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Lara, Enrique

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Lara, Enrique
Affiliation principale
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https://libra.unine.ch/handle/123456789/360

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  • Publication
    Accès libre
    Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing
    (2020-9-18)
    Reczuga, Monika 
    ;
    Seppey, Christophe Victor William
    ;
    Mulot, Matthieu 
    ;
    Jassey, Vincent E.J.
    ;
    Buttler, Alexandre
    ;
    Slowinska, Sandra
    ;
    Slowinski, Michal
    ;
    Lara, Enrique 
    ;
    Lamentowicz, Mariusz
    ;
    Mitchell, Edward 
    Current projections suggest that climate warming will be accompanied by more frequent and severe drought events. Peatlands store ca. one third of the world’s soil organic carbon. Warming and drought may cause peatlands to become carbon sources through stimulation of microbial activity increasing ecosystem respiration, with positive feedback effect on global warming. Micro-eukaryotes play a key role in the carbon cycle through food web interactions and therefore, alterations in their community structure and diversity may affect ecosystem functioning and could reflect these changes. We assessed the diversity and community composition of Sphagnum-associated eukaryotic microorganisms inhabiting peatlands and their response to experimental drought and warming using high throughput sequencing of environmental DNA. Under drier conditions, micro-eukaryotic diversity decreased, the relative abundance of autotrophs increased and that of osmotrophs (including Fungi and Peronosporomycetes) decreased. Furthermore, we identified climate change indicators that could be used as early indicators of change in peatland microbial communities and ecosystem functioning. The changes we observed indicate a shift towards a more “terrestrial” community in response to drought, in line with observed changes in the functioning of the ecosystem.
  • 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
    (2020)
    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
    We are ready for faunistic surveys of bdelloid rotifers through DNA barcoding: the example of Sphagnum bogs of the Swiss Jura Mountains
    (2019)
    Fontaneto, Diego
    ;
    Eckert, Ester M
    ;
    Anicic, Nikoleta
    ;
    Lara, Enrique 
    ;
    Mitchell, Edward 
    The identification of biological diversity through DNA barcoding and metabarcoding of the organisms living in the field has the potential to revolutionise the way biological surveys and monitoring are performed. Yet, we still do not know if the current representativeness of the reference database of DNA sequence data is sufficient to allow such approaches. Here, we show that, at least for bdelloid rotifers (Metazoa; Rotifera; Bdelloidea) in Europe, current knowledge is ripe to perform such surveys. We show the results of an exercise performed on bdelloid rotifers in Sphagnum bogs of the Swiss Jura Mountain. The results of DNA-based identifications were rather consistent with the morphology-based identifications, and the few cases of mismatch could be used as a cautionary tale to avoid potential misinterpretations of results. The mismatches were due to cases of the closest match not being genetically very close, and to the occurrence of cryptic species., La identificación de la diversidad biológica a través de DNA barcoding y metabarcoding de los organismos en el medio ambiente tiene el potencial de revolucionar la forma en que se realizan los inventarios biológicos y el monitoreo. Sin embargo, todavía no se sabe si las bases de datos genéticos de referencia a disposición hoy en día son lo suficientemente representativas como para permitir tales enfoques. Aquí, mostramos que, al menos para los rotíferos bdelloideos (Metazoa; Rotifera; Bdelloidea) de Europa, el nivel de conocimiento es suficiente para realizar tales estudios. Mostramos los resultados de un ejercicio realizado sobre rotíferos bdelloideos en turberas de Sphagnum del Jura suizo. Los resultados de las identificaciones basadas en el ADN fueron bastante consistentes con las identificaciones basadas en la morfología, y los pocos casos de desajuste podrían utilizarse como una advertencia para evitar posibles interpretaciones erróneas de los resultados. Estos desajustes se debieron a que las secuencias más cercanas seguían alejadas de los organismos realmente encontrados y a la presencia de especies crípticas.
  • Publication
    Accès libre
    Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists
    (2019)
    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
    En garde! Redefinition of Nebela militaris (Arcellinida, Hyalospheniidae) and erection of Alabasta gen. nov.
    (2018)
    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.
  • Publication
    Accès libre
    NAD9/NAD7 (mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene): A new “Holy Grail” phylogenetic and DNA-barcoding marker for Arcellinida (Amoebozoa)?
    (2017)
    Blandenier, Quentin 
    ;
    Lara, Enrique 
    ;
    Mitchell, Edward 
    ;
    Alcantara, Daniel M.C
    ;
    Siemensma, Ferry J
    ;
    Todorov, Milcho
    ;
    Lahr, Daniel J.G
    Molecular phylogeny is an indispensable tool for assessing evolutionary relationships among protists. The most commonly used marker is the small subunit ribosomal RNA gene, a conserved gene present in many copies in the nuclear genomes. However, this marker is not variable enough at a fine-level taxonomic scale, and intra-genomic polymorphism has already been reported. Finding a marker that could be useful at both deep and fine taxonomic resolution levels seemed like a utopic dream. We designed Amoebozoa-specific primers to amplify a region including partial sequences of two subunits of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene (NAD9/NAD7). We applied them to arcellinids belonging to distantly related genera (Arcella, Difflugia, Netzelia and Hyalosphenia) and to Arcellinid-rich environmental samples to obtain additional Amoebozoa sequences. Tree topology was congruent with previous phylogenies, all nodes being highly supported, suggesting that this marker is well-suited for deep phylogenies in Arcellinida and perhaps Amoebozoa. Furthermore, it enabled discrimination of close-related taxa. This short genetic marker (ca. 250 bp) can therefore be used at different taxonomic levels, due to a fast-varying intergenic region presenting either a small intergenic sequence or an overlap, depending on the species.
  • Publication
    Accès libre
    A contribution to the phylogeny of agglutinating Arcellinida (Amoebozoa) based on SSU rRNA gene sequences
    (2017)
    Gomaa, Fatma
    ;
    Lahr, Daniel J. G
    ;
    Todorov, Milcho
    ;
    Li, Jingchun
    ;
    Lara, Enrique 
    Arcellinid testate amoebae include a wide variety of amoeboid organisms whose test (shell) varies in shape, composition and size. A decade ago, we initiated molecular phylogenetic analyses based on SSU rRNA gene sequences and a taxonomic revision of Arcellinida. However, many lineages within Arcellinida still lack molecular data, and the phylogeny of this group is largely incomplete. In this study, we obtained SSU rRNA gene sequences from seven taxa, of which six have agglutinated shell (Difflugia oblonga, D. labiosa, D. gramen, Mediolus corona, Netzelia wailesi, and N. tuberculata), and one has an entirely proteinaceous shell (Arcella intermedia). All species but Difflugia oblonga branched within the recently erected suborder Sphaerothecina, confirming the synapomorphic value of an oviform or discoid shell. Thus, we propose that species with an oviform or discoid shell currently classified within genus Difflugia must be transferred to other genera, thus continuing the process of taxonomic revision of genus Difflugia, the largest Arcellinida genus. We therefore transferred the current and the previously sequenced oviform Difflugia spp. to Netzelia spp., based on the shared globular/oviform shell shape and their monophyly. Another species, D. labiosa, formed an independent lineage that branched as a sister clade to Arcella spp.; based on the shell morphology and their phylogenetic position, we considered D. labiosa as incertae sedis.
  • Publication
    Accès libre
    Mycamoeba gemmipara nov. gen., nov. sp., the First Cultured Member of the Environmental Dermamoebidae Clade LKM74 and its Unusual Life Cycle
    (2017)
    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
    Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests
    (2017)
    Mahé, Frédéric
    ;
    de Vargas, Colomban
    ;
    Bass, David
    ;
    Czech, Lucas
    ;
    Stamatakis, Alexandros
    ;
    Lara, Enrique 
    ;
    Singer, David 
    ;
    Mayor, Jordan
    ;
    Bunge, John
    ;
    Sernaker, Sarah
    ;
    Siemensmeyer, Tobias
    ;
    Trautmann, Isabelle
    ;
    Romac, Sarah
    ;
    Berney, Cédric
    ;
    Kozlov, Alexey
    ;
    Mitchell, Edward 
    ;
    Seppey, Christophe V. W
    ;
    Egge, Elianne
    ;
    Lentendu, Guillaume 
    ;
    Wirth, Rainer
    ;
    Trueba, Gabriel
    ;
    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
    Soil protistology rebooted: 30 fundamental questions to start with
    (2017)
    Geisen, Stefan
    ;
    Mitchell, Edward 
    ;
    Wilkinson, David M
    ;
    Adl, Sina
    ;
    Bonkowski, Michael
    ;
    Brown, Matthew W
    ;
    Fiore-Donno, Anna Maria
    ;
    Heger, Thierry 
    ;
    Jassey, Vincent E.J
    ;
    Krashevska, Valentyna
    ;
    Lahr, Daniel J.G
    ;
    Marcisz, Katarzyna
    ;
    Mulot, Matthieu 
    ;
    Payne, Richard
    ;
    Singer, David 
    ;
    Anderson, Roger O
    ;
    Charman, Dan J
    ;
    Ekelund, Flemming
    ;
    Griffiths, Bryan S
    ;
    Rønn, Regin
    ;
    Smirnov, Alexey
    ;
    Bass, David
    ;
    Belbahri, Lassaâd 
    ;
    Berney, Cédric
    ;
    Blandenier, Quentin 
    ;
    Blandenier, Quentin
    ;
    Chatzinotas, Antonis
    ;
    Clarholm, Marianne
    ;
    Dunthorn, Micah
    ;
    Feest, Alan
    ;
    Fernández, Leonardo D
    ;
    Foissner, Wilhelm
    ;
    Fournier, Bertrand 
    ;
    Gentekaki, Eleni
    ;
    Hájek, Michal
    ;
    Helder, Johannes
    ;
    Jousset, Alexandre
    ;
    Koller, Robert
    ;
    Kumar, Santosh
    ;
    La Terza, Antonietta
    ;
    Lamentowicz, Mariusz
    ;
    Mazei, Yuri
    ;
    Santos, Susana S
    ;
    Seppey, Christophe V.W
    ;
    Spiegel, Frederick W
    ;
    Walochnik, Julia
    ;
    Winding, Anne
    ;
    Lara, Enrique 
    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.