Publications

@article{nokey,

title = {Unlocking Foraminiferal Genetic Diversity on Estuarine Mudflats with eDNA Metabarcoding},

author = {David Singer and Marie P. A. Fouet and Magali Schweizer and Aurélia Mouret and Sophie Quinchard and Frans J. Jorissen},

url = {https://doi.org/10.1016/j.scitotenv.2023.165983, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_et_al_2023_Unlocking_foraminiferal_genetic_diversity_on_estuarine_mudflats_with_eDNA_metabarcoding.pdf, PDF

},

issn = {0048-9697},

year  = {2023},

date = {2023-12-01},

urldate = {2023-01-01},

journal = {Science of the Total Environment},

pages = {165983},

abstract = {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 to 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 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.},

keywords = {Diversity, Ecology, First-Last-Author, Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {A Needle in a Haystack: A New Metabarcoding Approach to Survey Diversity at the Species Level of Arcellinida (Amoebozoa: Tubulinea)},

author = {Rubén González-Miguéns and Emilio Cano and Antonio Guillén-Oterino and Antonio Quesada and Daniel J. G. Lahr and Daniel Tenorio-Rodríguez and David Salvador-Velasco and David Velázquez and María Isabel Carrasco-Braganza and R. Timothy Patterson and Enrique Lara and David Singer},

url = {https://doi.org/10.1111/1755-0998.13771, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Gonzalez‐Miguens_2023_-A_needle_in_a_haystack_A_new_metabarcoding_approach_to_survey.pdf, PDF},

issn = {1755-098X},

year  = {2023},

date = {2023-11-01},

urldate = {2023-11-01},

journal = {Molecular Ecology Resources},

volume = {23},

issue = {5},

pages = {1034-1049},

publisher = {John Wiley & Sons, Ltd},

abstract = {Environmental DNA-based diversity studies have increased in popularity with the development of high throughput sequencing technologies. This permits the potential simultaneous retrieval of vast amounts of molecular data from many different organisms and species, thus contributing to a wide range of biological disciplines. Environmental DNA protocols designed for protists often focused on the highly conserved small subunit of the ribosome gene, that does not permit species-level assignments. On the other hand, eDNA protocols aiming at species-level assignments allow a fine level ecological resolution and reproducible results. These protocols are currently applied to organisms living in marine and shallow lotic freshwater ecosystems, often in a bioindication purpose. Therefore, in this study, we present a species-level eDNA protocol designed to explore diversity of Arcellinida (Amoebozoa: Tubulinea) testate amoebae taxa that is based on mitochondrial cytochrome oxidase subunit I (COI). These organisms are widespread in lentic water bodies and soil ecosystems. We applied this protocol to 42 samples from peatlands, estuaries and soil environments, recovering all the infraorders in Glutinoconcha (with COI data), except for Hyalospheniformes. Our results revealed an unsuspected diversity in morphologically homogeneous groups such as Cylindrothecina, Excentrostoma or Sphaerothecina. With this protocol we expect to revolutionize the design of modern distributional Arcellinida surveys. Our approach involves a rapid and cost-effective analysis of testate amoeba diversity living in contrasted ecosystems. Therefore, the order Arcellinida has the potential to be established as a model group for a wide range of theoretical and applied studies.},

keywords = {Diversity, Ecology, First-Last-Author, Metabarcoding, Testate-amoebae},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Protist Taxonomic and Functional Diversity in Soil, Freshwater and Marine Ecosystems},

author = {David Singer and Christophe V. W. Seppey and Guillaume Lentendu and Micah Dunthorn and David Bass and Lassâad Belbahri and Quentin Blandenier and Didier Debroas and G. Arjen Groot and Colomban Vargas and Isabelle Domaizon and Clément Duckert and Irina Izaguirre and Isabelle Koenig and Gabriela Mataloni and M. Romina Schiaffino and Edward A. D. Mitchell and Stefan Geisen and Enrique Lara},

url = {https://doi.org/10.1016/j.envint.2020.106262, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_and_Seppey_2021_Protist_taxonomic_and_functional_diversity_in_soil_freshwater_and_marine_ecosystems.pdf, PDF},

issn = {0160-4120},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Environment International},

volume = {146},

pages = {106262},

abstract = {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 comparison of protist diversity based on standardized high throughput 18S rRNA gene sequencing of soil, freshwater and marine environmental DNA. Soil and freshwater protist communities were more similar to each other than to marine protist communities, with virtually no overlap of Operational Taxonomic Units (OTUs) between terrestrial and marine habitats. Soil protists showed higher γ diversity than aquatic samples. Differences in taxonomic composition of the communities led to changes in a functional diversity among ecosystems, as expressed in relative abundance of consumers, phototrophs and parasites. Phototrophs (eukaryotic algae) dominated freshwater systems (49% of the sequences) and consumers soil and marine ecosystems (59% and 48%, respectively). The individual functional groups were composed of ecosystem- specific taxonomic groups. Parasites were equally common in all ecosystems, yet, terrestrial systems hosted more OTUs assigned to parasites of macro-organisms while aquatic systems contained mostly microbial parasitoids. Together, we show biogeographic patterns of protist diversity across major ecosystems on Earth, preparing the way for more focused studies that will help understanding the multiple roles of protists in the biosphere.},

keywords = {Diversity, First-Last-Author, Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {High-Throughput Sequencing of Litter and Moss eDNA Reveals a Positive Correlation between the Diversity of Apicomplexa and Their Invertebrate Hosts across Alpine Habitats},

author = {David Singer and Clément Duckert and Petr Heděnec and Enrique Lara and Erika Hiltbrunner and Edward A. D. Mitchell},

url = {https://doi.org/10.1016/j.soilbio.2020.107837, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_and_Duckert_2020_High-throughput_sequencing_of_litter_and_moss_eDNA_reveals_a_positive.pdf, PDF},

issn = {0038-0717},

year  = {2020},

date = {2020-12-01},

urldate = {2020-12-01},

journal = {Soil Biology and Biochemistry},

pages = {107837},

abstract = {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.},

keywords = {Ecology, First-Last-Author, Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Dispersal Limitations and Historical Factors Determine the Biogeography of Specialized Terrestrial Protists},

author = {David Singer and Edward A. D. Mitchell and Richard J. Payne and Quentin Blandenier and Clément Duckert and Leonardo D. Fernández and Bertrand Fournier and Cristián E. Hernández and Gustaf Granath and Håkan Rydin and Luca Bragazza and Natalia G. Koronatova and Irina Goia and Lorna I. Harris and Katarzyna Kajukało and Anush Kosakyan and Mariusz Lamentowicz and Natalia P. Kosykh and Kai Vellak and Enrique Lara},

url = {https://doi.org/10.1111/mec.15117, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_2019_Dispersal_limitations_and_historical_factors_determine_the_biogeography_of_specialized_terrestrial_protists.pdf, PDF

},

issn = {0962-1083},

year  = {2019},

date = {2019-01-01},

urldate = {2019-01-01},

journal = {Molecular Ecology},

issue = {ja},

abstract = {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 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 phylogeographic patterns in \textit{Hyalosphenia papilio}, a large testate amoeba restricted to Holarctic \textit{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 habitat. Phylogenetic diversity was higher in Western North America, corresponding to the inferred geographical origin of the \textit{H. papilio} complex, and was lower in Eurasia despite extensive suitable habitat. These results suggest that patterns of phylogenetic diversity and distribution can be explained by the history of Holarctic \textit{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 \textit{H. papilio}. This implies that, at least for large and specialized terrestrial microorganisms, propagule dispersal is slow enough that historical processes may contribute to their diversification and phylogeographic patterns and may partly explain their very high overall diversity.},

keywords = {Biogeography, First-Last-Author, Peatland, Testate-amoebae},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Contrasted Micro-Eukaryotic Diversity Associated with \textit{Sphagnum} Mosses in Tropical, Subtropical and Temperate Climatic Zones},

author = {David Singer and Sebastian Metz and Fernando Unrein and Satoshi Shimano and Yuri Mazei and Edward A. D. Mitchell and Enrique Lara},

url = {https://doi.org/10.1007/s00248-019-01325-7, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_2019_Contrasted_Micro_Eukaryotic_Diversity_Associated_with_Sphagnum.pdf, PDF},

issn = {0095-3628},

year  = {2019},

date = {2019-01-01},

urldate = {2019-01-01},

journal = {Microbial Ecology},

volume = {78},

number = {3},

pages = {714–724},

abstract = {\textit{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 characterised the taxonomic diversity, and from this, inferred the functional diversity of microeukaryotes in \textit{Sphagnum} mosses in tropical, subtropical and temperate climatic zones through an environmental DNA diversity metabarcoding survey of the V9 region of the gene coding for the RNA of the small subunit of the ribosomes (SSU rRNA). As microbial processes are strongly driven by temperatures, we hypothesised that saprotrophy would be highest in warm regions, whereas mixotrophy, an optimal strategy in oligotrophic environments, would peak under colder climates. Phylotype richness was higher in tropical and subtropical climatic zones than in the temperate region, mostly due to a higher diversity of animal parasites (i.e. Apicomplexa). Decomposers, and especially opportunistic yeasts and moulds, were more abundant under warmer climates, while mixotrophic organisms were more abundant under temperate climates. The dominance of decomposers, suggesting a higher heterotrophic activity under warmer climates, is coherent with the generally observed faster nutrient cycling at lower latitudes; this phenomenon is likely enhanced by higher inputs of nutrients most probably brought in the system by Metazoa, such as arthropods.},

keywords = {Biogeography, First-Last-Author, Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Environmental Filtering and Phylogenetic Clustering Correlate with the Distribution Patterns of Cryptic Protist Species},

author = {David Singer and Anush Kosakyan and Christophe V. W. Seppey and Amandine Pillonel and Leonardo D. Fernández and Diego Fontaneto and Edward A. D. Mitchell and Enrique Lara},

url = {https://doi.org/10.1002/ecy.2161, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_2018_Environmental_filtering_and_phylogenetic_clustering_correlate_with_the_distribution_patterns_of_cryptic_protist_species.pdf, PDF

},

issn = {1939-9170},

year  = {2018},

date = {2018-12-01},

urldate = {2018-12-01},

journal = {Ecology},

volume = {99},

number = {4},

pages = {904–914},

abstract = {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 significance of such diversity and the degree to which they obey to the same rules as macroscopic organisms. The fast-growing cultivable protist species on which hypotheses are usually experimentally tested represent only a minority of the protist diversity. Addressing these questions for the lesser known majority can only be inferred through observational studies. We conducted an environmental DNA survey of the genus \textit{Nebela}, a group of closely related testate (shelled) amoeba species, in different habitats within \textit{Sphagnum}-dominated peatlands. Identification based on the mitochondrial cytochrome c oxidase 1 gene, allowed species-level resolution as well as phylogenetic reconstruction. Community composition varied strongly across habitats and associated environmental gradients. Species showed little overlap in their realized niche, suggesting resource partitioning, and a strong influence of environmental filtering driving community composition. Furthermore, phylogenetic clustering was observed in the most nitrogen-poor samples, supporting phylogenetic inheritance of adaptations in the group of \textit{N. guttata}. This study showed that the studied free-living unicellular eukaryotes follow to community assembly rules similar to those known to determine plant and animal communities; the same may be true for much of the huge functional and taxonomic diversity of protists.},

keywords = {Diversity, Ecology, First-Last-Author, Peatland, Testate-amoebae},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {En Garde! Redefinition of \textit{Nebela} \textit{Militaris} (Arcellinida, Hyalospheniidae) and Erection of \textit{Alabasta} Gen. Nov.},

author = {Clément Duckert and Quentin Blandenier and Fanny A. L. Kupferschmid and Anush Kosakyan and Edward A. D. Mitchell and Enrique Lara and David Singer},

url = {https://doi.org/10.1016/j.ejop.2018.08.005, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Duckert_Blandenier_2018_En_garde_Redefinition_of_Nebela_militaris_Arcellinida_Hyalospheniidae_and_erection_of_Alabasta_gen_nov.pdf, PDF},

year  = {2018},

date = {2018-11-01},

urldate = {2018-11-01},

journal = {European Journal of Protistology},

volume = {66},

pages = {156–165},

abstract = {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 \textit{Nebela militaris}. A phylogenetic reconstruction of the Hyalospheniidae using partial sequences of the mitochondrial Cytochrome Oxidase Subunit 1 (COI) gene shows that \textit{N. militaris} does not belong to genus \textit{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: \textit{Alabasta} gen. nov. Based on their morphology, we include in this genus \textit{Nebela kivuense} and \textit{Nebela longicollis}. We discuss the position of genus \textit{Alabasta} within Hyalospheniidae, and the species that could integrate this new genus based on their morphological characteristics.},

keywords = {Diversity, First-Last-Author, Peatland, Testate-amoebae},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {High-Throughput Sequencing Reveals Diverse Oomycete Communities in Oligotrophic Peat Bog Micro-Habitat},

author = {David Singer and Enrique Lara and Mónica M. Steciow and Christophe V. W. Seppey and Noelia Paredes and Amandine Pillonel and Tomasz Oszako and Lassâad Belbahri},

url = {https://doi.org/10.1016/j.funeco.2016.05.009, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_2016_High_throughput_sequencing_reveals_diverse_oomycete_communities_in_oligotrophic_peat_bog_micro-habitat.pdf, PDF},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Fungal Ecology},

volume = {23},

pages = {42–47},

abstract = {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 ( \textit{Aphanomyces astaci}: X1100 and \textit{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.},

keywords = {Diversity, Ecology, First-Last-Author, Metabarcoding, Peatland},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Eight Species in the \textit{Nebela} \textit{Collaris} Complex: \textit{Nebela} \textit{Gimlii} (Arcellinida, Hyalospheniidae), a New Species Described from a Swiss Raised Bog},

author = {David Singer and Anush Kosakyan and Amandine Pillonel and Edward A. D. Mitchell and Enrique Lara},

url = {https://doi.org/10.1016/j.ejop.2014.11.004, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_2015_Eight_species_in_the_Nebela_collaris_complex_Nebela_gimlii_Arcellinida_Hyalospheniidae_a_new_species_described_from_a_Swiss_raised_bog.pdf, PDF},

issn = {0932-4739},

year  = {2015},

date = {2015-01-01},

urldate = {2015-01-01},

journal = {European Journal of Protistology},

volume = {51},

number = {1},

pages = {79–85},

abstract = {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 \textit{Nebela gimlii} was placed in a phylogenetic tree based on mitochondrial cytochrome oxidase sequences (COI), and branched robustly within the \textit{N. collaris} complex next to the morphologically similar \textit{N. guttata} and \textit{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 \textit{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.},

keywords = {Diversity, First-Last-Author, Peatland, Testate-amoebae},

pubstate = {published},

tppubtype = {article}

}