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PEOPLE@HES-SO – Annuaire et Répertoire des compétences
PEOPLE@HES-SO – Annuaire et Répertoire des compétences

PEOPLE@HES-SO
Annuaire et Répertoire des compétences

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Singer David

Singer David

Adjoint scientifique

Compétences principales

Protists

Biodiversity

Ecology

Microbiology

Molecular biology

Bioinformatics

Statistics

  • Contact

  • Publications

Contrat principal

Adjoint scientifique

Changins- Haute école de viticulture et œnologie
Route de Duillier, 1260 Nyon, CH
EIC
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2024

Conception d'itinéraires innovants de couverture du sol sans herbicide en viticulture :
Article professionnel ArODES
réseau on-farm du projet de recherche CV-VIGNESOL (article2/2)

David Marchand, Robin Sonnard, Matteo Mota, Serena Fantasia, Antoine Faggion, Frédéric Lamy, David Singer, Markus Rienth, Thierry Heger, Nicolas Delabays, Vivian Zufferey

Vignes et vergers,  2024, 8, 11-14

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The symbiotic alga Trebouxia fuels a coherent soil ecosystem on the landscape scale in the Atacama Desert
Article scientifique ArODES

Patrick Jung, Rebekah Brand, Laura Briegel-Williams, Lina Werner, Emily Jost, Guillaume Lentendu, David Singer, Rujuta Athavale, Dennis J. Nürnberg, Fernando D. Alfaro, Burkhard Büdel

Environmental Microbiome,  2024, 19, 1

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Résumé:

Biocrusts represent associations of lichens, green algae, cyanobacteria, fungi and other microorganisms, colonizing soils in varying proportions of principally arid biomes. The so-called grit crust represents a recently discovered type of biocrust situated in the Coastal Range of the Atacama Desert (Chile) made of microorganisms growing on and in granitoid pebbles, resulting in a checkerboard pattern visible to the naked eye on the landscape scale. This specific microbiome fulfills a broad range of ecosystem services, all probably driven by fog and dew-induced photosynthetic activity of mainly micro-lichens. To understand its biodiversity and impact, we applied a polyphasic approach on the phototrophic microbiome of this biocrust, combining isolation and characterization of the lichen photobionts, multi-gene phylogeny of the photobionts and mycobionts based on a direct sequencing and microphotography approach, metabarcoding and determination of chlorophylla+b contents. Metabarcoding showed that yet undescribed lichens within the Caliciaceae dominated the biocrust together with Trebouxia as the most abundant eukaryote in all plots. Together with high mean chlorophylla+b contents exceeding 410 mg m−2, this distinguished the symbiotic algae Trebouxia as the main driver of the grit crust ecosystem. The trebouxioid photobionts could be assigned to the I (T. impressa/gelatinosa) and A (T. arboricola) clades and represented several lineages containing five potential species candidates, which were identified based on the unique phylogenetic position, morphological features, and developmental cycles of the corresponding isolates. These results designate the grit crust as the only known coherent soil layer with significant landscape covering impact of at least 440 km2, predominantly ruled by a single symbiotic algal genus.

Conception d'itinéraires innovants de couverture du sol sans herbicides en viticulture :
Article professionnel ArODES
présentation de la parcelle expérimentale on-station du projet CV-VIGNESOL

Matteo Mota, Serena Fantasia, Antoine Faggion, Frédéric Lamy, David Singer, Markus Rienth, Thierry Heger, Nicolas Delabays, Vivian Zufferey, Robin Sonnard, David Marchand

Vignes et vergers,  2024, 7, 14-16

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Amoebozoan testate amoebae illuminate the diversity of heterotrophs and the complexity of ecosystems throughout geological time
Article scientifique ArODES

Alfredo L. Porfirio-Sousa, Alexander K. Tice, Luana Morais, Giulia M. Ribeiro, Quentin Blandenier, Kenneth Dumack, Yana Eglit, Nicholas W. Fry, Maria Beatriz Gomes Souza, Tristan C. Henderson, Felicity Kleitz-Singleton, David Singer, Matthew W. Brown, Daniel J. G. Lahr

Proceedings of the National Academy of Sciences,  2024, 121, 30, e2319628121

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Résumé:

Heterotrophic protists are vital in Earth’s ecosystems, influencing carbon and nutrient cycles and occupying key positions in food webs as microbial predators. Fossils and molecular data suggest the emergence of predatory microeukaryotes and the transition to a eukaryote-rich marine environment by 800 million years ago (Ma). Neoproterozoic vase-shaped microfossils (VSMs) linked to Arcellinida testate amoebae represent the oldest evidence of heterotrophic microeukaryotes. This study explores the phylogenetic relationship and divergence times of modern Arcellinida and related taxa using a relaxed molecular clock approach. We estimate the origin of nodes leading to extant members of the Arcellinida Order to have happened during the latest Mesoproterozoic and Neoproterozoic (1054 to 661 Ma), while the divergence of extant infraorders postdates the Silurian. Our results demonstrate that at least one major heterotrophic eukaryote lineage originated during the Neoproterozoic. A putative radiation of eukaryotic groups (e.g., Arcellinida) during the early-Neoproterozoic sustained by favorable ecological and environmental conditions may have contributed to eukaryotic life endurance during the Cryogenian severe ice ages. Moreover, we infer that Arcellinida most likely already inhabited terrestrial habitats during the Neoproterozoic, coexisting with terrestrial Fungi and green algae, before land plant radiation. The most recent extant Arcellinida groups diverged during the Silurian Period, alongside other taxa within Fungi and flowering plants. These findings shed light on heterotrophic microeukaryotes’ evolutionary history and ecological significance in Earth’s ecosystems, using testate amoebae as a proxy.

Can we accurately predict the distribution of soil microorganism presence and relative abundance ?
Article scientifique ArODES

Valentin Verdon, Lucie Malard, Flavien Collart, Antoine Adde, Erika Yashiro, Enrique Lara Pandi, Heidi Mod, David Singer, Hélène Niculita-Hirzel, Nicolas Guex, Antoine Guisan

Ecography,  To be published

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Résumé:

Soil microbes play a key role in shaping terrestrial ecosystems. It is therefore essential to understand what drives their distribution. While multivariate analyses have been used to characterise microbial communities and drivers of their spatial patterns, few studies have focused on predicting the distribution of amplicon sequence variants (ASVs). Here, we evaluate the potential of species distribution models (SDMs) to predict the presence–absence and relative abundance distribution of bacteria, archaea, fungi, and protist ASVs in the western Swiss Alps. Advanced automated selection of abiotic covariates was used to circumvent the lack of knowledge on the ecology of each ASV. Presence–absence SDMs could be fitted for most ASVs, yielding better predictions than null models. Relative abundance SDMs performed less well, with low fit and predictive power overall, but displayed a good capacity to differentiate between sites with high and low relative abundance of the modelled ASV. SDMs for bacteria and archaea displayed better predictive power than for fungi and protists, suggesting a closer link of the former with the abiotic covariates used. Microorganism distributions were mostly related to edaphic covariates. In particular, pH was the most selected covariate across models. The study shows the potential of using SDM frameworks to predict the distribution of ASVs obtained from topsoil DNA. It also highlights the need for further development of precise edaphic mapping and scenario modelling to enhances prediction of microorganism distributions in the future.

Unravelling the distribution of three Ammonia species (Foraminifera, Rhizaria) in French Atlantic Coast estuaries using morphological and metabarcoding approaches
Article scientifique ArODES

Marie P. A. Fouet, Magali Schweizer, David Singer, Julien Richirt, Sophie Quinchard, Frans J. Jorisen

Marine Micropaleontology,  2024, 188, 102353

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Résumé:

Assessing the distribution of species in natural environments is essential for their use in environmental surveys. Here, we investigate the distribution of three pseudo-cryptic species formerly lumped in the morphospecies Ammonia tepida (Cushman, 1926), commonly found on estuarine mudflats along the European coasts: Ammonia veneta Schultze, 1854 (T1), Ammonia aberdoveyensis Haynes, 1973 (T2) and Ammonia confertitesta Zheng, 1978 (T6). We studied their distribution at 51 sites located in seven estuaries of the French North Atlantic coast (Elorn, Aulne, Odet, Crac'h, Auray, Vilaine, Vie), using both morphological and molecular identification methods. Ammonia veneta was detected by both approaches at most of the stations. While A. aberdoveyensis was frequently identified by the morphological method but not detected with metabarcoding, the presence of A. confertitesta in the eDNA data often contrasted with its absence in the morphological analysis. The absence of A. aberdoveyensis in eDNA of sites where it was identified morphologically could be the consequence of its relative scarcity, and eventually a patchy distribution. Concerning A. confertitesta, we hypothesise that these contradictory results can be explained by the supposedly invasive character of this species. Despite the widespread presence of A. confertitesta genetic material (including adults, juveniles and propagules), a mature population has not yet fully developed everywhere. The seven investigated estuaries seem to represent different stages of replacement of the autochthonous species A. veneta and A. aberdoveyensis by A. confertitesta. Our study demonstrates that the combination of visual observations and molecular approaches is ideal for monitoring the progressive spreading of exotic species.

It's time to consider the Arcellinida shell as a weapon
Article scientifique ArODES

Kenneth Dumack, Enrique Lara, Clément Duckert, Elizaveta Ermolaeva, Ferry Siemensma, David Singer, Valentyna Krashevska, Mariusz Lamentowicz

European Journal of Protistology,  2024, 92, 126051

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Résumé:

The shells of testate amoebae are morphologically diverse and persistent in the environment. Accordingly, the examination of the morphology and composition of shells became a standard tool in ecological, palaeoecological, and evolutionary studies. However, so far the function of the shell remains poorly understood and, although based on limited evidence, the shell was considered as a defense mechanism. Based on recent evidence, we propose that the shell of arcellinid testate amoebae is a crucial component facilitating the amoebae’s attack of large prey. Accordingly, the shell is not purely protective, but must be considered also as a weapon. This change in perspective opens up numerous new avenues in protistology and will lead to a substantial change in ecological, palaeoecological, and evolutionary research.

2023

Unlocking foraminiferal genetic diversity on estuarine mudflats with eDNA metabarcoding
Article scientifique ArODES

David Singer, Marie P. A. Fouet, Magali Schweizer, Aurélia Mouret, Sophie Quinchard, Frans J. Jorissen

Science of The Total Environment,  2023, vol. 902, article no. 165983

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Résumé:

Environmental biomonitoring is a prerequisite for efficient evaluation and remediation of ecosystem degradation due to anthropogenic pressure or climate change. Estuaries are key habitats subject to multiple anthropogenic and natural stressors. Due to these multiple stressors, the detection of anthropogenic pressure is challenging. The fact that abundant natural stressors often lead to negative quality assessments has been coined the “estuarine quality paradox”. To solve this issue, the application of molecular approaches with successful bioindicators like foraminifera is promising. However, sampling protocols, molecular procedures and data analyses need to be validated before such tools can be routinely applied. We conducted an environmental DNA survey of estuarine mudflats along the French Atlantic coast, using a metabarcoding approach targeting foraminifera. Our results demonstrate that estuarine environments have only a few active OTUs dominating the community composition and a large stock of dormant or propagule stages. This last genetic diversity components constitute an important reservoir, with different species which can potentially develop in response to the temporal variability of the multiple stressors. In fact, different OTUs were dominant in the studied estuaries. Our statistical model shows that the physical and chemical characteristics of the sediment and the climatic conditions explain only 43 % of the community composition variance. This suggests that other, less easily quantifiable factors, such as the history and use of the estuaries or the ecological drift could play an important role as well. Environmental DNA biomonitoring opens new perspectives to better characterize the genetic diversity in estuaries.

Global distribution modelling of a conspicuous Gondwanian soil protist reveals latitudinal dispersal limitation and range contraction in response to climate warming
Article scientifique ArODES

Estelle P. Bruni, Olivia Rusconi, Olivier Broennimann, Antoine Adde, Raphaël Jauslin, Valentyna Krashevska, Anush Kosakyan, Eric Armynot du Châtelet, João P. B. Alcino, Louis Beyens, Quentin Blandenier, Anatoly Bobrov, Luciana Burdman, Clément Duckert, Leonardo D. Fernández, Maria Beatriz Gomes e Souza, Thierry Heger, Isabelle Koenig, Daniel J. G. Lahr, Michelle McKeown, Ralf Meisterfeld, David Singer, Eckhard Voelcker, Janet Wilmshurst, Sebastien Wohlhauser, David M. Wilkinson, Antoine Guisan, Edward A. D. Mitchell

Diversity and Distributions,

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Résumé:

The diversity and distribution of soil microorganisms and their potential for long-distance dispersal (LDD) are poorly documented, making the threats posed by climate change difficult to assess. If microorganisms do not disperse globally, regional endemism may develop and extinction may occur due to environmental changes. Here, we addressed this question using the testate amoeba Apodera vas, a morphologically conspicuous model soil microorganism in microbial biogeography, commonly found in peatlands and forests mainly of former Gondwana. We first documented its distribution. We next assessed whether its distribution could be explained by dispersal (i.e. matching its climatic niche) or vicariance (i.e. palaeogeography), based on the magnitude of potential range expansions or contractions in response to past and on-going climatic changes. Last, we wanted to assess the likelihood of cryptic diversity and its potential threat from climate and land-use changes (e.g. due to limited LDD). Documented records: Southern Hemisphere and intertropical zone; modelling: Global. We first built an updated global distribution map of A. vas using 401 validated georeferenced records. We next used these data to develop a climatic niche model to predict its past (LGM, i.e. 21 ± 3 ka BP; PMIP3 IPSL-CM5A-LR), present and future (IPSL-CMP6A-LR predictions for 2071–2100, SSP3 and 5) potential distributions in responses to climate, by relating the species occurrences to climatic and topographic predictors. We then used these predictions to test our hypotheses (dispersal/vicariance, cryptic diversity, future threat from LDD limitation). Our models show that favourable climatic conditions for A. vas currently exist in the British Isles, an especially well-studied region for testate amoebae where this species has never been found. This demonstrates a lack of interhemispheric LDD, congruent with the palaeogeography (vicariance) hypothesis. Longitudinal LDD is, however, confirmed by the presence of A. vas in isolated and geologically young peri-Antarctic islands. Potential distribution maps for past, current and future climates show favourable climatic conditions existing on parts of all southern continents, with shifts to higher land from LGM to current in the tropics and a strong range contraction from current to future (global warming IPSL-CM6A-LR scenario for 2071–2100, SSP3.70 and SSP5.85) with favourable conditions developing on the Antarctic Peninsula. This study illustrates the value of climate niche models for research on microbial diversity and biogeography, along with exploring the role played by historical factors and dispersal limitation in shaping microbial biogeography. We assess the discrepancy between latitudinal and longitudinal LDD for A. vas, which is possibly due to contrast in wind patterns and/or likelihood of transport by birds. Our models also suggest that climate change may lead to regional extinction of terrestrial microscopic organisms, thus illustrating the pertinence of including microorganisms in biodiversity conservation research and actions.

Diversity of DNA sequences from pathogenic and potentially pathogenic eukaryotic microorganisms in protected granite mountain rocks
Article scientifique ArODES

Ismael Velasco-Gonzalez, Enrique Lara, David Singer, Amaya de Cos-Gandoy, Manuel Garcia-Rodriguez, Antonio Murciano, Blanca Pérez-Uz, Richard Williams, Abel Sanchez-Jimenez, Mercedes Martin-Cereceda

Diversity,  2023, vol. 15, no. 5, article no. 594

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Résumé:

Rain-fed mountain granite rock basins are temporary habitats conditioned by a fluctuating environment and the unpredictability of precipitation or flooding rates. These small highland freshwater habitats remain largely unexplored at the microbial level. The aim of this work is to report the presence in these habitats of genetic sequences of microbial eukaryotes that are pathogens and potential pathogens of humans, wildlife, cattle, crops as well as of other microorganisms. We sequenced the hypervariable region v4 of the 18S rDNA gene from environmental DNA of sediments taken from 21 rock basins in a National Park in Spain. More than a fifth (21%) of the eukaryotic Operational Taxonomic Units (OTUs) found are ascribed to pathogenic (within 11 Phyla) and potential pathogenic (within 1 phylum, the Chytridiomycota) microorganisms. Some OTUs retrieved are of agro-economic and public health importance (e.g., Pythium spp., Lagenidium spp., Candida spp. and Vermamoeba vermiformis). In 86% of the basins, the most abundant OTUs were affiliated to Chytridiomycota, a broad fungal group including saprozoic and parasitic taxa. Two OTUs affiliated to chytrids were significantly correlated with high concentrations of heavy metals. The high proportion of chytrid-like microbial sequences found emphasises the role of these freshwater habitats for adding knowledge regarding the ecological trade-offs of the still rather unknown Chytridiomycota. Our results show that rain-fed rock basins may be model habitats for the study and surveillance of microbial community dynamics and genetics of (mainly opportunistic) microbial pathogens.

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