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L'étude de la biodiversité de la macrofaune et des Oniscoïdes dans l'agroécosystème Majerda (BVM) a été réalisée sur 2 années successives sur 15 parcelles durant 4 saisons de l'année 2008-2009 et sur 11 parcelles de l'année 2009-2010. L'analyse a été faite en fonction des cultures les plus représentées dans la BVM (l'arboriculture, culture maraîchère, fourragère et légumineuse). L'échantillonnage a été réalisé par piégeage. Au total, 19 groupes taxonomiques ont été collectés. Les résultats montrent une variation saisonnière de la diversité de la macrofaune en fonction des parcelles. Les Coléoptères, les Oniscoïdes, les Hyménoptères, les Diptères, les Orthoptères et les Araignées sont les plus constants et abondants dans la BVM. Les Oniscoïdes sont abondants dans les parcelles en cultures fourragères. En passant des parcelles du milieu terrestre vers celui côtier, un gradient ascendant de la diversité de la macrofaune a été observé. Neuf espèces ont été collectées. Porcellio laevis est la plus fréquente durant toutes les saisons d'étude. En fonction de cultures, l'effectif et la richesse spécifique les plus importants ont été enregistrés dans les cultures fourragères et dans la céréaliculture. En fonction des secteurs, les Isopodes terrestres sont abondants dans les parcelles du secteur Pont de Bizerte qui sont irriguées par le mode aspersion et par les eaux usées. L'étude de la variation interannuelle montre qu'il existe un effet du facteur année sur la diversité de la macrofaune et des espèces d'Oniscoïdes. Les espèces d'Oniscoïdes sont corrélées avec la conductivité, la teneur du sol en Mg2+ Ca2+, K+ et de la granulométrie du sol. / In Tunisia, few studies on the macrofauna and species diversity of terrestrial isopods in the agroecosystems were performed. To fill this gap, the spatio-tempral (plots, sectors and season) diversity of macrofauna and Oniscidea was analysed. We studied the distribution of Isopods in Majerda agroecosystems related to cultivation types (orchards, market gardening, vegetable crops), irrigations systems (sprinkler, surface and drip) and soil physico-chemical characteristics. Sampling was carried out with pitfalls traps during in 15 plots during 2008-2009 and 11 plots during 2009-2010. Nineteen groups of macrofauna was found. Coleoptera, Oniscidea, Hymenoptera, Diptera, Othoptera and Aranea were the most present and abundant. Isopods were abundant in autum in the vegetable crops cultivation. In the coastal plots (Ghar El Melh sector) diversity was higher than in the terrestrial plots (Utique sector). Nine species of terrestrial isopods belonging to 6 genera were identified. Porcellio laevis was the most frequent species in all seasons. According to cultivation types, the number of individuals and the species richness were important in vegetable crops and barely cultivation. The spatial distribution of Oniscidea showed that isopods were abundant in the plots of Pont of Bizerte irrigated by sprinkler systems and wastewater. Year factor affected the diversity of fauna and isopods. Oniscidea species distribution was correlated to conductivity, texture and the content of Mg2+ Ca2+ and K+ of soil.

Au cours des dernières décennies, d'énormes quantités de haies, de lisières ont étédétruites en Europe tandis que le régime des incendies majeurs augmente dans les milieuxméditerranéens. La perte de ces milieux de type lisières s'accompagne d'une chutecatastrophique de la biodiversité. Notamment par la perte des refuges disponibles pour lafaune. Cette thèse s'intéresse à l'importance des abris à différentes échelles et sur différentsmodèles biologiques. Premièrement, l'influence de la disponibilité en abris au pied des haiessur la biodiversité a été démontrée à l'aide d'inventaires et grâce à une expérimentation surle terrain. Pour cela, une nouvelle approche d'inventaire qui combine les avantages desinventaires rapides et des techniques non létales a été mise au point. A une échelleintermédiaire, l'impact positif de l'ouverture du milieu forestier sur des populations dereptiles a été mis en évidence. Enfin, un suivi au niveau individuel de tortues d'Hermann apermis de suivre les conséquences de modifications l'habitat suite à un incendie majeur ; ilsuggère que les habitats brûlés restent favorables sur le long terme.En conclusion, l'importance des abris pour la biodiversité a été démontrée à plusieurséchelles d'espace, de temps et de précision. La conséquence pratique est que les fichestechniques de gestion des haies et des lisières devraient en tenir compte, ce qui n'est pas lecas actuellement. / During the last decencies, massive amounts of hedgerows and forest hedges have beendestroyed in Europe whereas increasing fire regimes threatened Mediterranean habitats.The loss of these hedge habitats is concomitant to a drastic loss of biodiversity. Notablythrough the decrease of shelter available to the fauna. This thesis aims to investigate therole of refuges considering different scales and biological systems. First, the positiveinfluence of the availability of shelter at the base of hedgerows on biodiversity has beendemonstrated using surveys and a field experiment. For that, a novel technique has beendeveloped by combining the advantages of rapid biodiversity assessments with non-lethalprocedures. At an intermediary scale, the positive impact of habitat opening on ophidianpopulations has been shown in a forest context. Finally, individual monitoring of Hermanntortoises allowed us to examine the impact of a major fire in habitat changes; the resultssuggest that burnt habitats remain suitable on the long term.In conclusion, the importance of refuges on biodiversity have been demonstrated atdifferent time, spatial and accuracy scales. In practice, technical recommendations shouldtake into account this key element to manage hedgerows and other hedge habitats; thiscurrently not the case.

Les zoonoses constituent plus des deux tiers des pathologies virales qui concernent l’homme. Le développement et la démocratisation des outils de métagénomique en font de bons outils d’inventaire et de surveillance de virus potentiellement émergents.Dans un premier temps j’ai développé et validé un protocole expérimental de purification des viromes à ARN qui permettait le maintien de l’infectivité des particules virales. Ce protocole a ensuite été appliqué pour caractériser les communautés virales d’arthropodes hématophages et de prélèvements de faune sauvage. J’ai par la suite réalisé l’inventaire des communautés virales de viande de singe fumée illégalement importée en France et confisquée par les douanes, qui a révélé la présence de nombreux bactériophages, dont certains pourraient infecter des bactéries potentiellement pathogènes pour l’homme.Enfin j’ai caractérisé les communautés virales de culicoïdes collectés au Sénégal, ce qui a permis de mettre en évidence la présence de nombreux virus géants à ADN infectant les amibes. Le séquençage des viromes à ARN a quant à lui révélé la présence d'un certain nombre d'arbovirus qui pourraient constituer un risque d’émergence pour la santé humaine. Du fait de nombreux facteurs intrinsèques et extérieurs à l’agent infectieux, la prédiction des futures émergences de virus zoonotiques est très compliquée voire utopique, mais elle reste un challenge crucial et d’actualité. La stratégie de réalisation d’inventaires des communautés virales présentes dans les différents acteurs des cycles de transmission zoonotique est un premier pas indispensable dans la connaissance des risques potentiels d’émergence en population humaine. / Zoonoses are responsible of more than two thirds of human viral infections. The development of high-throughput sequencing tools and their application in metagenomics allow inventorying the viral communities of various reservoirs in order to detect the emergence of viruses before their infection to humans. In this context, I characterized the viral communities of simian bushmeat illegally imported into France and of Culicoides biting midges, recognized vectors of several viruses of human and veterinary medicine importance. I have first developed a protocol for the purification of RNA viromes which allowed maintaining the infectivity of viral particles. This protocol was subsequently applied to characterize viral communities of bloodsucking arthropods and wildlife samples. In a second part I realized the inventory of viral communities of smoked simian bushmeat illegally imported into France and confiscated by the French customs. This study revealed the presence of a wide diversity of bacteriophages, in which some of them could infect bacteria potentially pathogenic for humans.Finally I characterized the viral communities of Culicoides biting midges collected in Senegal, which revealed the presence of sequences related to several giant DNA viruses infecting amoeba. Sequencing of the RNA virome revealed the presence of several arboviruses that could constitute a risk of emergence of zoonoses for humans.The prediction of future emerging zoonotic viruses is very difficult, if not impossible. However the characterization of viral communities present in the different actors of zoonotic transmission cycle is a first step to evaluate potential risks of transmission to humans.

Human activities have being responsible for the global environmental changes, resulting in an increase number of incident of vector- and rodent-borne diseases worldwide. Rodents and arthropods-borne viruses are important globally emerging and re-emerging viruses and most of them are RNA viruses. Efficient and early diagnosis of these infections are very important to prevent their spread, to improve clinical management of the patients, as wells to protect livestock and domestic animals. Currently, available diagnostic methods such as immunoassays, polymerase chain reaction and virus isolation can detect only one or few viruses in a single assay. The DNA microarray platform has emerged as diagnostic tool suitable for high throughput screening of pathogenic agents. The aim of this study was to develop a DNA microarray platform (RoboArboVirusChip) for detecting rodent- and arthropod-borne viruses, which belong to seven families: Bunyaviridae (genera Orthobunyavirus, Nairovirus and Phlebovirus), Flaviviridae (genus Flavivirus), Togaviridae (genus Alphavirus), Reoviridae (genera Orbivirus, Seadornavirus and Coltvivirus), Rhabdoviridae (genera Vesiculovirus and Ephemerovirus), and Asfarviridae (genus Asfarvirus). Specific oligonucleotide probes of 60-mer (n=4209) targeting 412 virus species and generic probes of 25-35-mer (n=87) targeting viruses at the genus level were designed. A total of 17 reference viruses belonging to the Bunyaviridae, Flaviviridae, Rhabdoviridae and Togaviridae families were used to standardize RoboArboVirusChip. All reference viruses were specifically detected without any cross hybridization; however, the generic probes were not able to identify the viruses at the genus level. The RoboArboVirusChip was able to specifically identify four viruses contained in three different mixtures: i) virus of different families, ii) virus of the Flavivirus genus, and iii) the Dengue virus (DENV) serotypes. The four DENV serotypes were use to evaluate the sensitivity of the RoboArboVirusChip, which was able to detect a minimum of 25 RNA copies/mL of the viruses, confirming its high sensitivity. The applicability of the RoboArboVirusChip to detect viruses in clinical samples was tested with serum samples obtained from dengue suspected cases (four positive cases and 40 negative cases). DENV was detected in the four positive serum samples, while in the 40 negative serum samples, it was not detected any virus. The results obtained in this study suggest that the RoboArboVirusChip platform could be a useful tool for early diagnosis of robovirus and arbovirus infections during epidemic outbreaks, helping in the rapid implementation of disease containment strategies / As atividades humanas têm sido responsável por mudanças ambientais globais, resultando num aumento do número de casos de doenças transmitidas por vetores e roedores em todo o mundo. Os vírus transmitidos por roedores e artrópodes são vírus emergentes e re-emergentes de importância global, sendo que a maioria deles são vírus de RNA. O diagnóstico eficiente e precoce dessas infecções são muito importantes para evitar a sua propagação, para melhorar o manejo clínico dos pacientes e também, para proteger o gado e os animais domésticos. Atualmente, os métodos de diagnóstico disponíveis, tais como os imunoensaios, a reação em cadeia da polimerase e o isolamento viral podem detectar apenas um ou poucos vírus em um único ensaio. A plataforma de microarranjo de DNA tem surgido como uma ferramenta de diagnóstico apropriada para o monitoramento em larga escala de agentes patogênicos. O objetivo deste estudo foi desenvolver uma plataforma de microarranjo de DNA (RoboArboVirusChip) para a detecção de vírus transmitidos por roedores e artrópodes, os quais pertencem a sete famílias: Bunyaviridae (gêneros Orthobunyavirus, Nairovirus e Phlebovírus), Flaviviridae (gênero Flavivirus), Togaviridae (gênero Alphavirus), Reoviridae (gênero Orbivirus, Seadornavirus e Coltvivirus), Rhabdoviridae (géneros Vesiculovirus e Ephemerovirus), e Asfarviridae (gênero Asfarvirus). Sondas oligonucleotídicas de 60-mer (n=4209) específicas contra 412 espécies virais, e sondas genéricas de 25-35-mer (n=87) para detecção de vírus a nível do gênero foram desenhados. Um total de 17 vírus de referência, pertencentes às famílias Bunyaviridae, Flaviviridae, Rhabdoviridae e Togaviridae foram utilizados para padronizar o RoboArboVirusChip. Todos os vírus de referência foram detectados especificamente sem apresentação de hibridação cruzada, porem as sondas genéricas não foram capazes de detectar os vírus a nível do gênero. O RoboArboVirusChip foi capaz de identificar especificamente quatro vírus contidos em diferentes misturas: i) vírus de diferentes famílias, ii) vírus pertencentes ao gênero a Flavivirus, e iii) os sorotipos do vírus da dengue (DENV). Os quatro sorotipos do DENV foram utilizados para determinar a sensibilidade do RoboArboVirusChip, o qual foi capaz de detectar um mínimo de 25 copias de RNA/mL. A aplicabilidade do RoboArboVirusChip para detectar vírus em amostras clínicas foi avaliada testando amostras de soro de pacientes com suspeita de dengue (quatro casos positivos e 40 casos negativos). Os resultados obtidos neste estudo sugerem que o RoboArboVirusChip poderá ser uma ferramenta útil para o diagnóstico precoce da infecção causada por robovírus e arbovírus, auxiliando na rápida implementação de estratégias de contenção das doenças causadas por esses vírus

Os artrópodes constituem o grupo mais diverso do Reino Animal, apresentando uma distribuição muito ampla nos ecossistemas e habitats. O fato de esses animais terem mudado muito pouco durante sua evolução e estarem bem adaptados aos ambientes inóspitos e com uma alta presença de microorganismos patogênicos, torna interessante a realização de estudos sobre o seu sistema imunológico. Parte importante deste sistema são os peptídeos antimicrobianos, que controlam a invasão dos diferentes patógenos. Estas moléculas não só podem fornecer informação sobre o sistema imune e o funcionamento deste, como também pode ajudar a buscar alternativas nas lutas contra as doenças infecciosas. Sendo assim, se torna interessante a purificação e a caracterização dos peptídeos antimicrobianos presentes nesses animais como também o conhecimento do funcionamento de seu sistema imune. Neste trabalho foram utilizadas duas espécies da ordem quilópoda: Scolopendra viridicornis e Otostigmus cavalcanti como modelo experimental. Foi avaliada a presença de moléculas bioativas na hemolinfa (plasma e hemócitos) e no extrato total do corpo, bem como a produção destas moléculas após o animal receber um estímulo ou injúria. Foi observada a presença de diferentes frações com atividade antimicrobiana na hemolinfa (plasma e hemócitos) e no extrato total de animais desafiados e não desafiados em Otostigmus cavalcanti, apresentando um aumento na atividade antimicrobiana nos animais do grupo estimulado. O que pode significar que algumas das moléculas antimicrobianas estão presentes constitutivamente no animal enquanto outras precisam de um estímulo para ser expressas. No plasma de S. viridicornis foram observadas diferentes frações com atividade antimicrobiana, observando-se atividade contra a bactéria Gram-negativa E coli e contra a levedura C. albicans. No entanto, nos hemocitos, diferentes frações apresentaram atividade somente contra a bactéria Gram-positiva M. luteus. Na porção hidrofóbica do extrato total do corpo de S. viridicornis também foram observadas diferentes frações com atividade antimicrobiana. No material eluído em 5% de ACN, por análise de ESI-MS de uma fração com atividade contra M. luteus foram observadas duas moléculas com massa molecular baixa (848,49 e 861,94 Da). Ainda no extrato total da fração hidrofóbica foram observadas duas moléculas que se apresentaram puras. A primeira destas mostrou uma massa molecular de 1,7 kDa mas ainda não foi caracterizada. Enquanto a segunda evidenciou um peptídeo de 925,4658 Da e cuja estrutura primaria apresentou um composto de 8 resíduos de aminoácidos (RYPAVGYT). Esta molécula foi nomeada Lacraina. Entretanto na porção hidrofílica do extrato total de S. viridicornis e de Otostigmus cavalcanti foram observadas frações de baixa massa molecular com atividade antiparasítica contra Leishmania amazonensis e Trypanosoma brucei e antibacteriana contra E. coli e M. luteus. Também nesta fração foi observada uma molécula semelhante à Gomesina um peptídeo antimicrobiano da aranha caranguejeira Acanthoscurria gomesiana. A análise e caracterização desta molécula ainda esta em progresso. / Arthropods constitute the most diverse group in the Animal Kingdom, representing a very wide distribution in different ecosystems and habitats. The fact that these animals have changed very little during their evolution and that theyre well adapted to harsh environments with a high presence of pathogenic microorganisms, makes it interesting to conduct studies on their immune system. An important part of these systems are antimicrobial peptides that control the invasion of various pathogens. These molecules not only provide us with information on their immune system and its functioning, but can also help us find alternatives in the struggle against infectious diseases. Therefore, the purification and characterization of antimicrobial peptides present in these animals becomes important, as well as gaining knowledge on how their immune systems work. In this work two specimens of the Chilopoda order, Scolopendra viridicornis and Otostigmus cavalcanti, were used as an experimental model for the characterization of bioactive molecules present in the hemolymph and total body extract as well as the production of these molecules after stimulating or injuring the animal. The presence of different fractions with antimicrobial activity in the hemolymph (plasma and hemocytes) and the total body extract of defied and not defied animals in Otostigmus cavalcanti was observed. Presenting an increase in the antimicrobial activity in the stimulated group of animals, this could mean that some of the antimicrobial molecules are constitutively present in the animal, while others need to be induced to be expressed. In the plasma of S. viridicornis different fractions with antimicrobial activity and with activity against the Gram-negative bacteria E coli and against the C. albicans yeast were observed. Notwithstanding, in the hemocytes, there are different fractions that presented activity only against the Gram-positive M. luteus bacteria. In the hydrophobic portion of the total extract of the S. viridicorniss body, different fractions with anti-microbial activity were also observed. In the 5% ACN eluted material, by an ESI-MS analysis of a fraction with activity against M. luteus two molecules with low molecular mass (848.49 and 861.94 Da) were present and two pure molecules were observed in the total extract of the hydrophobic fraction. The first one presented a molecular mass of 1.7 kDa that remains to be characterized. The second one was a 925.4658 Da peptide, whose primary structure presented a compound of 8 amino acid residues (RYPAVGYT). This molecule was named Lacrain. However, in the hydrophilic portion of the total extract of S. viridicornis and O. cavalcanti low molecular mass fractions with antiparasitic activity against Leishmania amazonensis and Trypanosoma brucei as well as antibacterial activity against E. coli and M. luteus were observed. Also in this fraction a molecule similar to Gomesin, an antimicrobial peptide from the spider Acanthoscurria gomesiana. was present. The analysis and characterization of this molecule is still in progress.

In the Arctic tundra, wood ants play an important ecological role in aerating the soil, cycling nutrients, for seed dispersal and, as biological control by preying on forest pest insects during outbreaks. The increase in temperature, caused by climate change, is positively associated with ant abundance.  This could accelerate the wood ants’ effects on the ecosystem, with potentially dramatic consequences for associated taxa. It is, however, still unclear to what extent the ants influence the vegetation and arthropod community. The aim of this study is to investigate the effects ants have on the Arctic tundra ecosystem and how climate change may modify these effects. The study was conducted in Abisko national park, north Sweden, were two study sites were selected: one at low altitude and one at high altitude. I found that wood ants had a substantial effect on the vegetation community close to the mound, with a positive effect on different kind of vascular plant species, and a negative effect on rushes, mosses, and lichens. All the arthropods taxonomic orders and most of the families were positively affected by the presence of ant mounds. Ant mound abundance and volume were positively related with annual insolation and GPP, which indicates that climate change will increase ant abundance in the Arctic tundra. Thus, my results suggest that future climate change will have significant effects on Arctic tundra vegetation and arthropod communities, via positive effects on ant abundance.

The diet of an animal plays a fundamental role in its ecology, and the consequence of a specific diet may be more pronounced in mammals with a specialised diet that are more reliant on a specific food type. This can have a dramatic effect on its activity patterns, home range size and the interaction with heterospecifics. Investigating the diet of specialist mammals and the subsequent effects it will have on their ecology is thus vital to the management and subsequent conservation of the species, and crucial to our understanding of how the animal can survive and reproduce. In this thesis I investigate the effect that the diet of the aardwolf, a highly specialised myrmecophage, has on its ecology. Aardwolves feed predominantly on one genus of termite, Trinervoides spp., and are thus extremely dependent on the abundance and distribution of this arthropod. I firstly investigated the effect of temperature and rainfall on arthropod abundance and diversity, and further investigated the variation of arthropod abundance and diversity across the four habitat types at study site. This is one of a few studies that have been conducted on arthropod abundance and diversity in an arid environment and the findings show that in an arid environment arthropods are mainly influenced by temperature rather than rainfall. This is in contrast to studies in temperate and forest habitats where rainfall is the most important abiotic factor determining the abundance and diversity of arthropod assemblages. Habitat type still plays a major role in the abundance and diversity of arthropods, and habitat types that are more complex and diverse have both a higher diversity, and abundance of arthropods than other habitats. Due to the absence of prey items during the colder months of the year I investigated the diet of aardwolves to see if they display a switch in diet. This included an investigation into the seasonal variation of diet from a detailed scat analysis, using a newly developed method to assess scat content. The analysis of scats revealed that, contrary to previous studies, aardwolves showed no switch in diet and continued to feed on Trinervitermes. Using the data from the scat analyses and the information from the abundance and diversity of arthropods at the study site I expanded the study to investigate the functional responses of the aardwolf to change in prey abundance at the locality. Aardwolves demonstrate a Type I functional response to changes in prey abundance, a response that is normally found in plankton feeders. The expected functional response for specialist animals would be Type II response, and I propose that the Type I response seen in aardwolves is probably as a result of a limited handling time which reduces time spent foraging. The abundance of termites thus had a clear effect on the diet of aardwolves, showing that they feed on fewer when they are unavailable, and as such I investigated the effect of termite densities on home range sizes. The number of termite mounds in a home range influenced the size of the home range, and aardwolves with larger home ranges had a lower density of termite mounds. In contrast to previous studies, large overlaps between neighbouring individuals were recorded and indeed three male aardwolves shared a common den. I propose that the reason behind the overlap of home ranges is that a higher prey abundance during my study period occurred and as a consequence aardwolves did not need to defend an area to protect this resource. T. trinervoides has thus played a keystone role in driving the biology of the aardwolf and shaping many aspects of its ecology. / Thesis (PhD)--University of Pretoria, 2021. / South African Research Chair Initiative chair of Mammal Behavioural Ecology and Physiology / Zoology and Entomology / PhD / Unrestricted

No description available.

In the Arctic tundra, wood ants play an important ecological role in aerating the soil, cycling nutrients, for seed dispersal and, as biological control by preying on forest pest insects during outbreaks. The increase in temperature, caused by climate change, is positively associated with ant abundance.  This could accelerate the wood ants’ effects on the ecosystem, with potentially dramatic consequences for associated taxa. It is, however, still unclear to what extent the ants influence the vegetation and arthropod community. The aim of this study is to investigate the effects ants have on the Arctic tundra ecosystem and how climate change may modify these effects. The study was conducted in Abisko national park, north Sweden, were two study sites were selected: one at low altitude and one at high altitude. I found that wood ants had a substantial effect on the vegetation community close to the mound, with a positive effect on different kind of vascular plant species, and a negative effect on rushes, mosses, and lichens. All the arthropods taxonomic orders and most of the families were positively affected by the presence of ant mounds. Ant mound abundance and volume were positively related with annual insolation and GPP, which indicates that climate change will increase ant abundance in the Arctic tundra. Thus, my results suggest that future climate change will have significant effects on Arctic tundra vegetation and arthropod communities, via positive effects on ant abundance.