David Singer

David Singer
University of Angers | UA · Laboratoire d’études des Bio-Indicateurs Actuels et Fossiles (LPGN-BIAF)

PhD

About

34
Publications
15,842
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Introduction
Hello, I'm a Doctor in Biology and I started my research in 2012 in the university of Neuchâtel in the laboratory of Soil Biodiversity. My main interests are the study of the diversity, the ecology and the Biogeography of the Micro-eukaryotes.
Additional affiliations
April 2017 - present
Université de Neuchâtel
Position
  • PostDoc Position
Description
  • The effect of cadavers, blood, urine and faeces on soil ecology
February 2013 - February 2017
Université de Neuchâtel
Position
  • PhD Student
Description
  • Is everything everywhere A metabarcoding approach to protist biogeography and ecology.
Education
February 2009 - February 2012
Université de Neuchâtel
Field of study
  • Biogeosciences-Biology
February 2006 - February 2009
Université de Neuchâtel
Field of study
  • Biology

Publications

Publications (34)
Article
Full-text available
Metabarcoding approaches are exponentially increasing our understanding of soil biodiversity, with a major focus on the bacterial part of the microbiome. Part of the soil diversity are also eukaryotes that include fungi, algae, protists, and Metazoa. Nowadays, soil eukaryotes are targeted with the same approaches developed for bacteria and archaea...
Article
Full-text available
In this paper, we propose a marine influence index (MII), which is thought to give an integrated quantitative description of the complex of the environmental parameters controlling the foraminiferal fauna in estuarine intertidal mudflats. The MII contains three components, as follows: (1) the relative distance along the salinity gradient, (2) the e...
Article
Full-text available
This study focuses on the foraminiferal distribution on intertidal mudflats of two contrasted estuaries (Auray and Vie) along the French Atlantic coast. In both estuaries, the foraminiferal communities are dominated by Haynesina germanica and the Ammonia tepida group. Stations located near the outlets show a high diversity and abundance of species...
Article
Full-text available
Protist biogeography and macroecology are often explained in terms of current climate (temperature and water availability). Here, we provide evidence suggesting that the often-observed association between broad-scale diversity patterns of soil protists and climate may have an evolutionary origin rooted in the conservatism of ancestral thermal regim...
Article
Full-text available
Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning...
Article
Full-text available
Previous studies conducted in summer in the lakes at Hope Bay (Antarctic Peninsula) between 1991 and 2007 showed a large numerical contribution of flagellated Chrysophyceae to the phytoplankton communities, particularly in the oligotrophic lakes, as evidenced by light microscopy observations and molecular fingerprinting. Given the ecological releva...
Article
Full-text available
Protists dominate eukaryotic diversity and play key functional roles in all ecosystems, particularly by catalyzing carbon and nutrient cycling. To date, however, a comparative analysis of their taxonomic and functional diversity that compares the major ecosystems on Earth (soil, freshwater and marine systems) is missing. Here, we present a comparis...
Article
Full-text available
Testate lobose amoebae of the order Arcellinida are a diverse, cosmopolitan group of shelled protists found in many environments, including freshwater habitats, peatlands, and soils. Their decay-resistant tests make them an important fossil group for reconstructing Quaternary environments. Within the family Difflugidae Stein, 1859 more than 300 spe...
Article
Full-text available
This review provides a synthesis of current knowledge on the morphological and functional traits of testate amoebae, a polyphyletic group of protists commonly used as proxies of past hydrological changes in paleoecological investigations from peatland, lake sediment and soil archives. A trait-based approach to understanding testate amoebae ecology...
Article
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Assessing the degree to which climate explains the spatial distributions of different taxonomic and functional groups is essential for anticipating the effects of climate change on ecosystems. Most effort so far has focused on aboveground organisms, which offer only a partial view on the response of biodiversity to environmental gradients. Here, in...
Article
Full-text available
The relative importance of global versus local environmental factors for growth and thus carbon uptake of the bryophyte genus Sphagnum—the main peat-former and ecosystem engineer in northern peatlands—remains unclear. We measured length growth and net primary production (NPP) of two abundant Sphagnum species across 99 Holarctic peatlands. We tested...
Article
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Rain fed granite rock basins are ancient geological landforms of worldwide distribution and structural simplicity. They support habitats that can switch quickly from terrestrial to aquatic along the year. Diversity of animals and plants, and the connexion between communities in different basins have been widely explored in these habitats, but hardl...
Article
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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 met...
Article
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The purpose of this application, under Article 23.9.3 of the Code, is to conserve the specific name Nebela militaris Penard, 1890, a junior subjective synonym of Nebela bursella Taranek, 1881 – referred to as Nebela bursella Vejdovský in the literature. Due to the absence of any type or reference specimen and due to the confusing original descripti...
Article
Full-text available
Trends in spatial patterns of diversity in macroscopic organisms can be well predicted from correlative models, using topo‐climatic variables for plants and animals allowing inference over large scales. By contrast, diversity in soil microorganisms is generally considered as mostly driven by edaphic variables and, therefore, difficult to extrapolat...
Article
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Sphagnum-dominated ecosystem plays major roles as carbon sinks at the global level. Associated microbial communities, in particular, eukaryotes, play significant roles in nutrient fixation and turnover. In order to understand better the ecological processes driven by these organisms, the first step is to characterise these associated organisms. We...
Article
Trebouxiophyceae are a ubiquitous class of Chlorophyta encountered in aquatic and terrestrial environments. Most taxa are photosynthetic, and many acts as photobionts in symbiotic relationships, while others are free‐living. Trebouxiophyceae have also been widely investigated for their use for biotechnological applications. In this work, we aimed a...
Article
Recent studies show that soil eukaryotic diversity is immense and dominated by microorganisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to microorganisms. Major diversification events in multicellular organisms have often been attributed to long‐term climatic and g...
Preprint
Full-text available
Aim: General trends in spatial patterns of macroscopic organisms diversity can be reasonably well predicted from correlative models, using for instance topo-climatic variables for plants and animals allowing inference over large scales. By contrast, soil microorganisms diversity is generally considered as mostly driven by edaphic variables and, the...
Article
Full-text available
Rain-fed peatlands are dominated by peat mosses (Sphagnum sp.), which for their growth depend on nutrients, water and CO2 uptake from the atmosphere. As the isotopic composition of carbon (12,13C) and oxygen (16,18O) of these Sphagnum mosses are affected by environmental conditions, Sphagnum tissue accumulated in peat constitutes a potential long-t...
Article
Soil microorganisms are recognized as key players in all biogeochemical cycles. However, little effort has been paid to incorporate them in predictive models for future climate change. Here, we investigated the variation of prokaryotic community composition in alpine meadow soil from the Qinghai-Tibet Plateau under dry-rewetting stress using MiSeq...
Article
Protists include all eukaryotes except plants, fungi and animals. They are an essential, yet often forgotten, component of the soil microbiome. Method developments have now furthered our understanding of the real taxonomic and functional diversity of soil protists. They occupy key roles in microbial foodwebs as consumers of bacteria, fungi and othe...
Article
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The community composition of any group of organisms should theoretically be determined by a combination of assembly processes including resource partitioning, competition, environmental filtering, and phylogenetic legacy. Environmental DNA studies have revealed a huge diversity of protists in all environments, raising questions about the ecological...
Article
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Criminal investigations of suspected murder cases require estimating the post-mortem interval (PMI, or time after death) which is challenging for long PMIs. Here we present the case of human remains found in a Swiss forest. We have used a multidisciplinary approach involving the analysis of bones and soil samples collected beneath the remains of th...
Article
High-throughput sequencing (HTS) of soil environmental DNA (eDNA) allows assessing the full diversity of soil micro-eukaryotes. The resulting operational taxonomic units (OTUs) can be assigned to potential taxonomic and functional identities using increasingly complete reference databases. HTS of soil eDNA is revealing a high diversity and abundanc...
Article
Full-text available
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...
Article
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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 m...
Article
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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...
Article
Full-text available
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, clos...
Article
Full-text available
We investigated the composition of the smallest size fraction (<3 µm) 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,...
Article
Full-text available
Decomposing cadavers modify the soil environ-ment, 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, ampl...

Projects

Projects (2)
Project
Testate amoebae are a common group of amoeboid protists that build shells (called tests). They occur in soils, freshwater habitats, and to a lesser extent marine environments. They play a key role in microbial foodwebs and are useful bioindicators due to their responses to major ecological gradients (e.g. water availability, pH and nutrients). Their shells allow species-level identification and are preserved in sediments, peat and dried or frozen soil or moss samples, and they are commonly used in palaeoecology for quantitative inference and as model organisms for microbial biogeography. The literature on testate amoebae includes many ancient publications, in different languages and is often hard to find and stored in different private archives. Our goal is to compile the existing data in a user-friendly, open database which will facilitate the study of testate amoebae. This will have positive implications for their use in the study of testate amoeba biodiversity, biogeography, their functional roles and interactions with other organisms. It will also allow defining knowledge gaps and research priorities. In this global effort, we aim to build several databases for testate amoebae: 1) Original taxonomic descriptions (and translations) 2) Biometry and trait data 3) Geographical distribution 4) Diversity and community data (density, relative abundance) and associated metadata (especially quantitative ecological information, vegetation etc.). International Society for Testate Amoeba Research http://istar.wikidot.com/
Project
Knowledge on soil protists in all aspects such as on community structure and functioning remains poorly known. In this global effort we aim at increasing this knowledge and link soil protistology with other fields such as more general soil microbecology, plant and general ecology.