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Mitchell, Edward
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Mitchell, Edward
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Professeur ordinaire
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edward.mitchell@unine.ch
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- PublicationRestriction temporaireUnveiling the biogeography of terrestrial protists through microscopy, metabarcoding, and species distribution modelling : from testate amoebae as model organisms to community patterns(Neuchâtel : Université de Neuchâtel, 2024)
; ; Ma thèse de doctorat porte sur la biogéographie et l'écologie des protistes terrestres libres en tant que communauté et des amibes à thèque de l’ordre des arcellinides (Amoebozoa: Arcellinida) en tant qu’organismes modèles. Mes recherches s’articulent autour de deux objectifs principaux: (1) le développement d'une stratégie d'échantillonnage pour étudier, à l’aide du métabarcoding de l’ADN environnemental, l’ensemble de la communauté des protistes du sol le long de gradients d'altitude en tenant compte de leur dynamique spatiotemporelle, et (2) le développement de modèles de distribution d’espèces d’amibes à thèque pour évaluer si les prédictions de distribution à l’échelle globale corroborent l'hypothèse selon laquelle les micro-organismes ont une distribution géographique restreinte. De plus, ces modèles prédictifs visent également à étudier la capacités et les limitations de distribution des amibes à thèque à atteindre des écosystèmes insulaires isolés, et à évaluer leurs risques d'extinction en réponse aux futurs changements climatiques. Dans la première étude, mes recherches ont porté sur la dynamique spatio-temporelle de l’ensemble de la communauté des protistes du sol le long de multiples gradients d’altitude dans les Alpes suisses et la Sierra Nevada espagnole. L’objectif était de déterminer, à l’aide du métabarcoding de l’ADN environnemental, si la dynamique temporelle des communautés de protistes du sol pourrait introduire des biais dans l’études de leur biodiversité lorsque plusieurs gradients d’altitude échantillonnés à travers différentes saisons, habitats, régions ou latitudes sont comparés. Mes analyses ont révélé que la bêta-diversité des communautés de protistes du sol est principalement influencée par l’hétérogénéité spatiale plutôt que par le turnover temporel. Ainsi, les résultats indiquent que, dans les climats tempérés, un seul échantillonnage le long d’un gradient d'altitude n'introduit pas de biais dû aux différences phénologiques entre les saisons. Par conséquent, la bêta-diversité entre plusieurs gradients et plusieurs régions peut être comparée de manière fiable, même si l'échantillonnage n'est pas simultané. Mon deuxième projet a permis d’étudier la distribution et le potentiel de dispersion à longue distance de l'amibe à thèque Apodera vas (Certes) Loeblich & Tappan à l'aide d'un modèle de distribution d’espèce à l’échelle mondiale et basé sur la niche climatique. Les résultats ont révélé de surprenantes divergences entre le potentiel de dispersion à longue distance latitudinale et longitudinale. En effet, alors que le modèle indique de nombreuses zones propices à A. vas dans l’hémisphère nord, le potentiel de distribution interhémisphérique du taxon semble limité, contrairement au potentiel de dispersion longitudinale par le vent ou par les oiseaux qui a été confirmé, notamment dans les îles péri-antarctiques. En outre, en extrapolant le modèle aux climats passés et futurs, j'ai évalué les expansions et contractions des zones propices à A. vas au fil du temps. Jusqu’à la fin du 21ème siècle, les prévisions annoncent une forte réduction des zones propices à ce taxon sur tous les continents en raison du changement climatique. Apodera vas étant un complexe d’espèces cryptiques, mes résultats mettent en évidence d’importants risques d'extinctions régionaux et souligne la nécessité de stratégies de conservation ciblées qui incluent les protistes du sol. J'ai utilisé la même approche de modélisation dans le cadre de la troisième étude pour déterminer les aires propices à l'amibe à thèque Hyalosphenia papilio Leidy à l’échelle globale et étudier les raisons de son absence dans l'archipel des Açores (Portugal) malgré la présence de vastes tourbières à sphaignes. Comme pour A. vas, le modèle de distribution de H. papilio suggère une absence de potentiel de distribution interhémisphérique, mais confirme qu'une dispersion sur de courtes distances est possible. Alors que plusieurs espèces de la même taille que H. papilio ont été trouvées dans des échantillons de sphaigne des Açores, H. papilo ainsi que d'autres espèces mixotrophes étaient absentes, et ceci malgré un climat favorable et la présence d'un habitat approprié. Ce cas de disharmonie insulaire est probablement dû davantage au développement récent des tourbières à sphaignes déclenché par des changements hydrologiques liés au déboisement qu'à une limitation de la dispersion. Pour conclure, en évaluant la robustesse des méthodes d'échantillonnage le long des gradients d'altitude, mon étude a mis en évidence que, dans les régions tempérées, un effort d'échantillonnage réduit (c'est-à-dire une fois par an au lieu d'un échantillonnage répété) ne fausserait pas la comparaison de la bêta-diversité dans le cadre d’études à large échelle. En utilisant la modélisation et les amibes à thèque comme organismes modèles, mes deux autres chapitres de thèse approfondissent les connaissances sur les potentiels mécanismes de dispersion, les filtres environnementaux et l’héritage de l’impact humain passé qui régissent la biogéographie des protistes du sol et soulignent qu'en effet, au moins certains microorganismes ont une biogéographie. De plus, la modélisation permet non seulement d'orienter les études futures, mais met également en exergue les menac es climatiques importantes qui pèsent sur la diversité microbienne. Par conséquent, mes résultats soutiennent l'idée que, à l'instar des plantes et des animaux, les protistes du sol sont fortement structurés dans l'espace à la fois à l'échelle régionale (le long des gradients d'altitude) et à l'échelle mondiale. En outre, ces motifs de distribution peuvent être observés à différents niveaux taxonomiques . En définitive, ma thèse met en lumière l’utilité de combiner différentes approches méthodologiques et différents niveaux taxonomiques pour étudier la biogéographie de protistes du sol. Elle souligne également le besoin urgent de combler les lacunes taxonomiques (‘Linnean shortfall’) et de distribution (‘Wallacean shortfall’) des protistes du sol. Finalement, mon travail illustre l'importance de la collaboration entre les chercheurs et chercheuses en protistologie, en modélisation et en conservation afin d'élaborer des mesures de conservation concrètes pour ces communautés microbiennes vitales et les écosystèmes qu'elles habitent. ABSTRACT My PhD thesis delves into the biogeography and ecology of terrestrial free-living protists, as a community, and on arcellinid testate amoebae (Amoebozoa: Arcellinida) as model organisms. My research is centred on two principal objectives:(1) the development of a metabarcodingbased sampling strategy to study spatio-temporal dynamics of soil protist communities across elevation gradients, and (2) the development of global-scale testate amoebae species distribution models to evaluate if these models corroborate the hypothesis that microorganisms possess restricted geographical distributions. These predictions further aim to investigate the dispersal capabilities and limitations of testate amoebae to reach isolated island ecosystems and to assess their extinction risks in response to future climate change. In the first study, my research investigated the spatio-temporal dynamics of the entire soil protist community along multiple elevation gradients in the Swiss Alps and Spanish Sierra Nevada using environmental DNA metabarcoding. The aim was to determine if temporal dynamics in soil protist communities could introduce biases in biodiversity studies when multiple elevation gradients sampled across different seasons, habitats, regions, or latitudes are compared. My analyses revealed that soil protist community beta-diversity is primarily influenced by spatial heterogeneity rather than temporal turnover. Thus, the results indicate that conducting a single sampling across an elevation gradient in temperate climates does not introduce biases due to phenological differences between seasons. Consequently, beta diversity patterns can be reliably compared between gradients and regions, even if the sampling is not simultaneous. My second project allowed to investigate the distribution and long-distance dispersal (LDD) potential of the testate amoeba Apodera vas (Certes) Loeblich & Tappan using a global climate niche modelling approach. The results revealed intriguing discrepancies between latitudinal and longitudinal LDD for A. vas, with no evidence of interhemispheric LDD, whereas longitudinal LDD, either by wind or by birds, was confirmed, notably in peri-Antarctic islands. Furthermore, by extrapolating the model to past and future climates, I assessed range expansions and contractions over time. Until the end of the 21st century, the predictions forecast a strong reduction in climate suitability for this taxon on all continents due to future climate change. Apodera vas being a complex of cryptic species, this underscores significant risks of regional extinctions and emphasizes the need for targeted conservation strategies that include soil protists. I employed the same modelling approach in the third project and investigated the global climate niche suitability of the testate amoeba Hyalosphenia papilio Leidy and the reasons for its absence in the Azores archipelago (Portugal), despite the presence of extensive Sphagnum-dominated peatlands. Similar to A. vas, the model suggested a lack of interhemispheric LDD for H. papilio but confirmed that short distance dispersal is likely. While several species of the same size range of H. papilio were found in Sphagnum samples from the Azores, H. papilo was absent as well as other mixotrophic species, despite favourable climatic and the presence of the appropriate habitat. This case of island disharmony may be due more to the recent development of Sphagnum peatlands triggered by hydrological changes due to forest clearance than to dispersal limitation. To conclude, by assessing the robustness of the sampling design along elevation gradients, my study highlighted that, in temperate regions, reduced sampling effort (i.e., once per year versus repeated sampling) would not bias beta diversity comparison of large-scale studies. By using species distribution modelling and testate amoebae as model organisms, my two other studies provide insights into the potential dispersal mechanisms, environmental filtering and legacy of past human impact governing the biogeography of soil protists and emphasize that at least some microorganisms do have a biogeography. Additionally, species distribution modelling not only has the potential to guide future studies but also highlights the significant climate threats to microbial diversity. Overall, my results support the notion that soil protist diversity is strongly structured spatially at both regional (along elevation gradients) and global scales, akin to plants and animals. Furthermore, these distribution patterns can be observed at different taxonomic levels (i.e., single testate amoeba taxa vs. entire soil protist community). Consequently, my thesis underscores the utility of combining different methodological approaches and focusing on different taxonomical levels to study soil protist biogeography. It also stresses the urgent need to address the Linnean (taxonomic) and Wallacean (distributional) shortfalls in soil protists. Finally, my work highlights the importance of collaboration among protist researchers, species distribution modeller and conservationists to develop concrete conservation measures for these vital microbial communities and the ecosystems they inhabit. - PublicationRestriction temporaireMorphological and molecular taxonomy of aquatic and terrestrial protists as a prerequisite for studies of evolution, biodiversity, biogeography, bioindication and ecosystem functioning –examples from euglyphid and arcellinid testate amoebaeMacro-eukaryotes (i.e., organisms that do not need magnification to be seen) appear to being the dominant component of ecosystems, but they are not the only driving forces of ecological processes. Microorganisms are known to play important roles in ecological processes such as elements, and nutrients cycling and are also known to shape macro-eukaryotic communities via parasitism or symbiosis (e.g., mycorrhiza). Now we are starting to assess the diversity and the impact on ecological processes of freshwater and marine micro-organisms but little is known of the soil-dwelling microbes, especially non-fungal and non-plant unicellular microeukaryotes (known as the protists). Maybe because most do not form recognizable colonies like the bacteria and the fungi, soil protists have been overlooked even by microbiologists. Some protists such as the diatoms, radiolarians, foraminiferans and coccolithophores have proved to be potent proxies and are commonly used to evaluate current or past environmental changes, but it concerns only a fraction of the protistan diversity. Furthermore, those are mostly marine organisms. Among the plethora of soil protists and their possible uses, only testate amoebae are regularly used as proxies to monitor the evolution of peatlands. And probably, one of the major reasons that could be invoked is the largely incomplete taxonomy of soil protists. The use of protists as bioindicators implies a sound taxonomic framework. However, the diversity and the taxonomy of these organisms is still far from being understood, as most species have not been described. Protists were mainly characterized with light microscopy, but the absence of characteristic morphological traits - and the fact that the phenotypical plasticity of protists was considered as being extremely high - has led naturalists to underestimate their diversity for a long time. It is only recently with the appearance of staining protocols, electron microscopy and molecular biology that we start to assess the true diversity of these organisms. With these new tools, it appears that many described species were in fact morphospecies complexes including more than one biological species that, sometimes, could be completely unrelated. Among these tools, High Throughput Sequencing (HTS) allows to evaluate more easily the micro-eukaryotic community of an environmental sample, revealing that many clades of protists have not been characterized and are still to be discovered. There is then a need for taxonomists to describe this hidden diversity and to update old descriptions in order to build a sound taxonomy. The aim of this thesis is to cover the several steps required to improve the taxonomy of soil protists, with a focus on testate amoebae, so that they can be used in larger surveys to study their ecology, diversity and evolution.
- PublicationAccès libreFrom fundamental questions to practical conservation actions: a study of the ecological niche (soil and vegetation), the pollination system, population genetics, population demography and mycorrhizal associations of "Cypripedium calceolus" (Orchidaceae)The current epoch, the Anthropocene, is witnessing a generalized and rapid extinction of species worldwide. As the causes of such extinctions, often related to global change drivers (e.g., habitat destruction, pollution, climate change), might not be hampered immediately, conservation actions should focus on preserving, restoring and regenerating the disappearing species through concrete action plans. Rare and endangered plant species, for instance, can be preserved by reintroducing seedlings in the same habitat, or introducing them into yet unoccupied habitats to generate novel populations. While this approach holds several good promises, it often generates mixed results, likely due to the fact that the current or novel habitat do not actually offer the optimal conditions for the target species to grow and thrive. With this thesis, we have tackled the problem of how to better characterize the ecological requirements of an endangered plant species in order to increase the success rate of future (re)introduction actions and to develop more efficient and targeted conservation measures. By focusing on the iconic and endangered orchid species Cypripedium calceolus (Lady’s Slipper) as a model species, we have taken a broad-range perspective, including both geomatics and field work to study the links between multiple ecological factors (soil properties, climate, association with local vegetation and health of 34 C. calceolus populations across Switzerland). In the first chapter, we propose a two-step approach to identify (re)introductions sites for endangered plant species using C. calceolus as a model species. The first step involves modelling its niche and its distribution with bioclimatic and topographical predictors. The second step consists in refining these bioclimatic predictions by analysing stationary ecological factors, such as edaphic conditions, and relating them to populations-level fitness values. The first results show that climatic predictions alone were not precise enough, but nevertheless could highlight a likely decline of the species range during the next 50 years due to predicted climate warming. Moreover, when incorporating topographical layers for the modelling approach at the regional scale, we show that the species is more likely to occur near forest edges. Finally, by analysing in situ soil factors, we show that soil organic matter, cation-exchange capacity and pH correlated most strongly with C. calceolus population fitness variables as described by multivariate function trait space. We thus advocate for the combination of modelling tools with fine scale on-site ecological surveys to identify suitable reintroduction sites for this, and potentially other, endangered plant species. In the second chapter, we aimed to determine the relationships between the performance of C. calceolus populations and soil and vegetation factors, to improve this species conservation and but also to advance the theoretical underpinning of which facets of an ecosystem most influence this species fitness. By studying C. calceolus functional traits of 34 sites across Switzerland, we found that large (>20 individuals) populations of C. calceolus displayed a specific assemblage of measurable characteristics that discriminate them from small (<10 individuals) populations, indicating that it is possible to assess the health of a population of a rare plant species by measuring a specific set of traits. While we could not direct predict population health status from vegetation (phytosociological alliances) and soil types, we show that a unique combination of companion plants and several edaphic variables, such as soil organic matter (SOM), CaCO3, pH, and P could be used to potentially assess the optimal sites to implement (re)-introduction actions for this emblematic and patrimonial orchid species. In the third chapter, we addressed the pollination ecology of C. calceolus by studying the links between plant vegetative and floral traits and local pollinator biodiversity. Moreover, we studied potential variation at the population level of how plants attract their pollinators and subsequently how this variation relates to the overall reproductive effort of C. calceolus individuals. We found that small C. calceolus populations occur in less diverse sites, both in terms of surrounding plants and insects. However, while plants from larger populations were physically larger and produced more flowers per capita, they produce the same number of seeds per capita (i.e., seed set) as small populations. This occurred despite the lower pollinator diversity present at the small population sites, meaning that plants from small populations must compensate by providing a stronger attraction to pollinators. Indeed, we discovered that floral volatile organic compounds are produced in higher quantity from the flowers of plants from small populations, suggesting that small populations compensate for low pollinator diversity by producing a stronger floral scent. Two additional perspective chapters deal with the genetic structure of the Swiss C. calceolus populations and their association with mycorrhizal fungi. While these data opens new interesting venues, these topics merits further investigations in the future. In summary, our results do not only increase the fundamental knowledge about C. calceolus biology and ecology but also allow to establish concrete conservation measures and to select more appropriate translocation sites. Moreover, this thesis emphasizes the complexity of orchid ecology and supports the use of integrated research and practical protection measures for this family of plants, and likely others. In a context of global climatic changes and due to the fragility of orchid ecological needs, this kind of approach is more relevant than ever. From a broader perspective, the method we developed is transposable to other plant taxa. Therefore, we advocate for the use of comprehensive methodologies based on multiple aspects of plant biology and ecology, as presented here, to study and protect a broad range rare and endangered plants.
- PublicationAccès libreAssessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing(2020-9-18)
; ; ; - PublicationAccès libreLes pesticides: lacunes et alternatives(2020-2-9)
; Les études de l’impact des néonicotinoïdes sur les abeilles ont permis une prise de conscience sur la toxicité de ces molécules. Mais ces insectes ne sont pas les seuls à subir les conséquences de l’usage massif des pesticides en agriculture conventionnelle. En nous focalisant sur l’abeille, ne risque-t-on pas de négliger les effets sur les autres organismes vivants? - PublicationAccès libreExploration and characterization of "Amoebozoa" diversity and investigation of their diversity patterns at regional and global scales(2020)
; ; La diversité mondiale des eucaryotes est dominée par des organismes (principalement) unicellulaires appelés protistes. Parmi eux, les Amoebozoa sont l'un des groupes les plus abondants, diversifiés et caractéristiques du sol, jouant ainsi des rôles importants dans le fonctionnement des écosystèmes. Cependant, leur étude a été entravée par la difficulté de les détecter et le manque de traits morphologiques stables dans la plupart des groupes. Toutefois, certains amibozoaires comme les Hyalospheniformes (Arcellinida) produisent une thèque (c.-à-d. une coquille) caractéristique qui facilite leur identification, et sont donc considérées comme un groupe modèle approprié pour étudier les schémas de répartition de la diversité. Le développement récent du barcoding moléculaire a considérablement aidé pour l’identification taxonomique, tandis que le métabarcoding a permis de révéler la composition des communautés microbiennes sans biais d'observation et de culture. Ces méthodes se sont révélées efficaces pour plusieurs groupes microbiens, mais seulement quelques études ont été conçues pour les Amoebozoa et les protocoles disponibles sont encore assez rares. Les objectifs de ma thèse étaient alors 1) améliorer et développer des méthodes moléculaires pour étudier la diversité et l'écologie des amibozoaires, 2) estimer la diversité taxonomique et fonctionnelle présente dans le sol, 3) améliorer la taxonomie et phylogénie de cette diversité afin d'établir une base solide pour de futures recherches et 4) caractériser les facteurs écologiques susceptibles d'influencer la diversité microbienne à l'échelle locale, continentale et mondiale. Nous avons d'abord identifié un nouveau marqueur moléculaire pour étudier plusieurs groupes d’arcellinides, qui s'est révélé efficace pour discriminer des taxons proches et étudier simultanément les relations phylogénétiques profondes entre des taxons éloignés (chapitre 2). De plus, nous avons également adapté un protocole de métabarcoding pour étudier le genre Nebela avec des amorces COI spécifiques et une résolution taxonomique fine (chapitre 6). Ensuite, nous avons isolé, cultivé et décrit le premier membre d'un clade environnemental d’amibozoaires évolutivement très divergent (chapitre 3). Cette amibe, l'une des plus petites espèces d'amibes décrites, présente un cycle de vie unique avec une alternance de trophozoïtes actifs phagotrophes et de ramifications osmotrophes ressemblant aux champignons. Sa présence a été fréquemment reportée dans de nombreuses études de métabarcoding du sol, mais cet organisme n'avait jamais été caractérisé auparavant. En revanche, les Hyalospheniformes sont connus depuis les travaux d’Ehrenberg au XIXe siècle. Cependant, leur diversité au niveau de l’espèce reste mal caractérisée. Dans le chapitre 4, nous avons montré que l'espèce emblématique d’amibe à thèque, Nebela militaris, n'appartenait pas au genre Nebela, mais constituait une entité distincte dans l'arbre des Hyalospheniformes. Par conséquent, nous avons érigé le nouveau genre Alabasta pour cette espèce (chapitre 4). De plus, nous avons montré que la diversité des Hyalospheniformes avait été largement sous-estimée. En effet, nos résultats morphologiques et moléculaires ont révélé la présence de plusieurs espèces au sein des genres Apodera, Alocodera et Padaungiella. Cette nouvelle diversité a des impacts sur la biogéographie microbienne, car Apodera vas et Alocodera cockayni étaient auparavant considérées comme deux espèces non-cosmopolites avec des aires de répartition géographique très étendues et de grandes tolérances écologiques. Par conséquent, nous avons montré que la situation était beaucoup plus complexe, suggérant l'existence d'endémismes locaux étroits et de spécialistes écologiques, à l'instar des genres Hyalosphenia et Nebela (chapitre 5). Finalement, nous avons exploré la diversité du genre Nebela le long d’un gradient d’élévation (chapitre 6). Nous avons observé une diminution de l’abondance et de la diversité en haute altitude ce qui correspond à un effet typique de « milieu de domaine ». Notre étude a également révélé plusieurs phylotypes inconnus limités à de hautes altitudes qui semblent présenter une exclusion réciproque avec des taxons généralistes présents à des altitudes inférieures. En conclusion, cette thèse met en évidence que des méthodes moléculaires associées à des observations morphologiques robustes sont efficaces pour révéler et décrire la diversité des Amoebozoa. De plus, ces organismes microbiens possèdent des schémas biogéographiques et macro-écologiques similaires aux animaux, plantes et champignons, dès lors que ces groupes sont étudiés au même rang taxonomique, c'est-à-dire au niveau de l'espèce. ABSTRACT The world eukaryotic diversity is dominated by (mostly) single-celled organisms referred to as protists. Among them, the Amoebozoa are one of the most numerous, diverse and characteristic groups in soil, thus playing important roles in ecosystem functioning. However, their study has been impeded by the difficulty in detecting them and the lack of stable morphological traits in most groups. Nevertheless, some amoebozoans such as the Hyalospheniformes (Arcellinida) are characterized by a self-constructed test (i.e. shell) which facilitates their identification, and are then considered as a suitable model group for investigating diversity patterns of repartition. The recent development of DNA barcoding has helped considerably taxonomic identification, whereas metabarcoding has allowed revealing microbial community composition without observational and cultivation biases. These methods have proved efficient for several microbial groups, but only few studies have been designed for Amoebozoa and available protocols are still rather scarce. The aims of my thesis were then to 1) improve and develop molecular methods to study the amoebozoan diversity and ecology, 2) estimate their taxonomic and functional diversity in the soil, 3) improve the taxonomic and phylogenetic frame for this diversity in order to build a sound basis for further research and 4) characterize the ecological drivers which are likely to influence microbial diversity at local, continental and global scales. We first identified a new molecular marker to survey arcellinids taxa, which proved to be efficient for discriminating closely-related taxa and simultaneously investigating deep relationships among distant taxa (Chapter 2). In addition, we also adapted a metabarcoding protocol with specific COI primers to survey the diversity within the genus Nebela at a fine taxonomical resolution (Chapter 6). Then, we isolated, cultivated and described the first member of a deep-branching environmental clade of Amoebozoa (Chapter 3). This amoeba, one of the smallest amoeboid species described, presents a unique life cycle with an alternation of phagotrophic active trophozoites and osmotrophic fungi-like ramifications. Its presence has been pervasively reported in many soil metabarcoding studies, but this organism had never been characterized. By contrast, Hyalospheniformes are known since the works of Ehrenberg in the 19th century. However, their diversity at the species level remains poorly characterized. In chapter 4, we showed that the iconic testate amoeba species Nebela militaris did not belong to genus Nebela but branched as a separate entity in the Hyalospheniformes tree. Therefore, we erected the new genus Alabasta for this species (Chapter 4). In addition, we demonstrated that Hyalospheniformes diversity had been greatly underestimated. Indeed, our morphological and molecular results have revealed the presence for several species within the genera Apodera, Alocodera and Padaungiella. This new diversity has implications on microbial biogeography as Apodera vas and Alocodera cockayni were previously considered as two non-cosmopolite species with very broad geographical ranges and large ecological tolerances. Furthermore, we showed that the situation was far more complex, suggesting the existence of narrow local endemisms and ecological specialists, similarly to genera Hyalosphenia and Nebela (Chapter 5). Finally, we explored the diversity patterns of the genus Nebela along an elevation gradient (Chapter 6). We observed a decrease of abundance and diversity in high elevation corresponding to a typical mid-domain effect. Our study also revealed several unknown phylotypes restricted to the higher elevation that seemed to present competitive exclusion with the generalist taxa from lower elevation. In conclusion, this thesis highlights that molecular methods associated to robust morphological observations are efficient to reveal and describe the diversity of Amoebozoa. Furthermore, these microbial organisms display biogeographical and macroecological patterns similarly to animals, plants and fungi, when all groups are studied at the same taxonomical rank, i.e. species level. - PublicationAccès libreUltra-trace level determination of neonicotinoids in honey as a tool for assessing environmental contamination(2019-2-5)
; ; Glauser, GaetanNeonicotinoids and the closely related insecticide classes sulfoximines and butenolides have recently attracted growing concerns regarding their potential negative effects on non-target organisms, including pollinators such as bees. Indeed, it is becoming increasingly clear that these effects may occur at much lower levels than those considered to be safe for humans. To properly assess the ecological and environmental risks posed by neonicotinoids, appropriate sampling and analytical procedures are needed. Here, we used honey as reliable environmental sampler and developed an unprecedentedly sensitive method based on QuEChERS and UHPLC-MS/MS for the simultaneous determination of the nine neonicotinoids and related molecules currently present on the market (acetamiprid, clothianidin, dinotefuran, flupyradifurone, imidacloprid, nitenpyram, sulfoxaflor, thiacloprid and thiamethoxam). The method was validated and provided excellent levels of precision and accuracy over a wide concentration range of 3–4 orders of magnitude. Lowest limits of quantification (LLOQs) as low as 2–20 pg/g of honey depending on the analytes were reached. The method was then applied to the analysis of 36 honey samples from various regions of the World which had already been analysed for the five most common neonicotinoids (acetamiprid, clothianidin, imidacloprid, thiacloprid and thiamethoxam) in a previous study. This allowed us to determine the long-term stability (i.e. up to 40 months) of these molecules in honey, both at room temperature and −20 °C. We found that the five pesticides were stable over a period of several years at −20 °C, but that acetamiprid and thiacloprid partially degraded at room temperature. Finally, we also measured the levels of dinotefuran, nitenpyram, sulfoxaflor and flupyradifurone and found that 28% of the samples were contaminated by at least one of these pesticides. - PublicationAccès librePesticides: Berne doit jouer la transparence(2018-11-25)
; OPINION. Deux chercheurs de l’Université de Neuchâtel, Alexandre Aebi et Edward Mitchell, demandent à l’Office fédéral de l’agriculture de publier les informations détaillées sur l’usage des pesticides en Suisse, après une première communication insatisfaisante - PublicationAccès libreComment promouvoir une agriculture qui protège et profite de la biodiversité?(2018-11-1)
; - PublicationAccès libreSoil chemistry changes beneath decomposing cadavers over a one-year period(2018-3-6)
; ; ; Decomposing vertebrate cadavers release large, localized inputs of nutrients. These temporally limited resource patches affect nutrient cycling and soil organisms. The impact of decomposing cadavers on soil chemistry is relevant to soil biology, as a natural disturbance, and forensic science, to estimate the postmortem interval. However, cadaver impacts on soils are rarely studied, making it difficult to identify common patterns. We investigated the effects of decomposing pig cadavers (Sus scrofa domesticus) on soil chemistry (pH, ammonium, nitrate, nitrogen, phosphorous, potassium and carbon) over a one-year period in a sprucedominant forest. Four treatments were applied, each with five replicates: two treatments including pig cadavers (placed on the ground and hung one metre above ground) and two controls (bare soil and bags filled with soil placed on the ground i.e. “fake pig” treatment). In the first two months (15–59 days after the start of the experiment), cadavers caused significant increases of ammonium, nitrogen, phosphorous and potassium (p < 0.05) whereas nitrate significantly increased towards the end of the study (263–367 days; p < 0.05). Soil pH increased significantly at first and then decreased significantly at the end of the experiment. After one year, some markers returned to basal levels (i.e. not significantly different from control plots), whereas others were still significantly different. Based on these response patterns and in comparison with previous studies, we define three categories of chemical markers that may have the potential to date the time since death: early peak markers (EPM), late peak markers (LPM) and late decrease markers (LDM). The marker categories will enhance our understanding of soil processes and can be highly useful when changes in soil chemistry are related to changes in the composition of soil organism communities. For actual casework further studies and more data are necessary to refine the marker categories along a more precise timeline and to develop a method that can be used in court.