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Mitchell, Edward
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Mitchell, Edward
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Professeur ordinaire
Email
edward.mitchell@unine.ch
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Voici les éléments 1 - 10 sur 21
- PublicationAccès libreMorphological 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 libreAssessing the ecological value of small testate amoebae (<45 μm) in New Zealand peatlands(2019)
- PublicationAccès libreTaxonomic and functional traits responses of Sphagnum peatland testate amoebae to experimentally manipulated water table(2018)
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Testate amoebae are good indicators of surface moisture conditions in Sphagnum peatlands and are routinely used in palaeoecology. Their shells (tests), on which identification is based, can also be used to define functional traits and thus to infer changes in ecosystem functioning.
We investigated the response of testate amoeba communities to manipulated water table depth (wet: −4 cm, intermediate: −15 cm, and dry: −25 cm) over time (seven time points, 19 months) using mesocosms by comparing two approaches: community structure and functional traits responses, using a combination of morphological (biovolume, length, aperture size and position) and physiological (mixotrophy/heterotrophy, shell material) traits.
This is the first study investigating the effect of water table depth on testate amoeba assemblages over time using a mesocosm approach. Taxonomical and functional approaches showed similar response patterns, confirming that water level acted as a strong environmental filter. After one year Hyalosphenia papilio decreased in the dry treatment, and the community structure shifted towards a dominance of dry indicators (Nebela tincta complex, Corythion dubium, Euglypha compressa) and the selected functional traits (smaller, heterotrophic, compressed species, with a ventral aperture) corresponded to drought adaptations.
In line with recent observational and transfer function studies exploring the use of testate amoebae functional traits, our experimental results illustrate how well-selected traits could be used to monitor the impact of present and past climatic changes on Sphagnum peatlands. - PublicationAccès librePalaeoecology of Sphagnum riparium (Ångström) in Northern Hemisphere peatlands: Implications for peatland conservation and palaeoecological research(2018)
; - PublicationAccès libreTowards a Holarctic synthesis of peatland testate amoeba ecology: Development of a new continental-scale palaeohydrological transfer function for North America and comparison to European data(2018)
; - PublicationAccès libreResponse of Sphagnum Testate Amoebae to Drainage, Subsequent Re-wetting and Associated Changes in the Moss Carpet: Results from a Three Year Mesocosm Experiment(2017)
; ; Sphagnum peatlands represent a globally significant pool and sink of carbon but these functions are threatened by ongoing climate change. Testate amoebae are useful bioindicators of hydrological changes, but little experimental work has been done on the impact of water table changes on communities.
Using a mesocosm experimental setting that was previously used to assess the impact of drought disturbance on communities and ecosystem processes with three contrasted water table positions: wet (–4 cm), intermediate (–15 cm) and dry (–25 cm), we studied the capacity of testate amoeba communities to recover when the water table was kept at –10 cm for all plots. The overall experiment lasted three years. We assessed the taxonomic and functional trait responses of testate amoeba communities. The selected traits were hypothesised to be correlated to moisture content (response traits: shell size, aperture position) or trophic role (effect traits: mixotrophy, aperture size controlling prey range).
During the disturbance phase, the mixotrophic species Hyalosphenia papilio dominated the wet and intermediate plots, while the community shifted to a dominance of “dry indicators” (Corythion dubium, Nebela tincta, Cryptodifflugia oviformis) and corresponding traits (loss of mixotrophy, and dominance of smaller taxa with ventral or ventral-central aperture) in dry plots. During the recovery phase we observed two contrasted trends in the previously wet and intermediate plots: communities remained similar where the Sphagnum carpet remained intact but species and traits indicators of drier conditions increased in plots where it had degraded. In the former dry plots, indicators and traits of wet conditions increased by the end of the experiment.
This is one of the first experiment simulating a disturbance and subsequent recovery in ex-situ mesocosms of Sphagnum peatland focusing on the response of testate amoebae community structure as well as functional traits to water table manipulation. The results generally confirmed that testate amoebae respond within a few months to hydrological changes and thus represent useful bioindicators for assessing current and past hydrological changes in Sphagnum peatlands. - PublicationAccès libreComparative ecology of vascular plant, bryophyte and testate amoeba communities in four Sphagnum peatlands along an altitudinal gradient in Switzerland(2015-3-4)
; - PublicationAccès libreEnvironmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa;Arcellinida; Hyalospheniidae)(2015)
; ; ; Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community com-position estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matches the ratio of mitochondria and that within closely-related taxa the density of mitochondria per unit biovolume is approximately constant. Further developments of this metabarcoding approach including quantifying the mitochondrial density among closely-related taxa, experiments on other taxonomic groups and using high throughput sequencing should make if possible to quantitatively estimate community composition of different groups, which would be invaluable for microbial food webs studies. - PublicationAccès libreComparative ecology of vascular plant, bryophyte and testate amoeba communities in four Sphagnum peatlands along an altitudinal gradient in Switzerland(2015)
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We compared the relationships of testate amoebae, bryophytes, and vascular plants with soil temperature, water table depth, micro-habitats and the carbon and nitrogen content of Sphagnum mosses in four peatlands along a 1300 m altitudinal gradient in Switzerland. We used the full diversity of vascular plants and bryophyte but only a selection of ten easily identifiable testate amoeba morpho-taxa (i.e. species or species-complexes).
Indirect and direct gradient ordinations, multiple factor analysis (MFA) and transfer function models for inferring water table depth showed that a selection of ten testate amoeba taxa are more powerful (% variance explained in RDA) and accurate (discrimination among habitats) indicators of local conditions (micro-habitat type, water table depth and Sphagnum C/N ratio) than the vegetation (vascular plants and bryophytes either individually or combined and considering the full diversity).
Our study showed that a limited list of ten easily identifiable testate amoeba taxa have higher bioindication value than the full bryophytes and vascular plants. Furthermore, testate amoebae can be analyzed on samples collected at any season (accessibility allowing and if precise sampling sites are well marked) – a clear advantage for biomonitoring and can be used to infer past changes from the peat record at the same taxonomic resolution. This simple approach could therefore be very useful for biomonitoring of peatlands. - PublicationAccès libreThe Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems(2015)
; The terrestrial cycling of Si is thought to have a large influence on the terrestrial and marine primary production, as well as the coupled biogeochemical cycles of Si and C. Biomineralization of silica is widespread among terrestrial eukaryotes such as plants, soil diatoms, freshwater sponges, silicifying flagellates and testate amoebae. Two major groups of testate (shelled) amoebae, arcellinids and euglyphids, produce their own silica particles to construct shells. The two are unrelated phylogenetically and acquired biomineralizing capabilities independently. Hyalosphenids, a group within arcellinids, are predators of euglyphids.We demonstrate that hyalosphenids can construct shells using silica scales mineralized by the euglyphids. Parsimony analyses of the current hyalosphenid phylogeny indicate that the ability to “steal” euglyphid scales is most likely ancestral in hyalosphenids, implying that euglyphids should be older than hyalosphenids. However, exactly when euglyphids arose is uncertain. Current fossil record contains unambiguous euglyphid fossils that are as old as 50 million years, but older fossils are scarce and difficult to interpret. Poor taxon sampling of euglyphids has also prevented the development of molecular clocks. Here, we present a novel molecular clock reconstruction for arcellinids and consider the uncertainties due to various previously used calibration points. The new molecular clock puts the origin of hyalosphenids in the early Carboniferous (~370 mya). Notably, this estimate coincides with the widespread colonization of land by Si-accumulating plants, suggesting possible links between the evolution of Arcellinid testate amoebae and the expansion of terrestrial habitats rich in organic matter and bioavailable Si.
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