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  • Publication
    Métadonnées seulement
    Microbial eukaryote communities from Patagonian-Antarctic gradient of lakes evidence robust biogeographical patterns
    (2016-9-30)
    Schiaffino, M. Romina
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    ; ;
    Balagué, Vanessa
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    ; ;
    Massana, Ramon
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    Izaguirre, Irina
    Microbial eukaryotes play important roles in aquatic ecosystem functioning. Unravelling their distribution patterns and biogeography provides important baseline information to infer the underlying mechanisms that regulate the biodiversity and complexity of eco- systems. We studied the distribution patterns and factors driving diversity gradients in microeukaryote communities (total, abundant, uncommon and rare community composition) along a latitudinal gradient of lakes distributed from Argentinean Patagonia to Maritime Antarctica using both denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (Illumina HiSeq). DGGE and abundant Illumina operational taxonomic units (OTUs) showed both decreasing richness with latitude and significant differences between Patagonian and Antarctic lakes communities. In contrast, total richness did not change significantly across the latitudinal gradient, although evenness and diversity indices were significantly higher in Patagonian lakes. Beta-diversity was characterized by a high species turnover, influenced by both environmental and geographical descriptors, although this pattern faded in the rare community. Our results suggest the co-existence of a ‘core biosphere’ containing reduced number of abundant/dominant OTUs on which classical ecological rules apply, together with a much larger seedbank of rare OTUs driven by stochastic and reduced dispersal processes. These findings shed new light on the biogeographical patterns and forces structuring inland microeukaryote composition across broad spatial scales.
  • Publication
    Accès libre
    Mycamoeba gemmipara nov. gen., nov. sp., the First Cultured Member of the Environmental Dermamoebidae Clade LKM74 and its Unusual Life Cycle
    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
    Métadonnées seulement
    High-throughput sequencing reveals diverse oomycete communities in oligotrophic peat bog micro-habitat
    (2016-4-21) ; ;
    Steciow, Mónica M.
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    Noelia, Paredes
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    Tomasz, Oszako
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    Oomycete diversity has been generally underestimated, despite their ecological and economic importance. Surveying unexplored natural ecosystems with up-to-date molecular diversity tools can reveal the existence of unsuspected organisms. Here, we have explored the molecular diversity of five microhabitats located in five different oligotrophic peat bogs in the Jura Mountains using a high-throughput sequencing approach (Illumina HiSeq 2500). We found a total of 34 different phylotypes distributed in all major oomycete clades, and comprising sequences affiliated to both well-known phylotypes and members of undescribed, basal clades. Parasitic species, including obligate forms were well-represented, and phylotypes related to highly damaging invasive pathogens (Aphanomyces astaci: X1100 and Saprolegnia parasitica: X1602) were retrieved. Microhabitats differed significantly in their community composition, and many phylotypes were strongly affiliated to free water habitats (pools). Our approach proved effective in screening oomycete diversity in the studied habitat, and could be applied systematically to other environments and other fungal and fungal-like groups.
  • Publication
    Métadonnées seulement
    Response of forest soil euglyphid testate amoebae (Rhizaria: Cercozoa) to pig cadavers assessed by high-throughput sequencing
    Decomposing cadavers modify the soil environment, but the effect on soil organisms and especially on soil protists is still poorly documented. We conducted a 35-month experiment in a deciduous forest where soil samples were taken under pig cadavers, control plots and fake pigs (bags of similar volume as the pigs). We extracted total soil DNA, amplified the SSU ribosomal RNA (rRNA) gene V9 region and sequenced it by Illumina technology and analysed the data for euglyphid testate amoebae (Rhizaria: Euglyphida), a common group of protozoa known to respond to micro- environmental changes. We found 51 euglyphid operational taxonomic units (OTUs), 45 of which did not match any known sequence. Most OTUs decreased in abundance underneath cadavers between days 0 and 309, but some responded positively after a time lag. We sequenced the full-length SSU rRNA gene of two common OTUs that responded positively to cadavers; a phylogenetic analysis showed that they did not belong to any known euglyphid family. This study confirmed the existence of an unknown diversity of euglyphids and that they react to cadavers. Results suggest that metabarcoding of soil euglyphids could be used as a forensic tool to estimate the post-mortem interval (PMI) particularly for long-term (>2 months) PMI, for which no reliable tool exists.
  • Publication
    Métadonnées seulement
    Planktonic eukaryote molecular diversity: discrimination of minerotrophic and ombrotrophic peatland pools in Tierra del Fuego (Argentina)
    (2015-5-1) ; ;
    González Garraza, Gabriela
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    Quiroga, Maria Victoria
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    Mataloni, Gabriela
    We investigated the composition of the smallest size fraction (<3µm) of eukaryotic plankton communities of five pools located in the Rancho Hambre peat bog in Argentinean Tierra del Fuego with an IlluminaHiSeq massive sequencing approach applied to the v9 region of the eukaryotic SSU rRNA gene. Communities were generally dominated by chrysophytes, with a good representation of Perkinsea and Cercozoa clade NC-10. A community composition analysis performed using GUniFraC separated minerotrophic and ombrotrophic sites, reflecting perfectly the classification of the sites based on environmental data. However, this separation disappeared when more weight was given to abundant phylotypes, suggesting that subordinate phylotypes were responsible for site discrimination. The 5% best indicators for, respectively, minerotrophic and ombrotrophic environments were searched using an IndVal analysis. Among these, autotrophic taxa were more common in minerotrophic environments, whereas mixotrophic taxa represented best ombrotrophic water bodies. However, the ecological traits of many taxa have still not been determined, and still needs to be investigated for a better understanding of freshwater systems ecology.
  • Publication
    Accès libre
    Eight species in the Nebela collaris complex: Nebela gimlii (Arcellinida,Hyalospheniidae), a new species described from a Swiss raised bog
    We describe here a new species of sphagnicolous testate amoeba found abundantly in the forested part of the Le Cachot peatland (Jura Mountains, Neuchâtel, Switzerland) based on microscopical observations (LM, SEM). The new species, called Nebela gimlii was placed in a phylogenetic tree based on mitochondrial cytochrome oxidase sequences (COI), and branched robustly within the N. collaris complex next to the morphologically similar N. guttata and N. tincta. It is however genetically clearly distinct from these two species, and differs morphologically from them by its smaller size and stouter shape of the shell. This new species completes the phylogeny of the Nebela collaris species complex, with now eight species described, mostly from peatlands and acidic forest litter, and further demonstrates the existence of an unknown diversity within testate amoebae. Improving the taxonomy of testate amoebae in peatlands and clarifying the ecology of newly discovered species should make these organisms even more valuable as bioindicator and for palaeoecological reconstruction.
  • Publication
    Accès libre
    Soil protistology rebooted: 30 fundamental questions to start with
    Geisen, Stefan
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    Wilkinson, David M
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    Adl, Sina
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    Bonkowski, Michael
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    Brown, Matthew W
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    Fiore-Donno, Anna Maria
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    Jassey, Vincent E.J
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    Krashevska, Valentyna
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    Lahr, Daniel J.G
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    Marcisz, Katarzyna
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    Payne, Richard
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    Anderson, Roger O
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    Charman, Dan J
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    Ekelund, Flemming
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    Griffiths, Bryan S
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    Rønn, Regin
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    Smirnov, Alexey
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    Bass, David
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    Berney, Cédric
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    Blandenier, Quentin
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    Chatzinotas, Antonis
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    Clarholm, Marianne
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    Dunthorn, Micah
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    Feest, Alan
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    Fernández, Leonardo D
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    Foissner, Wilhelm
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    Gentekaki, Eleni
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    Hájek, Michal
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    Helder, Johannes
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    Jousset, Alexandre
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    Koller, Robert
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    Kumar, Santosh
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    La Terza, Antonietta
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    Lamentowicz, Mariusz
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    Mazei, Yuri
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    Santos, Susana S
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    Seppey, Christophe V.W
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    Spiegel, Frederick W
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    Walochnik, Julia
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    Winding, Anne
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    Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this, protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in soil studies. Recent methodological advances, particularly in molecular biology techniques, have made the study of soil protists more accessible, and have created a resurgence of interest in soil protistology. This ongoing revolution now enables comprehensive investigations of the structure and functioning of soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive review, we provide a synthesis of research gaps that should be prioritized in future studies of soil protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics that will establish soil protistology as a hub discipline connecting different fundamental and applied fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers in biology.
  • Publication
    Accès libre
    Microbial eukaryote communities exhibit robust biogeographical patterns along a gradient of Patagonian and Antarctic lakes
    Schiaffino, M. Romina
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    Fernández, Leonardo D
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    Balagué, Vanessa
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    Seppey, Christophe C. W
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    Massana, Ramon
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    Izaguirre, Irina
    Microbial eukaryotes play important roles in aquatic ecosystem functioning. Unravelling their distribution patterns and biogeography provides important baseline information to infer the underlying mechanisms that regulate the biodiversity and complexity of ecosystems. We studied the distribution patterns and factors driving diversity gradients in microeukaryote communities (total, abundant, uncommon and rare community composition) along a latitudinal gradient of lakes distributed from Argentinean Patagonia to Maritime Antarctica using both denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (Illumina HiSeq). DGGE and abundant Illumina operational taxonomic units (OTUs) showed both decreasing richness with latitude and significant differences between Patagonian and Antarctic lakes communities. In contrast, total richness did not change significantly across the latitudinal gradient, although evenness and diversity indices were significantly higher in Patagonian lakes. Beta-diversity was characterized by a high species turnover, influenced by both environmental and geographical descriptors, although this pattern faded in the rare community. Our results suggest the co-existence of a ‘core biosphere’ containing reduced number of abundant/dominant OTUs on which classical ecological rules apply, together with a much larger seedbank of rare OTUs driven by stochastic and reduced dispersal processes. These findings shed new light on the biogeographical patterns and forces structuring inland microeukaryote composition across broad spatial scales.
  • Publication
    Accès libre
    Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests
    Mahé, Frédéric
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    de Vargas, Colomban
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    Bass, David
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    Czech, Lucas
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    Stamatakis, Alexandros
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    Mayor, Jordan
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    Bunge, John
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    Sernaker, Sarah
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    Siemensmeyer, Tobias
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    Trautmann, Isabelle
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    Romac, Sarah
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    Berney, Cédric
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    Kozlov, Alexey
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    Seppey, Christophe V. W
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    Egge, Elianne
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    Wirth, Rainer
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    Trueba, Gabriel
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    Dunthorn, Micah
    High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms.
  • 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
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    Duckert, Clément
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    Heděnec, Petr
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    Hiltbrunner, Erika
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    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.