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 = {Environmental Drivers of \textit{Sphagnum} Growth in Peatlands across the Holarctic Region},

author = {Fia Bengtsson and Håkan Rydin and Jennifer L. Baltzer and Luca Bragazza and Zhao-Jun Bu and Simon J. M. Caporn and Ellen Dorrepaal and Kjell Ivar Flatberg and Olga Galanina and Mariusz Gałka and Anna Ganeva and Irina Goia and Nadezhda Goncharova and Michal Hájek and Akira Haraguchi and Lorna I. Harris and Elyn Humphreys and Martin Jiroušek and Katarzyna Kajukało and Edgar Karofeld and Natalia G. Koronatova and Natalia P. Kosykh and Anna M. Laine and Mariusz Lamentowicz and Elena Lapshina and Juul Limpens and Maiju Linkosalmi and Jin-Ze Ma and Marguerite Mauritz and Edward A. D. Mitchell and Tariq M. Munir and Susan M. Natali and Rayna Natcheva and Richard J. Payne and Dmitriy A. Philippov and Steven K. Rice and Sean Robinson and Bjorn J. M. Robroek and Line Rochefort and David Singer and Hans K. Stenøien and Eeva-Stiina Tuittila and Kai Vellak and James Michael Waddington and Gustaf Granath},

url = {https://doi.org/10.1111/1365-2745.13499, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Bengtsson_2020_Environmental_drivers_of_Sphagnum_growth_in_peatlands_across_the_Holarctic_region.pdf, PDF},

issn = {0022-0477},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Journal of Ecology},

volume = {109},

number = {1},

pages = {417–431},

publisher = {John Wiley & Sons, Ltd},

abstract = {The relative importance of global versus local environmental factors for growth and thus carbon uptake of the bryophyte genus \textit{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 \textit{Sphagnum} species across 99 Holarctic peatlands. We tested the importance of previously proposed abiotic and biotic drivers for peatland carbon uptake (climate, N deposition, water table depth and vascular plant cover) on these two responses. Employing structural equation models (SEMs), we explored both indirect and direct effects of drivers on \textit{Sphagnum} growth. Variation in growth was large, but similar within and between peatlands. Length growth showed a stronger response to predictors than NPP. Moreover, the smaller and denser \textit{Sphagnum fuscum} growing on hummocks had weaker responses to climatic variation than the larger and looser \textit{Sphagnum magellanicum} growing in the wetter conditions. Growth decreased with increasing vascular plant cover within a site. Between sites, precipitation and temperature increased growth for \textit{S. magellanicum}. The SEMs indicate that indirect effects are important. For example, vascular plant cover increased with a deeper water table, increased nitrogen deposition, precipitation and temperature. These factors also influenced \textit{Sphagnum} growth indirectly by affecting moss shoot density. Synthesis. Our results imply that in a warmer climate, \textit{S. magellanicum} will increase length growth as long as precipitation is not reduced, while \textit{S. fuscum} is more resistant to decreased precipitation, but also less able to take advantage of increased precipitation and temperature. Such species-specific sensitivity to climate may affect competitive outcomes in a changing environment, and potentially the future carbon sink function of peatlands.},

keywords = {Peatland},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Testate Amoeba Functional Traits and Their Use in Paleoecology},

author = {Katarzyna Marcisz and Vincent E. J. Jassey and Anush Kosakyan and Valentyna Krashevska and Daniel J. G. Lahr and Enrique Lara and Łukasz Lamentowicz and Mariusz Lamentowicz and Andrew Macumber and Yuri Mazei and Edward A. D. Mitchell and Nawaf A. Nasser and R. Timothy Patterson and Helen M. Roe and David Singer and Andrey N. Tsyganov and Bertrand Fournier},

url = {https://doi.org/10.3389/fevo.2020.575966, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Marcisz_et_al_2020_Testate-amoeba_functional_traits_and_their_use_in_paleoecology.pdf, PDF

},

issn = {2296-701X},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Frontiers in Ecology and Evolution},

volume = {8},

pages = {340},

abstract = {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 and paleoecology has gained in popularity in recent years, with research showing that morphological characteristics provide complementary information to the commonly used environmental inferences based on testate amoeba (morpho-)species data. We provide a broad overview of testate amoeba morphological and functional traits and trait-environment relationships in the context of ecology, evolution, genetics, biogeography, and paleoecology. As examples we report upon previous ecological and paleoecological studies that used trait-based approaches, and describe key testate amoebae traits that can be used to improve the interpretation of environmental studies. We also highlight knowledge gaps and speculate on potential future directions for the application of trait-based approaches in testate amoeba research.},

note = {3},

keywords = {Peatland, Testate-amoebae},

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 = {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 = {Environmental and Taxonomic Controls of Carbon and Oxygen Stable Isotope Composition in \textit{Sphagnum} across Broad Climatic and Geographic Ranges},

author = {G. Granath and H. Rydin and J. L. Baltzer and F. Bengtsson and N. Boncek and L. Bragazza and Z. -J. Bu and S. J. M. Caporn and E. Dorrepaal and O. Galanina and M. Gałka and A. Ganeva and D. P. Gillikin and I. Goia and N. Goncharova and M. Hájek and A. Haraguchi and L. I. Harris and E. Humphreys and M. Jiroušek and K. Kajukało and E. Karofeld and N. G. Koronatova and N. P. Kosykh and M. Lamentowicz and E. Lapshina and J. Limpens and M. Linkosalmi and J. -Z. Ma and M. Mauritz and T. M. Munir and S. M. Natali and R. Natcheva and M. Noskova and R. J. Payne and K. Pilkington and S. Robinson and B. J. M. Robroek and L. Rochefort and D. Singer and H. K. Stenøien and E. -S. Tuittila and K. Vellak and A. Verheyden and J. M. Waddington and S. K. Rice},

url = {https://doi.org/10.5194/bg-15-5189-2018, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Granath_2018_Environmental_and_taxonomic_controls_of_carbon_and_oxygen.pdf, PDF

},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {Biogeosciences},

volume = {15},

number = {16},

pages = {5189–5202},

abstract = {Rain-fed peatlands are dominated by peat mosses (\textit{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 \textit{Sphagnum} mosses are affected by environmental conditions, \textit{Sphagnum} tissue accumulated in peat constitutes a potential long-term archive that can be used for climate reconstruction. However, there is inadequate understanding of how isotope values are influenced by environmental conditions, which restricts their current use as environmental and palaeoenvironmental indicators. Here we tested (i) to what extent C and O isotopic variation in living tissue of \textit{Sphagnum} is species-specific and associated with local hydrological gradients, climatic gradients (evapotranspiration, temperature, precipitation) and elevation; (ii) whether the C isotopic signature can be a proxy for net primary productivity (NPP) of \textit{Sphagnum}; and (iii) to what extent \textit{Sphagnum} tissue δ18O tracks the δ18O isotope signature of precipitation. In total, we analysed 337 samples from 93 sites across North America and Eurasia using two important peat-forming \textit{Sphagnum} species ( \textit{S. magellanicum}, \textit{S. fuscum}) common to the Holarctic realm. There were differences in δ13C values between species. For \textit{S. magellanicum} δ13C decreased with increasing height above the water table (HWT},

keywords = {Peatland},

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}

}