Publications

@article{nokey,

title = {Global Distribution Modelling of a Conspicuous Gondwanian Soil Protist Reveals Latitudinal Dispersal Limitation and Range Contraction in Response to Climate Warming},

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

url = {https://doi.org/10.1111/ddi.13779, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Bruni_2023_Global_distribution_modelling_of_a_conspicuous_Gondwanian.pdf, PDF},

issn = {1366-9516},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Diversity and Distributions},

volume = {30},

number = {2},

pages = {e13779},

publisher = {John Wiley & Sons, Ltd},

abstract = {Aim 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 \textit{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). Location Documented records: Southern Hemisphere and intertropical zone; modelling: Global. Methods We first built an updated global distribution map of \textit{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±3ka 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). Results Our models show that favourable climatic conditions for \textit{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 \textit{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. Main Conclusions 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 \textit{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.},

keywords = {Biogeography, Peatland, Testate-amoebae},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Unravelling the Distribution of Three \textit{Ammonia} Species (Foraminifera, Rhizaria) in French Atlantic Coast Estuaries Using Morphological and Metabarcoding Approaches},

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

url = {https://doi.org/10.1016/j.marmicro.2024.102353, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Fouet_2024_Unravelling_the_distribution_of_three_Ammonia_species_Foraminifera_Rhizaria_in_French_Atlantic_Coast_estuaries_using_morphological_and_metabarcoding_approaches.pdf, PDF},

issn = {0377-8398},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Marine Micropaleontology},

volume = {188},

pages = {102353},

abstract = {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 \textit{Ammonia tepida} (Cushman, 1926), commonly found on estuarine mudflats along the European coasts: \textit{Ammonia veneta} Schultze, 1854 (T1), \textit{Ammonia aberdoveyensis} Haynes, 1973 (T2) and \textit{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. \textit{Ammonia veneta} was detected by both approaches at most of the stations. While \textit{A. aberdoveyensis} was frequently identified by the morphological method but not detected with metabarcoding, the presence of \textit{A. confertitesta} in the eDNA data often contrasted with its absence in the morphological analysis. The absence of \textit{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 \textit{A. confertitesta}, we hypothesise that these contradictory results can be explained by the supposedly invasive character of this species. Despite the widespread presence of \textit{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 \textit{A. veneta} and \textit{A. aberdoveyensis} by \textit{A. confertitesta}. Our study demonstrates that the combination of visual observations and molecular approaches is ideal for monitoring the progressive spreading of exotic species.},

keywords = {Biogeography, Diversity, Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Global Distribution of Trebouxiophyceae Diversity Explored by High-Throughput Sequencing and Phylogenetic Approaches},

author = {Sebastian Metz and David Singer and Isabelle Domaizon and Fernando Unrein and Enrique Lara},

url = {https://doi.org/10.1111/1462-2920.14738, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Metz_2019_Global_distribution_of_Trebouxiophyceae_diversity.pdf, PDF},

issn = {1462-2912},

year  = {2019},

date = {2019-01-01},

urldate = {2019-01-01},

journal = {Environmental microbiology},

volume = {21},

number = {10},

pages = {3885–3895},

abstract = {Summary 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 at obtaining a comprehensive image of their diversity by compiling the information of 435 freshwater, soil and marine environmental DNA samples surveyed with Illumina sequencing technology in order to search for the most relevant environments for bioprospecting. Freshwater and soil were most diverse and shared more than half of all operational taxonomic units (OTUs), however, their communities were significantly distinct. Oceans hosted the highest genetic novelty, and did not share any OTUs with the other environments; also, marine samples host more diversity in warm waters. Symbiotic genera usually found in lichens such as \textit{Trebouxia}, \textit{Myrmecia} and \textit{Symbiochloris} were also abundantly detected in the ocean, suggesting either free-living lifestyles or unknown symbiotic relationships with marine planktonic organisms. Altogether, our study opens the way to new prospection for trebouxiophycean strains, especially in understudied environments like the ocean.},

keywords = {Biogeography, 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 = {Soil Protists: A Fertile Frontier in Soil Biology Research},

author = {Stefan Geisen and Edward A. D. Mitchell and Sina Adl and Michael Bonkowski and Micah Dunthorn and Flemming Ekelund and Leonardo D. Fernández and Alexandre Jousset and Valentyna Krashevska and David Singer and Frederick W. Spiegel and Julia Walochnik and Enrique Lara},

url = {https://doi.org/10.1093/femsre/fuy006, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Geisen_2018_Soil_protists_a_fertile_frontier_in_soil_biology_research.pdf, PDF},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {FEMS Microbiology Reviews},

volume = {42},

number = {3},

pages = {293–323},

abstract = {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 other small eukaryotes. As parasites of plants, animals and even of larger protists, they regulate populations and shape communities. Pathogenic forms play a major role in public health issues as human parasites, or act as agricultural pests. Predatory soil protists release nutrients enhancing plant growth. Soil protists are of key importance for our understanding of eukaryotic evolution and microbial biogeography. Soil protists are also useful in applied research as bioindicators of soil quality, as models in ecotoxicology and as potential biofertilizers and biocontrol agents. In this review, we provide an overview of the enormous morphological, taxonomical and functional diversity of soil protists, and discuss current challenges and opportunities in soil protistology. Research in soil biology would clearly benefit from incorporating more protistology alongside the study of bacteria, fungi and animals.},

keywords = {Biogeography, Diversity, Ecology, Protists},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Microbial Eukaryote Communities Exhibit Robust Biogeographical Patterns along a Gradient of Patagonian and Antarctic Lakes},

author = {M. Romina Schiaffino and Enrique Lara and Leonardo D. Fernández and Vanessa Balagué and David Singer and Christophe V. W. Seppey and Ramon Massana and Irina Izaguirre},

url = {https://doi.org/10.1111/1462-2920.13566, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Schiaffino_2016_Microbial_eukaryote_communities_exhibit_robust_biogeographical_patterns_along_a_gradient_of_Patagonian_and_Antarctic_lakes.pdf, PDF},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Environmental microbiology},

volume = {18},

number = {12},

pages = {5249–5264},

abstract = {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 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.},

keywords = {Biogeography, Diversity, Metabarcoding},

pubstate = {published},

tppubtype = {article}

}