Publications
2025
Verdon, Valentin; Malard, Lucie; Collart, Flavien; Adde, Antoine; Yashiro, Erika; Pandi, Enrique Lara; Mod, Heidi; Singer, David; Niculita-Hirzel, Hélène; Guex, Nicolas; Guisan, Antoine
Can We Accurately Predict the Distribution of Soil Microorganism Presence and Relative Abundance? Journal Article
In: Ecography, vol. 2025, no. 3, pp. e07086, 2025, ISSN: 0906-7590.
Abstract | PDF/Link | Tags: Diversity, Metabarcoding, Protists
@article{nokey,
title = {Can We Accurately Predict the Distribution of Soil Microorganism Presence and Relative Abundance?},
author = {Valentin Verdon and Lucie Malard and Flavien Collart and Antoine Adde and Erika Yashiro and Enrique Lara Pandi and Heidi Mod and David Singer and Hélène Niculita-Hirzel and Nicolas Guex and Antoine Guisan},
url = {https://doi.org/10.1111/ecog.07086, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Verdon_2024_Can_we_accurately_predict_the_distribution_of_soil_microorganism_presence_and_relative_abundance.pdf, PDF},
issn = {0906-7590},
year = {2025},
date = {2025-01-01},
urldate = {2025-01-01},
journal = {Ecography},
volume = {2025},
number = {3},
pages = {e07086},
publisher = {John Wiley & Sons, Ltd},
abstract = {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.},
keywords = {Diversity, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
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.
2024
Fouet, Marie P. A.; Schweizer, Magali; Singer, David; Richirt, Julien; Quinchard, Sophie; Jorissen, Frans J.
In: Marine Micropaleontology, vol. 188, pp. 102353, 2024, ISSN: 0377-8398.
Abstract | PDF/Link | Tags: Biogeography, Diversity, Metabarcoding, Protists
@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}
}
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.
Jung, Patrick; Brand, Rebekah; Briegel-Williams, Laura; Werner, Lina; Jost, Emily; Lentendu, Guillaume; Singer, David; Athavale, Rujuta; Nürnberg, Dennis J.; Alfaro, Fernando D.; Büdel, Burkhard; Lakatos, Michael
The Symbiotic Alga Trebouxia Fuels a Coherent Soil Ecosystem on the Landscape Scale in the Atacama Desert Journal Article
In: Environmental Microbiome, vol. 19, no. 1, pp. 59, 2024, ISSN: 2524-6372.
Abstract | PDF/Link | Tags: Diversity, Ecology, Metabarcoding, Protists
@article{nokey,
title = {The Symbiotic Alga Trebouxia Fuels a Coherent Soil Ecosystem on the Landscape Scale in the Atacama Desert},
author = {Patrick Jung and Rebekah Brand and Laura Briegel-Williams and Lina Werner and Emily Jost and Guillaume Lentendu and David Singer and Rujuta Athavale and Dennis J. Nürnberg and Fernando D. Alfaro and Burkhard Büdel and Michael Lakatos},
url = {https://doi.org/10.1186/s40793-024-00601-5, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Jung_2024_The_symbiotic_alga_Trebouxia_fuels_a_coherent_soil_ecosystem_on_the_landscape_scale_in_the_Atacama_Desert.pdf, PDF
},
issn = {2524-6372},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Environmental Microbiome},
volume = {19},
number = {1},
pages = {59},
abstract = {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 chlorophyll a+b contents. Metabarcoding showed that yet undescribed lichens within the Caliciaceae dominated the biocrust together with \textit{Trebouxia} as the most abundant eukaryote in all plots. Together with high mean chlorophyll a+b contents exceeding 410 mg m−2, this distinguished the symbiotic algae \textit{Trebouxia} as the main driver of the grit crust ecosystem. The trebouxioid photobionts could be assigned to the I ( \textit{T. impressa/gelatinosa}) and A ( \textit{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.},
keywords = {Diversity, Ecology, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
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 chlorophyll a+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 chlorophyll a+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.
Porfirio-Sousa, Alfredo L.; Tice, Alexander K.; Morais, Luana; Ribeiro, Giulia M.; Blandenier, Quentin; Dumack, Kenneth; Eglit, Yana; Fry, Nicholas W.; Souza, Maria Beatriz Gomes E; Henderson, Tristan C.; Kleitz-Singleton, Felicity; Singer, David; Brown, Matthew W.; Lahr, Daniel J. G.
Amoebozoan Testate Amoebae Illuminate the Diversity of Heterotrophs and the Complexity of Ecosystems throughout Geological Time Journal Article
In: PNAS, vol. 121, no. 30, pp. e2319628121, 2024.
Abstract | PDF/Link | Tags: Diversity, Testate-amoebae
@article{nokey,
title = {Amoebozoan Testate Amoebae Illuminate the Diversity of Heterotrophs and the Complexity of Ecosystems throughout Geological Time},
author = {Alfredo L. Porfirio-Sousa and Alexander K. Tice and Luana Morais and Giulia M. Ribeiro and Quentin Blandenier and Kenneth Dumack and Yana Eglit and Nicholas W. Fry and Maria Beatriz Gomes E Souza and Tristan C. Henderson and Felicity Kleitz-Singleton and David Singer and Matthew W. Brown and Daniel J. G. Lahr},
url = {https://doi.org/10.1073/pnas.2319628121, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Porfirio-Sousa_2024_Amoebozoan_testate_amoebae_illuminate_the_diversity_of_heterotrophs_and_the_complexity.pdf, PDF},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {PNAS},
volume = {121},
number = {30},
pages = {e2319628121},
publisher = {Proceedings of the National Academy of Sciences},
abstract = {Arcellinida shelled amoebae are heterotrophic microbial eukaryotes with an extensive Neoproterozoic fossil record, the vase-shaped microfossils (VSMs), a diverse group that is abundant and widespread in late Tonian rocks. We combined phylogenomic sampling and the fossil record to generate time-calibrated trees. Our results illuminate key events in the history of life, including: i) the Tonian origin of extant microbial eukaryote lineages; ii) a speculative proposed radiation of eukaryotes before the Cryogenian, "Tonian revolution"; iii) the establishment of complex terrestrial habitats before the Cryogenian; iv) a post-Silurian divergence of modern Arcellinida subclades in terrestrial (including freshwater) habitats. Our results provide insights into the evolution of life throughout geological time and are congruent with recent discoveries regarding the early diversification of eukaryotes. 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.},
keywords = {Diversity, Testate-amoebae},
pubstate = {published},
tppubtype = {article}
}
Arcellinida shelled amoebae are heterotrophic microbial eukaryotes with an extensive Neoproterozoic fossil record, the vase-shaped microfossils (VSMs), a diverse group that is abundant and widespread in late Tonian rocks. We combined phylogenomic sampling and the fossil record to generate time-calibrated trees. Our results illuminate key events in the history of life, including: i) the Tonian origin of extant microbial eukaryote lineages; ii) a speculative proposed radiation of eukaryotes before the Cryogenian, "Tonian revolution"; iii) the establishment of complex terrestrial habitats before the Cryogenian; iv) a post-Silurian divergence of modern Arcellinida subclades in terrestrial (including freshwater) habitats. Our results provide insights into the evolution of life throughout geological time and are congruent with recent discoveries regarding the early diversification of eukaryotes. 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.
2023
Singer, David; Fouet, Marie P. A.; Schweizer, Magali; Mouret, Aurélia; Quinchard, Sophie; Jorissen, Frans J.
Unlocking Foraminiferal Genetic Diversity on Estuarine Mudflats with eDNA Metabarcoding Journal Article
In: Science of the Total Environment, pp. 165983, 2023, ISSN: 0048-9697.
Abstract | PDF/Link | Tags: Diversity, Ecology, First-Last-Author, Metabarcoding, Protists
@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}
}
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.
González-Miguéns, Rubén; Cano, Emilio; Guillén-Oterino, Antonio; Quesada, Antonio; Lahr, Daniel J. G.; Tenorio-Rodríguez, Daniel; Salvador-Velasco, David; Velázquez, David; Carrasco-Braganza, María Isabel; Patterson, R. Timothy; Lara, Enrique; Singer, David
A Needle in a Haystack: A New Metabarcoding Approach to Survey Diversity at the Species Level of Arcellinida (Amoebozoa: Tubulinea) Journal Article
In: Molecular Ecology Resources, vol. 23, iss. 5, pp. 1034-1049, 2023, ISSN: 1755-098X.
Abstract | PDF/Link | Tags: Diversity, Ecology, First-Last-Author, Metabarcoding, Testate-amoebae
@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}
}
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.
Velasco-González, Ismael; Lara, Enrique; Singer, David; Cos-Gandoy, Amaya; García-Rodríguez, Manuel; Murciano, Antonio; Pérez-Uz, Blanca; Williams, Richard; Sanchez-Jimenez, Abel; Martín-Cereceda, Mercedes
Diversity of DNA Sequences from Pathogenic and Potentially Pathogenic Eukaryotic Microorganisms in Protected Granite Mountain Rocks Journal Article
In: Diversity, vol. 15, no. 5, 2023, ISSN: 1424-2818.
Abstract | PDF/Link | Tags: Diversity, Ecology, Metabarcoding, Protists
@article{nokey,
title = {Diversity of DNA Sequences from Pathogenic and Potentially Pathogenic Eukaryotic Microorganisms in Protected Granite Mountain Rocks},
author = {Ismael Velasco-González and Enrique Lara and David Singer and Amaya Cos-Gandoy and Manuel García-Rodríguez and Antonio Murciano and Blanca Pérez-Uz and Richard Williams and Abel Sanchez-Jimenez and Mercedes Martín-Cereceda},
url = {https://doi.org/10.3390/d15050594, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Velasco-Gonzalez_2023_Diversity_of_DNA_Sequences_from_Pathogenic_and_Potentially_Pathogenic_Eukaryotic_Microorganisms_in_Protected_Granite_Mountain_Rocks.pdf, PDF
},
issn = {1424-2818},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Diversity},
volume = {15},
number = {5},
abstract = {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., \textit{Pythium} spp., \textit{Lagenidium} spp., \textit{Candida} spp. and \textit{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.},
keywords = {Diversity, Ecology, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
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.
2022
Jorissen, Frans J.; Fouet, Marie P. A.; Singer, David; Howa, Hélène
The Marine Influence Index (MII): A Tool to Assess Estuarine Intertidal Mudflat Environments for the Purpose of Foraminiferal Biomonitoring Journal Article
In: Water, vol. 14, no. 4, pp. 676, 2022, ISSN: 2073-4441.
Abstract | PDF/Link | Tags: Diversity, Ecology, Protists
@article{nokey,
title = {The Marine Influence Index (MII): A Tool to Assess Estuarine Intertidal Mudflat Environments for the Purpose of Foraminiferal Biomonitoring},
author = {Frans J. Jorissen and Marie P. A. Fouet and David Singer and Hélène Howa},
url = {https://doi.org/10.3390/w14040676, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Jorissen_2022_The-Marine-Influence-Index-MII-A-Tool-to-Assess-Estuarine.pdf, PDF
},
issn = {2073-4441},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Water},
volume = {14},
number = {4},
pages = {676},
abstract = {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 emergence time relative to a reference tidal cycle, and (3) the relative importance of river outflow in the 30 days before sampling the foraminiferal fauna. Although these three parameters all have a strong relation with salinity, they also implicitly include other environmental parameters, such as the introduction of marine and continental organic matter and biota, hydrodynamic energy, or temperature. In order to show the functioning of this new index, MII is calculated for 28 stations in the Auray and Vie estuaries, for two different periods. The next step will be to compare the MII with faunal data sets. Ideally, this comparison should allow us to find strong correlations between some characteristics of the foraminiferal assemblages and the MII. If such strong correlations were indeed found, any major deviation of this relationship could then be interpreted as being due to strong anthropogenic disturbance.},
keywords = {Diversity, Ecology, Protists},
pubstate = {published},
tppubtype = {article}
}
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 emergence time relative to a reference tidal cycle, and (3) the relative importance of river outflow in the 30 days before sampling the foraminiferal fauna. Although these three parameters all have a strong relation with salinity, they also implicitly include other environmental parameters, such as the introduction of marine and continental organic matter and biota, hydrodynamic energy, or temperature. In order to show the functioning of this new index, MII is calculated for 28 stations in the Auray and Vie estuaries, for two different periods. The next step will be to compare the MII with faunal data sets. Ideally, this comparison should allow us to find strong correlations between some characteristics of the foraminiferal assemblages and the MII. If such strong correlations were indeed found, any major deviation of this relationship could then be interpreted as being due to strong anthropogenic disturbance.
2021
Singer, David; Seppey, Christophe V. W.; Lentendu, Guillaume; Dunthorn, Micah; Bass, David; Belbahri, Lassâad; Blandenier, Quentin; Debroas, Didier; Groot, G. Arjen; Vargas, Colomban; Domaizon, Isabelle; Duckert, Clément; Izaguirre, Irina; Koenig, Isabelle; Mataloni, Gabriela; Schiaffino, M. Romina; Mitchell, Edward A. D.; Geisen, Stefan; Lara, Enrique
Protist Taxonomic and Functional Diversity in Soil, Freshwater and Marine Ecosystems Journal Article
In: Environment International, vol. 146, pp. 106262, 2021, ISSN: 0160-4120.
Abstract | PDF/Link | Tags: Diversity, First-Last-Author, Metabarcoding, Protists
@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}
}
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.
Izaguirre, Irina; Unrein, Fernando; Schiaffino, M. Romina; Lara, Enrique; Singer, David; Balagué, Vanessa; Gasol, Josep M.; Massana, Ramon
Phylogenetic Diversity and Dominant Ecological Traits of Freshwater Antarctic Chrysophyceae Journal Article
In: Polar Biology, vol. 44, pp. 941–957, 2021, ISSN: 1432-2056.
Abstract | PDF/Link | Tags: Diversity, Ecology, Metabarcoding, Protists
@article{nokey,
title = {Phylogenetic Diversity and Dominant Ecological Traits of Freshwater Antarctic Chrysophyceae},
author = {Irina Izaguirre and Fernando Unrein and M. Romina Schiaffino and Enrique Lara and David Singer and Vanessa Balagué and Josep M. Gasol and Ramon Massana},
url = {https://doi.org/10.1007/s00300-021-02850-3, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Izaguirre_2021_Phylogenetic_diversity_and_dominant_ecological_tra.pdf, PDF},
issn = {1432-2056},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Polar Biology},
volume = {44},
pages = {941–957},
abstract = {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 relevance of this group in these Antarctic microbial foodwebs, we carried out further molecular analyses (clone libraries and 18S Illumina high throughput sequencing) to characterize their phylogenetic diversity. The results of this study significantly increased the retrieved Chrysophyceae biodiversity. Clone libraries in two selected lakes (one oligotrophic and one mesotrophic) yielded 12 different chrysophycean OTUs, whereas 81 Swarm OTUs were recovered from six lakes using Illumina HiSeq. With the combination of both methods, we observed sequences of all the chrysophyte known clades, although most of the diversity belonged to Clade D, a group comprising mixotrophic and heterotrophic species. The percentage of reads for this clade in Illumina HiSeq ranged from 30% to 96% of the total Chrysophyceae reads. Based on experiments and observations, we also describe the main ecological traits of this group: the dominant taxa were small pigmented flagellates, well adapted to survive in oligotrophic systems, sometimes abundant under ice-cover subjected to low light intensities, and that have phagotrophic behavior. The used combination of methods allowed us to characterize the biodiversity and ecology of the Chrysophyceae, the dominant phytoplankton group in the oligotrophic lakes of this Maritime Antarctic region.},
keywords = {Diversity, Ecology, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
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 relevance of this group in these Antarctic microbial foodwebs, we carried out further molecular analyses (clone libraries and 18S Illumina high throughput sequencing) to characterize their phylogenetic diversity. The results of this study significantly increased the retrieved Chrysophyceae biodiversity. Clone libraries in two selected lakes (one oligotrophic and one mesotrophic) yielded 12 different chrysophycean OTUs, whereas 81 Swarm OTUs were recovered from six lakes using Illumina HiSeq. With the combination of both methods, we observed sequences of all the chrysophyte known clades, although most of the diversity belonged to Clade D, a group comprising mixotrophic and heterotrophic species. The percentage of reads for this clade in Illumina HiSeq ranged from 30% to 96% of the total Chrysophyceae reads. Based on experiments and observations, we also describe the main ecological traits of this group: the dominant taxa were small pigmented flagellates, well adapted to survive in oligotrophic systems, sometimes abundant under ice-cover subjected to low light intensities, and that have phagotrophic behavior. The used combination of methods allowed us to characterize the biodiversity and ecology of the Chrysophyceae, the dominant phytoplankton group in the oligotrophic lakes of this Maritime Antarctic region.
Nawaf, A. Nasser; Braden, R. B. Gregory; Singer, David; Patterson, R. Timothy; Roe, Helen M.
Erugomicula, a New Genus of Arcellinida (Testate Lobose Amoebae) Journal Article
In: Palaeontologia Electronica, vol. 24(1), iss. a16, 2021.
Abstract | PDF/Link | Tags: Diversity, Protists, Testate-amoebae
@article{nokey,
title = {\textit{Erugomicula}, a New Genus of Arcellinida (Testate Lobose Amoebae)},
author = {A. Nasser Nawaf and R. B. Gregory Braden and David Singer and R. Timothy Patterson and Helen M. Roe},
url = {https://doi.org/10.26879/807, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Nasser_2021_Erugomicula_a_new_genus_of_Arcellinida.pdf, PDF
},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Palaeontologia Electronica},
volume = {24(1)},
issue = {a16},
abstract = {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 species and 200 sub-species have been attributed to the genus Difflugia Leclerc, 1815. Although carried out on only a few taxa, molecular evidence has demonstrated that test morphology is more important than test composition in categorizing distinct taxa within the Arcellinida. The type species of \textit{Difflugia, D. proteiformis} Lamarck, 1816, is characterized by a terminal aperture and an elongate acuminate test. The morphology of \textit{D. proteiformis} is vastly different from most species assigned to \textit{Difflugia}, explaining its polyphyletic status. We reclassify \textit{Difflugia bidens} Penard, 1902 as type species of \textit{Erugomicula}, a new genus within the Difflugidae, which is distinguished from other taxa within \textit{Difflugia} by its broad, ovoid test, and distinct compression. Based on the compressed morphology of the test, which is not a characteristic of the Difflugiidae, we tentatively assign \textit{Erugomicula} to the family Hyalospheniidae.},
keywords = {Diversity, Protists, Testate-amoebae},
pubstate = {published},
tppubtype = {article}
}
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 species and 200 sub-species have been attributed to the genus Difflugia Leclerc, 1815. Although carried out on only a few taxa, molecular evidence has demonstrated that test morphology is more important than test composition in categorizing distinct taxa within the Arcellinida. The type species of Difflugia, D. proteiformis Lamarck, 1816, is characterized by a terminal aperture and an elongate acuminate test. The morphology of D. proteiformis is vastly different from most species assigned to Difflugia, explaining its polyphyletic status. We reclassify Difflugia bidens Penard, 1902 as type species of Erugomicula, a new genus within the Difflugidae, which is distinguished from other taxa within Difflugia by its broad, ovoid test, and distinct compression. Based on the compressed morphology of the test, which is not a characteristic of the Difflugiidae, we tentatively assign Erugomicula to the family Hyalospheniidae.
2020
Velasco-González, Ismael; Sanchez-Jimenez, Abel; Singer, David; Murciano, Antonio; Díez-Hermano, Sergio; Lara, Enrique; Martín-Cereceda, Mercedes
Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes Journal Article
In: Microbial Ecology, vol. 79, no. 4, pp. 882–897, 2020, ISSN: 1432-184X, (5).
Abstract | PDF/Link | Tags: Diversity, Metabarcoding, Protists
@article{nokey,
title = {Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes},
author = {Ismael Velasco-González and Abel Sanchez-Jimenez and David Singer and Antonio Murciano and Sergio Díez-Hermano and Enrique Lara and Mercedes Martín-Cereceda},
url = {https://doi.org/10.1007/s00248-019-01463-y, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Velasco_Gonzalez_2019_Rain_Fed_Granite_Rock_basins_accumulate_a_high_diversity_of_dormant_microbial_eukaryote.pdf, PDF
},
issn = {1432-184X},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Microbial Ecology},
volume = {79},
number = {4},
pages = {882–897},
abstract = {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 hardly any research has been carried out on microorganisms. The aim of this study is to provide the first insights on the diversity of eukaryotic microbial communities from these environments. Due to the ephemeral nature of these aquatic environments, we predict that the granitic basins should host a high proportion of dormant microeukaryotes. Based on an environmental DNA diversity survey, we reveal diverse communities with representatives of all major eukaryotic taxonomic supergroups, mainly composed of a diverse pool of low abundance OTUs. Basin communities were very distinctive, with alpha and beta diversity patterns non-related to basin size or spatial distance respectively. Dissimilarity between basins was mainly characterised by turnover of OTUs. The strong microbial eukaryotic heterogeneity observed among the basins may be explained by a complex combination of deterministic factors (diverging environment in the basins), spatial constraints, and randomness including founder effects. Most interestingly, communities contain organisms that cannot coexist at the same time because of incompatible metabolic requirements, thus suggesting the existence of a pool of dormant organisms whose activity varies along with the changing environment. These organisms accumulate in the pools, which turns granitic rock into high biodiversity microbial islands whose conservation and study deserve further attention.},
note = {5},
keywords = {Diversity, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
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 hardly any research has been carried out on microorganisms. The aim of this study is to provide the first insights on the diversity of eukaryotic microbial communities from these environments. Due to the ephemeral nature of these aquatic environments, we predict that the granitic basins should host a high proportion of dormant microeukaryotes. Based on an environmental DNA diversity survey, we reveal diverse communities with representatives of all major eukaryotic taxonomic supergroups, mainly composed of a diverse pool of low abundance OTUs. Basin communities were very distinctive, with alpha and beta diversity patterns non-related to basin size or spatial distance respectively. Dissimilarity between basins was mainly characterised by turnover of OTUs. The strong microbial eukaryotic heterogeneity observed among the basins may be explained by a complex combination of deterministic factors (diverging environment in the basins), spatial constraints, and randomness including founder effects. Most interestingly, communities contain organisms that cannot coexist at the same time because of incompatible metabolic requirements, thus suggesting the existence of a pool of dormant organisms whose activity varies along with the changing environment. These organisms accumulate in the pools, which turns granitic rock into high biodiversity microbial islands whose conservation and study deserve further attention.
2018
Singer, David; Kosakyan, Anush; Seppey, Christophe V. W.; Pillonel, Amandine; Fernández, Leonardo D.; Fontaneto, Diego; Mitchell, Edward A. D.; Lara, Enrique
Environmental Filtering and Phylogenetic Clustering Correlate with the Distribution Patterns of Cryptic Protist Species Journal Article
In: Ecology, vol. 99, no. 4, pp. 904–914, 2018, ISSN: 1939-9170.
Abstract | PDF/Link | Tags: Diversity, Ecology, First-Last-Author, Peatland, Testate-amoebae
@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}
}
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 Nebela, a group of closely related testate (shelled) amoeba species, in different habitats within 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 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.
Duckert, Clément; Blandenier, Quentin; Kupferschmid, Fanny A. L.; Kosakyan, Anush; Mitchell, Edward A. D.; Lara, Enrique; Singer, David
En Garde! Redefinition of Nebela Militaris (Arcellinida, Hyalospheniidae) and Erection of Alabasta Gen. Nov. Journal Article
In: European Journal of Protistology, vol. 66, pp. 156–165, 2018.
Abstract | PDF/Link | Tags: Diversity, First-Last-Author, Peatland, Testate-amoebae
@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}
}
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 Nebela militaris. A phylogenetic reconstruction of the Hyalospheniidae using partial sequences of the mitochondrial Cytochrome Oxidase Subunit 1 (COI) gene shows that N. militaris does not belong to genus 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: Alabasta gen. nov. Based on their morphology, we include in this genus Nebela kivuense and Nebela longicollis. We discuss the position of genus Alabasta within Hyalospheniidae, and the species that could integrate this new genus based on their morphological characteristics.
Geisen, Stefan; Mitchell, Edward A. D.; Adl, Sina; Bonkowski, Michael; Dunthorn, Micah; Ekelund, Flemming; Fernández, Leonardo D.; Jousset, Alexandre; Krashevska, Valentyna; Singer, David; Spiegel, Frederick W.; Walochnik, Julia; Lara, Enrique
Soil Protists: A Fertile Frontier in Soil Biology Research Journal Article
In: FEMS Microbiology Reviews, vol. 42, no. 3, pp. 293–323, 2018.
Abstract | PDF/Link | Tags: Biogeography, Diversity, Ecology, Protists
@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}
}
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.
Szelecz, Ildikó; Lösch, Sandra; Seppey, Christophe V. W.; Lara, Enrique; Singer, David; Sorge, Franziska; Tschui, Joelle; Perotti, M. Alejandra; Mitchell, Edward A. D.
In: Scientific Reports, vol. 8, no. 1, pp. 25, 2018.
Abstract | PDF/Link | Tags: Diversity, Metabarcoding, Protists
@article{nokey,
title = {Comparative Analysis of Bones, Mites, Soil Chemistry, Nematodes and Soil Micro-Eukaryotes from a Suspected Homicide to Estimate the Post-Mortem Interval},
author = {Ildikó Szelecz and Sandra Lösch and Christophe V. W. Seppey and Enrique Lara and David Singer and Franziska Sorge and Joelle Tschui and M. Alejandra Perotti and Edward A. D. Mitchell},
url = {https://doi.org/10.1038/s41598-017-18179-z, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Szelecz_2018_Comparative_analysis_of_bones_mites_soil_chemistry_nematodes_and_soil_microeukaryotes_from_a_suspected_homicide_to_estimate_the_post_mortem_interval.pdf, PDF},
year = {2018},
date = {2018-01-01},
urldate = {2018-01-01},
journal = {Scientific Reports},
volume = {8},
number = {1},
pages = {25},
abstract = {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 the head, upper and lower body and “control” samples taken a few meters away. We analysed soil chemical characteristics, mites and nematodes (by microscopy) and micro-eukaryotes (by Illumina high throughput sequencing). The PMI estimate on hair ¹⁴C-data via bomb peak radiocarbon dating gave a time range of 1 to 3 years before the discovery of the remains. Cluster analyses for soil chemical constituents, nematodes, mites and micro-eukaryotes revealed two clusters 1) head and upper body and 2) lower body and controls. From mite evidence, we conclude that the body was probably brought to the site after death. However, chemical analyses, nematode community analyses and the analyses of micro-eukaryotes indicate that decomposition took place at least partly on site. This study illustrates the usefulness of combining several lines of evidence for the study of homicide cases to better calibrate PMI inference tools.},
keywords = {Diversity, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
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 the head, upper and lower body and “control” samples taken a few meters away. We analysed soil chemical characteristics, mites and nematodes (by microscopy) and micro-eukaryotes (by Illumina high throughput sequencing). The PMI estimate on hair ¹⁴C-data via bomb peak radiocarbon dating gave a time range of 1 to 3 years before the discovery of the remains. Cluster analyses for soil chemical constituents, nematodes, mites and micro-eukaryotes revealed two clusters 1) head and upper body and 2) lower body and controls. From mite evidence, we conclude that the body was probably brought to the site after death. However, chemical analyses, nematode community analyses and the analyses of micro-eukaryotes indicate that decomposition took place at least partly on site. This study illustrates the usefulness of combining several lines of evidence for the study of homicide cases to better calibrate PMI inference tools.
2017
Mahé, Frédéric; Vargas, Colomban; Bass, David; Czech, Lucas; Stamatakis, Alexandros; Lara, Enrique; Singer, David; Mayor, Jordan; Bunge, John; Sernaker, Sarah; Siemensmeyer, Tobias; Trautmann, Isabelle; Romac, Sarah; Berney, Cédric; Kozlov, Alexey; Mitchell, Edward A. D.; Seppey, Christophe V. W.; Egge, Elianne; Lentendu, Guillaume; Wirth, Rainer; Trueba, Gabriel; Dunthorn, Micah
Parasites Dominate Hyperdiverse Soil Protist Communities in Neotropical Rainforests Journal Article
In: Nature Ecology & Evolution, vol. 1, no. 4, pp. 0091, 2017, ISSN: 2397-334X.
Abstract | PDF/Link | Tags: Diversity, Metabarcoding, Protists
@article{nokey,
title = {Parasites Dominate Hyperdiverse Soil Protist Communities in Neotropical Rainforests},
author = {Frédéric Mahé and Colomban Vargas and David Bass and Lucas Czech and Alexandros Stamatakis and Enrique Lara and David Singer and Jordan Mayor and John Bunge and Sarah Sernaker and Tobias Siemensmeyer and Isabelle Trautmann and Sarah Romac and Cédric Berney and Alexey Kozlov and Edward A. D. Mitchell and Christophe V. W. Seppey and Elianne Egge and Guillaume Lentendu and Rainer Wirth and Gabriel Trueba and Micah Dunthorn},
url = {https://doi.org/10.1038/s41559-017-0091, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Mahe_2017_Parasites_dominate_hyperdiverse_soil_protist_communities_in_Neotropical_rainforests.pdf, PDF},
issn = {2397-334X},
year = {2017},
date = {2017-01-01},
urldate = {2017-01-01},
journal = {Nature Ecology & Evolution},
volume = {1},
number = {4},
pages = {0091},
abstract = {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 in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms.},
keywords = {Diversity, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
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 in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms.
Blandenier, Quentin; Seppey, Christophe V. W.; Singer, David; Vlimant, Michèle; Simon, Anaële; Duckert, Clément; Lara, Enrique
Mycamoeba Gemmipara Nov. Gen., Nov. Sp., the First Cultured Member of the Environmental Dermamoebidae Clade LKM74 and Its Unusual Life Cycle Journal Article
In: Journal of Eukaryotic Microbiology, vol. 64, no. 2, pp. 257–265, 2017, ISSN: 1066-5234.
Abstract | PDF/Link | Tags: Diversity, Protists
@article{nokey,
title = {\textit{Mycamoeba Gemmipara} Nov. Gen., Nov. Sp., the First Cultured Member of the Environmental Dermamoebidae Clade LKM74 and Its Unusual Life Cycle},
author = {Quentin Blandenier and Christophe V. W. Seppey and David Singer and Michèle Vlimant and Anaële Simon and Clément Duckert and Enrique Lara},
url = {https://doi.org/10.1111/jeu.12357, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Blandenier_2016_Mycamoeba_gemmipara_nov_gen_nov_sp_the_First_Cultured_Member_of_the_Environmental_Dermamoebidae_Clade_LKM74_and_its_Unusual_Life_Cycle.pdf, PDF},
issn = {1066-5234},
year = {2017},
date = {2017-01-01},
urldate = {2017-01-01},
journal = {Journal of Eukaryotic Microbiology},
volume = {64},
number = {2},
pages = {257–265},
abstract = {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, close related to freshwater clones. We described \textit{Mycamoeba gemmipara} based on observations made with light- and transmission electron microscopy. It is an extremely small amoeba with typical lingulate shape. Unlike other Dermamoebidae, it lacked ornamentation on its cell membrane, and condensed chromatin formed characteristic patterns in the nucleus. \textit{M. gemmipara} displayed a unique life cycle: trophozoites formed walled coccoid stages which grew through successive buddings and developed into branched structures holding cysts. These structures, measuring hundreds of micrometres, are built as the exclusive product of osmotrophic feeding. To demonstrate that \textit{M. gemmipara} is a genuine soil inhabitant, we screened its presence in an environmental soil DNA diversity survey performed on an experimental setup where pig cadavers were left to decompose in soils to follow changes in eukaryotic communities. \textit{Mycamoeba gemmipara} was present in all samples, although related reads were uncommon underneath the cadaver.},
keywords = {Diversity, Protists},
pubstate = {published},
tppubtype = {article}
}
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, close related to freshwater clones. We described Mycamoeba gemmipara based on observations made with light- and transmission electron microscopy. It is an extremely small amoeba with typical lingulate shape. Unlike other Dermamoebidae, it lacked ornamentation on its cell membrane, and condensed chromatin formed characteristic patterns in the nucleus. M. gemmipara displayed a unique life cycle: trophozoites formed walled coccoid stages which grew through successive buddings and developed into branched structures holding cysts. These structures, measuring hundreds of micrometres, are built as the exclusive product of osmotrophic feeding. To demonstrate that M. gemmipara is a genuine soil inhabitant, we screened its presence in an environmental soil DNA diversity survey performed on an experimental setup where pig cadavers were left to decompose in soils to follow changes in eukaryotic communities. Mycamoeba gemmipara was present in all samples, although related reads were uncommon underneath the cadaver.
2016
Schiaffino, M. Romina; Lara, Enrique; Fernández, Leonardo D.; Balagué, Vanessa; Singer, David; Seppey, Christophe V. W.; Massana, Ramon; Izaguirre, Irina
Microbial Eukaryote Communities Exhibit Robust Biogeographical Patterns along a Gradient of Patagonian and Antarctic Lakes Journal Article
In: Environmental microbiology, vol. 18, no. 12, pp. 5249–5264, 2016.
Abstract | PDF/Link | Tags: Biogeography, Diversity, Metabarcoding
@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}
}
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.
Singer, David; Lara, Enrique; Steciow, Mónica M.; Seppey, Christophe V. W.; Paredes, Noelia; Pillonel, Amandine; Oszako, Tomasz; Belbahri, Lassâad
High-Throughput Sequencing Reveals Diverse Oomycete Communities in Oligotrophic Peat Bog Micro-Habitat Journal Article
In: Fungal Ecology, vol. 23, pp. 42–47, 2016.
Abstract | PDF/Link | Tags: Diversity, Ecology, First-Last-Author, Metabarcoding, Peatland
@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}
}
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 ( Aphanomyces astaci: X1100 and 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.
2015
Seppey, Christophe V. W.; Fournier, Bertrand; Szelecz, Ildikò; Singer, David; Mitchell, Edward A. D.; Lara, Enrique
Response of Forest Soil Euglyphid Testate Amoebae (Rhizaria: Cercozoa) to Pig Cadavers Assessed by High-Throughput Sequencing Journal Article
In: International Journal of Legal Medicine, vol. 130, no. 2, pp. 551–562, 2015, ISSN: 0937-9827.
Abstract | PDF/Link | Tags: Diversity, Ecology, Metabarcoding
@article{nokey,
title = {Response of Forest Soil Euglyphid Testate Amoebae (Rhizaria: Cercozoa) to Pig Cadavers Assessed by High-Throughput Sequencing},
author = {Christophe V. W. Seppey and Bertrand Fournier and Ildikò Szelecz and David Singer and Edward A. D. Mitchell and Enrique Lara},
url = {https://link.springer.com/article/10.1007/s00414-015-1149-7, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Seppey_2015_Response_of_forest_soil_euglyphid_testate_amoebae_Rhizaria_Cercozoa_to_pig_cadavers_assessed_by_high_throughput_sequencing.pdf, PDF},
issn = {0937-9827},
year = {2015},
date = {2015-01-01},
urldate = {2015-01-01},
journal = {International Journal of Legal Medicine},
volume = {130},
number = {2},
pages = {551–562},
abstract = {Decomposing cadavers modify the soil environment, 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, amplified the SSU ribosomal RNA (rRNA) gene V9 region and sequenced it by Illumina technology and analysed the data for euglyphid testate amoebae (Rhizaria: Euglyphida), a common group of protozoa known to respond to micro-environmental changes. We found 51 euglyphid operational taxonomic units (OTUs), 45 of which did not match any known sequence. Most OTUs decreased in abundance underneath cadavers between days 0 and 309, but some responded positively after a time lag. We sequenced the full-length SSU rRNA gene of two common OTUs that responded positively to cadavers; a phylogenetic analysis showed that they did not belong to any known euglyphid family. This study confirmed the existence of an unknown diversity of euglyphids and that they react to cadavers. Results suggest that metabarcoding of soil euglyphids could be used as a forensic tool to estimate the post-mortem interval (PMI) particularly for long-term (>2 months) PMI, for which no reliable tool exists.},
keywords = {Diversity, Ecology, Metabarcoding},
pubstate = {published},
tppubtype = {article}
}
Decomposing cadavers modify the soil environment, 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, amplified the SSU ribosomal RNA (rRNA) gene V9 region and sequenced it by Illumina technology and analysed the data for euglyphid testate amoebae (Rhizaria: Euglyphida), a common group of protozoa known to respond to micro-environmental changes. We found 51 euglyphid operational taxonomic units (OTUs), 45 of which did not match any known sequence. Most OTUs decreased in abundance underneath cadavers between days 0 and 309, but some responded positively after a time lag. We sequenced the full-length SSU rRNA gene of two common OTUs that responded positively to cadavers; a phylogenetic analysis showed that they did not belong to any known euglyphid family. This study confirmed the existence of an unknown diversity of euglyphids and that they react to cadavers. Results suggest that metabarcoding of soil euglyphids could be used as a forensic tool to estimate the post-mortem interval (PMI) particularly for long-term (>2 months) PMI, for which no reliable tool exists.
Lara, Enrique; Seppey, Christophe V. W.; Garraza, Gabriela González; Singer, David; Quiroga, Maria Victoria; Mataloni, Gabriela
Planktonic Eukaryote Molecular Diversity: Discrimination of Minerotrophic and Ombrotrophic Peatland Pools in Tierra Del Fuego (Argentina) Journal Article
In: Journal of Plankton Research, vol. 37, no. 3, pp. 645–655, 2015.
Abstract | PDF/Link | Tags: Diversity, Ecology, Metabarcoding
@article{nokey,
title = {Planktonic Eukaryote Molecular Diversity: Discrimination of Minerotrophic and Ombrotrophic Peatland Pools in Tierra Del Fuego (Argentina)},
author = {Enrique Lara and Christophe V. W. Seppey and Gabriela González Garraza and David Singer and Maria Victoria Quiroga and Gabriela Mataloni},
url = {https://doi.org/10.1093/plankt/fbv016, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Lara_2015_Planktonic_eukaryote_molecular_diversity_discrimination_of_minerotrophic_and_ombrotrophic_peatland_pools_in_Tierra_del_Fuego_Argentina.pdf, PDF},
year = {2015},
date = {2015-01-01},
urldate = {2015-01-01},
journal = {Journal of Plankton Research},
volume = {37},
number = {3},
pages = {645–655},
abstract = {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, with a good representation of Perkinsea and Cercozoa clade NC-10. A community composition analysis performed using GUniFraC separated minerotrophic and ombrotrophic sites, reflecting perfectly the classification of the sites based on environmental data. However, this separation disappeared when more weight was given to abundant phylotypes, suggesting that subordinate phylotypes were responsible for site discrimination. The 5% best indicators for, respectively, minerotrophic and ombrotrophic environments were searched using an IndVal analysis. Among these, autotrophic taxa were more common in minerotrophic environments, whereas mixotrophic taxa represented best ombrotrophic water bodies. However, the ecological traits of many taxa have still not been determined, and still needs to be investigated for a better understanding of freshwater systems ecology.},
keywords = {Diversity, Ecology, Metabarcoding},
pubstate = {published},
tppubtype = {article}
}
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, with a good representation of Perkinsea and Cercozoa clade NC-10. A community composition analysis performed using GUniFraC separated minerotrophic and ombrotrophic sites, reflecting perfectly the classification of the sites based on environmental data. However, this separation disappeared when more weight was given to abundant phylotypes, suggesting that subordinate phylotypes were responsible for site discrimination. The 5% best indicators for, respectively, minerotrophic and ombrotrophic environments were searched using an IndVal analysis. Among these, autotrophic taxa were more common in minerotrophic environments, whereas mixotrophic taxa represented best ombrotrophic water bodies. However, the ecological traits of many taxa have still not been determined, and still needs to be investigated for a better understanding of freshwater systems ecology.
Singer, David; Kosakyan, Anush; Pillonel, Amandine; Mitchell, Edward A. D.; Lara, Enrique
Eight Species in the Nebela Collaris Complex: Nebela Gimlii (Arcellinida, Hyalospheniidae), a New Species Described from a Swiss Raised Bog Journal Article
In: European Journal of Protistology, vol. 51, no. 1, pp. 79–85, 2015, ISSN: 0932-4739.
Abstract | PDF/Link | Tags: Diversity, First-Last-Author, Peatland, Testate-amoebae
@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}
}
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 Nebela gimlii was placed in a phylogenetic tree based on mitochondrial cytochrome oxidase sequences (COI), and branched robustly within the N. collaris complex next to the morphologically similar N. guttata and 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 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.