Mitchell, Edward

2015-3-4, Koenig, Isabelle, Feldmeyer-Christe, Elizabeth, Mitchell, Edward

Monitoring tools are needed to assess changes in peatland biotic communities and ecosystem functions inresponse to on-going climate and other environmental changes. Although the responses of soil organismsand plants to ecological gradients and perturbations do not always correlate, peatland monitoring ismainly based on vegetation surveys. Testate amoebae, a group of protists, are important contributorsto carbon and nitrogen cycling in organic soils and are useful bioindicators in peatland ecology andpaleoecology. There is however little comparative data on the value of testate amoebae, vascular plantsand bryophytes as bioindicators of micro-environmental gradients in peatlands.We compared the relationships of testate amoebae, bryophytes, and vascular plants with soil tempera-ture, water table depth, micro-habitats and the carbon and nitrogen content of Sphagnum mosses in fourpeatlands along a 1300 m altitudinal gradient in Switzerland. We used the full diversity of vascular plantsand bryophyte but only a selection of ten easily identifiable testate amoeba morpho-taxa (i.e. species orspecies-complexes).Indirect and direct gradient ordinations, multiple factor analysis (MFA) and transfer function modelsfor 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 andbryophytes 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 bioindi-cation value than the full bryophytes and vascular plants. Furthermore, testate amoebae can be analyzedon 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 thesame taxonomic resolution. This simple approach could therefore be very useful for biomonitoring ofpeatlands.

2009, Payne, Richard J., Mitchell, Edward

Testate amoebae are increasingly used in ecological and palaeoecological studies of wetlands. To characterise the amoeba community a certain number of individuals need to be counted under the microscope. To date, most studies have aimed for 150 individuals, but that sample size is not based on adequate evidence. When testate amoeba concentrations are low, it can be difficult or impossible to reach this total. The impacts of lower count totals have never been seriously scrutinised. We investigated the impact of count size on number of taxa identified, quantitative inferences of environmental variables and the strength of the links between amoebae and environmental data in the context of predicting depth to water table. Low counts were simulated by random selection of individuals from four existing datasets. Results show progressively diminishing returns by all criteria as count size increases from low numbers to counts of 150. A higher count is required to identify all taxa than to adequately characterise the community for transfer function inference. We suggest that in most cases, it will be a more efficient use of time to count a greater number of samples to a lower count. While a count of 50 individuals may be sufficient for some samples from some sites we recommend that counts of 100 individuals should be sufficient for most samples. Counts need only be increased to 150 or more where the aim is to identify relatively minor, but still potentially ecologically relevant community changes. This approach will help reduce lack of replication and low resolution, which are common limitations in testate amoeba-based palaeoecological and ecological studies.

2008, Lamentowicz, Mariucz, Cedro, A., Gałka, M., Goslar, T., Miotk-Szpiganowicz, G., Mitchell, Edward, Pawlyta, J.

The Baltic coast of Northern Poland is an interesting region for palaeoclimatic studies because of the mixed oceanic and continental climatic influences and the fact that the dominance of one or the other of these two influences might have changed over time. Also, unlike many more intensively studied regions of Europe, human impact in the region was rather limited until the 19th century. We present a 1200-year high-resolution record from Stążki mire, an ombrotrophic bog located 35 km from the Baltic Sea coast. Using testate amoebae, stable isotopes (δ¹³C) of Sphagnum stems, pollen, plant macrofossils and dendroecological analyses, our aims were to: 1) reconstruct the last millennium palaeoenvironment in the study site and its surroundings, 2) identify the major wet–dry shifts, 3) determine if those events correlate with climate change and human impact, 4) assess the resilience of the Baltic bog ecosystem following human impact, and 5) compare the palaeo-moisture signal from the Baltic coast with records from more oceanic regions. Two dry periods are inferred at AD 1100–1500 and 1650–1900 (–2005). The first dry shift is probably climate-driven as pollen record shows little evidence of human indicators. The second dry shift can be related to local peat exploitation of the mire. In the 20th century additional limited drainage took place and since ca. AD 1950 the mire has been recovering. From 1500 AD onwards all proxies indicate wetter condition. The beginning of this wet shift occurred during the Little Ice Age and may therefore be a climatic signal. The macrofossil data show that Sphagnum fuscum dominated the pristine mire vegetation but then declined and finally disappeared at ca. AD 1900. This pattern is comparable with the timing of extinction of Sphagnum austinii (Sphagnum imbricatum) in the UK. This study illustrates the value of high-resolution multi-proxy studies of peat archives to assess the magnitude of anthropogenic land-use changes. This study presents the first direct comparison of testate amoebae and stable isotope data from the same core. The two proxies correlate significantly throughout the record and most strongly for the latter part of the record when most of the variability was recorded.

, Koenig, Isabelle, Feldmeyer-Christe, Elizabeth, Mitchell, Edward

Monitoring tools are needed to assess changes in peatland biotic communities and ecosystem functions in response to on-going climate and other environmental changes. Although the responses of soil organisms and plants to ecological gradients and perturbations do not always correlate, peatland monitoring is mainly based on vegetation surveys. Testate amoebae, a group of protists, are important contributors to carbon and nitrogen cycling in organic soils and are useful bioindicators in peatland ecology and paleoecology. There is however little comparative data on the value of testate amoebae, vascular plants and bryophytes as bioindicators of micro-environmental gradients in peatlands.
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.

2012, Gomaa, Fatma, Mitchell, Edward, Lara, Enrique

Les recherches en phylogénie moléculaire ont considérablement avancé notre compréhension des relations entre eucaryotes. Les classifications récentes placent les protistes amoeboides dans plus de 30 lignées au sein des Amoebozoa, Rhizaria, Stramenopiles, Opisthokonta, et Excavata. Parmi celles-ci, certaines branches ont développé des thèques ou coquilles, souvent ornementées et caractéristiques qui ont été utilisées depuis plus de 150 ans comme caractère diagnostique pour décrire plus de 2000 espèces. Les thécamoebiens sont caractérisés par des pseudopodes lobés ou filamenteux et une thèque à une chambre pouvant être agglutinée, protéinique, calcaire ou siliceuse. L’acquisition de la thèque s’est faite plusieurs fois de manière indépendante au cours de l’évolution. De plus, et malgré la longue tradition de recherche en taxonomie sur les thécamoebiens, les relations entre les différents taxons demeurent largement non-résolue, l’affiliation phylogénétique de certains genres restant inconnue.
Le but de cette thèse était de construire une phylogénie fiable du plus grand ordre d’amibes, les Arcellinida, en utilisant des séquences du gène SSU rRNA et des analyses par microscopie électronique (chapitres 2 et 5). Les résultats révèlent des contradictions drastiques avec la taxonomie traditionnelle. Le genre Difflugia, le plus grand genre des Arcellinida, n’est pas monophylétique et est divisé en deux clades bien distincts regroupant respectivement les espèces allongées/pyriformes et les espèces globulaires. Le genre Netzelia est phylogénétiquement proche des Difflugia globulaires malgré les différences de structures de leur thèque.
Par ailleurs, les Arcellinida démontrent un conservatisme morphologique marqué; les types morphologiques similaires correspondant possiblement à des taxons génétiquement très distants. Nous démontrons la possibilité d’une évolution morphologique rapide an sein de ce groupe. Difflugia tuberspinifera, une espèce endémique d’Asie possède deux morpho-types (avec et sans cornes) possédant des séquences similaire du gène SSU rRNA gene (99.8%) et des introns et insertions identiques, mais pouvant toutefois être discriminés sur la base de leur séquences. Ceci suggère une évolution morphologique récente, possiblement liée à des facteurs écologiques à déterminer.
Nous avons déterminé la position phylogénétique des deux genresincertae sedis bien connus de la famille des Amphitrematidae, Amphitrema et Archerella (chapitre 3), qui de manière surprenante sont apparentés Labyrinthulomycetes (Stramenopiles), formant ainsi un nouveau clade de thécamoebiens indépendants des autres (c.à.d. Amoebozoa & Rhizaria). Cette étude illustre également que la taxonomie et la phylogénie des protistes en général est d’une importance cruciale pour comprendre l’évolution de la diversité des eucaryotes.
Les thécamoebiens forment souvent des associations avec les organismes photosynthétiques dont l’identité demeure toutefois inconnue. Nous avons identifié les symbiontes de quatre thécamoebiens différents sur la base du gène chloroplastique rbcL (ribulose-1, 5-diphosphate carboxylase/oxygénase grande sub-unité) utilisé comme gène de barcoding. La majorité des symbiontes de thécamoebiens ont pu être raisonnablement associés à une seule espèce, malgré le fait que leurs hôtes étaient taxonomiquement très distants. Fait intéressant, les Chlorelles symbiontes des thécamoebiens étaient très proches de Chlorella variabilis ainsi que des symbiontes de Paramecium bursaria. A la lumière de ces résultats, nous proposons un scénario d’évolution de l’association entre hôtes hétérotrophes et leur symbiontes photosynthétiques.
De manière générale, ma thèse illustre qu’une phylogénie fiable des thécamobiens basée sur les approches morphologiques et moléculaires est non-seulement un prérequis essentiel pour comprendre leur évolution, mais contribuera aussi à résoudre des débats concernant leur diversité et leur biogéographie, et en augmentera en général leur utilisé comme groupe modèle d’organismes pour les recherches en écologie appliquée., Molecular phylogenetic studies have considerably advanced our understanding of the relationships among eukaryotes. In recent classification schemes, amoeboid protists appeared scattered in more than 30 lineages within Amoebozoa, Rhizaria, Stramenopiles, Opisthokonta, and Excavata. Amongst these, some branches tended to develop a test or shell, often ornamented and conspicuous, which has been used for more than 150 years as a diagnostic character to describe more than 2000 species. Testate amoebae are characterized by lobose or filose pseudopodia and one chamber shell that can be agglutinated, proteinaceous, calcareous or siliceous. The acquisition of the shell happened several times independently in the course of evolution. Furthermore, and in spite of the long taxonomic tradition in testate amoebae research, the relationships between the different taxa remained largely unresolved, some genera remaining still without known phylogenetic affiliation.
In this thesis, we aimed at constructing a reliable phylogeny of the largest testate amoebae order, the Arcellinida, using SSU rRNA gene sequences and scanning electron microscopy analyses (chapters 2 and 5). Our results revealed drastic contradictions with traditional taxonomy. Genus Difflugia, the largest Arcellinid genus appeared not monophyletic, and divided in two major and distantly related clades that grouped respectively the elongated/pyriform and the globular species. Genus Netzelia was phylogenetically very closely related to the globular Difflugia despite the inconsistencies in their shell structure.
In addition, Arcellinida tended to show an important morphological conservatism, and closely related morphologies can possibly hide important genetic distances. We also demonstrated that fast morphological evolution could also be possible in this group. Difflugia tuberspinifera, an Asian endemic species had two morphotypes (spiny and spineless) which shared highly similar SSU rRNA gene sequences (99.8%) and identical introns and insertions, but could be nevertheless discriminated on the base of their sequences. This result suggested a recent morphological evolution, presumably due to some differing ecological factors that still need to be clarified.
We determined also the phylogenetic position of two well known incertae sedis genera of family Amphitremida, Amphitrema and Archerella (chapter 3), which appeared surprisingly to be related to Labyrinthulomycetes (Stramenopiles), thus forming a new clade of testate amoebae independent from others (i.e Amoebozoa, Rhizaria). This study also illustrated that accurate taxonomy and phylogeny of protists in general is of crucial important for understanding the evolution and diversity of eukaryotes.
Testate amoebae have been also often found in association with some photosynthetic organisms whose identity remained unknown. We identified the symbionts of four different testate amoeba species using the chloroplastic gene rbcL (ribulose-1, 5-diphosphate carboxylase/oxygenase large subunit) as a barcoding gene. The majority of testate amoeba symbionts formed a consistent group with very few sequence diversity that could be reasonably associated to a single species, in spite of the fact that host species were taxonomically distantly related. Interestingly, testate amoebae Chlorella symbionts were very closely related to Chlorella variabilis and to Paramecium bursaria Chlorella symbionts. In the light of these results, we proposed a general evolutionary scenario for association between heterotrophic hosts and their photosynthetic symbionts.
Overall, my thesis illustrated that the reliable phylogeny of testate amoebae based on molecular and morphological approaches is not only essential prerequisite for understanding their evolution, but it also will contribute in resolving debates concerning their diversity and biogeography, and in general will increase their utility as a model group of organisms for applied ecological research.

2008, Mitchell, Edward, Payne, Richard J., Lamentowicz, Mariucz

Testate amoebae are now commonly used in paleoenvironmental studies but little is known of their taphonomy. There is some experimental evidence for differential preservation of some testate amoeba shell types over others, but it is unclear what, if any impact this has on palaeoenvironmental reconstruction. To investigate this issue we looked at palaeoecological evidence for the preservation of different shell types. We then investigated the possible impact of selective preservation on quantitative palaeoenvironmental inference. We first used existing palaeoecological data sets to assess the vertical patterns of relative abundance in four testate amoeba shell types: (1) shells made of secreted biosilica plates (idiosomes, e.g. Euglypha), (2) idiosomes with thick organic coating (Assulina), (3) proteinaceous shells (e.g. Hyalosphenia), (4) shells built from recycled organic or mineral particles (xenosomes) (e.g. Difflugia, Centropyxis). In three diagrams a clear pattern of decay was only observed for the idiosome type. In order to assess the implications of differential preservation of testate amoeba taxa for paleoenvironmental reconstruction we then carried out simulations using three existing transfer functions and a wide range of scenarios, downweighting different test categories to represent the impact of selective test decomposition. Simulation results showed that downweighting generally reduced overall model performance. However downweighting a shell type only produced a consistent directional bias in inferred water table depth where that shell type is both dominant and shows a clear preference along the ecological gradient. Applying a scenario derived from previous experimental work did not lead to significant difference in inferred water table. Our results show that differential shell preservation has little impact on paleohydrological reconstruction from Sphagnum-dominated peatlands. By contrast, for the minerotrophic peatlands data-set loss of idiosome tests leads to consistent underestimation of water table depth. However there are few studies from fens and it is possible that idiosome tests are not always dominant, and/or that differential decomposition is less marked than in Sphagnum peatlands. Further work is clearly needed to assess the potential of testate amoebae for paleoecological studies of minerotrophic peatlands.

, Mitchell, Edward, Lamentowicz, Mariusz, Payne, Richard J, Mazei, Yuri

Sound taxonomy is a major requirement for quantitative environmental reconstruction using biological data. Transfer function performance should theoretically be expected to decrease with reduced taxonomic resolution. However for many groups of organisms taxonomy is imperfect and species level identification not always possible. We conducted numerical experiments on five testate amoeba water table (DWT) transfer function data sets. We sequentially reduced the number of taxonomic groups by successively merging morphologically similar species and removing inconspicuous species. We then assessed how these changes affected model performance and palaeoenvironmental reconstruction using two fossil data sets. Model performance decreased with decreasing taxonomic resolution, but this had only limited effects on patterns of inferred DWT, at least to detect major dry/wet shifts. Higher-resolution taxonomy may however still be useful to detect more subtle changes, or for reconstructed shifts to be significant.

2010, Heger, Thierry J., Mitchell, Edward, Todorov, Milcho, Golemansky, Vassil, Lara, Enrique, Leander, Brian S., Pawlowski, Jan

Marine and freshwater ecosystems are fundamentally different regarding many biotic and abiotic factors. The physiological adaptations required for an organism to pass the salinity barrier are considerable. Many eukaryotic lineages are restricted to either freshwater or marine environments. Molecular phylogenetic analyses generally demonstrate that freshwater species and marine species segregate into different sub-clades, indicating that transitions between these two environments occur only rarely in the course of evolution. It is, however, unclear if the transitions between freshwater and environments characterized by highly variable salinities, such as the marine supralittoral zone, are also infrequent. Here, we use testate amoebae within the Euglyphida to assess the phylogenetic interrelationships between marine supralittoral and freshwater taxa. Euglyphid testate amoebae are mainly present in freshwater habitats but also occur in marine supralittoral environments. Accordingly, we generated and analyzed partial SSU rRNA gene sequences from 49 new marine/supralittoral and freshwater Cyphoderiidae sequences, 20 sequences of the Paulinellidae, Trinematidae, Assulinidae, and Euglyphidae families as well as 21 GenBank sequences of unidentified taxa derived from environmental PCR surveys. Both the molecular and morphological data suggest that the diversity of Cyphoderiidae is strongly underestimated. The results of our phylogenetic analyses demonstrated that marine supralittoral and freshwater euglyphid testate amoeba species are segregated into distinct sub-clades, suggesting that transitions between these two habitats occurred only infrequently.

2008, Mitchell, Edward, Charman, Daniel J., Warner, Barry G.

Testate amoebae are an abundant and diverse polyphyletic group of shelled protozoa living in aquatic to moist habitats ranging from estuaries to lakes, rivers, wetlands, soils, litter, and moss habitats. Owing to the preservation of shells in sediments, testate amoebae are useful proxy indicators complementary to long-established indicators such as pollen and spores or macrofossils. Their primary use to date has been for inferring past moisture conditions and climate in ombrotrophic peatlands and, to a lesser extent, to infer pH in peatlands and the trophic or nutrient status of lakes. Recent research on these organisms suggests other possible uses in paleoecology and ecology such as sea-level reconstruction in estuarine environments, as indicators of soil or air pollution, and monitoring recovery of peatland. We review the past and present use of testate amoebae, the challenges in current research, and provide some ideas on future research directions.

, Lahr, Daniel J.G, Bosak, Tanja, Lara, Enrique, Mitchell, Edward

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.