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Singer, David

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Singer, David
Affiliation principale
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https://libra.unine.ch/handle/123456789/774

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  • Publication
    Accès libre
    Mycamoeba gemmipara nov. gen., nov. sp., the First Cultured Member of the Environmental Dermamoebidae Clade LKM74 and its Unusual Life Cycle
    (2016-8-20)
    Blandenier, Quentin 
    ;
    Seppey, Christophe 
    ;
    Singer, David 
    ;
    Vlimant, Michèle 
    ;
    Simon, Anaele 
    ;
    Duckert, Clément
    ;
    Lara, Enrique 
    Since the first environmental DNA surveys, entire groups of sequences called “environmental clades” did not have any cultured representative. LKM74 is an amoebozoan clade affiliated to Dermamoebidae, whose presence is pervasively reported in soil and freshwater. We obtained an isolate from soil that we assigned to LKM74 by molecular phylogeny, close related to freshwater clones. We described Mycamoeba gemmipara based on observations made with light- and transmission electron microscopy. It is an extremely small amoeba with typical lingulate shape. Unlike other Dermamoebidae, it lacked ornamentation on its cell membrane, and condensed chromatin formed characteristic patterns in the nucleus. M. gemmipara displayed a unique life cycle: trophozoites formed walled coccoid stages which grew through successive buddings and developed into branched structures holding cysts. These structures, measuring hundreds of micrometres, are built as the exclusive product of osmotrophic feeding. In order to demonstrate that M. gemmipara is a genuine soil inhabitant, we screened its presence in an environmental soil DNA diversity survey performed on an experimental setup where pig cadavers were left to decompose in soils in order to follow changes in eukaryotic communities. M. gemmipara was present in all samples, although related reads were uncommon underneath the cadaver.
  • Publication
    Accès libre
    High-throughput sequencing of litter and moss eDNA reveals a positive correlation between the diversity of Apicomplexa and their invertebrate hosts across alpine habitats
    Singer, David 
    ;
    Duckert, Clément
    ;
    Heděnec, Petr
    ;
    Lara, Enrique 
    ;
    Hiltbrunner, Erika
    ;
    Mitchell, Edward 
    A high diversity of Apicomplexa was recently found in tropical soils presumably reflecting the diversity of their invertebrate hosts, but such patterns have not been explored in colder regions. We analysed the diversity of Apicomplexa and their potential metazoan hosts in litter and mosses collected in 11 different alpine habitats using an eDNA metabarcoding approach. The abundance and diversity of Apicomplexa phylotypes and of their potential invertebrate hosts were positively correlated. This confirms that eDNA metabarcoding is a useful tool to explore the unknown biodiversity of free-living eukaryotes, as well as potential host-parasite interactions. Future studies should aim at describing this diversity using a combination of morphological and molecular approaches.
  • Publication
    Accès libre
    Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists
    Singer, David 
    ;
    Mitchell, Edward 
    ;
    Payne, Richard J
    ;
    Blandenier, Quentin 
    ;
    Duckert, Clément
    ;
    Fernández, Leonardo D
    ;
    Fournier, Bertrand 
    ;
    Hernández, Cristián E
    ;
    Granath, Gustaf
    ;
    Rydin, Håkan
    ;
    Bragazza, Luca
    ;
    Koronatova, Natalia G
    ;
    Goia, Irina
    ;
    Harris, Lorna I
    ;
    Kajukało, Katarzyna
    ;
    Kosakyan, Anush 
    ;
    Lamentowicz, Mariusz
    ;
    Kosykh, Natalia P
    ;
    Vellak, Kai
    ;
    Lara, Enrique 
    Recent studies show that soil eukaryotic diversity is immense and dominated by micro‐organisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to micro‐organisms. Major diversification events in multicellular organisms have often been attributed to long‐term climatic and geological processes, but the impact of such processes on protist diversity has received much less attention as their distribution has often been believed to be largely cosmopolitan. Here, we quantified phylogeographical patterns in Hyalosphenia papilio, a large testate amoeba restricted to Holarctic Sphagnum‐dominated peatlands, to test if the current distribution of its genetic diversity can be explained by historical factors or by the current distribution of suitable habitats. Phylogenetic diversity was higher in Western North America, corresponding to the inferred geographical origin of the H. papilio complex, and was lower in Eurasia despite extensive suitable habitats. These results suggest that patterns of phylogenetic diversity and distribution can be explained by the history of Holarctic Sphagnum peatland range expansions and contractions in response to Quaternary glaciations that promoted cladogenetic range evolution, rather than the contemporary distribution of suitable habitats. Species distributions were positively correlated with climatic niche breadth, suggesting that climatic tolerance is key to dispersal ability in H. papilio. This implies that, at least for large and specialized terrestrial micro‐organisms, propagule dispersal is slow enough that historical processes may contribute to their diversification and phylogeographical patterns and may partly explain their very high overall diversity.
  • Publication
    Accès libre
    Mycamoeba gemmipara nov. gen., nov. sp., the First Cultured Member of the Environmental Dermamoebidae Clade LKM74 and its Unusual Life Cycle
    Blandenier, Quentin 
    ;
    Seppey, Christophe V. W
    ;
    Singer, David 
    ;
    Vlimant, Michèle 
    ;
    Simon, Anaële
    ;
    Duckert, Clément
    ;
    Lara, Enrique 
    Since the first environmental DNA surveys, entire groups of sequences called “environmental clades” did not have any cultured representative. LKM74 is an amoebozoan clade affiliated to Dermamoebidae, whose presence is pervasively reported in soil and freshwater. We obtained an isolate from soil that we assigned to LKM74 by molecular phylogeny, close related to freshwater clones. We described Mycamoeba gemmipara based on observations made with light- and transmission electron microscopy. It is an extremely small amoeba with typical lingulate shape. Unlike other Dermamoebidae, it lacked ornamentation on its cell membrane, and condensed chromatin formed characteristic patterns in the nucleus. M. gemmipara displayed a unique life cycle: trophozoites formed walled coccoid stages which grew through successive buddings and developed into branched structures holding cysts. These structures, measuring hundreds of micrometres, are built as the exclusive product of osmotrophic feeding. To demonstrate that M. gemmipara is a genuine soil inhabitant, we screened its presence in an environmental soil DNA diversity survey performed on an experimental setup where pig cadavers were left to decompose in soils to follow changes in eukaryotic communities. Mycamoeba gemmipara was present in all samples, although related reads were uncommon underneath the cadaver.
  • Publication
    Accès libre
    En garde! Redefinition of Nebela militaris (Arcellinida, Hyalospheniidae) and erection of Alabasta gen. nov.
    Duckert, Clément
    ;
    Blandenier, Quentin 
    ;
    Kupferschmid, Fanny A. L
    ;
    Kosakyan, Anush 
    ;
    Mitchell, Edward 
    ;
    Lara, Enrique 
    ;
    Singer, David 
    Molecular data have considerably contributed to building the taxonomy of protists. Recently, the systematics of Hyalospheniidae (Amoebozoa; Tubulinea; Arcellinida) has been widely revised, with implications extending to ecological, biogeographical and evolutionary investigations. Certain taxa, however, still have an uncertain phylogenetic position, including the common and conspicuous species Nebela militaris. A phylogenetic reconstruction of the Hyalospheniidae using partial sequences of the mitochondrial Cytochrome Oxidase Subunit 1 (COI) gene shows that N. militaris does not belong to genus Nebela, but should be placed in its own genus. The morphological singularities (strongly curved pseudostome and a marked notch in lateral view) and phylogenetic placement of our isolates motivated the creation of a new genus: Alabasta gen. nov. Based on their morphology, we include in this genus Nebela kivuense and Nebela longicollis. We discuss the position of genus Alabasta within Hyalospheniidae, and the species that could integrate this new genus based on their morphological characteristics.