mineral nitrogen content within the gut. To assess these different hypotheses in-vitro short-term N2O emission rates were assessed for either live macrofauna (30 species collected from Africa, South America and Europe) or their biogenic materials or both under aerobic incubations. Genes abundance of nitrifiers (AOA and AOB) and denitrifiers (nirK, nirS, nosZ) were quantified by real time quantitative PCR. Soil-feeders and fungus-growing termites and scarabaeid grubs emitted in-vivo N2O while ants did not. Surprisingly, wood- and grass-feeding termites revealed an uptake of N2O. Biogenic structures of earthworms and ants emitted substantial amount of N2O while those of termites did not. The emission difference between macrofauna or their biogenic materials and their control materials was significant for most of the macrofaunal groups studied confirming our first hypothesis. We also confirmed that the feeding behavior (total N content and C:N ratio of food material) is the main factor explaining the observed N2O emission pattern of each macrofaunal group investigated whereas genes abundances, particularly of denitrifiers and gut N mineral content did not appear to be relevant proxies of the N2O emissions rates. A back-on-the-envelope data upscaling suggests that soil macrofauna could contribute from 0.1–11.7% and 0.1–8.8% of the total soil N2O emissions, respectively, for the tropical rainforest and dry savanna ecosystems. This work should contribute to a better estimation of the soil biotic compartment in the different models of greenhouse gas emissions from tropical soils.

Le secteur du tri des déchets est en pleine expansion. De par la nature de leurs activités, les centres de tri des déchets sont une source d’émission de bioaérosols dont l’exposition peut entrainer diverses troubles sur la santé des travailleurs. La composition des bioaérosols dans les centres de tri est peu documentée. Dans ce contexte, les objectifs de la thèse étaient de caractériser et de déployer dans un centre de tri (pour un suivi d’un an) une méthode d’analyse de la biodiversité microbienne dans les bioaérosols par séquençage à haut débit. Les travaux ont permis de connaitre les avantages et les limites de plusieurs méthodes d’analyse de la biodiversité et de mettre en lumière la nécessité de standardiser un processus de mesure dans le cadre d’études de comparaison. Le suivi de la biodiversité microbienne dans les bioaérosols émis en centre de tri a permis de mettre en évidence la grande complexité et la variabilité des taxons bactériens et fongiques à différents postes de l’entreprise. L’analyse statistique a mis en évidence le caractère multifactoriel de la variation et de la composition des bioaérosols émis en environnement professionnel. La quantité importante de données a permis d’améliorer les connaissances sur la composition des bioaérosols émis en centre de tri des déchets et sur la stratégie de prélèvement à adopter pour une évaluation du risque biologique représentative de l’entreprise / The waste sorting activities is constantly increasing. Due to the nature of their activities, waste sorting plants are a source of bioaerosol emissions whose exposure can lead to various health problems for workers. The composition of bioaerosols in sorting centers is poorly documented. In this context, the aims of the thesis were to characterize and deploy in a sorting center (for a follow- up of one year) a method of analysis of microbial biodiversity in bioaerosols using high throughput sequencing. The work provided information about the advantages and the limits of several methods of analysis of the biodiversity and highlighted the need to standardize a process of measurements for comparative studies. The monitoring of microbial biodiversity in bioaerosols emitted in a sorting plant revealed the high complexity and the variability of bacterial and fungal taxa at different places in the company. Statistical analysis highlighted the multifactorial nature of the variation and composition of bioaerosols emitted in this occupational environment. The large amount of collected data improved the knowledge on the composition of bioaerosols emitted in the waste sorting plant and the sampling strategy to be conducted for a representative biological risk assessment in the company

Micro-organismos oriundos de ecossistemas restritivos e pouco explorados como o continente Antártico têm despertado grande interesse na comunidade científica, visto que pesquisas biotecnológicas podem resultar em produtos de alto valor agregado. Dentre estes produtos, enzimas de psicrófilos ou psicrotolerantes, que apresentam alta atividade catalítica aliada à flexibilidade, estimulam a busca de condições que favoreçam a sua produção. Assim, as proteases se destacam neste universo, visto que respondem por cerca de 60% do mercado mundial de enzimas. Neste contexto, o objetivo do presente trabalho foi o de selecionar, dentre os isolados de diferentes amostras do continente Antártico, leveduras produtoras destas enzimas, bem como de estabelecer condições de cultivo laboratorial para o favorecimento da atividade proteolítica. Foram utilizadas 99 leveduras previamente isoladas na Divisão de Recursos Microbianos da Coleção Brasileira de Micro-organismos de Ambiente e Indústria da UNICAMP, das quais 14,14% (n= 14) foram selecionadas como produtoras de proteases por meio de ensaios em placas contendo ágar Sabouraud com leite desnatado (10%). O perfil da atividade proteolítica extracelular, o crescimento e o consumo de açúcar das leveduras selecionadas foram avaliados a partir do cultivo das mesmas em caldo Sabouraud, pH 5,5, a 150rpm, a 25°C por 120h. Todos os isolados selecionados mostraram alguma atividade proteolítica em meio líquido. A levedura Rhodotorula mucilaginosa L07 foi então selecionada para a etapa seguinte, em função da máxima atividade proteolítica (33,36 U.mL-1) observada em meio líquido. Para avaliar o impacto da suplementação do meio de cultivo e da variação de parâmetros físico-químicos sobre a atividade proteolítica desta levedura, e ainda visando o favorecimento da produção de proteases, foi utilizado o planejamento fatorial fracionado 26-2, seguido de planejamento fatorial completo (DCCR 23). Os resultados obtidos permitiram estabelecer um modelo matemático que foi validado, elevando a atividade proteolítica inicial em 45,53%. A caracterização da protease produzida por R. mucilaginosa L07 revelou seu caráter ácido, cuja máxima atividade (71,14 U.ml-1) foi obtida em pH 5,0 a 50°C. Verificou-se ainda que 70% da atividade proteolítica foi conservada quando os ensaios foram realizados a 37°C e 80% em 45 e 60°C. Esta enzima mostrou-se altamente estável após incubação por 1h em temperaturas até 50°C, verificando-se a manutenção da atividade proteolítica. Estas características combinadas com a atividade proteolítica sugerem que esta protease exibe potencial para ser utilizada em processos biotecnológicos. / Microorganisms from restrictive and unexplored ecosystems as the Antarctic continent have been of great interest in the scientific community, because they can synthesize biotechnological products with high added value. Among these products, psychrotolerants or psychrophilic enzymes, which present high activity coupled with flexibility, stimulates the studies regarding to optimize conditions in order to favor their production. Proteases are highlighted in this universe, because that account for about 60 % of the enzymes world market. In this context, the aim of this work was to select among microorganisms strains isolated from Antarctica, specifically protease-producing yeast, as well as establishing its growth conditions at laboratory scale focusing on its proteolytic activity. Ninety-nine previously isolated yeasts (DRM CPQBA / UNICAMP), from different samples of the Antarctic continent were evaluated and 14,14% (n = 14) were selected as protease producers in Sabouraud Agar containing skim milk (10%). The profile of the extracellular proteolytic activity, growth conditions and sugar consumption by selected yeast strains was reported in Sabouraud broth at pH 5.5, agitation rate of 150 rpm, 25 ° C for 120h. The results showed that all selected strains presented proteolytic activity. The maximum activity values was observed with Rhodotorula mucilaginosa L07 (33,36 U.mL-1), which was selected to continue the experiments. In the next step it was studied the effect of nutrients supplementation of the culture medium and the variation of physicochemical parameters on the proteolytic activity of R. mucilaginosa L07 by using an experimental design consisting of 26-2 fractional factorial followed by a full factorial design (CCRD 23). The results obtained allowed to stablish a mathematical model, which was validated, allowing the increase of the initial proteolytic activity in 45.53%. Characterization of protease produced by R. mucilaginosa L07 showed an acid character, and a maximum activity of 71.14 U.ml-1 was obtained at pH 5.0 at 50°C. It was also found that 70% of the proteolytic activity was preserved when the assays were performed at 37°C and 80% at 45 and 60°C. This enzyme was highly stable after incubation at temperatures <= 50°C/ 1 h, maintaining the proteolytic activity. These characteristics combined with enzymatic activity, suggests that this protease exhibits potential use in biotechnological processes.