The coexistence of humans and rodents lasts from the beginnings of the history of agriculture. Many rodent populations accepted to synanthropic way of life and as commensals accompany human societies until today. In the first study we wanted to find out, how the evolution of non-commensal rodent species, a Cypriot mouse (Mus cypriacus), was influenced by people. This endemic island species evolved on the Cyprus Island without presence of any mammalian competitors or predators. In last 10.000 years humans arrived on the island, bringing several mammalian species, which affected the environment markedly. A black rat (Rattus rattus) is now dominant species there and presumably it is an important competitor for the Cypriot mouse. We supposed that the mice should avoid its odour. Nevertheless the rats odour was preferred by the mouse, probably as an odour of phylogenetically related species. On the contraty, the odour of domestic cat (species, which is also widespread on the island), was avoided. In conclusion, the long-term isolation from mammalian predators did not affect the antipredatory reactions of the Cypriot mouse. Our next study was focuse on changes in behavioural strategies of different populations of mice: the main question was how the commensal way of life affects their exploratory...

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. / 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.

This study investigated commensal feeding interactions between the European harvestman (P. opilio L.) and the predatory mites Balaustium spp. and Anystis baccarum L. It also investigated the feeding behaviour of P. opilio. Experiments were conducted in the laboratory using standardised temperature, humidity, photoperiod and experimental arenas, with eggs of the brown blowfly (Calliphora stygia F.) as prey facsimiles. Due to initial difficulties in obtaining enough predatory mites, mite feeding was manually simulated piercing blowfly eggs with a minuten pin. P. opilio consumed significantly more freeze-killed than live blowfly eggs, indicating that freezing induced chemical and/or physical changes to blowfly eggs that are detected by P. opilio. Significantly more manually pierced eggs were consumed by P. opilio compared with unpierced ones, demonstrating that piercing caused a chemical and/or physical to the egg and increased the feeding rates of P. opilio. Different densities of eggs had no effect on the numbers eaten by P. opilio and placing single pierced eggs next to groups of unpierced eggs also had no effect on the numbers of unpierced eggs eaten. These results suggest that P. opilio does not exhibit klinokinesis or orthokinesis to intensify its search for prey around the area where previous prey were located. P. opilio ate significantly more brown blowfly eggs that had previously been fed on by mites, demonstrating that a short term commensal interaction existed. However, further work is required to demonstrate if the relationship is commensal in the longer term. A comparison between hand-pierced and mite-pierced eggs showed that P. opilio ate significantly more of the former indicating that mite and hand piercing were quantitatively different. The potential for, and importance of, other commensal or mutual relationships between predators in agroecosystems is discussed. The lack of klinokinesis and orthokinesis in P. opilio is compared with other predators and parasitoids that do exhibit these behaviours. The means by which prey are detected by P. opilio are discussed in relation to interpreting behaviours such as prey inspection. Concerns about the effect of pre-treatment and handling of sentinel prey and the problems of using prey facsimiles are raised.

Symbiosis is the close and protracted interaction between organisms. The molecular interactions that occur during symbiosis are complex with multiple barriers that must be overcome. Many Gram-negative, host-associated bacteria use a type III secretion system to mediate associations with their eukaryotic hosts. This secretion system is a specialized apparatus for the injection of type III effector proteins directly into host cells, which in the case of plant pathogens, are collectively necessary to modulate host defense. The type III secretion system is not a mechanism exclusive to pathogens, however, as many strains of commensal Pseudomonas fluorescens and mutualistic rhizobia demonstrably require a type III secretion system to interact with their host plants. The work presented in this thesis describes genome-enabled approaches for characterizing type III effector genes across the range of plant symbiosis. Using high-throughput sequencing technology, draft genome sequences were generated for the plant pathogen, Xanthomonas hortorum pv. carotae M081, the plant commensal, Pseudomonas fluorescens WH6, and six strains from the plant mutualists Sinorhizobium fredii and Bradyrhizobium japonicum. Analyses of the draft genome sequences and publicly available finished sequences contributed insights into mechanisms of host-association and to increasing the inventory of type III effector sequences as well as developing methods directly applicable for agriculture. Finally, characterization of the genetic diversity of type III effectors from rhizobia shows that collections of type III effectors of mutualists are static, with little diversity in content and sequence variation. This represents the first comprehensive cataloging of type III effector from species of mutualistic bacteria and the first to provide evidence for purifying selection of this important class of genes. / Graduation date: 2012

The primary objectives of this research were to demonstrate that: 1.) antibiotic resistant bacteria can promote the survival of antibiotic sensitive organisms when grown simultaneously as biofilms in antibiotics, 2.) community-level multiple antibiotic resistance of polymicrobial consortia can lead to biofilm formation despite the presence of multiple antibiotics, and 3.) biofilms may benefit plasmid retention and heterologous protein production in the absence of selective pressure. Quantitative analyses of confocal data showed that ampicillin resistant organisms supported populations of ampicillin sensitive organisms in steady state ampicillin concentrations 13 times greater than that which would inhibit sensitive cells inoculated alone. The rate of reaction of the resistance mechanism influenced the degree of protection. Spectinomycin resistant organisms did not support their sensitive counterparts, although flow cytometry indicated that GFP production by the sensitive strain was improved. When both organisms were grown in both antibiotics, larger numbers of substratum-attached pairs at 2 hours resulted in greater biofilm formation at 48 hours. For biofilms grown in both antibiotics, a benefit to spectinomycin resistant organism’s population size was detectable, but the only benefit to ampicillin resistant organisms was in terms of GFP production. Additionally, an initial attachment ratio of 5 spectinomycin resistant organisms to 1 ampicillin resistant organism resulted in optimal biofilm formation at 48 hours. Biofilms also enhanced the stability of high-copy number plasmids and heterologous protein production. In the absence of antibiotic selective pressure, plasmid DNA was not detected after 48 hours in chemostats, where the faster growth rate of plasmid-free cells contributed to the washout of plasmid retaining cells. The plasmid copy number per cell in biofilms grown without antibiotic selective pressure steadily increased over a six day period. Flow cytometric monitoring of bacteria grown in biofilms indicated that 95 percent of the population was producing GFP at 48 hours. This research supports the idea that ecological interactions between bacteria contribute to biofilm development in the presence of antibiotics, and demonstrates that community-level multiple antibiotic resistance is a factor in biofilm recalcitrance against antibiotics. Additionally, biofilms may provide an additional tool for stabilizing high copy number plasmids used for heterologous protein production.

The objective of this work was to investigate whether there are differences between commensal and non-commensal populations of spiny mice (Acomys spp.). There is a good evidence that some populations of Acomys cahirinus have been commensal since the time of ancient Egypt, that is for at least 3,500 years. Therefore, it could be expected that some adaptation for a commensal way of life have evolved. To find out, I tested twelve populations of spiny mice in two types of open field test - a vertical test and a hole board test. In the vertical test, a wire mesh was added and offered to spiny mice to climb on. Since human settlements represent an environment with a new predation pressure as well as new hiding opportunities like those in heights above the ground, I hypothesized that commensal populations of A. cahirinus would (1) explore less on the ground and (2) prefer to spend more time on the wire mesh than the non-commensal populations. Results supported the first hypothesis as in both tests commensal spiny mice spent less time exploring on the ground than other populations. The second hypothesis, however, was not supported - all populations showed approximately equal interest in the wire mesh and commensal spiny mice did not spend more time on it compared to the others. Nevertheless, an overall...

Uppsatsen ämnar belysa kommensala gnagare inom arkeologin och förmedla potentialen för vidare forskning. Den medeltida bebyggelsen i Västergarn, Gotland agerar fallstudie där benen från små gnagare analyserats och diskuterats utifrån mikro- och makroarkeologins teoretiska vinklar. För den osteologiska analysen undersöktes benen med mikroskop för att se till ålder, spår av sjukdom och minsta individantal. I en rumslig analys sattes benen i jämförelse med de husgrunder som påträffats på platsen. Resultatet visade att materialet som fanns tillhandahållet endast innehöll de större benelementen, mest troligt till följd av den alltför stormaskiga sållen som användes vid utgrävningen. Benen som analyserades härrörde från mestadels mycket unga individer som befann sig i eller i anslutning till husgrunderna. Ett ben hade även en sjuklig förändring. Materialet visar på stor potential för framtida tvärvetenskaplig forskning där eventuella handelsrutter, sjukdomsrisker och matkonsumtion kan belysas. / This thesis aims to shed light on commensal rodents in archaeology and convey the potential for future research. The medieval settlement in Västergarn, Gotland was chosen for a case study where the rodent bones were analyzed and discussed based on micro- and macroarchaeological theoretical views. For the osteological analysis the bones were examined through a microscope to determine age, signs of disease and minimum number of individuals. The bones were put into context through a spatial analysis with the building foundations of the archaeological site. The results showed that the material at hand only contained the larger bone elements from the bodies, possibly because of the smaller bones falling through the big mesh sieve. The individuals were mostly very young and encountered near or within the building foundations. One bone had a pathological alteration. The material showed great promises for future interdisciplinary research where potential trading routes, risks of diseases and food consumption can all be made clearer.

Le commensalisme est une association biologique au sein de laquelle le commensal obtient un avantage, alors que son hôte n'obtient ni avantage, ni désavantage. Ce type d'association est théorisé durant la seconde moitié du dix-neuvième siècle, notamment par Pierre-Joseph Van Beneden (1809-1894). Zoologiste belge, professeur à l'université de Louvain, il propose dans son ouvrage de 1875 intitulé Les commensaux et les parasites dans le règne animal, 264 exemples d'associations qu'il classe parmi le commensalisme. Ses travaux ont un retentissement majeur dans l'univers des zoologistes de son époque. Le concept de commensalisme perdure alors jusqu'au vingt-et-unième siècle et interroge sur les notions d'individualité, d'individuation et d'association. Notre étude porte non seulement sur le développement de ce concept au cours du dix-neuvième siècle, que nous démontrons par de nombreux documents inédits issus des archives de Pierre-Joseph Van Beneden, mais aussi sur la pérennité du concept jusqu'à nos jours. Le commensalisme est interprété comme un « marqueur » de l'émergence de nouvelles sciences du vivant : la microbiologie et l'écologie. Plus qu'un concept scientifique, le commensalisme apparaît alors comme un concept illustrant la complexité du vivant / Commensalism is a biological association in which one partner (the commensal) benefits while neither harming nor benefitting the host. Parasitism and mutualism were well defined during the nineteenth century and commensalism was theorized during the second part of that century. Pierre- Joseph Van Beneden (1809-1894), a Belgian professor at the University of Louvain, developed this concept of commensalism. In his 1875 publication Animal Parasites and Messmates, Van Beneden presented 264 examples of commensalism. His conception was widely accepted by his contemporaries and commensalism has continued to be used as a concept right up to the present day. Our thesis examines the development of commensalism during the nineteenth century and the use of the concept in modern science. We have used hitherto unpublished archival material for Pierre-Joseph Van Beneden to explore the pertinence of his concept. From an epistemological point of view, commensalism can be seen as a marker of the new domains in the life sciences: microbiology and ecology. Through their use of different models of the concept, these two sciences gave a new sense to commensalism. Beyond being simply a scientific concept, commensalism illustrates the complexity of life

This study investigated commensal feeding interactions between the European harvestman (P. opilio L.) and the predatory mites Balaustium spp. and Anystis baccarum L. It also investigated the feeding behaviour of P. opilio. Experiments were conducted in the laboratory using standardised temperature, humidity, photoperiod and experimental arenas, with eggs of the brown blowfly (Calliphora stygia F.) as prey facsimiles. Due to initial difficulties in obtaining enough predatory mites, mite feeding was manually simulated piercing blowfly eggs with a minuten pin. P. opilio consumed significantly more freeze-killed than live blowfly eggs, indicating that freezing induced chemical and/or physical changes to blowfly eggs that are detected by P. opilio. Significantly more manually pierced eggs were consumed by P. opilio compared with unpierced ones, demonstrating that piercing caused a chemical and/or physical to the egg and increased the feeding rates of P. opilio. Different densities of eggs had no effect on the numbers eaten by P. opilio and placing single pierced eggs next to groups of unpierced eggs also had no effect on the numbers of unpierced eggs eaten. These results suggest that P. opilio does not exhibit klinokinesis or orthokinesis to intensify its search for prey around the area where previous prey were located. P. opilio ate significantly more brown blowfly eggs that had previously been fed on by mites, demonstrating that a short term commensal interaction existed. However, further work is required to demonstrate if the relationship is commensal in the longer term. A comparison between hand-pierced and mite-pierced eggs showed that P. opilio ate significantly more of the former indicating that mite and hand piercing were quantitatively different. The potential for, and importance of, other commensal or mutual relationships between predators in agroecosystems is discussed. The lack of klinokinesis and orthokinesis in P. opilio is compared with other predators and parasitoids that do exhibit these behaviours. The means by which prey are detected by P. opilio are discussed in relation to interpreting behaviours such as prey inspection. Concerns about the effect of pre-treatment and handling of sentinel prey and the problems of using prey facsimiles are raised.