Dissertations / Theses on the topic 'Micromys'

L’effet des inondations sur la structure génétique des populations de petits mammifères et sur leur réponse comportementale demeure encore peu étudié. Le Rat des moissons (Micromys minutus) est un modèle d’étude intéressant parce que plusieurs traits de sa biologie suggèrent qu’il doit être bien adapté à ce type de perturbation. Cette thèse a pour objectifs d’identifier la structure génétique d’une population de Rats des moissons à l’échelle d’un paysage, de déterminer les capacités de déplacements et de dispersion des animaux, et d’évaluer l’effet des inondations sur leurs déplacements et sur la structure génétique des populations. L’étude combine des approches directes sur le terrain (CMR, radiopistage, pièges-photos) avec des inférences issues d’analyses génétiques sur un grand nombre d’individus, grâce à neuf nouveaux microsatellites polymorphes décrits pour cette espèce. Le Rat des moissons forme une population unique à l’échelle du paysage considéré, avec un très faible isolement par la distance dû à des flux de gènes importants. Ses capacités de dispersions sont élevées. Pendant les inondations, les animaux restent dans la roselière sans mouvement de fuite apparent. Les inondations ont un effet sur les flux géniques qui est différent selon les possibilités de refuge fournies par les habitats. Ces résultats montrent que le Rat des moissons est une espèce adaptée aux inondations. Plus généralement, il mérite d’être considéré comme une espèce porte-drapeau des zones humides<br>The effect of flooding on the genetic structure of small mammal populations and their behavioural response remains unstudied. The Harvest mouse (Micromys minutus) is an interesting study model because several traits of its biology suggest that it should be well adapted to this type of disturbance. The purpose of this thesis is to identify the genetic structure of a population of Harvest mouse on a landscape scale, to determine the ability of animals to move and disperse, and to assess the effect of floods on their movements and on the genetic structure of populations. The study combines direct field approaches (CMR, radiotracking, camera traps) with inferences from genetic analyses on a large number of individuals, using nine new polymorphic microsatellites described for this species. The Harvest mouse forms a unique population at the landscape scale, with very little isolation by distance due to large gene flows. Its dispersal abilities are high. During the floods, the Harvest mouse stays in the reedbed without any apparent leak. Floods have an effect on gene flows that is different, depending on the refuge possibilities provided by habitats. These outcomes show that the Harvest mouse is a flood-friendly species. More generally, it should be considered as a wetland flagship species

Establecer las relaciones existentes entre las especies y definir los límites entre las mismas ha sido uno de los objetos principales de estudio de la biología evolutiva durante las últimas décadas. El establecimiento de estos límites se hace más complejo cuanto más cercanas son las especies entre sí debido a que comparten más características, tanto genéticas como morfológicas, lo que hace que en algunas ocasiones estos límites sean muy difusos, generando una mayor complejidad en la búsqueda de los criterios más precisos y menos sesgados para establecer los límites entre las especies. Bajo este marco conceptual, el objetivo principal de esta tesis doctoral ha sido la búsqueda, sirviéndose de herramientas morfológicas y filogenéticas, de los criterios que explican con un mayor grado de exactitud la relación existente entre dos especies cercanas de topillos, Microtus duodecimcostatus y Microtus lusitanicus, que se distribuyen a lo largo de la Península Ibérica. Estos dos topillos ibéricos pertenecen al orden Rodentia y, teniendo en cuenta que los roedores componen la mitad de las especies de los mamíferos y que además cuentan con un genoma con ciertas particularidades con respecto al del resto de los mamíferos, se desarrolló un conjunto de marcadores nucleares intrónicos específicos para los roedores. A partir de genomas de las bases de datos y mediante la aplicación de una serie de filtros bioinformáticos se seleccionaron 208 marcadores con unas determinadas características (tamaño, copia única, alta divergencia y evolución ajustada a la del resto del genoma) que permitieran usar estos intrones para resolver cuestiones filogenéticas a los niveles taxonómicos más bajos dentro del orden Rodentia. Una vez obtenido este conjunto de marcadores se escogió un subconjunto de ellos y se comprobó su validez mediante la amplificación y posterior uso para la reconstrucción filogenética en especies pertenecientes a varias familias representativas del orden Rodentia. Se obtuvo un elevado éxito de amplificación (78%) y las reconstrucciones filogenéticas de máxima verosimilitud y de inferencia Bayesiana con estos marcadores seleccionados reflejaron las filogenias propuestas para este orden en la literatura. Por otro lado, se empleó la técnica de la morfometría geométrica para determinar las características morfológicas principales que diferencian las dos especies de topillos, M. duodecimcostatus y M. lusitanicus, en las zonas de distribución alopátrica. Se identificaron cinco caracteres óseos que permitían una clara diferenciación morfológica entre las dos especies. Posteriormente se llevó a cabo, mediante estos caracteres, la asignación de especie a los individuos de las zonas de distribución solapada de las dos especies de topillos. A pesar de que en las zonas de distribución solapada se detectó una convergencia en forma entre las dos especies, se obtuvo una clasificación muy robusta de los individuos en una de las dos especies Por último, se llevó a cabo la caracterización de las dos especies de topillos ibéricos a nivel filogenético mediante el uso de un marcador mitocondrial, citocromo b, y de seis intrones de los desarrollados en la primera parte de la tesis. Se estimó, usando metodologías de reconstrucción de árboles de especies, que el tiempo de especiación entre estas dos especies es de 0,65 millones de años y que ambas especies sufren procesos de expansión poblacional, siendo este mayor en el caso de M. lusitanicus. A pesar de que estas dos especies se comportan como dos entidades separadas se detectó la existencia de una discordancia mitocondrial. Utilizando diferentes metodologías basadas en la teoría de la coalescencia se determinó que la causa más plausible de esta discordancia es un proceso antiguo de introgresión por hibridación de la especie M. duodecimcostatus hacia M. lusitanicus, originado así secuencias mitocondriales introgresadas en individuos de M. lusitanicus, siendo posiblemente los machos de M. lusitanicus los que invadieron las áreas de distribución de M. duodecimcostatus.<br>Establishing the relationships among species and particularly defining the boundaries among them has been one of the main goals of Evolutionary Biology in recent decades. Assessing these limits becomes more complex when species are closely related, since they share more features, both genetic and morphological, and their boundaries are more diffuse. In such cases, it is crucial to identify accurate criteria to set the limits among species. In this scenario, the aim of this thesis has been to explore, using morphological and phylogenetic tools, wich are the criteria that explain with a higher degree of accuracy the relationship between two closely related species of voles, Microtus duodecimcostatus and Microtus lusitanicus (order Rodentia), that are distributed along the Iberian Peninsula, with a partial range overlap. In order to perform a multi-locus analysis of these species, a bioinformatic pipeline to extract intron sequences from already available rodent genomes was used, which allowed the identification of 208 introns. These introns were shown to be optimal to solve phylogenetic questions of closely related species in the Rodentia order. In addition, geometric morphometrics on skull bones and teeth was used to identify five characters to discriminate between the two species in their allopatric ranges. These characters also proved to be very powerful to discriminate species in the overlapped range, despite the existence of morphological convergence processes in this area in the two species. Finally, by multi-locus coalescence methods applied to the cytochrome b marker and a selection of six of the developed introns, a divergence time of 0.65 million years ago was estimated for these two species. Although these species behave as two separate entities, the existence of a mitochondrial discordance was detected. Using different methodologies based on the coalescent theory, it was determined that the most plausible cause of this discordance is due to an ancient process of introgression by hybridization from M. duodecimcostatus to M. lusitanicus.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2015.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>Marine microbes play a fundamental role in driving ocean ecosystem dynamics and biogeochemistry. While their importance is global in scale, microbial processes unfold at the level of single cells and are intimately dependent on interactions between microorganisms, their neighbors, and the surrounding physical and chemical environment. Furthermore, traditional imaging techniques often provide frozen snapshots of the marine microbial world, yet microbial interactions are inherently dynamic, as for example in the case of motility, chemotaxis, and the encounter of microbes with viruses and animal hosts. These biological processes are frequently driven by physical mechanisms, and our understanding of them can benefit from a focus on the physical ecology of marine microbes. This is the approach pursued in this thesis, by directly applying dynamic imaging and microfluidics, which offer powerful new opportunities to study microbial processes in a time resolved manner and with exquisite environmental control. Through single-cell, live imaging of three fundamental marine microbial processes - motility, chemotaxis and viral adsorption - we demonstrate how capturing previously unseen biophysical processes in microbial ecology at their natural timescales can both shed light on unexplained mechanisms and provide robust quantifications of interaction rates. We first study a newly discovered nanoscale motility adaptation in the marine bacterium Vibrio alginolyticus using high-speed imaging. We found that marine bacteria can exploit a buckling instability of their flagellum to change direction during swimming, achieving the same functionality as multi-flagellated cells, but with the cost of synthesizing and operating only one flagellum. This finding not only reveals a new role of flexibility in prokaryotic flagella, but also highlights the exquisite motility adaptations of marine microbes to the resource-poor environment of the ocean. We then determine how this motility adaptation affects the cells' ability to climb chemical gradients ('chemotaxis'). We found that, counter- to current models, chemotaxis in V. alginolyticus is speed-dependent. Faster cells exhibited not only faster chemotactic migration, but also tighter accumulation around the resource peak. This result adds a new dimension to our understanding of bacterial chemotaxis pathways, by demonstrating that swimming speed can be an important and counter-intuitive control parameter in how marine microbes encounter and exploit chemical resources. Finally, we consider an encounter process that is motility-independent - that between a nonmotile host and a virus. Using the globally abundant marine cyanobacterium Prochlorococcus and a cyanobacterial virus ('cyanophage') as a model system, we directly imaged the encounter and adsorption dynamics of the virus and the host at the level of single cells, using dual-wavelength epifluorescent microscopy. By applying this non-invasive approach to quantify thousands of encounter events using automated image acquisition and analysis, we directly measured the rate at which viruses encounter and adsorb to hosts. We found that the probability of adsorption is considerably lower than was obtained with traditional, bulk measurement approaches, suggesting the need for a revision of viral infection dynamics in marine ecosystem models and opening the door for studies of microbial individuality in the context of viral infection. In summary, this thesis demonstrates that physical processes in microbial ecology, studied by means of new approaches including microfluidics and dynamic imaging at the single-cell scale, can contribute fundamental new insights into the ecology of marine microbes.<br>by Kwangmin Son.<br>Ph. D.

La compréhension des interactions qui associent les plantes et les microorganismes du sol est une étape incontournable pour une gestion durable de nos écosystèmes notamment en agriculture. Parmi les services écosystémiques résultant de leurs interactions, on peut citer la productivité végétale répondant, en partie, aux besoins alimentaires de la population mondiale et la régulation des cycles biogéochimiques. Les services écosystémiques, qui émergent de telles interactions, reposent sur des liens trophiques pouvant être représentés par un compromis entre coûts et bénéfices pour les différents partenaires de l’interaction. Les plantes, organismes autotrophes ou producteurs primaires, sont des organismes clefs qui font entrer le carbone dans l’écosystème, via la photosynthèse. Une partie de ce carbone est libérée sous forme de molécules plus ou moins complexes, au niveau de leurs racines, par le processus de rhizodéposition. Ces composés servent de molécules signal et de nutriments pour les microorganismes du sol, essentiellement hétérotrophes, c’est l’effet rhizosphère. Ce processus est donc coûteux pour la plante mais bénéfique aux microorganismes. Les microorganismes contribuent, en retour, à la nutrition et la santé des plantes ce qui est coûteux mais leur assure une source bénéfique de nutriments. Ces échanges trophiques reposent néanmoins sur un équilibre dépendant des conditions biotiques et abiotiques qui affectent chaque partenaire. La biodiversité microbienne, de par la multitude d’interactions au sein des communautés microbiennes, est un facteur biotique important. Parmi les facteurs abiotiques, le contexte environnemental actuel, soumis aux changements globaux, est propice à une déstabilisation de ces interactions. L’objectif de ce travail est donc de comprendre comment vont varier les coûts et bénéfices, pour chaque partenaire, suite à des modifications de l’environnement affectant l’un ou l’autre. L’intérêt étant de savoir si les bénéfices pour les plantes et les microorganismes, qui permettent les services écosystémiques, seront affectés. Pour répondre à cet objectif, un cadre d’interaction plantes-microbes simplifié a été choisi et une déstabilisation, au niveau de la plante, a été effectuée au moyen d’une augmentation en CO2 atmosphérique. L’interaction entre Medicago truncatula et Pseudomonas fluorescens a ainsi été étudiée. Les interactions ont ensuite été complexifiées en utilisant une communauté microbienne dans son ensemble et, cette fois, la modification a été appliquée au compartiment microbien soumis à une dilution de sa diversité. L’effet du gradient de diversité microbienne obtenu a été mesuré sur la croissance et la reproduction de trois espèces végétales modèles (Medicago truncatula, Brachypodium distachyon et Arabidopsis thaliana). Enfin, l’analyse s’est focalisée sur la communauté microbienne en identifiant la part active, c'est-à-dire les microorganismes qui utilisent les composés libérés par la plante. Ces microorganismes, qui interagissent réellement avec la plante, ont été détectés grâce à une analyse ADN SIP utilisant l’isotope 13C. Les principaux résultats observés, que la modification affecte l’un ou l’autre des partenaires, sont une déstabilisation des coûts et bénéfices. La première étude montre une variation temporaire des interactions en faveur de la plante en condition de CO2 augmenté. Dans le cas d’une dilution de la diversité microbienne, les coûts pour la plante sont conditionnés par la dépendance naturelle des plantes vis-à-vis des microorganismes symbiotiques qui interagissent avec le reste de la communauté. Cela est confirmé par la dernière expérimentation qui met en évidence les interactions microbes-microbes qui conditionnent la structure de la communauté microbienne interagissant avec la plante. [...]<br>Understanding the interactions that bind plants and soil microorganisms is an essential step for the sustainable management of ecosystems, especially in agriculture. The ecosystem services resulting from such interactions include plant productivity which responds, in part, to the food requirements of the world's population and the regulation of biogeochemical cycles. These ecosystem services depend on trophic links between the two partners in the interaction and can be represented by a tradeoff between the costs and benefits for each partner. Plants, being autotrophic organisms or primary producers, are key organisms which introduce carbon into the ecosystem, through photosynthesis. Part of this carbon is released as more or less complex molecules at the roots level, thanks to the rhizodeposition process. These compounds act as signal molecules and nutrients for soil microorganisms, which are mainly heterotrophic, in the so-called rhizosphere effect. This process is costly for the plant but beneficial to the microorganisms. In return, microorganisms contribute to plant nutrition and health, which is costly but provides them with a beneficial source of nutrients. These trophic exchanges, however, are based on a balance which depends on the biotic and abiotic conditions that affect each partner. Microbial biodiversity, through the multitude of interactions occurring within microbial communities, is a significant biotic factor. Among the abiotic factors, the current environmental context, subject to global change, is tending to destabilize these interactions. The objective of this work was to understand how environmental changes affect the costs and benefits for each partner by applying changes to one or the other, the aim being to determine whether these changes would affect the benefits for plants and microorganisms that provide ecosystem services. To achieve this objective, a simplified framework for plants-microbes interaction was first chosen. Destabilization at the plant level was carried out by increasing the atmospheric CO2 and studying the interaction between Medicago truncatula and Pseudomonas fluorescens. The interactions were then made more complex by using a whole microbial community but this time the change was applied to the microbial compartment by subjecting it to diversity dilution. The effect of the resulting microbial diversity gradient was measured on the growth and reproduction of three model plant species (Medicago truncatula, Brachypodium distachyon and Arabidopsis thaliana). Finally, the microbial community was subjected to a DNA SIP analysis, with the isotope 13C, to identify the active portion, i.e., those microorganisms which really interacted with the plant and used compounds released by it. The main result, when the change affected one or other partner, was a destabilization of the costs and benefits. The first study showed a transient variation in the interactions in favour of the plant under increased CO2 conditions. In the case of a dilution of microbial diversity, the costs for the plant are conditioned by the natural dependency of plants on symbiotic microorganisms that interact with the rest of the community. This was confirmed by the last experiment that highlighted the between-microbes interactions which determined the composition of the microbial community that interacted with the plant. This work has helped to clarify the functioning of relationships between plants and soil microbes and the factors that contribute to their maintenance which is essential to the functioning of ecosystems. These studies also provide ways for predicting the impacts of global change on ecosystems. The conservation or restoration of ecosystem services is essential for human well-being

Previous studies of the control of reproduction in Rhabdomys pumilio have shown that day length alone does not inhibit spermatogenesis, that a reduction in food availability and ambient temperature results in an inhibition of gametogenesis, that females are more susceptible to inhibition than are males, and that mice that are able to maintain a body fat store in the face of an energetic challenge, are less likely to show reproductive inhibition than those that lose their fat store. In the present study, field and laboratory experiments were conducted to examine the effects of winter food supplementation on reproduction and population dynamics, and the effects of exogenous GnRH, leptin and mercaptoacetate (MA) on reproductive activity of Rhabdomys pumilio exposed to an energetic challenge. In the field food supplementation experiments in Thomas Baines Nature Reserve (2000, 2001), there was no winter inhibition of reproduction and provision of supplementary food had little effect. While at Mountain Zebra National Park (2002) winter was harsher, females became reproductively inactive, spermatogenesis continued and the provision of extra food resulted in higher rates of individual growth and larger reproductive organs. Treatment of mice that had been exposed to a prolonged energetic challenge, with exogenous GnRH (1µg/mouse/treatment) resulted in an increase in the masses of the testes and epididymides, and in the activity of the reproductive organs. Treatment with exogenous leptin (40µg/mouse/treatment), concurrently with an energetic challenge, countered the negative effects of the energetic challenge, and treated males had larger reproductive organs. MA (600µmol/kg body mass), given concurrently with an energetic challenge, did not inhibit fat metabolism, although the high-fat diet countered the effects of the energetic challenge. Results suggest that the first response of male Rhabdomys pumilio to an energetic challenge is a reduction in the size of the reproductive organs, without an inhibition of spermatogenesis. It is likely that this effect is mediated via white fat and leptin, and leptin’s influence on the hypothalamic-pituitary-gonad axis. Results of the study support the suggestion that females are more sensitive to reproductive inhibition than males and that reproduction in Rhabdomys pumilio is truly opportunistic.

Insgesamt 1746 Kleinsäuger aus den Familien Muridae (Murinae, Arvicolinae) und Soricidae aus dem Naturschutzgebiet ”Großer Hakel” (Sachsen-Anhalt) und der Tagebaufolgelandschaft ”Phönix-Ost und Rusendorf” Meuselwitz (Thüringen) wurden auf einen Befall mit Capillaria hepatica und Metazestoden von Bandwürmern (Cyclophyllida) untersucht. Das Tiermaterial stammte aus genehmigten faunistischen Untersuchungen aus den Jahren 1993 bis 1997 in Zusammenarbeit mit der Universität Halle und dem Naturkundemuseum "Mauritianum" Altenburg. Alle Mäuse wurden seziert und der Brust- und Bauchraum einschließlich aller Organoberflächen, der Subkutis, des Gehirns und der Leber untersucht. Eine Altersbestimmung der Wirte erfolgte bei den untersuchten Rötelmäusen (Clethrionomys glareolus). Erstmals in Deutschland konnte im Hakel ein stabiles Endemiegebiet von Capillaria hepatica bei Wildmäusen nachgewiesen werden. Die aus dem ”Großen Hakel” stammenden Gelbhals- (Apodemus flavicollis) und Rötelmäuse wiesen Befallshäufigkeiten von 8,5 bzw. 15,1 % auf, die Eizahlen pro Leber lagen zwischen 67 und 3 600 000. Weibliche Mäuse zeigten eine höhere Befallshäufigkeit als männliche Mäuse. Bei den Rötelmäusen konnte ein Anstieg der Befallshäufigkeit von 5,8 % der bis zu 3 Monate alten bis auf 28,6 % der bis zu einem Jahr alten Tiere beobachtet werden. Patente Infektionen waren erst in der Altersgruppe 3-6 Monate nachzuweisen. In dem Untersuchungsgebiet Meuselwitz war Capillaria hepatica bei den untersuchten 1069 Muridae und Soricidae nicht nachweisbar. Eine aktuelle Übersicht der weltweit in 53 Ländern festgestellten 137 Wirtsarten aus 25 Säugetierfamilien von Capillaria hepatica wurde zusammengestellt. Die Familie Muridae stellt mit 83 Arten die bedeutendste Wirtsgruppe dar. Bisher wurde über 56 Capillaria-hepatica-Infektionen beim Menschen (davon 39 Kinder) aus 18 Ländern berichtet. Die Leitsymptome der Erkrankung beim Menschen sind intermittierendes Fieber, Hepatomegalie, Leukozytose mit hochgradiger, persistierender Eosinophilie, Anämie, Hypergammaglobulinämie und Hypoalbuminämie. Die Serumaktivitäten von AST, ALT und LDH sind erhöht. Die Diagnose der zum Teil tödlich verlaufenden Erkrankung ist intra vitam bisher nur durch Leberbiopsie oder Laparotomie möglich. Einzelne Versuche mit serologischen Tests scheinen erfolgversprechend. Die Einzelnachweise von Capillaria hepatica bei Mensch, Hase und Sumpfbiber in Deutschland (Bayern, Sachsen und Sachsen-Anhalt) sind als Hinweise auf bestehende Endemiegebiete zu werten. Aufgrund der weiteren Verbreitung und der diagnostischen Probleme kann von einer höheren Gefährdung des Menschen (insbesondere Kleinkinder) und der Haustiere durch den Zoonoseerreger Capillaria hepatica ausgegangen werden. Bei 10,5 % aller untersuchten Mäuse wurden Metazestoden gefunden. Die Rötelmaus wies insgesamt mit durchschnittlich 23,5 % (Meuselwitz 30,2 %, Hakel 15,1 %) die signifikant höchsten Befallshäufigkeiten mit Metazestoden auf. Insgesamt konnten bei Muridae und Soricidae in Sachsen-Anhalt und Thüringen Metazestoden von 8 Bandwurmgattungen bzw. -arten (Cladotaenia globifera, Mesocestoides spp., T. crassiceps, T. martis martis, T. martis americana, T. mustelae, T. polyacantha, T. taeniaeformis) nachgewiesen werden. Die breiteste Metazestodenfauna mit insgesamt 7 Arten wurde bei der Feldmaus (Microtus arvalis), nur jeweils eine Metazestodenart dagegen bei Brandmaus (Apodemus agrarius), Zwergmaus (Micromys minutus), Feldspitzmaus (Crocidura leucodon) und Waldspitzmaus (Sorex araneus) gefunden. Die Zwergspitzmaus (Sorex minutus) war nicht von Metazestoden befallen. Eine deutliche Wirtsspezifität (Feldmaus) konnte für T.-crassiceps- und T.-polyacantha-Metazestoden festgestellt werden. Im Gebiet Meuselwitz dominierten bei Muridae Metazestoden von T. mustelae (Befallshäufigkeit 9,3 %) sowie von T. martis martis (Befallshäufigkeit 6,4 %), im Hakel von T. martis martis (Befallshäufigkeit 2,5 %) sowie T. mustelae (Befallshäufigkeit 2,2 %). Während in Meuselwitz die höchsten Befallshäufigkeiten mit Metazestoden von T. mustelae (24,7 %) bei der Rötelmaus und von T. martis martis (13 %) bei der Gelbhalsmaus vorlagen, waren im Hakel die Rötelmäuse am häufigsten mit T.-mustelae- (8,2 %) und T.-martis-martis- Metazestoden (4,8 %) befallen. Mit zunehmendem Alter der Rötelmäuse stieg die Befallshäufigkeit mit Metazestoden bei dieser Tierart an. Rötelmäuse unter einem Alter von 2 Monaten waren noch nicht von Metazestoden befallen. Infektionen mit 2 Metazestodenarten traten erstmals bei 4 Monate alten Rötelmäusen auf, bei zwei Tieren im Alter von 9 bzw. 12 Monaten wurden Infektionen mit 3 Metazestodenarten (Cladotaenia globifera + T. martis americana + T. mustelae; Cladotaenia globifera + T. martis martis + T. mustelae) nachgewiesen. Bei insgesamt 10 Muriden konnten Mischinfektionen mit Capillaria hepatica und Metazestoden von Bandwürmern festgestellt werden. Bei Mäusen der Familie Soricidae sind ausschließlich Metazestoden von Cladotaenia globifera gefunden worden. Erstnachweise für Deutschland stellen Funde der Metazestoden von Cladotaenia globifera bei der Feldspitzmaus, T. martis americana bei der Rötelmaus, T. mustelae bei Erd- und Zwergmaus und T. polyacantha bei der Waldmaus dar. Das erste Mal in Europa konnten T.-martis-americana-Metazestoden bei der Feldmaus gefunden werden. Eine wichtige Einflußgröße auf die Metazestodenfauna war das Aufeinandertreffen von End- und Zwischenwirt in bestimmten Biotopen<br>The occurrence of Capillaria hepatica and metacestodes of Cyclophillida was investigated in 1746 small mammals of the families Muridae (Murinae, Arvicolinae) and Soricidae from the nature reserve ”Grosser Hakel” (Saxony-Anhalt) and the former open-cast mining area "Phoenix-Ost and Rusendorf" Meuselwitz (Thuringia). The animals came from approved faunistic surveys in co-operation with the University of Halle and the natural history museum ”Mauritianum” Altenburg. All mice were sectioned and the thoracic as well as the abdominal cavity including all organ surfaces, subcutaneous tissue, brain and liver were examined. The age of all bank voles (Clethrionomys glareolus) was determined. In the nature reserve "Grosser Hakel"an stable endemic area of Capillaria hepatica in wild mice could be detected for the first time in Germany. The percentage of yellow-necked mice (Apodemus flavicollis) infected with Capillaria hepatica in that area was 8.5 %, the percentage of bank voles infected with Capillaria hepatica in that area reached 15.1 % respectively. The number of eggs per liver ranged from 67 to 3,600,000. The proportion of infected mice was higher in female than in male mice. In bank voles the frequency of infection increased with age (from 5.8 % in the age of 3 months to 28.6 % in the age of one year). Patent infections were first detected in the age group of 3 to 6 month. No Capillaria hepatica could be found in 1069 Muridae and Soricidae examined in the Meuselwitz area. A current survey of the world-wide occurrence of Capillaria hepatica in 137 hosts of 25 mammal families was prepared. The family of Muridae (with 83 species) is the most important host group. Up to now 56 Capillaria-hepatica-infections in humans (including 39 children) from 18 different countries were reported. Major symptoms in humans are intermittent fever, hepatomegaly, leucocytosis with severe, persistent eosinophilia, anaemia, hypergammaglobulinaemia and hypoalbuminaemia. The serum activities of AST, ALT and LDH are elevated. Intra-vitam diagnosis of this partly lethal disease is only possible by liver biopsy or laparatomy. First serological tests are promising. Sporadic detection of Capillaria hepatica in humans, hares and nutria in Germany (Bavaria, Saxony and Saxony-Anhalt) can be regarded as an indication of existing endemic areas. A higher risk of Capillaria-hepatica-infection in humans (especially in small children) and domestic animals can be assumed on the basis of the wide distribution and the diagnostic problems. Metacestodes were found in 10.5 % of all examined mice. The bank voles showed the significantly highest rate of infection with 23.5 % (Meuselwitz 30.2 % and Hakel 15.1 %). Altogether metacestodes of 8 tapeworm genuses (Cladotaenia globifera, Mesocestoides spp., T. crassiceps, T. martis martis, T. martis americana, T. mustelae, T. polyacantha, T. taeniaeformis) could be detected in Muridae and Soricidae in Saxony-Anhalt and Thuringia. The broadest metacestode-fauna (with 7 species) was found in the common vole (Microtus arvalis). Only one metacestode-species was detected in the stripped field mouse (Apodemus agrarius), the harvest mouse (Micromys minutus), the bicoloured whitetoothed shrew (Crocidura leucodon) and the eurasion common shrew (Sorex araneus). The pygmy shrew (Sorex minutus) was not infected by metacestodes. A distinct host specificity (in the common vole) could be established for T. crassiceps and T. polyacantha. Metacestodes of T. mustelae (infection rate 9.3 %) and T. martis martis (infection rate 6.4 %) dominated in Muridae of the Meuselwitz area. In the Hakel area T. martis martis (infection rate 2.5 %) and T. mustelae (infection rate 2.2 %) dominated as well. Whereas metacestodes of T. mustelae occurred in the bank vole with an infection rate of 24.7 % and T. martis martis in yellow-necked mice with an infection rate of 13.0 % in the Meuselwitz area, T. mustelae occurred in bank voles with an infection rate of 8.2 % and T. martis martis in yellow-necked mice with an infection rate of 4.8 % in the Hakel area. The infection rate of bank voles with metacestodes increased with age. No metacestodes were found in bank voles younger than 2 month of age. Infection with 2 different metacestode-species occurred in bank voles for the first time at the age of 4 month. 3 metacestode-species were found in 2 animals at the age of 9 to 12 months (Cladotaenia globifera + T. martis americana + T. mustelae; Cladotaenia globifera + T. martis martis + T. mustelae). In 10 Muridae occurred a mixed infection with Capillaria hepatica and metacestodes of tapeworms. In mice of the Soricidae-family only metacestodes from Cladotaenia globifera could be found. For the first time in Germany were detected metacestodes of Cladotaenia globifera in the bicoloured whitetoothed shrew, of T. martis americana in bank voles, of T. mustelae in the common field vole and the harvest mouse and of T. polyacantha in the wood mouse. For the first time in Europe T. martis americana-metacestodes could be detected in the common vole. Of high importance to the metacestode-fauna was the encounter of final host and intermediate host in certain biotopes

Superbug infection is one of the greatest public health threat with grave implications across all levels of society. Towards a new solution to combat infection by multi-drug resistant bacteria, this thesis presents an engineering framework and genetic tools applied to repurpose commensal bacteria into 'micro-robots' for the treatment of superbug infection. Specifically, a prototype of designer probiotic was developed using the human commensal bacteria Escherichia coli. The engineered commensal was reprogrammed with user-specified functions to sense superbug, produced pathogen-specific killing molecules and released the killing molecules via a lytic mechanism. The engineered commensal was effective in suppressing ~99% of planktonic Pseudomonas and preventing ~ 90% of biofilm formation. To enhance the sensing capabilities of engineered commensal, genetic interfaces comprising orthogonal AND & OR logic devices were developed to mediate the integration and interpretation of binary input signals. Finally, AND, OR and NOT logic gates were networked to generate a myriad of cellular logic operations including half adder and half subtractor. The creation of half adder logic represents a significant advancement of engineering human commensal to be biological equivalent of microprocessor chips in programmable computer with the ability to process input signals into diversified actions. Importantly, this thesis provides exemplary case studies to the attenuation of cellular and genetic context dependent effects through principles elucidated herein, thereby advancing our capability to engineer commensal bacteria.

Antibiotics are designed to inhibit the growth of or kill bacteria. Of the many classes of antibiotics that have been synthesized two particular classes of antibiotic have been frequently detected in the natural environment, namely the tetracyclines and sulfonamides. Following use, these compounds can enter the environment via the application of animal manures or domestic seawage sludge to land as a fertiliser or from wastewater treatment plant effluents. Once in the environment the compounds can persist and, depending on their properties, are distributed around the different environmental media (i.e. surface waters, groundwaters, soils and sediments). Several studies have suggested that tetracyclines and sulfonamides may have significant impacts on microbial function in the natural environment. However most of these studies have used existing standardised test procedures and/or unrealistic exposure conditions. The aim of the current study therefore was to develop a more environmentally realistic test system for assessing the effects of antibiotics on aquatic microbial communities and to apply this to assess the potential impacts of a sulphonamide and a tetracycline antibiotic on aquatic microbial communities. The developed system, which was an aquatic microcosm composed of fresh river water, return line treated sewage and OECD synthetic sewage, was initially used to assess the effects of 3, 5-dichlorophenol, an OECD reference toxicant. Effects of DCP were seen within the concentration range that is considered valid by other standard microbial toxicity tests, such as OECD method 209 (3.2-32 mg/L). Since the developed system was able to quantify effects on aquatic microbial communities, it can be seen as being more environmentally relevant than existing standard tests, which rely on testing single microbial species or sludge communities. The test system was then used to test the effects of chlortetracycline (CTC) and sulfamethoxazole (SMX) on multisubstrate utilization. Following addition of the study antibiotics, effects were observed for both antibiotics on total substrate utilization and on the utilization of specific, ecologically relevant end-points (such as nutrient cycling and polymer degradation) also. Effects were also observed on the structure of microbial communities and on the functional diversity of substrate utilization (especially in the case of SMX exposure) and these effects generally persisted for up to 3 d after addition of the study compounds at a lower concentration of 0.1 mg/L for both compounds. The results indicate that both antibiotics were inhibiting various aspects of substrate utilization, most of which were related to ecologically relevant processes that occur in the aquatic environment. The results also suggest that SMX and CTC exposure result in changes in the community structure of ecologically relevant groups of microbes (such as bacteria involved in the nitrogen and carbon cycle bacteria). Microbial communities that were exposed to CTC and SMX showed a varying degree of recovery, although more long term effects were seen in SMX exposures; functional effects were observed for the duration of the exposure. It was hypothesized that the observed recovery may have been caused by the selection of antibiotic resistance in the exposed communities. Culture based resistance studies showed that there was a significant temporal rise in CTC resistance at all CTC concentrations, but not SMX resistance, across the dose range. In addition, a greater number of distinct microbial morphotypes could be isolated from combined microcosms on day 7 compared with day 1. An increase in CTC and SMX resistance in control exposures was also observed. In addition, distinct resistant morphotypes developed in both dosed and undosed microcosms on day 7 of the study. Furthermore, the results of a series of different culture based experiments suggested that multidrug resistance was present in morphotypes that were isolated from dosed and control microcosms. These data therefore suggest that multidrug resistance was present at the start of the exposure and may also have been co-selected by exposure to CTC and SMX. In general, CTC and SMX show signs that they may pose a risk to the environment and possibly the wider health of humans and animals.

The Tasmanian lacewing (Micromus tasmaniae Walker) is one of the most common aphid predators occurring in lucerne crops in New Zealand. A comparison of sampling techniques, and the output from a simulation model, suggest that the abundance of this lacewing may have been significantly underestimated in the past. Although the occurrence of aphid predators was erratic M. tasmaniae occurred more often and in far greater numbers (up to 100 m⁻²) than any other predator species. A simulation model for lacewing development in the field indicated that the large adult populations which occurred could be accounted for on the basis of reproductive recruitment. Independent evidence that immigration was not involved in the occurrence of these large populations was gathered using directional flight traps around the field perimeter. The major factors influencing lacewing population dynamics were the availability of aphid prey and, in the autumn, parasitism. Otherwise, survival of all life-histoty stages was high with no evidence of egg or larval cannibalism. Several instances of high lacewing mortality were identified by the model and the lack of any obvious cause for these highlights inadequacies in the understanding of lacewing bionomics. The model, which used a linear relationship (day-degrees) between development and temperature, was incapable of accurately predicting lacewing emergence under field temperatures which fluctuated outside the linear region of the development rate curve. Temperature thresholds and thermal requirements estimated under fluctuating temperatures similar to those in the field produced almost identical model output to those estimated under constant temperatures in the laboratory. Prey species was capable of influencing the rate of lacewing development. M. tasmaniae has the attributes necessary to produce large populations in the short time available between lucerne harvests. The asymptote of the functional response curve is low but the efficiency at converting aphids to eggs is high. Therefore, the lacewing is able to attain maximun reproductive output at low prey densities. A low temperature threshold for development (4-5° C), rapid development and short preoviposition period results in a short generation time (49 days at 15° C). Long adult life, high fecundity and the absence of any form of estivation or diapause, results in complete overlap of generations and multiple generations per year. M. tasmaniae's role as an aphid predator is restricted by its low appetite for prey and by the lucerne management regime currently practiced in New Zealand. Because it consumes relatively few aphids per day the lacewing's ability to destroy large aphid populations is limited. However, this may be offset by its ability to attack aphids early in the aphid population growth phase, and by the large numbers of lacewings which may occur. Under the present lucerne management schemes the large lacewing populations which do occur are forced out of the fields, or die, following harvest. A number of management options for increasing the lacewings impact as an aphid predator are briefly discussed.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2013<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>Iron is a cofactor of a number biochemical reactions that are essential for life. In the marine environment, this micronutrient is a scarce resource that limits processes of global importance such as photosynthesis and nitrogen fixation. Given that marine microorganisms play a central role in modulating such biogeochemical cycles, understanding how their distribution, diversity and activity may be affected by changes in iron availability is key. This thesis explores how the availability of iron affects the ecology of marine microbial populations and communities. At the population level, I characterized the prevalence and diversity of iron acquisition strategies in specific populations of marine vibrios with distinct micro-habitat preferences. Using a combination of genomics and functional screens, I showed that siderophore-based iron acquisition is not conserved at the organismlevel but represents a stable trait at the population level. This population-level trait further appears to play a role in driving the diversification of specific vibrio populations, especially of those that are thought to prefer particles as a micro-habitat. At the community level, I measured whole microbial community responses to iron addition in microcosm experiments in different regions of the Pacific Ocean. Using metagenomics, I characterized the impact of iron availability on the microbial community structure of the Central Equatorial Pacific Ocean. This study showed that addition of iron to an iron-limited ecosystem triggers a phytoplankton bloom dominated by Pseudo-nitZschia-like diatoms, which in turn stimulate a Bacteroidetes population functionally distinct from the ambient free-living population. In the North Pacific Subtropical Gyre, I explored how iron availability impacts microbial community gene expression dynamics. Using a metatranscriptomic approach I showed that in that environment, the impact of iron was tightly connected to the supply of other limiting macronutrients, and seems to mostly affect photosynthetic organisms. This initial study paves the way for more in depth and longer-term studies to further investigate the effects of iron on the dynamics of the microbial community in the North Pacific Subtropical Gyre. Taken together data and analyses presented in this thesis demonstrate how iron availability can shape the ecology of marine microorganisms at population, community and functional levels.<br>by Laure-Anne Ventouras.<br>Ph.D.

This study was initiated in an attempt toadd the four-striped field mouse (Rhabdomys pumilio) to the small group of mammals that are used to study and develop assisted reproductive technologies. To accomplish this, a complete knowledge of both the male and female gametes was necessary, as well as a repeatable and successful IVF protocol. The gametes of the field mouse, both the falciformspermand the mature oocytes, were shown to be similar in several respects to those of many other rodent species. The induction of both the capacitated state and the acrosome reaction in the sperm were readily achieved. The success of retrieving mature oocytes was very low, with the rare occurrence of polar bodies within ovulated oocytes. The difficulties with oocytes was either related to the lack of a regular oestrous cycle, or to the hormonal regime used to induce superovulation. Although several protocols were used to accomplish superovulation in this species, it was seldom achieved. In in vitro fertilization trials, sperm were found to attach to both the cumulus oophorus and the zona pellucida of the oocytes. However, fertilization was never accomplished. This failure to achieve fertilization was probably related to the immaturity of the oocytes. Without further studies on Rhabdomys pumilio and further attempts at accomplishing in vitro fertilization, it would seem that this species would not easily be introduced as an animalmodelfor assisted reproduction.

L'acquisition, en laboratoire, des génomes mitochondriaux complets de plusieurs espèces de rongeurs Arvicolinae permet la définition de l'histoire évolutive du groupe dans un cadre évolutif et temporel. Ces relations phylogénétiques sont inférés sur un grand nombre de caractères (16000 pb), grâce à des méthodes d'analyses statistiques novatrices.La base de données moléculaires constituée représente un échantillon de génomes mitochondriaux à évolution dite "rapide", ouvrant des perspectives quant à la description des points chauds mutationnels dans des études de génomique comparative, et permettant d'identifier plus globalement la source de l'hétérogénéité des taux de substitution mitochondriale au sein des génomes mitochondriaux des Mammifères<br>Experimental acquisition of complete mitochondrial genome for several Arvicolinae species allows defining evolutionary history of the group in evolutionary and temporal frames. These phylogenetic relationships are inferred on a great number of characters (16000 bp), thanks to innovator statistical analysis methods.Constituted molecular data set represents a sample of "fast evolving" mitochondrial genomes, and allows describing mutational hots spots in comparative genomic studies, and identifying globally the origin of mitochondrial substitution rate heterogeneity detected in Mammalian mitochondrial genomes

Thesis (Ph.D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2010.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>Biological activity has shaped the surface of the earth in numerous ways, but life's most pervasive and persistent global impact has been the secular oxidation of the surface environment. Through primary production - the biochemical reduction of carbon dioxide to synthesize biomass - large amounts of oxidants such as molecular oxygen, sulfate and ferric iron have accumulated in the ocean, atmosphere and crust, fundamentally altering the chemical environment of the earth's surface. This thesis addresses aspects of the role of marine microorganisms in driving this process. In the first section of the thesis, biomarkers (hydrocarbon molecular fossils) are used to investigate the early history of microbial diversity and biogeochemistry. Molecular fossils from the Transvaal Supergroup, South Africa, document the presence in the oceans of a diverse microbiota, including eukaryotes, as well as oxygenic photosynthesis and aerobic biochemistry, by ca. 2.7Ga. Experimental study of the oxygen requirements of steroid biosynthesis suggests that sterane biomarkers in late Archean rocks are consistent with the persistence of microaerobic surface ocean environments long before the initial oxygenation of the atmosphere. In the second part, using Prochlorococcus (a marine cyanobacterium that is the most abundant primary producer on earth today) as a model system, we explored how microbes use the limited nutrient resources available in the marine environment to make the protein catalysts that enable primary production. Quantification of the Prochlorococcus proteome over the diel cell-division cycle reveals that protein abundances are distinct from transcript-level dynamics, and that small temporal shifts in enzyme levels can redirect metabolic fluxes. This thesis illustrates how molecular techniques can contribute to a systems-level understanding of biogeochemical processes, which will aid in reconstructing the past of, and predicting future change in, earth surface environment<br>by Jacob Richard Waldbauer.<br>Ph.D.

Parce qu'ils sont constamment en contact avec toutes sortes de microorganismes présents dans leur environnement, les organismes pluricellulaires ont développé un système immunitaire qui leur permet de détecter leur présence et contrôler leur croissance. Les contacts se produisent naturellement au niveau des surfaces de l'animal qui sont exposés à l'environnement extérieur, comme la peau ou les muqueuses. Il existe au minimum deux types d'interactions : dans le premier cas, la présence de l'autre ne cause aucun problème pour chacun, et peut même éventuellement apporter un bénéfice. Dans le second, l'un des partenaires est aggressif envers l'autre, qui doit répondre à cette situation de stress en essayant de préserver son intégrité pour assurer sa survie. Du côté de l'hôte, cette réponse implique le système immunitaire et a généralement pour but de détruire le microorganisme. En utilisant l'insecte drosophila melanogaster comme organisme hôte modèle, j'ai étudié les interactions hôtes - microbes. Dans le cadre d'un premier projet, je me suis interessé aux cellules circulantes de la drosophiles, les plasmatocytes. Nous savions qu'elles sont capables de manifester certaines activités biologiques (sécrétion de cytokine et de facteurs coagulant, phagocytose), mais leur importance dans la résistance aux infections n'a jamais été évaluée. En générant des drosophiles dépourvues de plasmatocytes, j'ai pu montrer que ces cellules sont requises pour assurer la résistance à certaines infections bactériennes systémiques chez l'adulte, dont Staphylococcus aureus et Salmonella typhimurium, mais pas toutes<br>Because they are constantly exposed to contact with the various type of microorganisms present in their environment, multicellular organisms have evolved an immune system that allow them to sense their presence and control their growth. Close contact with these microbes naturally occurs in body parts that are exposed to the environment, like external body surfaces and internal mucosa, and at least two diffrerent kind of relations can be described. In the first case both the two parts do not harm the other, eventually allowing the relationship to go for a mutual benefit. In the second case, one part is agressive towards the other and lead it to induce a response to this stressful situation in order to preserve it's integrity and ultimately it's survival. From the host point of view, this response involves the immune system and most frequently aims at the eradication of the microbes. Using the fruitfly drosophila melanogaster as a model for the host side, i was interested in studying host-microbe interactions. A first project i worked on focused on drosophila circulating cells, the plasmatocytes, about which we knew some activities (secretion of cytokines, cloting factors, phagocytosis) but whose functional relevance to resist infection has never been tested. By generating plasmatocytes-depleted flies, I show that these cells are required for the survival of the adult upon some type of systemic bacterial infections, including Staphylococcus aureus and Salmonella typhimurium, but not all

Ticks (Ixodida) represent one of the most important vector groups affecting human and animal health, and in recent years there have been increasing concerns regarding the cause of tick-borne disease affecting Australians. Worldwide, wildlife health surveillance is recognised as a key tool for investigating tick-borne infections and a One Health approach is essential to understand the epidemiology of tick-associated microbes. Therefore, this research aimed to; i) identify ticks from Australian wildlife; ii) investigate bacteria and haemoprotozoa present in wildlife and ticks; and iii) characterise microbes and understand the interplay between host-microbetick. Molecular tools were used to assist in the identification of Australian ticks. Museum specimens of the human biting tick Amblyomma triguttatum were used to investigate the molecular systematics of this species complex. A set of molecular barcodes was developed for Australian ticks, which was important for the accurate identification of immature life stages and cryptic species. Additionally, a novel 12S rDNA metabarcoding assay was developed for high throughput identification of ticks. Free-ranging animals and their ticks were sampled from urban and periurban areas. The bacterial and haemoprotozoan diversity was characterised using a combination of amplicon high-throughput sequencing, targeted Sanger sequencing, and microscopy. Bacterial profiling generated over 100 million sequences. Statistical analysis using constrained ordination methods revealed blood, tick and tissues had distinct community signatures. A diverse range of tick associated microbes was identified, such as Anaplasmataceae, Bartonellaceae, Borreliaceae, Coxiellaceae, Midichloriaceae. Overall, these microbes were rare in wildlife hosts and generally confined to specific sample types. In addition, eight species of haemoprotozoa were identified, including species within the genera Babesia, Hepatozoon, Theileria and Trypanosoma. Lastly, this study further confirmed the absence of northern hemisphere tick-borne pathogens and provided further evidence of the unique microbes present in Australian wildlife and ticks.

Biology<br>Ph.D.<br>Polar regions impose harsh conditions, including low temperatures, and prolonged periods of darkness on resident microbial communities. Despite these challenges, the conditions in these environments can also create opportunities for organisms utilizing combined trophic strategies (Mixotrophy). Only a limited number of studies have identified mixotrophic behavior in polar microbial eukaryotes, and even fewer studies have quantified the response of mixotrophs to likely environmental drivers of trophic behavior (light and nutrients). The goal of this work is to provide an identification of mixotrophic behavior and elucidate of some of the factors that influence algae isolated from polar environments. First, a study of the Arctic prasinophyte, Micromonas pusilla is presented in the first species-specific identification of mixotrophy in a eukaryotic phytoflagellate of this size class. M. pusilla grazed on bacteria under all experimental conditions, responding to nutrient limitation with increased rates of bacterivory. M. pusilla also showed evidence of prey selection. In contrast to the phagotrophic response, photosynthetic production was decreased under low-nutrient conditions. In an additional study of microbial eukaryotes from the Antarctic environment, identification of phagotrophy in photosynthetic nanoflagellates representing multiple evolutionary lineages: Cryptophyceae (Geminigera cryophila) and Prasinophyceae (Pyramimonas tychotreta and Mantoniella antarctica), showed that mixotrophy is more widespread in the Southern ocean that previously thought. G. cryophila and M. antarctica increased ingestions in dark treatments, but did not respond to difference in nutrient concentrations. In contrast, no significant grazing activity was observed in P. tychotreta under high nutrient conditions. When nutrients were reduced, ingestion of bacteria by P. tychotreta was observed and grazing increased in dark as compared to illuminated treatments. Finally, through a series of experimental assays, the competitive advantages of mixotrophic flagellates as opposed to monotrophic specialists were evaluated, using organisms isolated from the Southern Ocean. In these experiments, G. cryophila is emerged as a dominant competitor against two solely autotrophic diatoms (Fragilaria sp. and Fragilariopsis sp.). In contrast, P. tychotreta was outcompeted by the solely heterotrophic chrysophyte Paraphysomonas antarctica. These results show that mixotrophic ability can confer advantages to organisms in some cases, while in other interactions the cost associated with maintenance of multiple trophic strategies results in competitive exclusion by a specialist. These results present novel identification as well as rigorous investigation of mixotrophic behaviors in phototrophic flagellates from both polar (Arctic and Antarctic) environments representing two evolutionary lineages. This work provides a significant contribution to our understanding of the versatile nature of the physiology and trophic ecology of microbial eukaryotic organisms occupying polar marine ecosystems.<br>Temple University--Theses

Im Rahmen einer Projektarbeit wurde im Jahr 2014 bei der microm eine bundesweite, flächendeckende, kleinräumige Bevölkerungsprognose erarbeitet. Dies greift auf eine Datenbasis zurück, welche es ermöglicht, Bevölkerungszahlen deutlich unterhalb der bis dato veröffentlichten Kreisebene fortzuschreiben. Dabei fußt der microm Ansatz initial auf den Einwohnerzahlen des Zensus 2011. Die Haupteinflüsse der Bevölkerungsentwicklung, die Zu- und Abwanderung von Personen, die Sterbequoten sowie die Geburtenraten wurden aus verschiedenen Quellen zusammengeführt und liegen auf der microm-eigenen sogenannten Postleitzahl-8-Ebene (N = 82 584; 500 Privathaushalte im bundesdeutschen Durchschnitt) vor. Methodisch erfolgte die Orientierung an den Vorarbeiten des BBSR. Ziel des Projektes war es, auf der insbesondere innerstädtisch differenzierenden Postleitzahlebene die Einwohnerzahlen entlang der 17 amtlichen nach Geschlecht getrennten Altersklassen in fünf Jahresschritten bis ins Jahr 2030 fortzuschreiben. Die Festlegung der Altersgrenzen orientiert sich dabei an den Ergebnissen der jährlichen Fortschreibung des Bevölkerungsstandes aus der Regionalstatistik der Statistischen Ämter des Bundes und der Länder (Statistische Ämter des Bundes und der Länder 2014).

All animals are adapted to the environmental conditions of the habitat they chose to live in. It was the aim of this PhD-project, to show which behavioral strategies are expressed as mechanisms to cope with the constraints, which contribute to the natural selection pressure acting on individuals. For this purpose, small mammals were exposed to different levels and types of predation risk while actively foraging. Individuals were either exposed to different predator types (airborne or ground) or combinations of both, or to indirect predators (nest predators). Risk was assumed to be distributed homogeneously, so changing the habitat or temporal adaptations where not regarded as potential options. Results show that wild-caught voles have strategic answers to this homogeneously distributed risk, which is perceived by tactile, olfactory or acoustic cues. Thus, they do not have to know an absolut quality (e.g., in terms of food provisioning and risk levels of all possible habitats), but they can adapt their behavior to the actual circumstances. Deriving risk uniform levels from cues and adjusting activity levels to the perceived risk is an option to deal with predators of the same size or with unforeseeable attack rates. Experiments showed that as long as there are no safe places or times, it is best to reduce activity and behave as inconspicuous as possible as long as the costs of missed opportunities do not exceed the benefits of a higher survival probability. Test showed that these costs apparently grow faster for males than for females, especially in times of inactivity. This is supported by strong predatory pressure on the most active groups of rodents (young males, sexually active or dispersers) leading to extremely female-biased operative sex ratios in natural populations. Other groups of animals, those with parental duties such as nest guarding, for example, have to deal with the actual risk in their habitat as well. Strategies to indirect predation pressure were tested by using bank vole mothers, confronted with a nest predator that posed no actual threat to themselves but to their young (Sorex araneus). They reduced travelling and concentrated their effort in the presence of shrews, independent of the different nutritional provisioning of food by varying resource levels due to the different seasons. Additionally, they exhibited nest-guarding strategies by not foraging in the vicinity of the nest site in order to reduce conspicuous scent marks. The repetition of the experiment in summer and autumn showed that changing environmental constraints can have a severe impact on results of outdoor studies. In our case, changing resource levels changed the type of interaction between the two species. The experiments show that it is important to analyze decision making and optimality models on an individual level, and, when that is not possible (maybe because of the constraints of field work), groups of animals should be classified by using the least common denominator that can be identified (such as sex, age, origin or kinship). This will control for the effects of the sex or stage of life history or the individual´s reproductive and nutritional status on decision making and will narrow the wide behavioral variability associated with the complex term of optimality.<br>Das Verhalten von Tieren ist das Ergebnis eines kontinuierlichen Anpassungsprozesses im Laufe der Evolution einer Art und damit der Veränderung der Umgebung in der es lebt und der Interaktion mit anderen Arten. Dies wird besonders deutlich im Verhalten von potentiellen Beutetieren, ihre Strategien beinhalten meist ein möglichst unauffälliges Verhalten im Zusammenspiel mit reduzierter Bewegung und möglichst guter Tarnung. Dementgegen stehen essentielle Bedürfnisse, wie zum Beispiel die Nahrungssuche, die Verteidigung von Ressourcen (zum Beispiel Territorien, Futterstellen) und die Suche nach Paarungspartnern. Beutetiere leben also in einem Spannungsfeld indem sie Ihr Verhalten optimieren müssen. Hierbei stehen die Ernährung, erfolgreiche Verpaarung und andere Chancen auf der einen Seite, die Vermeidung von Begegnungen mit Prädatoren auf der anderen. Vor allem Kleinsäuger sind häufig als Beutetiere mit einer Vielzahl von Prädatoren aus der Luft und auf dem Boden konfrontiert. Sie müssen für die verschiedenen Bedrohungen adaptive Verhaltensanpassungen bereit haben und in der Lage sein, auf die optischen, olfaktorischen oder akustischen Signale, die die Gefahr durch Prädatoren anzeigen, mit plastischen Verhaltensmustern zu reagieren. Die vorliegende Dissertation beschäftigt sich mit bisher als Konstanten behandelten Faktoren und untersucht anhand von Verhaltensexperimenten mit wilden Wühlmäusen (Microtus arvalis) folgende Fragestellungen: - Wie verhalten sich Tiere, die einer homogenen Risikoverteilung ausgesetzt sind, zum Beispiel weil ihr Prädator genauso gross ist wie sie, im gleichen Habitat lebt und es keinen sicheren Ort gibt? - Mit welchen Anpassungen reagieren Tiere, wenn sie gleichzeitig verschiedenen Prädatoren ausgesetzt sind? - Wie unterscheiden sich die Nahrungssuchstrategien von Männchen und Weibchen? - Wie verhalten sich laktierende Weibchen, die einer permanenten, indirekten Gefahr, z.B. durch einen Nestprädator ausgesetzt sind? Die Ergebnisse der verschiedenen Versuche in künstlichen Arenen und Aussengehegen zeigen, dass die Mäuse in der Lage sind, adaptive Verhaltensanpassung an homogenes Risiko und verschiedene Prädationstypen abzurufen. So sind sie in der Lage, Luft- von Bodenprädatoren zu unterscheiden und jeweils das Verhalten zu zeigen, dass die größtmögliche Sicherheit mit sich bringt. Die simultane Kombination von verschiedenen Prädatoren bewirkt hierbei additive Effekte. Gibt es keine Auswahl zwischen Habitaten, sondern nur unterschiedliche homogene Risikolevel, reagieren sie auf steigendes Risiko immer mit verminderter Aktivität und konzentrieren ihre Nahrungssuche auf weniger Futterstellen, beuten diese dafür jedoch länger aus. Die Wertigkeit von Futterstellen und alternativen Optionen verändert sich also mit dem Risikolevel. Ähnliches zeigt sich auch in den unterschiedlichen Futtersuchstrategien von Männchen und Weibchen. Die untersuchte Art ist polygyn und multivoltin, dementsprechend verbinden die Männchen mit ihrer Nahrungssuche Aktivitäten wie die Suche nach Paarungspartnern und unterscheiden sich die Aktivitätsmuster zwischen Männchen und Weibchen. Zusätzlich zeigen die Ergebnisse, das laktierende Weibchen in der Lage sind, das Risiko für sich und für Ihre Jungen abzuschätzen, wenn sie mit einem Nestprädator (Sorex araneus) konfrontiert werden. Für die Interaktion zwischen diesen beiden Arten ist jedoch die Saison (und damit die Ressourcenlage), in der sie sich begegnen, von entscheidender Bedeutung. Wühlmäuse reagieren mit entsprechenden Verhaltensanpassungen zum Schutz des Nestes um die Überlebenschancen ihrer letzten Würfe im Herbst zu erhöhen. Die vorliegende Arbeit konnte grundsätzliche Probleme der antiprädatorischen Verhaltensanpassung von Beutetieren klären und wichtige Faktoren der Entscheidungsfindung unter Prädationsdruck analysieren. Sie zeigt, dass Tiere das Risiko in ihrer Umgebung nicht unbedingt über direkt Signale wahrnehmen, sondern ihre Verhaltensstrategien einem empfundenen Gesamtrisikolevel anpassen. Dies ermöglicht ihnen, adaptive Strategien zu verfolgen, auch wenn sie keine Auswahl an sicheren Habitaten haben. Sie zeigt auch die unterschiedliche Wahrnehmung von Risiken durch Männchen und Weibchen, die durch die unterschiedlichen mit der Aktivität zusätzlich wahrgenommenen Chancen verknüpft zu sein scheint. Zusätzlich wurde der Einfluss des reproduktiven Status (z.B. laktierend), sowie der Ressourcenlage (z. B. je nach Saison) nachgewiesen.

Masters of Science<br>The study of the faint radio universe and of its properties has recently become a very active field of research not only because of the much improved capabilities of the SKA pathfinders but also because of the need to better plan for SKA surveys. These new facilities will map large areas of the sky to unprecedented depths and transform radio astronomy into the leading technique for investigating the complex processes which govern the formation and evolution of galaxies. This thesis combines multi-wavelength techniques, highly relevant to future deep radio surveys, to study the properties of faint radio sources. The nature of the faint radio sources is presented, over a large GMRT survey area of an area of 1.2 deg2 comprising 2800 sources. Utilising multi-wavelength data we have matched 85% of the radio population to Spitzer/IRAC and obtained a redshift estimate for 63%. The redshift associations are a combination of photometric and spectroscopic redshift estimates. This study investigates several multi-wavelength diagnostics used to identify AGN, using radio, infrared, optical and x-ray data . This analysis shows that various diagnostics (from the radio through the X-ray ones) select fairly different types of AGNs, with an evidence of a disagreement in the number of AGNs selected by each individual diagnostics. For the sources with redshift we use a classification scheme based on radio luminosity, x-ray emission, BOSS/SDSS spectroscopy, IRAC colors satisfying the Donley criterion, and MIPS 24ɥm radio-loud AGN criteria to separate them into AGNs and SFGs. On the basis of this classification, we find that at least 12.5% of the sources with redshifts are AGNs while the remaining 87.5% are adopted as SFGs. We explore the nature of the classified sources through the far-infrared radio correlation. We measure a median qIR value of 2:45± 0:01 for the SFGs and qIR value of 2:27 ± 0:05 for the AGNs. The decrease in the median value of qIR for the AGNs is a result of the additional AGN component to radio emission for the AGN-powered sources and find tentative evidence of an evolution of the qIR with redshift.

Rhabdomys pumilio, in the Eastern Cape of South Africa, does not use short day length as an inhibitory cue for reproductive activity, and, despite previous records indicating that these mice are strictly seasonal in their reproduction, litters have been found during the winters of some years,both in the Eastern Cape and in the Western Cape. This led me to believe that the reproductive activity of Rhabdomys pumilio is more opportunistic and that the cue or cues used to control reproduction are less predictable and, or more variable than the photoperiod cue used by many seasonally reproducing rodents. Two experiments were conducted, investigating the influence of low ambient temperature (15⁰C)and reduced food availability on the reproductive activity of both male and female four striped field mice. Mice were maintained in one of four conditions (food restricted at 15⁰C, food restricted at 26⁰C, ad lib. food at 15⁰C, and ad lib. food at 26⁰C) for 4 (males) and 8 weeks (females)(photoperiod 12L:12D, humidity 40%). Results indicated that the males reduced their reproductive activity slightly when exposed to either low temperature or low food availability and that maximum inhibition of reproduction occurred when mice were exposed to both low temperature and low food availability. However, female reproductive activity was inhibited when exposed to low food availability, irrespective of the temperature. Both sexes of mice showed varying abilities to resist fat loss and, in the males, the size of the fat store had a significant effect on reproduction. This varying ability to resist fat loss could be related to levels of activity and in the females (where activity was quantified), high activity scores were significantly associated with reproductive inhibition. These results support the hypothesis that reproduction in Rhabdomys pumilio is opportunistic and controlled by the availability of energy. I propose that the females will be more sensitive to reproductive inhibition due to their far greater post-fertilization responsibilities, where the reproductive activity of the females is rapidly inhibited by a reduction in food availability, while the males are less readily inhibited by low food availability or low temperature, unless the change in the controlling factors is severe enough, or prolonged, at which stage their reproductive activity will cease. The significance of opportunistic reproduction in the seasonal but unpredictable climate of the study area is discussed.

Thesis (Ph.D.)--Boston University<br>PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.<br>Seasonal differences in odor preference and social behavior existed among adult meadow voles. During the breeding season, a female preferred its own odor and the odor of males to the odor of another females. Males preferred the odor of females to the odor of other males. Paired encounters between breeding females were more agonistic than encounters between males or encounters between males and females. During the nonbreeding season, a female preferred the the odor of another female to the odor of males. Males did not display an odor preference for any conspecifics. Paired encounters between males were more agonistic than encounters between males and females or encounters between females. Encounters between nonbreeding females contained few agonistic acts. Seasonal differences also existed in the interactions between adults and juveniles. During the early breeding season, adult males were more agonistic than adult females toward juvenile males. During the late breeding season, adult females were more agonistic than adult males toward juvenile males. Encounters between an adult female and a juvenile female in the late breeding season contained few agonistic acts, indicating that overwintering groups are female-biased, and contain juvenile females. Juveniles did not display a shift in odor preferences. They preferred the odor of opposite-sex adults to the odor of same-sex adults, regardless of season. Familiarity, through association during rearing, reduced agonistic behavior between parents and young, and between siblings. Paired encounters between close-kin that were not familiar were agonistic, and similar to encounters between unfamiliar, and unrelated conspecifics. Conspecifics were more agonistic toward closely related males than females. Voles also preferred the odor of a familiar nestmate, independently of genetic relatedness. Familiarity decreased the number of agonistic behaviors between adult females, but increased the number of agonistic behaviors between adult males. Familiarity had no effect on the number of agonistic behaviors between a male and a female.<br>2031-01-01

Biogeochemical cycling of arsenic and speculation on mechanisms of arsenic removal are interest in the environmental remediation of contaminated sites. In the present study, combination of metagenomic molecular biology techniques with mineralogical analyses were used to study a biochemical reactor (BCR) that was successfully removing arsenic, zinc, copper and cadmium. First the metal and mineralogical content of the BCR solids was investigated. X-ray diffraction (XRD) and automated quantitative evaluation of minerals by scanning electron microscopy (QEMSCAN) were used for mineralogical characterization. Analysis indicated that sulfates and sulfides were the predominant types of Zn and As minerals formed in the BCR. Arsenic minerals were detected as sulfides (arsenopyrite, tennantite), arsenates(wihelmkleinite), oxides (unknown zinc arsenic oxides) and zincarsenic sulfides, which showed evidence of metal adsorption on the surfaces of other solids such as silicates. Energy-dispersive X-ray spectroscopy verified that arsenic was associated with iron, zinc and sometimes cadmium as arsenopyrite-type minerals. Using a SSU rRNA survey of the site, the following taxa were correlated with high metal content: Bacteroidetes, Synergistaceae, Victivallales, methanogens (Methanocorpusculum, Methanospirillum, Methanosarcina) and new phyla such as VadinHA17, M2PB4-65, candidate division WS6, RF3 and TM6. Next, enrichment culturing and arsenic chemical speciation monitoring were performed to assess potential for arsenic species transformations in the BCR. Most predominant groups in the As(III) and As(V) media, were Simplicispira (β-proteobacterium) and Sedimentibacter (Firmicutes), respectively. Chemical arsenic speciation monitoring of the enrichments suggested that arsenite oxidation and arsenate reduction occurred. These genera were not previously reported for arsenic transformation. Finally, functional metagenomic workflow was applied to study arsenic resistance genes. Functional screening and end-sequencing of large insert fosmid libraries demonstrated that arsenic(V) resistance genes were taxonomically widespread and different class of arsenic resistance genes related to periplasmic arsenate reduction, arsenite efflux, bioaccumulation (phosphate, metal transporters) and arsenite oxidation were present. Fewer genes were associated with dissimilatory arsenate reduction and arsenic volatilization mechanisms. Methanomicrobia were predominant in the BCR and identification of methanogen-related arsenic resistance genes indicated that methanogens potentially played a role in arsenic removal inside the BCR.<br>Applied Science, Faculty of<br>Chemical and Biological Engineering, Department of<br>Graduate

he chlorinated methanes carbon tetrachloride (CT), chloroform (CF), dichloromethane (DCM) and chloromethane (CM) are widespread groundwater pollutants that pose risks to human and ecosystem health. Although some progress has been made in elucidating the microbiology contributing to the aerobic degradation of DCM and CM, these efforts have had little impact on bioremediation practices aimed at restoring anoxic aquifers impacted by chlorinated methanes. Remaining knowledge gaps include the lack of understanding of the microbial mechanisms and pathways contributing to chlorinated methane transformations under anoxic conditions. Thus, the major goals of this research effort were to identify microbes that can contribute to the transformation of chlorinated methanes in the absence of oxygen, and to develop monitoring tools to assess anaerobic chlorinated methane bioremediation at contaminated sites. To accomplish these goals, freshwater and estuarine sediment samples from 45 geographically distinct locations, including 3 sites with reported chlorinated-methane contamination, were collected and screened for CT-, CF-, DCM- and/or CM-degrading activity. DCM degradation was observed in microcosms established with sediment materials from 15 locations, and the sediment-free, DCM-degrading enrichment culture RM was obtained from Rio Mameyes sediment. 16S rRNA-gene based community analysis characterized consortium RM, and identified a Dehalobacter sp. involved in DCM fermentation to non-toxic products. Organism- and process-specific monitoring tools were designed that target the 16S rRNA gene of the DCM-fermenting Dehalobacter sp. and the consortium’s specific 13C-DCM enrichment factor, respectively. Treatability studies using site materials that showed no chlorinated methane degradation activity demonstrated the feasibility of using CF- and DCM-degrading consortia for bioaugmentation applications. Collectively, this study expands our understanding of bacteria contributing to chlorinated methane degradation, provides new tools for monitoring anaerobic DCM degradation, and demonstrates that microbial remedies at chlorinated methane contaminated sites are feasible.

PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO<br>COORDENAÇÃO DE APERFEIÇOAMENTO DO PESSOAL DE ENSINO SUPERIOR<br>FUNDAÇÃO DE APOIO À PESQUISA DO ESTADO DO RIO DE JANEIRO<br>PROGRAMA DE EXCELENCIA ACADEMICA<br>Esta dissertação apresenta um framework para simulação de um ambiente de microbacias como serious game, onde o compromisso de representação mais realista de personagens, processos e ambientes está alinhado com as características usuais de jogos de entretenimento. O jogo tem por objetivo auxiliar na educação e na discussão de tópicos sobre sustentabilidade econômica e preservação do meio ambiente. Além da simulação física do terreno, este trabalho agrega uma nova funcionalidade ao simulador capaz de simular a interação dos habitantes de uma microbacia com o terreno e a interação entre eles na forma de um jogo. O framework permite a implementação de lógicas nos agentes, que simulam os habitantes, e as conjurações para atualização de preços e de valores de produção.<br>This dissertation presents a framework for the simulation of a watershed environment as a serious game, where the commitment of a more realistic representation of characters, processes and environment is aligned with the usual features of entertaining games. The game aims to assist education and discussing topics on economic sustainability and environmental preservation. In addition to the physical simulation of the terrain, this work adds a new functionality to the simulator which makes it capable of simulating the interaction of the inhabitants of a small watershed with the terrain and the interaction between them as a game. The framework allows us to implement logic in the agents that simulate inhabitants, and the settings for updating prices and values of production.

In order to satisfy the global requirement for transport fuel sustainably, renewable liquid biofuels must be developed. Currently, two biofuels dominate the market; bioethanol for spark ignition and biodiesel for compression ignition engines. However, both fuels exhibit technical issues such as low energy density, poor low temperature performance and poor stability. In addition, bioethanol and biodiesel sourced from first generation feedstocks use arable land in competition with food production, and can only meet a fraction of the current demand. To address these issues it is vital that biofuels be developed from truly sustainable sources, such as lignocellulosic waste resources, and possess improved physical properties. To improve and control the physical properties of a fuel for specific application, one must be able to tailor the products formed in its production process. All studies within this thesis, therefore, have the aim of assessing the fuels produced for their variability in physical property, or the aim of directing the process considered to specific fuel molecules. In Chapter 2, spent coffee grounds from a range of geographical locations, bean types and brewing processes were assessed as a potential feedstock for biodiesel production. While the lipid yield was comparable to that of conventional biodiesel sources, the fatty acid profile remained constant irrespective of the coffee source. Despite this lack of variation, the fuel properties varied widely, presumably due to a range of alternative biomolecules present in the lipid. Though coffee biodiesel was produced from a waste product, the fuel properties were found to be akin to palm oil biodiesel, with a high viscosity and pour point. The blend level would therefore be restricted. In Chapter 3 the coffee lipid, as well as a range of microbial oils potentially derived from renewable sources were transformed into a novel aviation and road transport fuel through cross-metathesis with ethene. Hoveyda-Grubbs 2nd generation catalyst was found to be the most suitable, achieving 41% terminal bond selectivity under optimum conditions. Metathesis yielded three fractions: an alkene hydrocarbon fraction suitable for aviation, a shorter chain triglyceride fraction that upon transesterification produced a short chain biodiesel fuel, and a multifunctional volatile alkene fraction that could potentially have application in the polymer industry. Though there was variation for the road transport fuel fraction due to the presence of long chain saturates, the compounds fell within the US standard for biodiesel. The aviation fraction lowered the viscosity, increased the energy density, and remained soluble with Jet A-1 down to the required freezing point. Oleaginous organisms generally only produce a maximum of 40% lipid, leaving a large portion of fermentable biomass. In Chapter 4, a variety of ethyl and butyl esters of organic acids – potentially obtainable from fermentation – were assessed for their suitability as fuels in comparison to bioethanol. One product, butyl butyrate, was deemed suitable as a Jet A-1 replacement while four products, diethyl succinate, dibutyl succinate, dibutyl fumarate and dibutyl malonate, were considered as potential blending agents for diesel. Diethyl succinate, being the most economically viable of the four, was chosen for an on-engine test using a 20 vol% blend of DES (DES 20) on a chassis dynamometer under pseudo-steady state conditions. DES20 was found to cause an increase in fuel demand and NOx emissions, and a decrease in exhaust temperature, wheel force, and CO emissions. While fermentation is generally directed to one product, producing unimolecular fuels, they do not convert the entirety of the biomass available. An alternative chemical transformation is pyrolysis. In Chapter 5, zeolite-catalysed fast pyrolysis of a model compound representative of the ketonic portion of biomass pyrolysis vapour – mesityl oxide – was carried out. The aim of this study was to understand the mechanistic changes that occur, which could lead to improved bio-oil yields and more directed fuel properties of the pyrolysis oil. While HZSM-5 and Cu ZSM-5 showed no activity for hydrogenation and little activity for oligomerisation, Pd ZSM-5 led to near-complete selective hydrogenation of mesityl oxide to methyl isobutyl ketone, though this reduced at higher temperatures. At lower temperature (150-250 °C), a small amount of useful oligomerisation was observed, which could potentially lead to a selective pyrolysis oligomerisation reaction pathway.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2016.<br>Cataloged from PDF version of thesis.<br>Includes bibliographical references.<br>Microbial dynamics in the environment are major drivers of global biogeochemical cycles; hence there is great interest in characterizing their rates and causes. While dynamics are affected by processes across many spatiotemporal scales, and even closely related microbes are known to vary in their ecological distributions, most work has characterized dynamics at bulk scales and with low genetic resolution. Thus, little is known about the effects of finer structure. In this thesis, I show that characterizing the dynamics of environmental microbes with finer spatiotemporal and genetic resolution reveals otherwise concealed dynamics. I use the Vibrionaceae, an ecologically diverse family of marine heterotrophs, as a model system. First, I review past studies on environmental associations of the Vibrionaceae, showing that few abiotic parameters have consistent predictive value, and that observed patterns vary based on taxonomic resolution. Biotic associations, however, may represent more specific predictors for fine-scale Vibrionaceae taxa, reflecting their diverse lifestyles. I then characterize Vibrionaceae dynamics within a high-resolution environmental time-series, with three months of daily sampling across four habitat partitions, population-level resolution, and large datasets of potential biological correlates. These data reveal diverse and spatially structured population dynamics. Individual populations varied from consistently abundant generalists to rare populations that occasionally displayed brief but intense peaks of abundance. Free-living and particle-attached habitat partitions were distinct in terms of diversity, turnover, and biotic interactors. These results emphasize the ecological differentiation of the Vibrionaceae populations, and the extent to which spatial partitions can function as distinct ecological regimes. Finally, I use sequence data from the Vibrionaceae populations to investigate a methodological question relating to phylogenetic resolution: how well does the standard taxonomic marker gene, 16S rRNA, resolve populations known to have distinct ecological distributions and dynamics? The analysis shows that even full-length 16S rRNA sequences collapse the majority of populations into only 2-3 taxa, concealing the breadth of ecological behavior within the family. Altogether, this thesis demonstrates that high resolution sampling techniques reveal a wealth of otherwise unobserved ecological diversity even within one family of closely related microbes, and suggests that fine-scale turnover and structure may have an unappreciated impact on microbial dynamics.<br>by Diana M. Chien.<br>Ph. D.

Abstract There is concern whether cabbage and beetroot wastes from the Fresh Produce Market are safe for feeding animals given the fact that some will have been discarded at the onset of putrefaction. This study evaluated the effects of sun-drying on microbiological load (E. coli, coliform, yeast and moulds and total bacterial count) in waste vegetables from the fresh produce market, since smallholder farmers tend to use the by-products without processing given the opportunity. Cabbage and beetroot wastes were sun dried to 14% moisture and micro-organisms were enumerated on both wet and dried samples. The results showed that sun drying reduced the level of micro-organisms significantly in both cabbage and beetroot. Although microbial load varied from batch to batch in the wet samples, coliforms were significantly more abundant in wet beetroot than in the dried samples. However, dried beetroot contained significantly more yeast and moulds. Wet cabbage contained more coliform and yeast and moulds compared to sun-dried cabbage. The sun drying process is thus an efficient processing method for resource poor farmers to reduce the microbial load in these animal feed sources and improve their shelf life.

Trillions of microorganisms inhabit mucosal surfaces of the human body. Despite increasing evidence of their impact on human health, many of the molecular mechanisms underlying hostmicrobial interactions (HMI) are poorly understood. To contribute to our understanding of HMI at mucosal surfaces, we investigated the novel family of M60-like/PF13402 domain-containing proteins and their putative functional partners. M60-like domains are shared by proteins from several mucosal microbes including two important human mucosal microbes; the bacterial mutualist Bacteroides thetaiotaomicron and the protist pathogen Trichomonas vaginalis, suggesting these proteins are important for interaction with the mucosal layer. We initially tested our hypothesis that these are glycoprotein-targeted metal dependent proteases in both these organisms. The three M60-like domains of B. thetaiotaomicron proteins (BT4244, BT3015 and BT4272) exhibited mucin protease activity. This proteolytic activity was shown to be inhibited in a mutant version of the protein (BT4244-FL-E575D) as well as in the presence of Ethylenediaminetetraacetic acid (EDTA), implying BT4244 and its relatives are metal dependent proteases. All M60-like proteins from B. thetaiotaomicron contained a carbohydrate binding module (CBM) from family 32 and these were shown to be capable of binding galacto-configured sugars that are common to mucin glycans, while in contrast the putative carbohydrate binding PA14 domain of the T. vaginalis TVAG339720 M60-like protein interacted with heparin and its sulphated derivatives. Mucins are glycoproteins and prominent components of the mucus secreted at mucosal surfaces while heparin is a close relative of heparan sulphate which typically exists as part of proteoglycans in the glycocalyx of mucosal epithelia. Although the actual target of the M60-like domain of TVAG339720 and its relatives in T. vaginalis are not currently known, the interaction of the TVAG339720 PA14 domain with heparin suggests that these may be proteases targeting proteoglycans and play a role in adhesion of the pathogen to the epithelial layer, a key initial step in pathogenesis. M60-like domain-containing proteins of B. thetaiotaomicron are also components of Sus-like systems. Sus-like systems are Bacteroidetes specific machinery that comprise a suite of cellenvelope located carbohydrate-active enzymes and sugar binding proteins that target complex glycans, with each Sus-like system tuned to the degradation of a specific glycan. The Sus-like system containing the BT4244 enzyme (BT4240-50), encoded by the polysaccharide locus (PUL) PULBT_4240-50 was characterised in this study. The results demonstrated that BT4244 is a surface protein and that its proteolytic activity is part of a concerted action of BT4240-50 components to utilise complex mucin glycoproteins containing the T (Galβ1-3GalNAc) and F (GalNAcα1-3GalNAc) antigens. Gene deletion studies revealed that PULBT_4240-50 provides a competitive advantage to the organism when grown on mucins, probably through its possession of the N-acetylgalactosamine (GalNAc) kinase BT4240, which was shown to be crucial for GalNAc utilisation. Finally, although variably conserved in closely related Bacteroides, the high frequency of PULBT_4240-50 components in this group of organisms suggests it may be an important evolutionary adaptation for survival at mucosal surfaces. Our findings not only set the stage for future functional studies on the novel M60-like/PF13402 family of proteins and their functional partners, but also further our understanding of host-microbial interactions at mucosal surfaces.

There has been an increasing emphasis placed on understanding microbial c, in order to enable the patterns and processes governing the spatial distribution of soil microbiota to be determined. Due to current food security issues, this is particularly important within agricultural systems given the fundamental role microorganisms play in the maintenance of crop health and productivity. With evidence in favour of both ubiquity and endemism, complicated by systems, scales and communities, there is a need to address the question of microbial biogeography within a single system. A range of field experimental resources were used to investigate factors controlling the assembly of soil microbial communities. Microorganisms across all three domains of life demonstrated spatial scaling, in which there was no single universal driver. Land-use management was an important driver of eukaryote distribution, but also impacted the drivers of bacterial and eukaryote taxa groups under land-use practice. When considering microbial community structure, a pan microbial relationship between abundance and distribution was shown for the first time, across all microbial groups. Furthermore, partitioning microbial communities into common and rare groups provided information on the processes operating on the community and highlighted the importance of land-use management for shaping the structure of communities. Finally, a case study on plasmodiophorids increased current estimates of plasmodiophorid diversity in the soil. Also different communities were associated with the rhizosphere compared with the bulk soil, under different hosts. Plant development stage was also an important consideration acting on this previously understudied but highly significant group of protists to crop health.

Studies were conducted to explore the interactions among rye grass, chlorophenols and microorganisms. The objectives were to examine some of the processes by which plants affect the fate of subsurface organic contaminants. The research was divided into three studies: interactions between live grasses and 2,4-dichlorophenol (DCP), 2,4,6-trichlorophenol (TCP), and pentachlorophenol (PCP); physico-chemical interactions between the three chlorophenols and root tissue; and effect of root exudates on biodegradation of TCP. To study the interactions between plants and organic contaminants, rye grass plants were grown in solutions containing DCP, TCP or PCP for one to three weeks. The grass removed substantial amounts of the chlorophenols throughout the incubation time. The majority of each chlorophenol removed from solution could not be recovered by non-destructive solvent extraction. The removal of the chlorophenols from solution and the unrecoverability of the removed compound followed different kinetics, indicating that the two are different processes. Both contaminant removal and unrecoverability were closely related to root surface area but not to transpiration. A qualitative model was developed to describe the uptake of organic contaminants by plants. The data demonstrate the importance of physico-chemical interactions between contaminants and roots and suggest that maximization of root surface area should be one consideration when selecting a plant species for phytoremediation. To study the physico-chemical interactions between plant roots and organic contaminants, the distribution of DCP, TCP and PCP within a three phase system was examined. The three phases were severed grass roots, water and an organic solvent, either hexane or ethyl acetate. The chlorophenol mass that partitioned into the solvent phase was inversely correlated with root mass and root surface area index. Partition coefficients calculated with respect to the organic liquid phase were inversely correlated with root mass and root surface area index. A similar partitioning experiment was conducted using PCP placed in a solution containing only the dissolved organic material released by roots. These resulting partition coefficients decreased with increasing organic carbon concentration. It appeared that the organic compounds released into solution by the roots affected the movement of the chlorophenol into the organic liquid phase. It is proposed that the presence of roots simultaneously promoted retention of the chlorphenols in the aqueous phase and provided a sorption site. The effect of grass root exudates and glucose on the lag time associated with 2,4,6-trichlorophenol (TCP) degradation by an unacclimated microbial inoculant and an acclimated microbial inoculant was investigated. The presence of an alternate organic carbon source reduced lag time for both the acclimated microbial inoculant and the inoculant that had not been previously exposed to chlorinated phenols. The lag time for acclimation of microbes to TCP mineralization was affected by the ratio of the alternate organic carbon source concentration to the biomass concentration. It is proposed that the presence of a readily available, alternate organic carbon source affected lag time through promotion of microbial population growth and provision of a preferred source of carbon and energy. The results indicate that rye grass may directly, through partitioning and uptake, and indirectly, through soil microbes, affect the fate of chlorophenols in the subsurface environment.<br>Ph. D.

1. Many ecologists have recently advocated the study of spatial patterns of abundance or growth rates as a means of better understanding population dynamics. In this study I described the spatial pattern of abundance of the field vole, Microtus agrestis, which has previously been shown to have cyclic temporal fluctuations of abundance in my study area in Kielder Forest, northern England. A combination of techniques was then used to investigate which processes determine the spatial pattern of dynamics in these vole populations.2. Previous analysis of spatial patterns in density of field voles from an area of approximately 80 km2 within Kielder forest over a 13-year period indicate that density varies as a periodic travelling wave moving across the landscape. I collected data on vole density from a larger area (approximately 600 km2) over a 2.5-year period and used the same analysis to show that the spatio-temporal variation in density was well explained by a travelling wave of density moving across the entire region. Estimates of the wave's speed of 14 kmyr-1 and direction of 66&deg; from north were consistent with the estimates obtained from the data set covering a smaller spatial extent but spanning a longer temporal scale.3. Processes that determine population abundance do so by acting on vital demographic rates. Spatial patterns in demographic rates were therefore described to help identify potential causes of the spatial patterns of density. Eight 0.3 ha live-trapping grids were established within the study area and animals were trapped at monthly intervals during a period of extended low density and during a period of increasing densities. Capture-mark-recapture techniques were used to estimate abundance, juvenile recruitment rate, apparent survival rate and immigration rate at these sampling sites. The synchrony of changes in these parameters between sites was measured as the cross-correlation coefficient between the time series of each parameter and the spatial patterns in the synchrony of each demographic rate were described using Mantel correlations. Field vole abundance, juvenile recruitment rate and a derived estimate of mortality rate were most synchronous between the closest sites, however no directionality was found in these patterns and they could not therefore be related to the travelling wave pattern of density. I concluded that the process responsible for the wave probably only acted during the period of declining density and that therefore the factors causing spatial patterns in abundance could differ at different stages of the population cycle.