Publications
2025
Lentendu, Guillaume; Singer, David; Agatha, Sabine; Bahram, Mohammad; Hannula, S. Emilia; Helder, Johannes; Tedersoo, Leho; Traunspurger, Walter; Geisen, Stefan; Lara, Enrique
EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes Journal Article
In: Molecular Ecology Resources, vol. 25, no. 7, pp. e14118, 2025, ISSN: 1755-098X.
Abstract | PDF/Link | Tags: Ecology, Metabarcoding, Protists
@article{nokey,
title = {EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes},
author = {Guillaume Lentendu and David Singer and Sabine Agatha and Mohammad Bahram and S. Emilia Hannula and Johannes Helder and Leho Tedersoo and Walter Traunspurger and Stefan Geisen and Enrique Lara},
url = {https://doi.org/10.1111/1755-0998.14118, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Lentendu_2025_EukFunc_A_Holistic_Eukaryotic_Functional_Reference_for_Automated_Profiling.pdf, PDF},
issn = {1755-098X},
year = {2025},
date = {2025-01-01},
urldate = {2025-01-01},
journal = {Molecular Ecology Resources},
volume = {25},
number = {7},
pages = {e14118},
publisher = {John Wiley & Sons, Ltd},
abstract = {The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we miss a standardised approach to functionally classify the soil eukaryome in a holistic way. Here we compiled EukFunc, the first functional reference database that characterises the most abundant and functionally important soil eukaryotic groups: fungi, nematodes and protists. We classified the 14,060 species in the database based on their mode of nutrient acquisition into the main functional classes of symbiotroph (40%), saprotroph (26%), phototroph (17%), predator (16%) and unknown (2%). EukFunc provides further detailed information about nutrition mode, including a secondary functional class (i.e., for organisms with multiple nutrition modes), and preyed or associated organisms for predatory or symbiotic taxa, respectively. EukFunc is available in multiple formats for user-friendly functional analyses of specific taxa or annotations of metabarcoding datasets, both embedded in the R package EukFunc. Using a soil dataset from alpine and subalpine meadows, we highlighted the extended ecological insights obtained from combining functional information across the entire soil eukaryome as compared to focusing on fungi, protists or nematodes individually. EukFunc streamlines the annotation process, enhances efficiency and accuracy, and facilitates the investigation of the functional roles of soil eukaryotes, a prerequisite to better understanding soil systems.},
keywords = {Ecology, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we miss a standardised approach to functionally classify the soil eukaryome in a holistic way. Here we compiled EukFunc, the first functional reference database that characterises the most abundant and functionally important soil eukaryotic groups: fungi, nematodes and protists. We classified the 14,060 species in the database based on their mode of nutrient acquisition into the main functional classes of symbiotroph (40%), saprotroph (26%), phototroph (17%), predator (16%) and unknown (2%). EukFunc provides further detailed information about nutrition mode, including a secondary functional class (i.e., for organisms with multiple nutrition modes), and preyed or associated organisms for predatory or symbiotic taxa, respectively. EukFunc is available in multiple formats for user-friendly functional analyses of specific taxa or annotations of metabarcoding datasets, both embedded in the R package EukFunc. Using a soil dataset from alpine and subalpine meadows, we highlighted the extended ecological insights obtained from combining functional information across the entire soil eukaryome as compared to focusing on fungi, protists or nematodes individually. EukFunc streamlines the annotation process, enhances efficiency and accuracy, and facilitates the investigation of the functional roles of soil eukaryotes, a prerequisite to better understanding soil systems.
Seppey, Christophe V. W.; Reczuga, Monika K.; Fournier, Bertrand; Lara, Enrique; Lentendu, Guillaume; Mulot, Matthieu; Singer, David; Szelecz, Ildikò; Mitchell, Edward A. D.
A Gruesome Garden of Earthly Delights: Cadaver Decomposition Fosters the Development of Specific Eukaryotic Microbial Biodiversity Journal Article
In: Acta Protozoologica, vol. 2025, iss. Volume 64, pp. 21–35, 2025, ISSN: 0065-1583.
Abstract | PDF/Link | Tags: Ecology, Metabarcoding, Protists
@article{nokey,
title = {A Gruesome Garden of Earthly Delights: Cadaver Decomposition Fosters the Development of Specific Eukaryotic Microbial Biodiversity},
author = {Christophe V. W. Seppey and Monika K. Reczuga and Bertrand Fournier and Enrique Lara and Guillaume Lentendu and Matthieu Mulot and David Singer and Ildikò Szelecz and Edward A. D. Mitchell},
url = {https://doi.org/10.4467/16890027AP.25.003.21935, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Seppey_2025_A-gruesome-garden-of-earthly-delights-Cadaver-decomposition-fosters-the-development-of-specific-eukaryotic-microbial-biodiversity.pdf, PDF},
issn = {0065-1583},
year = {2025},
date = {2025-01-01},
urldate = {2025-01-01},
journal = {Acta Protozoologica},
volume = {2025},
issue = {Volume 64},
pages = {21–35},
abstract = {Decomposing cadavers have a strong impact on the soil environment and the biodiversity of soil organisms. However, exploring these patterns in different natural settings, and beyond the first few weeks post-mortem remains a research priority. The response of soil communities to decomposing cadavers could be used for estimating the post-mortem interval (PMI), for which current models are lacking beyond 4–6 weeks. We conducted a 35-month field experiment using pig carcasses (Sus scrofa Linnaeus) in a deciduous forest in Switzerland to characterise the impact of decomposing cadavers on the diversity and community composition of soil micro-eukaryotes by high throughput sequencing of soil environmental DNA. The diversity of soil microbial eukaryotes strongly declined under decomposing cadavers. Several taxa which were rare in control soils became more abundant in cadaver-impacted soils. The clear temporal succession and turnover in soil microbial eukaryote diversity and community structure underneath cadavers offers potential for inferring the PMI. The diversity of soil micro-eukaryotes remains poorly documented, especially in under-studied habitats such as cadaver-impacted soils. Characterising this “rare biosphere” diversity will help better understand cadaver impacts on terrestrial ecosystems and is necessary to develop new PMI tools.},
keywords = {Ecology, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
Decomposing cadavers have a strong impact on the soil environment and the biodiversity of soil organisms. However, exploring these patterns in different natural settings, and beyond the first few weeks post-mortem remains a research priority. The response of soil communities to decomposing cadavers could be used for estimating the post-mortem interval (PMI), for which current models are lacking beyond 4–6 weeks. We conducted a 35-month field experiment using pig carcasses (Sus scrofa Linnaeus) in a deciduous forest in Switzerland to characterise the impact of decomposing cadavers on the diversity and community composition of soil micro-eukaryotes by high throughput sequencing of soil environmental DNA. The diversity of soil microbial eukaryotes strongly declined under decomposing cadavers. Several taxa which were rare in control soils became more abundant in cadaver-impacted soils. The clear temporal succession and turnover in soil microbial eukaryote diversity and community structure underneath cadavers offers potential for inferring the PMI. The diversity of soil micro-eukaryotes remains poorly documented, especially in under-studied habitats such as cadaver-impacted soils. Characterising this “rare biosphere” diversity will help better understand cadaver impacts on terrestrial ecosystems and is necessary to develop new PMI tools.
2024
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.
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.
Seppey, Christophe V. W.; Lara, Enrique; Broennimann, Olivier; Guisan, Antoine; Malard, Lucie; Singer, David; Yashiro, Erika; Fournier, Bertrand
Landscape Structure Is a Key Driver of Protist Diversity along Elevation Gradients in the Swiss Alps Journal Article
In: Landscape Ecology, vol. 38, no. 949–965, pp. 2022.04.13.488160, 2023.
Abstract | PDF/Link | Tags: Ecology, Metabarcoding, Protists
@article{nokey,
title = {Landscape Structure Is a Key Driver of Protist Diversity along Elevation Gradients in the Swiss Alps},
author = {Christophe V. W. Seppey and Enrique Lara and Olivier Broennimann and Antoine Guisan and Lucie Malard and David Singer and Erika Yashiro and Bertrand Fournier},
url = {https://doi.org/10.1007/s10980-022-01572-z, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Seppey_2023_Landscape_structure-is_a_key_driver_of_soil_protist_diversity_in_meadows_in_the_Swiss_Alps.pdf, PDF},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Landscape Ecology},
volume = {38},
number = {949–965},
pages = {2022.04.13.488160},
abstract = {Context Human-induced changes in landscape structure are among the main causes of biodiversity loss. Despite their important contribution to biodiversity and ecosystem functioning, microbes - and particularly protists - remain spatially understudied. Soil microbiota are most often driven by local soil properties, but the influence of the surrounding landscape is rarely assessed.Objectives We assessed the effect of landscape structure on soil protist alpha and beta diversity in meadows in the western Swiss Alps.Methods We sampled 178 plots along an elevation gradient representing a broad range of environmental conditions and land-use. We measured landscape structure around each plot at 5 successive spatial scales (i.e. neighbourhood windows of increasing radius, ranging from 100 to 2000 m around a plot). We investigated the changes of protist alpha and beta diversity as a function of landscape structure, local environmental conditions and geographic distance.Results Landscape structures played a key role for protist alpha and beta diversity. The percentage of meadows, forests, or open habitats had the highest influence among all landscape metrics. The importance of landscape structure was comparable to that of environmental conditions and spatial variables, and increased with the size of the neighbourhood window considered.Conclusions Our results suggest that dispersal from neighbouring habitats is a key driver of protist alpha and beta diversity which highlight the importance of landscape-scale assembly mechanisms for microbial diversity. Landscape structure emerges as a key driver of microbial communities which has profound implications for our understanding of the consequences of land-use change on soil microbial communities and their associated functions.Competing Interest StatementThe authors have declared no competing interest.},
keywords = {Ecology, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
Context Human-induced changes in landscape structure are among the main causes of biodiversity loss. Despite their important contribution to biodiversity and ecosystem functioning, microbes - and particularly protists - remain spatially understudied. Soil microbiota are most often driven by local soil properties, but the influence of the surrounding landscape is rarely assessed.Objectives We assessed the effect of landscape structure on soil protist alpha and beta diversity in meadows in the western Swiss Alps.Methods We sampled 178 plots along an elevation gradient representing a broad range of environmental conditions and land-use. We measured landscape structure around each plot at 5 successive spatial scales (i.e. neighbourhood windows of increasing radius, ranging from 100 to 2000 m around a plot). We investigated the changes of protist alpha and beta diversity as a function of landscape structure, local environmental conditions and geographic distance.Results Landscape structures played a key role for protist alpha and beta diversity. The percentage of meadows, forests, or open habitats had the highest influence among all landscape metrics. The importance of landscape structure was comparable to that of environmental conditions and spatial variables, and increased with the size of the neighbourhood window considered.Conclusions Our results suggest that dispersal from neighbouring habitats is a key driver of protist alpha and beta diversity which highlight the importance of landscape-scale assembly mechanisms for microbial diversity. Landscape structure emerges as a key driver of microbial communities which has profound implications for our understanding of the consequences of land-use change on soil microbial communities and their associated functions.Competing Interest StatementThe authors have declared no competing interest.
Brinkmann, Inda; Schweizer, Magali; Singer, David; Quinchard, Sophie; Barras, Christine; Bernhard, Joan M.; Filipsson, Helena L.
Through the eDNA Looking Glass: Responses of Fjord Benthic Foraminiferal Communities to Contrasting Environmental Conditions Journal Article
In: Journal of Eukaryotic Microbiology, vol. 70, no. 4, pp. e12975, 2023, ISSN: 1066-5234.
Abstract | PDF/Link | Tags: Ecology, Metabarcoding, Protists
@article{nokey,
title = {Through the eDNA Looking Glass: Responses of Fjord Benthic Foraminiferal Communities to Contrasting Environmental Conditions},
author = {Inda Brinkmann and Magali Schweizer and David Singer and Sophie Quinchard and Christine Barras and Joan M. Bernhard and Helena L. Filipsson},
url = {https://doi.org/10.1111/jeu.12975, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Brinkmann_2023_Through_the_eDNA_looking_glass_Responses_of_fjord_benthic_foraminiferal_communities_to_contrasting_environmental_conditions.pdf, PDF
},
issn = {1066-5234},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Journal of Eukaryotic Microbiology},
volume = {70},
number = {4},
pages = {e12975},
publisher = {John Wiley & Sons, Ltd},
abstract = {The health of coastal marine environments is severely declining with global changes. Proxies, such as those based on microeukaryote communities, can record biodiversity and ecosystem responses. However, conventional studies rely on microscopic observations of limited taxonomic range and size fraction, missing putatively ecologically informative community components. Here, we tested molecular tools to survey foraminiferal biodiversity in a fjord system (Sweden) on spatial and temporal scales: Alpha and beta diversity responses to natural and anthropogenic environmental trends were assessed and variability of foraminiferal environmental DNA (eDNA) compared to morphology-based data. The identification of eDNA-obtained taxonomic units was aided by single-cell barcoding. Our study revealed wide diversity, including typical morphospecies recognized in the fjords, and so-far unrecognized taxa. DNA extraction method impacted community composition outputs significantly. DNA extractions of 10g sediment more reliably represented present diversity than of 0.5-g samples and, thus, are preferred for environmental assessments in this region. Alpha- and beta diversity of 10-g extracts correlated with bottom-water salinity similar to morpho-assemblage diversity changes. Sub-annual environmental variability resolved only partially, indicating damped sensitivity of foraminiferal communities on short timescales using established metabarcoding techniques. Systematically addressing the current limitations of morphology-based and metabarcoding studies may strongly improve future biodiversity and environmental assessments.},
keywords = {Ecology, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
The health of coastal marine environments is severely declining with global changes. Proxies, such as those based on microeukaryote communities, can record biodiversity and ecosystem responses. However, conventional studies rely on microscopic observations of limited taxonomic range and size fraction, missing putatively ecologically informative community components. Here, we tested molecular tools to survey foraminiferal biodiversity in a fjord system (Sweden) on spatial and temporal scales: Alpha and beta diversity responses to natural and anthropogenic environmental trends were assessed and variability of foraminiferal environmental DNA (eDNA) compared to morphology-based data. The identification of eDNA-obtained taxonomic units was aided by single-cell barcoding. Our study revealed wide diversity, including typical morphospecies recognized in the fjords, and so-far unrecognized taxa. DNA extraction method impacted community composition outputs significantly. DNA extractions of 10g sediment more reliably represented present diversity than of 0.5-g samples and, thus, are preferred for environmental assessments in this region. Alpha- and beta diversity of 10-g extracts correlated with bottom-water salinity similar to morpho-assemblage diversity changes. Sub-annual environmental variability resolved only partially, indicating damped sensitivity of foraminiferal communities on short timescales using established metabarcoding techniques. Systematically addressing the current limitations of morphology-based and metabarcoding studies may strongly improve future biodiversity and environmental assessments.
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.
Fouet, Marie P. A.; Singer, David; Coynel, Alexandra; Héliot, Swann; Howa, Hélène; Lalande, Julie; Mouret, Aurélia; Schweizer, Magali; Tcherkez, Guillaume; Jorissen, Frans J.
Foraminiferal Distribution in Two Estuarine Intertidal Mudflats of the French Atlantic Coast: Testing the Marine Influence Index Journal Article
In: Water, vol. 14, no. 4, pp. 645, 2022, ISSN: 2073-4441.
Abstract | PDF/Link | Tags: Ecology, Protists
@article{nokey,
title = {Foraminiferal Distribution in Two Estuarine Intertidal Mudflats of the French Atlantic Coast: Testing the Marine Influence Index},
author = {Marie P. A. Fouet and David Singer and Alexandra Coynel and Swann Héliot and Hélène Howa and Julie Lalande and Aurélia Mouret and Magali Schweizer and Guillaume Tcherkez and Frans J. Jorissen},
url = {https://doi.org/10.3390/w14040645, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Fouet_2022_Foraminiferal_Distribution_in_Two_Estuarine_Intertidal_Mudflats_of_the_French_Atlantic_Coast_Testing_the_Marine_Influence_Index.pdf, PDF},
issn = {2073-4441},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Water},
volume = {14},
number = {4},
pages = {645},
abstract = {This study focuses on the foraminiferal distribution on intertidal mudflats of two contrasted estuaries (Auray and Vie) along the French Atlantic coast. In both estuaries, the foraminiferal communities are dominated by Haynesina germanica and the \textit{Ammonia tepida} group. Stations located near the outlets show a high diversity and abundance of species of the genus \textit{Elphidium}. Stations in the inner estuary show a higher proportion of agglutinated species ( \textit{Ammotium salsum, Ammobaculites agglutinans}). Multivariate statistical analysis suggests that the distance to the sea and the percentage of fine sediment (63micron) are the two main parameters explaining the foraminiferal distribution. Chemical analyses of the sediment show that the two studied estuaries are not affected by major anthropogenic pollution, so that the faunas should mainly reflect the natural controlling parameters. Three indices of environmental quality commonly used in coastal areas show counter-intuitive differences between stations, suggesting that these indices may be less reliable for use in intertidal estuarine mudflats. The newly developed Marine Influence Index (MII) integrates three major ecological factors: the position of the sampling point on the salinity gradient, the emergence time at low tide and the relative importance of fresh water discharge. In our dataset, MII shows significant correlations with the controlling environmental parameters (distance to the sea, percentage grains ; 63 micron), as well as with the foraminiferal patterns (PCA axis 1, species richness, percentage of \textit{Elphidium} spp. and \textit{Quinqueloculina} spp.). These results suggest that the MII explains a substantial part of the faunal variability on estuarine intertidal mudflats, and can be used to detect deviations from the natural distribution patterns in response to anthropogenic pollution.},
keywords = {Ecology, Protists},
pubstate = {published},
tppubtype = {article}
}
This study focuses on the foraminiferal distribution on intertidal mudflats of two contrasted estuaries (Auray and Vie) along the French Atlantic coast. In both estuaries, the foraminiferal communities are dominated by Haynesina germanica and the Ammonia tepida group. Stations located near the outlets show a high diversity and abundance of species of the genus Elphidium. Stations in the inner estuary show a higher proportion of agglutinated species ( Ammotium salsum, Ammobaculites agglutinans). Multivariate statistical analysis suggests that the distance to the sea and the percentage of fine sediment (63micron) are the two main parameters explaining the foraminiferal distribution. Chemical analyses of the sediment show that the two studied estuaries are not affected by major anthropogenic pollution, so that the faunas should mainly reflect the natural controlling parameters. Three indices of environmental quality commonly used in coastal areas show counter-intuitive differences between stations, suggesting that these indices may be less reliable for use in intertidal estuarine mudflats. The newly developed Marine Influence Index (MII) integrates three major ecological factors: the position of the sampling point on the salinity gradient, the emergence time at low tide and the relative importance of fresh water discharge. In our dataset, MII shows significant correlations with the controlling environmental parameters (distance to the sea, percentage grains ; 63 micron), as well as with the foraminiferal patterns (PCA axis 1, species richness, percentage of Elphidium spp. and Quinqueloculina spp.). These results suggest that the MII explains a substantial part of the faunal variability on estuarine intertidal mudflats, and can be used to detect deviations from the natural distribution patterns in response to anthropogenic pollution.
2021
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.
Fernández, Leonardo D.; Seppey, Christophe V. W.; Singer, David; Fournier, Bertrand; Tatti, Dylan; Mitchell, Edward A. D.; Lara, Enrique
Niche Conservatism Drives the Elevational Diversity Gradient in Major Groups of Free-Living Soil Unicellular Eukaryotes Journal Article
In: Microbial Ecology, vol. 83, pp. 459–469, 2021, ISSN: 1432-184X.
Abstract | PDF/Link | Tags: Ecology, Metabarcoding, Protists
@article{nokey,
title = {Niche Conservatism Drives the Elevational Diversity Gradient in Major Groups of Free-Living Soil Unicellular Eukaryotes},
author = {Leonardo D. Fernández and Christophe V. W. Seppey and David Singer and Bertrand Fournier and Dylan Tatti and Edward A. D. Mitchell and Enrique Lara},
url = {https://doi.org/10.1007/s00248-021-01771-2, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Fernandez_2021_Niche_conservatism_protists.pdf, PDF},
issn = {1432-184X},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Microbial Ecology},
volume = {83},
pages = {459–469},
abstract = {Ancestral adaptations to tropical-like climates drive most multicellular biogeography and macroecology. Observational studies suggest that this niche conservatism could also be shaping unicellular biogeography and macroecology, although evidence is limited to Acidobacteria and testate amoebae. We tracked the phylogenetic signal of this niche conservatism in far related and functionally contrasted groups of common soil protists (Bacillariophyta, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida) along a humid but increasingly cold elevational gradient in Switzerland. Protist diversity decreased, and the size of the geographic ranges of taxa increased with elevation and associated decreasing temperature (climate), which is consistent with a macroecological pattern known as the Rapoport effect. Bacillariophyta exhibited phylogenetically overdispersed communities assembled by competitive exclusion of closely related taxa with shared (conserved) niches. By contrast, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida exhibited phylogenetically clustered communities assembled by habitat filtering, revealing the coexistence of closely related taxa with shared (conserved) adaptations to cope with the humid but temperate to cold climate of the study site. Phylobetadiversity revealed that soil protists exhibit a strong phylogenetic turnover among elevational sites, suggesting that most taxa have evolutionary constraints that prevent them from colonizing the colder and higher sites of the elevation gradient. Our results suggest that evolutionary constraints determine how soil protists colonize climates departing from warm and humid conditions. We posit that these evolutionary constraints are linked to an ancestral adaptation to tropical-like climates, which limits their survival in exceedingly cold sites. This niche conservatism possibly drives their biogeography and macroecology along latitudinal and altitudinal climatic gradients.},
keywords = {Ecology, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
Ancestral adaptations to tropical-like climates drive most multicellular biogeography and macroecology. Observational studies suggest that this niche conservatism could also be shaping unicellular biogeography and macroecology, although evidence is limited to Acidobacteria and testate amoebae. We tracked the phylogenetic signal of this niche conservatism in far related and functionally contrasted groups of common soil protists (Bacillariophyta, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida) along a humid but increasingly cold elevational gradient in Switzerland. Protist diversity decreased, and the size of the geographic ranges of taxa increased with elevation and associated decreasing temperature (climate), which is consistent with a macroecological pattern known as the Rapoport effect. Bacillariophyta exhibited phylogenetically overdispersed communities assembled by competitive exclusion of closely related taxa with shared (conserved) niches. By contrast, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida exhibited phylogenetically clustered communities assembled by habitat filtering, revealing the coexistence of closely related taxa with shared (conserved) adaptations to cope with the humid but temperate to cold climate of the study site. Phylobetadiversity revealed that soil protists exhibit a strong phylogenetic turnover among elevational sites, suggesting that most taxa have evolutionary constraints that prevent them from colonizing the colder and higher sites of the elevation gradient. Our results suggest that evolutionary constraints determine how soil protists colonize climates departing from warm and humid conditions. We posit that these evolutionary constraints are linked to an ancestral adaptation to tropical-like climates, which limits their survival in exceedingly cold sites. This niche conservatism possibly drives their biogeography and macroecology along latitudinal and altitudinal climatic gradients.
Mazel, Florent; Malard, Lucie; Niculita-Hirzel, Hélène; Yashiro, Erika; Mod, Heidi K.; Mitchell, Edward A. D.; Singer, David; Buri, Aline; Pinto, Eric; Guex, Nicolas; Lara, Enrique; Guisan, Antoine
Soil Protist Function Varies with Elevation in the Swiss Alps Journal Article
In: Environmental Microbiology, vol. 24, iss. 4, pp. 1689-1702, 2021, ISSN: 1462-2912.
Abstract | PDF/Link | Tags: Ecology, Metabarcoding, Protists
@article{nokey,
title = {Soil Protist Function Varies with Elevation in the Swiss Alps},
author = {Florent Mazel and Lucie Malard and Hélène Niculita-Hirzel and Erika Yashiro and Heidi K. Mod and Edward A. D. Mitchell and David Singer and Aline Buri and Eric Pinto and Nicolas Guex and Enrique Lara and Antoine Guisan},
url = {https://doi.org/10.1111/1462-2920.15686, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Mazel_2021_Soil_protist_function_varies_with_elevation_in_the_Swiss_Alps.pdf, PDF},
issn = {1462-2912},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Environmental Microbiology},
volume = {24},
issue = {4},
pages = {1689-1702},
publisher = {John Wiley & Sons, Ltd},
abstract = {Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600m of elevation in the Swiss Alps (from 400 to 3000m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400-1000m), this ratio increases to 12 at high elevation (2000-3000m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.},
keywords = {Ecology, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600m of elevation in the Swiss Alps (from 400 to 3000m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400-1000m), this ratio increases to 12 at high elevation (2000-3000m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.
2020
Singer, David; Duckert, Clément; Heděnec, Petr; Lara, Enrique; Hiltbrunner, Erika; Mitchell, Edward A. D.
In: Soil Biology and Biochemistry, pp. 107837, 2020, ISSN: 0038-0717.
Abstract | PDF/Link | Tags: Ecology, First-Last-Author, Metabarcoding, Protists
@article{nokey,
title = {High-Throughput Sequencing of Litter and Moss eDNA Reveals a Positive Correlation between the Diversity of Apicomplexa and Their Invertebrate Hosts across Alpine Habitats},
author = {David Singer and Clément Duckert and Petr Heděnec and Enrique Lara and Erika Hiltbrunner and Edward A. D. Mitchell},
url = {https://doi.org/10.1016/j.soilbio.2020.107837, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_and_Duckert_2020_High-throughput_sequencing_of_litter_and_moss_eDNA_reveals_a_positive.pdf, PDF},
issn = {0038-0717},
year = {2020},
date = {2020-12-01},
urldate = {2020-12-01},
journal = {Soil Biology and Biochemistry},
pages = {107837},
abstract = {A high diversity of Apicomplexa was recently found in tropical soils presumably reflecting the diversity of their invertebrate hosts, but such patterns have not been explored in colder regions. We analysed the diversity of Apicomplexa and their potential metazoan hosts in litter and mosses collected in 11 different alpine habitats using an eDNA metabarcoding approach. The abundance and diversity of Apicomplexa phylotypes and of their potential invertebrate hosts were positively correlated. This confirms that eDNA metabarcoding is a useful tool to explore the unknown biodiversity of free-living eukaryotes, as well as potential host-parasite interactions. Future studies should aim at describing this diversity using a combination of morphological and molecular approaches.},
keywords = {Ecology, First-Last-Author, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
A high diversity of Apicomplexa was recently found in tropical soils presumably reflecting the diversity of their invertebrate hosts, but such patterns have not been explored in colder regions. We analysed the diversity of Apicomplexa and their potential metazoan hosts in litter and mosses collected in 11 different alpine habitats using an eDNA metabarcoding approach. The abundance and diversity of Apicomplexa phylotypes and of their potential invertebrate hosts were positively correlated. This confirms that eDNA metabarcoding is a useful tool to explore the unknown biodiversity of free-living eukaryotes, as well as potential host-parasite interactions. Future studies should aim at describing this diversity using a combination of morphological and molecular approaches.
Seppey, Christophe V. W.; Broennimann, Olivier; Buri, Aline; Yashiro, Erika; Pinto-Figueroa, Eric; Singer, David; Blandenier, Quentin; Mitchell, Edward A. D.; Niculita-Hirzel, Hélène; Guisan, Antoine; Lara, Enrique
Soil Protist Diversity in the Swiss Western Alps Is Better Predicted by Topo-Climatic than by Edaphic Variables Journal Article
In: Journal of Biogeography, vol. 47, no. 4, pp. 866–878, 2020, ISSN: 0305-0270, (4).
Abstract | PDF/Link | Tags: Ecology, Metabarcoding, Protists
@article{nokey,
title = {Soil Protist Diversity in the Swiss Western Alps Is Better Predicted by Topo-Climatic than by Edaphic Variables},
author = {Christophe V. W. Seppey and Olivier Broennimann and Aline Buri and Erika Yashiro and Eric Pinto-Figueroa and David Singer and Quentin Blandenier and Edward A. D. Mitchell and Hélène Niculita-Hirzel and Antoine Guisan and Enrique Lara},
url = {https://doi.org/10.1111/jbi.13755, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Seppey_2020_Soil_protist_diversity_in_the_Swiss_western_Alps_is_better_predicted_by_topo‐climatic_than_by_edaphic_variables.pdf, PDF
},
issn = {0305-0270},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Journal of Biogeography},
volume = {47},
number = {4},
pages = {866–878},
abstract = {Aim Trends in spatial patterns of diversity in macroscopic organisms can be well predicted from correlative models, using topo-climatic variables for plants and animals allowing inference over large scales. By contrast, diversity in soil microorganisms is generally considered as mostly driven by edaphic variables and, therefore, difficult to extrapolate on a large spatial scale based on predictive models. Here, we compared the power of topo-climatic versus edaphic variables for predicting the diversity of various soil protist groups at the regional scale. Location Swiss western Alps. Taxa Full protist community and nine clades belonging respectively to three functional groups: parasites (Apicomplexa, Peronosporomycetes and Phytomyxea), phagotrophs (Sarcomonadea, Tubulinea and Spirotrichea) and phototrophs (Chlorophyta, Trebouxiophyceae and Diatomeae). Methods We extracted soil DNA from 178 sites along a wide range of elevations with a random-stratified sampling design. We defined protist Operational Taxonomic Units assemblages by metabarcoding of the V4 region of the rRNA small subunit gene. We assessed and modelled the diversity (Shannon index) patterns of all above-mentioned taxonomic groups based on topo-climatic (topography, slope southness, slope steepness and average summer temperature) and edaphic (soil temperature, relative humidity, pH, electroconductivity, phosphorus percentage, carbon/nitrogen, loss on ignition and shale percentage) variables in Generalized Additive Models (GAM). Results The respective significance of topo-climatic and edaphic variables varied among taxonomic and to a certain extent functional groups: while many variables explained significantly the diversity of the three phototrophs this was less the case for the three parasites. Topo-climatic variables had a better predictive power than edaphic variables, yet predictive power varied among taxonomic groups. Main conclusions Topo-climatic variables (particularly slope steepness and summer temperature if we consider their significance in the GAMs) were, on average, better predictors of protist diversity at the landscape scale than edaphic variables. However, the predictive power of these variables on diversity differed considerably among taxonomic groups; such relationships may be due to direct and/or indirect (e.g. biotic) influences (like with parasitic taxa, where low predictive power is most likely explained by the absence of information on the hosts distribution). Future prospects include using such spatial models to predict hotspots of diversity and disease outbreaks.},
note = {4},
keywords = {Ecology, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
Aim Trends in spatial patterns of diversity in macroscopic organisms can be well predicted from correlative models, using topo-climatic variables for plants and animals allowing inference over large scales. By contrast, diversity in soil microorganisms is generally considered as mostly driven by edaphic variables and, therefore, difficult to extrapolate on a large spatial scale based on predictive models. Here, we compared the power of topo-climatic versus edaphic variables for predicting the diversity of various soil protist groups at the regional scale. Location Swiss western Alps. Taxa Full protist community and nine clades belonging respectively to three functional groups: parasites (Apicomplexa, Peronosporomycetes and Phytomyxea), phagotrophs (Sarcomonadea, Tubulinea and Spirotrichea) and phototrophs (Chlorophyta, Trebouxiophyceae and Diatomeae). Methods We extracted soil DNA from 178 sites along a wide range of elevations with a random-stratified sampling design. We defined protist Operational Taxonomic Units assemblages by metabarcoding of the V4 region of the rRNA small subunit gene. We assessed and modelled the diversity (Shannon index) patterns of all above-mentioned taxonomic groups based on topo-climatic (topography, slope southness, slope steepness and average summer temperature) and edaphic (soil temperature, relative humidity, pH, electroconductivity, phosphorus percentage, carbon/nitrogen, loss on ignition and shale percentage) variables in Generalized Additive Models (GAM). Results The respective significance of topo-climatic and edaphic variables varied among taxonomic and to a certain extent functional groups: while many variables explained significantly the diversity of the three phototrophs this was less the case for the three parasites. Topo-climatic variables had a better predictive power than edaphic variables, yet predictive power varied among taxonomic groups. Main conclusions Topo-climatic variables (particularly slope steepness and summer temperature if we consider their significance in the GAMs) were, on average, better predictors of protist diversity at the landscape scale than edaphic variables. However, the predictive power of these variables on diversity differed considerably among taxonomic groups; such relationships may be due to direct and/or indirect (e.g. biotic) influences (like with parasitic taxa, where low predictive power is most likely explained by the absence of information on the hosts distribution). Future prospects include using such spatial models to predict hotspots of diversity and disease outbreaks.
Mod, Heidi K.; Scherrer, Daniel; Cola, Valeria Di; Broennimann, Olivier; Blandenier, Quentin; Breiner, Frank T.; Buri, Aline; Goudet, Jérôme; Guex, Nicolas; Lara, Enrique; Mitchell, Edward A. D.; Niculita-Hirzel, Hélène; Pagni, Marco; Pellissier, Loïc; Pinto-Figueroa, Eric; Sanders, Ian R.; Schmidt, Benedikt R.; Seppey, Christophe V. W.; Singer, David; Ursenbacher, Sylvain; Yashiro, Erika; Meer, Jan R.; Guisan, Antoine
Greater Topoclimatic Control of Above- versus below-Ground Communities Journal Article
In: Global Change Biology, vol. n/a, no. n/a, 2020, ISSN: 1354-1013, (2).
Abstract | PDF/Link | Tags: Ecology, Metabarcoding, Protists
@article{nokey,
title = {Greater Topoclimatic Control of Above- versus below-Ground Communities},
author = {Heidi K. Mod and Daniel Scherrer and Valeria Di Cola and Olivier Broennimann and Quentin Blandenier and Frank T. Breiner and Aline Buri and Jérôme Goudet and Nicolas Guex and Enrique Lara and Edward A. D. Mitchell and Hélène Niculita-Hirzel and Marco Pagni and Loïc Pellissier and Eric Pinto-Figueroa and Ian R. Sanders and Benedikt R. Schmidt and Christophe V. W. Seppey and David Singer and Sylvain Ursenbacher and Erika Yashiro and Jan R. Meer and Antoine Guisan},
url = {https://doi.org/10.1111/gcb.15330, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Mod_2020_Greater_topoclimatic_control_of_above_versus_below-ground_communities.pdf, PDF
},
issn = {1354-1013},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Global Change Biology},
volume = {n/a},
number = {n/a},
publisher = {John Wiley & Sons, Ltd},
abstract = {Abstract Assessing the degree to which climate explains the spatial distributions of different taxonomic and functional groups is essential for anticipating the effects of climate change on ecosystems. Most effort so far has focused on above-ground organisms, which offer only a partial view on the response of biodiversity to environmental gradients. Here including both above- and below-ground organisms, we quantified the degree of topoclimatic control on the occurrence patterns of >1,500 taxa and phylotypes along a c. 3,000m elevation gradient, by fitting species distribution models. Higher model performances for animals and plants than for soil microbes (fungi, bacteria and protists) suggest that the direct influence of topoclimate is stronger on above-ground species than on below-ground microorganisms. Accordingly, direct climate change effects are predicted to be stronger for above-ground than for below-ground taxa, whereas factors expressing local soil microclimate and geochemistry are likely more important to explain and forecast the occurrence patterns of soil microbiota. Detailed mapping and future scenarios of soil microclimate and microhabitats, together with comparative studies of interacting and ecologically dependent above- and below-ground biota, are thus needed to understand and realistically forecast the future distribution of ecosystems.},
note = {2},
keywords = {Ecology, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
Abstract Assessing the degree to which climate explains the spatial distributions of different taxonomic and functional groups is essential for anticipating the effects of climate change on ecosystems. Most effort so far has focused on above-ground organisms, which offer only a partial view on the response of biodiversity to environmental gradients. Here including both above- and below-ground organisms, we quantified the degree of topoclimatic control on the occurrence patterns of >1,500 taxa and phylotypes along a c. 3,000m elevation gradient, by fitting species distribution models. Higher model performances for animals and plants than for soil microbes (fungi, bacteria and protists) suggest that the direct influence of topoclimate is stronger on above-ground species than on below-ground microorganisms. Accordingly, direct climate change effects are predicted to be stronger for above-ground than for below-ground taxa, whereas factors expressing local soil microclimate and geochemistry are likely more important to explain and forecast the occurrence patterns of soil microbiota. Detailed mapping and future scenarios of soil microclimate and microhabitats, together with comparative studies of interacting and ecologically dependent above- and below-ground biota, are thus needed to understand and realistically forecast the future distribution of ecosystems.
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.
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.
2017
Seppey, Christophe V. W.; Singer, David; Dumack, Kenneth; Fournier, Bertrand; Belbahri, Lassaâd; Mitchell, Edward A. D.; Lara, Enrique
In: Soil Biology and Biochemistry, vol. 112, pp. 68–76, 2017, ISSN: 0038-0717.
Abstract | PDF/Link | Tags: Ecology, Metabarcoding, Protists
@article{nokey,
title = {Distribution Patterns of Soil Microbial Eukaryotes Suggests Widespread Algivory by Phagotrophic Protists as an Alternative Pathway for Nutrient Cycling},
author = {Christophe V. W. Seppey and David Singer and Kenneth Dumack and Bertrand Fournier and Lassaâd Belbahri and Edward A. D. Mitchell and Enrique Lara},
url = {https://doi.org/10.1016/j.soilbio.2017.05.002, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Seppey_2017_Distribution_patterns_of_soil_microbial_eukaryotes_suggests_widespread_algivory_by_phagotrophic_protists_as_an_alternative_pathway_for_nutrient_cycling.pdf, PDF},
issn = {0038-0717},
year = {2017},
date = {2017-01-01},
urldate = {2017-01-01},
journal = {Soil Biology and Biochemistry},
volume = {112},
pages = {68–76},
abstract = {High-throughput sequencing (HTS) of soil environmental DNA (eDNA) allows assessing the full diversity of soil micro-eukaryotes. The resulting operational taxonomic units (OTUs) can be assigned to potential taxonomic and functional identities using increasingly complete reference databases. HTS of soil eDNA is revealing a high diversity and abundance of potential eukaryovorous protists, thus challenging the paradigm of the predominantly bacterivorous function of soil phagotrophic protists (i.e. microbial loop). Using Illumina sequencing of soil eDNA and targeting the V9 region of the SSU rRNA gene, we investigated the taxonomic and functional diversities, distribution and co-occurrence patterns of soil micro-eukaryotes in three land-use categories: forests, meadows and croplands located in Switzerland. Each OTU was assigned to a broad functional category (phototrophs, phagotrophs, osmotrophs, or parasites). Total OTU richness was similar in the three land-use categories, but community composition differed significantly between forests and other land-uses. The proportion of fungal sequences (especially Basidiomycota) was highest, and phototroph (i.e. soil microalgae) sequences least abundant in forests. Seven OTUs representing phagotrophic protists, together accounting for >25% of all phagotroph sequences, were significantly correlated to the total number of phototroph sequences, thus suggesting algivory. At least three of these OTUs corresponded to known algal predators. These results suggest that beyond plants, soil microalgae represent a functionally significant but rarely considered input of carbon in soils that should be taken into account when modelling soil nutrient cycling.},
keywords = {Ecology, Metabarcoding, Protists},
pubstate = {published},
tppubtype = {article}
}
High-throughput sequencing (HTS) of soil environmental DNA (eDNA) allows assessing the full diversity of soil micro-eukaryotes. The resulting operational taxonomic units (OTUs) can be assigned to potential taxonomic and functional identities using increasingly complete reference databases. HTS of soil eDNA is revealing a high diversity and abundance of potential eukaryovorous protists, thus challenging the paradigm of the predominantly bacterivorous function of soil phagotrophic protists (i.e. microbial loop). Using Illumina sequencing of soil eDNA and targeting the V9 region of the SSU rRNA gene, we investigated the taxonomic and functional diversities, distribution and co-occurrence patterns of soil micro-eukaryotes in three land-use categories: forests, meadows and croplands located in Switzerland. Each OTU was assigned to a broad functional category (phototrophs, phagotrophs, osmotrophs, or parasites). Total OTU richness was similar in the three land-use categories, but community composition differed significantly between forests and other land-uses. The proportion of fungal sequences (especially Basidiomycota) was highest, and phototroph (i.e. soil microalgae) sequences least abundant in forests. Seven OTUs representing phagotrophic protists, together accounting for >25% of all phagotroph sequences, were significantly correlated to the total number of phototroph sequences, thus suggesting algivory. At least three of these OTUs corresponded to known algal predators. These results suggest that beyond plants, soil microalgae represent a functionally significant but rarely considered input of carbon in soils that should be taken into account when modelling soil nutrient cycling.
2016
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.