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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
    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
    Métadonnées seulement
    Ecology of testate amoebae in peatlands of central China and development of a transfer function for paleohydrological reconstruction
    (2013) ; ;
    Lamentowicz, Mariusz
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    Payne, Richard J.
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    Gu, Yansheng
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    Huang, Xianyu
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    Wang, Hongmei
    Testate amoebae are a diverse and abundant group of protozoa that constitute a large proportion of biomass in many ecosystems and probably fill important roles in ecosystem function. These microorganisms have attracted the interest of paleoecologists because the preserved shells of testate amoebae and their known hydrological preferences enable reconstruction of past hydrological change. In ombrotrophic peatlands, surface wetness reflects hydroclimate, so testate amoebae can play an important role in reconstruction of Holocene climate change. Previous studies, however, have been geographically restricted, mostly to North America and Europe. We studied the ecology of testate amoebae in peatlands from central China in relation to hydrology, pH and metal concentrations. We found that testate amoeba community structure was correlated with depth to water table (DWT) and that the hydrological preferences of species generally matched those of previous studies. We developed a weighted average DWT transfer function that enables prediction of water table depth with a cross-validated mean error of < 5 cm. Our results demonstrate the potential for using testate amoebae to reconstruct paleohydrology in China. Such studies could contribute to our understanding of Holocene climate changes in China, particularly regarding past Asian monsoon activity.
  • Publication
    Métadonnées seulement
    Using DNA-barcoding for sorting out protist species complexes: A case study of the Nebela tincta-collaris-bohemica group (Amoebozoa; Arcellinida, Hyalospheniidae)
    (2013) ;
    Gomaa, Fatma
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    Heger, Thierry J.
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    Species identification by means of morphology is often problematic in protists. Nebela tincta-collaris-bohemica (Arcellinida) is a species complex of small to medium-sized (ca. 100 mu m) testate amoebae common in peat bogs and forest soils. The taxonomic validity of characters used to define species within this group is debated and causes confusion in studies of biogeography, and applications in palaeoecology. We examined the relationship between morphological and genetic diversity within this species complex by combined analyses of light microscopy imaging and Cytochrome Oxidase Subunit 1(COI) sequences obtained from the same individual amoeba cells. Our goals were (1) to clarify the taxonomy and the phylogenetic relationships within this group, and (2) to evaluate if individual genotypes corresponded to specific morphotypes and the extent of phenotypic plasticity. We show here that small variations in test morphology that have been often overlooked by traditional taxonomy correspond to distinct haplotypes. We therefore revise the taxonomy of the group. We redefine Nebela tincta (Leidy) Kosakyan et Lara and N. collaris (Ehrenberg 1848) Kosakyan et Gomaa, change N. tincta var. rotunda Penard to N. rotunda (Penard 1890), describe three new species: N. guttata n. sp. Kosakyan et Lara, N. pechorensis n. sp. Kosakyan et Mitchell, and N. aliciae n. sp. Mitchell et Lara. (C) 2012 Elsevier GmbH. All rights reserved.
  • Publication
    Métadonnées seulement
    Relationships between testate amoeba communities and water quality in Lake Donghu, a large alkaline lake in Wuhan, China
    (2013) ; ; ;
    Gu, Yansheng
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    Wang, Hongmei
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    Cui, Yongde
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    Zhang, Xiaoke
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    The middle Yangtze Reach is one of the most developed regions of China. As a result, most lakes in this area have suffered from eutrophication and serious environmental pollution during recent decades. The aquatic biodiversity in the lakes of the area is thus currently under significant threat from continuous human activities. Testate amoebae (TA) are benthic (rarely planktonic) microorganisms characterized by an agglutinated or autogenous shell. Owing to their high abundance, preservation potential in lacustrine sediments, and distinct response to environmental stress, they are increasingly used as indicators for monitoring water quality and reconstructing palaeoenvironmental changes. However this approach has not yet been developed in China. This study presents an initial assessment of benthic TA assemblages in eight lakes of Lake Donghu in the region of Wuhan, China. Testate amoeba community structure was most strongly correlated to water pH. In more alkaline conditions, communities were dominated by Centropyxis aculeata, Difflugia oblonga, Pontigulasia compressa, Pon. elisa and Lesquereusia modesta. These results are consistent with previous studies and show that TA could be useful for reconstructing past water pH fluctuations in China. To achieve this, the next step will be to expand the database and build transfer function models.
  • Publication
    Métadonnées seulement
    The Revised Classification of Eukaryotes (vol 59, pg 429, 2012)
    (2013)
    Adl, Sina M.
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    Simpson, Alastair G. B.
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    Lane, Christopher E.
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    Lukes, Julius
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    Bass, David
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    Bowser, Samuel S.
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    Brown, Matthew W.
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    Burki, Fabien
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    Dunthorn, Micah
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    Hampl, Vladimir
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    Heiss, Aaron
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    Hoppenrath, M.
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    le Gall, Line
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    Lynn, Denis H.
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    McManus, Hilary
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    Mozley-Stanridge, Sharon E.
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    Parfrey, Laura Wegener
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    Pawlowski, Jan
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    Rueckert, Sonja
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    Shadwick, Laura
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    Schoch, Conrad L.
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    Smirnov, Alexey
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    Spiegel, Frederick W.
  • Publication
    Métadonnées seulement
    Amphitremida (Poche, 1913) Is a New Major, Ubiquitous Labyrinthulomycete Clade
    (2013)
    Gomaa, Fatma
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    Micro-eukaryotic diversity is poorly documented at all taxonomic levels and the phylogenetic affiliation of many taxa - including many well-known and common organisms - remains unknown. Among these incertae sedis taxa are Archerella flavum (Loeblich and Tappan, 1961) and Amphitrema wrightianum (Archer, 1869) (Amphitremidae), two filose testate amoebae commonly found in Sphagnum peatlands. To clarify their phylogenetic position, we amplified and sequenced the SSU rRNA gene obtained from four independent DNA extractions of A. flavum and three independent DNA extractions of A. wrightianum. Our molecular data demonstrate that genera Archerella and Amphitrema form a fully supported deep-branching clade within the Labyrinthulomycetes (Stramenopiles), together with Diplophrys sp. (ATCC50360) and several environmental clones obtained from a wide range of environments. This newly described clade we named Amphitremida is diverse genetically, ecologically and physiologically. Our phylogenetic analysis suggests that osmotrophic species evolved most likely from phagotrophic ancestors and that the bothrosome, an organelle that produces cytoplasmic networks used for attachment to the substratum and to absorb nutrients from the environments, appeared lately in labyrithulomycete evolution.
  • Publication
    Métadonnées seulement
    Time to regulate microbial eukaryote nomenclature
    (2012)
    Lahr, Daniel J. G.
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    Nomenclature of microbial eukaryotes has been historically relegated to secondary importance. This is a legacy of the traditional classification of life into the most studied multicellular forms (plants, fungi, and animals). Despite the revolution in an understanding of eukaryotic diversity and relationships that has been achieved as a result of the use of molecular techniques, the description of microbial eukaryote genera and species is more difficult today than in the past. Researchers are at liberty to choose between the botanical (in the traditional sense) and zoological codes of nomenclature, although there is no obligation to comply with either. We demonstrate that, by combining the foci of different nomenclature codes with the current knowledge of relationships, a large number of genera and species end up being regulated by two codes (Patterson's ambiregnal taxa) and, in some cases, may even be regulated by none. We briefly present historically proposed types of solutions to this problem, and propose that an elaboration of authoritative guidelines to regulate the nomenclature of microbial eukaryotes by the community of researchers is most appropriate at this time. Most importantly, we plead to the community of researchers to resolve this centuries old outstanding issue. (C) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, , .