Publications
2024
Porfirio-Sousa, Alfredo L.; Tice, Alexander K.; Morais, Luana; Ribeiro, Giulia M.; Blandenier, Quentin; Dumack, Kenneth; Eglit, Yana; Fry, Nicholas W.; Souza, Maria Beatriz Gomes E; Henderson, Tristan C.; Kleitz-Singleton, Felicity; Singer, David; Brown, Matthew W.; Lahr, Daniel J. G.
Amoebozoan Testate Amoebae Illuminate the Diversity of Heterotrophs and the Complexity of Ecosystems throughout Geological Time Journal Article
In: PNAS, vol. 121, no. 30, pp. e2319628121, 2024.
Abstract | PDF/Link | Tags: Diversity, Testate-amoebae
@article{nokey,
title = {Amoebozoan Testate Amoebae Illuminate the Diversity of Heterotrophs and the Complexity of Ecosystems throughout Geological Time},
author = {Alfredo L. Porfirio-Sousa and Alexander K. Tice and Luana Morais and Giulia M. Ribeiro and Quentin Blandenier and Kenneth Dumack and Yana Eglit and Nicholas W. Fry and Maria Beatriz Gomes E Souza and Tristan C. Henderson and Felicity Kleitz-Singleton and David Singer and Matthew W. Brown and Daniel J. G. Lahr},
url = {https://doi.org/10.1073/pnas.2319628121, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Porfirio-Sousa_2024_Amoebozoan_testate_amoebae_illuminate_the_diversity_of_heterotrophs_and_the_complexity.pdf, PDF},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {PNAS},
volume = {121},
number = {30},
pages = {e2319628121},
publisher = {Proceedings of the National Academy of Sciences},
abstract = {Arcellinida shelled amoebae are heterotrophic microbial eukaryotes with an extensive Neoproterozoic fossil record, the vase-shaped microfossils (VSMs), a diverse group that is abundant and widespread in late Tonian rocks. We combined phylogenomic sampling and the fossil record to generate time-calibrated trees. Our results illuminate key events in the history of life, including: i) the Tonian origin of extant microbial eukaryote lineages; ii) a speculative proposed radiation of eukaryotes before the Cryogenian, "Tonian revolution"; iii) the establishment of complex terrestrial habitats before the Cryogenian; iv) a post-Silurian divergence of modern Arcellinida subclades in terrestrial (including freshwater) habitats. Our results provide insights into the evolution of life throughout geological time and are congruent with recent discoveries regarding the early diversification of eukaryotes. Heterotrophic protists are vital in Earth's ecosystems, influencing carbon and nutrient cycles and occupying key positions in food webs as microbial predators. Fossils and molecular data suggest the emergence of predatory microeukaryotes and the transition to a eukaryote-rich marine environment by 800 million years ago (Ma). Neoproterozoic vase-shaped microfossils (VSMs) linked to Arcellinida testate amoebae represent the oldest evidence of heterotrophic microeukaryotes. This study explores the phylogenetic relationship and divergence times of modern Arcellinida and related taxa using a relaxed molecular clock approach. We estimate the origin of nodes leading to extant members of the Arcellinida Order to have happened during the latest Mesoproterozoic and Neoproterozoic (1054 to 661 Ma), while the divergence of extant infraorders postdates the Silurian. Our results demonstrate that at least one major heterotrophic eukaryote lineage originated during the Neoproterozoic. A putative radiation of eukaryotic groups (e.g., Arcellinida) during the early-Neoproterozoic sustained by favorable ecological and environmental conditions may have contributed to eukaryotic life endurance during the Cryogenian severe ice ages. Moreover, we infer that Arcellinida most likely already inhabited terrestrial habitats during the Neoproterozoic, coexisting with terrestrial Fungi and green algae, before land plant radiation. The most recent extant Arcellinida groups diverged during the Silurian Period, alongside other taxa within Fungi and flowering plants. These findings shed light on heterotrophic microeukaryotes' evolutionary history and ecological significance in Earth's ecosystems, using testate amoebae as a proxy.},
keywords = {Diversity, Testate-amoebae},
pubstate = {published},
tppubtype = {article}
}
Arcellinida shelled amoebae are heterotrophic microbial eukaryotes with an extensive Neoproterozoic fossil record, the vase-shaped microfossils (VSMs), a diverse group that is abundant and widespread in late Tonian rocks. We combined phylogenomic sampling and the fossil record to generate time-calibrated trees. Our results illuminate key events in the history of life, including: i) the Tonian origin of extant microbial eukaryote lineages; ii) a speculative proposed radiation of eukaryotes before the Cryogenian, "Tonian revolution"; iii) the establishment of complex terrestrial habitats before the Cryogenian; iv) a post-Silurian divergence of modern Arcellinida subclades in terrestrial (including freshwater) habitats. Our results provide insights into the evolution of life throughout geological time and are congruent with recent discoveries regarding the early diversification of eukaryotes. Heterotrophic protists are vital in Earth's ecosystems, influencing carbon and nutrient cycles and occupying key positions in food webs as microbial predators. Fossils and molecular data suggest the emergence of predatory microeukaryotes and the transition to a eukaryote-rich marine environment by 800 million years ago (Ma). Neoproterozoic vase-shaped microfossils (VSMs) linked to Arcellinida testate amoebae represent the oldest evidence of heterotrophic microeukaryotes. This study explores the phylogenetic relationship and divergence times of modern Arcellinida and related taxa using a relaxed molecular clock approach. We estimate the origin of nodes leading to extant members of the Arcellinida Order to have happened during the latest Mesoproterozoic and Neoproterozoic (1054 to 661 Ma), while the divergence of extant infraorders postdates the Silurian. Our results demonstrate that at least one major heterotrophic eukaryote lineage originated during the Neoproterozoic. A putative radiation of eukaryotic groups (e.g., Arcellinida) during the early-Neoproterozoic sustained by favorable ecological and environmental conditions may have contributed to eukaryotic life endurance during the Cryogenian severe ice ages. Moreover, we infer that Arcellinida most likely already inhabited terrestrial habitats during the Neoproterozoic, coexisting with terrestrial Fungi and green algae, before land plant radiation. The most recent extant Arcellinida groups diverged during the Silurian Period, alongside other taxa within Fungi and flowering plants. These findings shed light on heterotrophic microeukaryotes' evolutionary history and ecological significance in Earth's ecosystems, using testate amoebae as a proxy.
Dumack, Kenneth; Lara, Enrique; Duckert, Clément; Ermolaeva, Elizaveta; Siemensma, Ferry; Singer, David; Krashevska, Valentyna; Lamentowicz, Mariusz; Mitchell, Edward A. D.
It's Time to Consider the Arcellinida Shell as a Weapon Journal Article
In: European Journal of Protistology, vol. 92, pp. 126051, 2024, ISSN: 0932-4739.
Abstract | PDF/Link | Tags: Testate-amoebae
@article{nokey,
title = {It's Time to Consider the Arcellinida Shell as a Weapon},
author = {Kenneth Dumack and Enrique Lara and Clément Duckert and Elizaveta Ermolaeva and Ferry Siemensma and David Singer and Valentyna Krashevska and Mariusz Lamentowicz and Edward A. D. Mitchell},
url = {https://doi.org/10.1016/j.ejop.2024.126051, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Dumack_2024_It_s_Time_to_Consider_the_Arcellinida_Shell_as_a_Weapon.pdf, PDF
},
issn = {0932-4739},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {European Journal of Protistology},
volume = {92},
pages = {126051},
abstract = {The shells of testate amoebae are morphologically diverse and persistent in the environment. Accordingly, the examination of the morphology and composition of shells became a standard tool in ecological, palaeoecological, and evolutionary studies. However, so far the function of the shell remains poorly understood and, although based on limited evidence, the shell was considered as a defense mechanism. Based on recent evidence, we propose that the shell of arcellinid testate amoebae is a crucial component facilitating the amoebae’s attack of large prey. Accordingly, the shell is not purely protective, but must be considered also as a weapon. This change in perspective opens up numerous new avenues in protistology and will lead to a substantial change in ecological, palaeoecological, and evolutionary research.},
keywords = {Testate-amoebae},
pubstate = {published},
tppubtype = {article}
}
The shells of testate amoebae are morphologically diverse and persistent in the environment. Accordingly, the examination of the morphology and composition of shells became a standard tool in ecological, palaeoecological, and evolutionary studies. However, so far the function of the shell remains poorly understood and, although based on limited evidence, the shell was considered as a defense mechanism. Based on recent evidence, we propose that the shell of arcellinid testate amoebae is a crucial component facilitating the amoebae’s attack of large prey. Accordingly, the shell is not purely protective, but must be considered also as a weapon. This change in perspective opens up numerous new avenues in protistology and will lead to a substantial change in ecological, palaeoecological, and evolutionary research.
Bruni, Estelle P.; Rusconi, Olivia; Broennimann, Olivier; Adde, Antoine; Jauslin, Raphaël; Krashevska, Valentyna; Kosakyan, Anush; du Châtelet, Eric Armynot; Alcino, João P. B.; Beyens, Louis; Blandenier, Quentin; Bobrov, Anatoly; Burdman, Luciana; Duckert, Clément; Fernández, Leonardo D.; Souza, Maria Beatriz Gomes E; Heger, Thierry J.; Koenig, Isabelle; Lahr, Daniel J. G.; McKeown, Michelle; Meisterfeld, Ralf; Singer, David; Voelcker, Eckhard; Wilmshurst, Janet; Wohlhauser, Sebastien; Wilkinson, David M.; Guisan, Antoine; Mitchell, Edward A. D.
In: Diversity and Distributions, vol. 30, no. 2, pp. e13779, 2024, ISSN: 1366-9516.
Abstract | PDF/Link | Tags: Biogeography, Peatland, Testate-amoebae
@article{nokey,
title = {Global Distribution Modelling of a Conspicuous Gondwanian Soil Protist Reveals Latitudinal Dispersal Limitation and Range Contraction in Response to Climate Warming},
author = {Estelle P. Bruni and Olivia Rusconi and Olivier Broennimann and Antoine Adde and Raphaël Jauslin and Valentyna Krashevska and Anush Kosakyan and Eric Armynot du Châtelet and João P. B. Alcino and Louis Beyens and Quentin Blandenier and Anatoly Bobrov and Luciana Burdman and Clément Duckert and Leonardo D. Fernández and Maria Beatriz Gomes E Souza and Thierry J. Heger and Isabelle Koenig and Daniel J. G. Lahr and Michelle McKeown and Ralf Meisterfeld and David Singer and Eckhard Voelcker and Janet Wilmshurst and Sebastien Wohlhauser and David M. Wilkinson and Antoine Guisan and Edward A. D. Mitchell},
url = {https://doi.org/10.1111/ddi.13779, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Bruni_2023_Global_distribution_modelling_of_a_conspicuous_Gondwanian.pdf, PDF},
issn = {1366-9516},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Diversity and Distributions},
volume = {30},
number = {2},
pages = {e13779},
publisher = {John Wiley & Sons, Ltd},
abstract = {Aim The diversity and distribution of soil microorganisms and their potential for long-distance dispersal (LDD) are poorly documented, making the threats posed by climate change difficult to assess. If microorganisms do not disperse globally, regional endemism may develop and extinction may occur due to environmental changes. Here, we addressed this question using the testate amoeba \textit{Apodera vas}, a morphologically conspicuous model soil microorganism in microbial biogeography, commonly found in peatlands and forests mainly of former Gondwana. We first documented its distribution. We next assessed whether its distribution could be explained by dispersal (i.e. matching its climatic niche) or vicariance (i.e. palaeogeography), based on the magnitude of potential range expansions or contractions in response to past and on-going climatic changes. Last, we wanted to assess the likelihood of cryptic diversity and its potential threat from climate and land-use changes (e.g. due to limited LDD). Location Documented records: Southern Hemisphere and intertropical zone; modelling: Global. Methods We first built an updated global distribution map of \textit{A.vas} using 401 validated georeferenced records. We next used these data to develop a climatic niche model to predict its past (LGM, i.e. 21±3ka BP; PMIP3 IPSL-CM5A-LR), present and future (IPSL-CMP6A-LR predictions for 2071 2100, SSP3 and 5) potential distributions in responses to climate, by relating the species occurrences to climatic and topographic predictors. We then used these predictions to test our hypotheses (dispersal/vicariance, cryptic diversity, future threat from LDD limitation). Results Our models show that favourable climatic conditions for \textit{A.vas} currently exist in the British Isles, an especially well-studied region for testate amoebae where this species has never been found. This demonstrates a lack of interhemispheric LDD, congruent with the palaeogeography (vicariance) hypothesis. Longitudinal LDD is, however, confirmed by the presence of \textit{A.vas} in isolated and geologically young peri-Antarctic islands. Potential distribution maps for past, current and future climates show favourable climatic conditions existing on parts of all southern continents, with shifts to higher land from LGM to current in the tropics and a strong range contraction from current to future (global warming IPSL-CM6A-LR scenario for 2071 2100, SSP3.70 and SSP5.85) with favourable conditions developing on the Antarctic Peninsula. Main Conclusions This study illustrates the value of climate niche models for research on microbial diversity and biogeography, along with exploring the role played by historical factors and dispersal limitation in shaping microbial biogeography. We assess the discrepancy between latitudinal and longitudinal LDD for \textit{A.vas}, which is possibly due to contrast in wind patterns and/or likelihood of transport by birds. Our models also suggest that climate change may lead to regional extinction of terrestrial microscopic organisms, thus illustrating the pertinence of including microorganisms in biodiversity conservation research and actions.},
keywords = {Biogeography, Peatland, Testate-amoebae},
pubstate = {published},
tppubtype = {article}
}
Aim The diversity and distribution of soil microorganisms and their potential for long-distance dispersal (LDD) are poorly documented, making the threats posed by climate change difficult to assess. If microorganisms do not disperse globally, regional endemism may develop and extinction may occur due to environmental changes. Here, we addressed this question using the testate amoeba Apodera vas, a morphologically conspicuous model soil microorganism in microbial biogeography, commonly found in peatlands and forests mainly of former Gondwana. We first documented its distribution. We next assessed whether its distribution could be explained by dispersal (i.e. matching its climatic niche) or vicariance (i.e. palaeogeography), based on the magnitude of potential range expansions or contractions in response to past and on-going climatic changes. Last, we wanted to assess the likelihood of cryptic diversity and its potential threat from climate and land-use changes (e.g. due to limited LDD). Location Documented records: Southern Hemisphere and intertropical zone; modelling: Global. Methods We first built an updated global distribution map of A.vas using 401 validated georeferenced records. We next used these data to develop a climatic niche model to predict its past (LGM, i.e. 21±3ka BP; PMIP3 IPSL-CM5A-LR), present and future (IPSL-CMP6A-LR predictions for 2071 2100, SSP3 and 5) potential distributions in responses to climate, by relating the species occurrences to climatic and topographic predictors. We then used these predictions to test our hypotheses (dispersal/vicariance, cryptic diversity, future threat from LDD limitation). Results Our models show that favourable climatic conditions for A.vas currently exist in the British Isles, an especially well-studied region for testate amoebae where this species has never been found. This demonstrates a lack of interhemispheric LDD, congruent with the palaeogeography (vicariance) hypothesis. Longitudinal LDD is, however, confirmed by the presence of A.vas in isolated and geologically young peri-Antarctic islands. Potential distribution maps for past, current and future climates show favourable climatic conditions existing on parts of all southern continents, with shifts to higher land from LGM to current in the tropics and a strong range contraction from current to future (global warming IPSL-CM6A-LR scenario for 2071 2100, SSP3.70 and SSP5.85) with favourable conditions developing on the Antarctic Peninsula. Main Conclusions This study illustrates the value of climate niche models for research on microbial diversity and biogeography, along with exploring the role played by historical factors and dispersal limitation in shaping microbial biogeography. We assess the discrepancy between latitudinal and longitudinal LDD for A.vas, which is possibly due to contrast in wind patterns and/or likelihood of transport by birds. Our models also suggest that climate change may lead to regional extinction of terrestrial microscopic organisms, thus illustrating the pertinence of including microorganisms in biodiversity conservation research and actions.
2023
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.
2021
Nawaf, A. Nasser; Braden, R. B. Gregory; Singer, David; Patterson, R. Timothy; Roe, Helen M.
Erugomicula, a New Genus of Arcellinida (Testate Lobose Amoebae) Journal Article
In: Palaeontologia Electronica, vol. 24(1), iss. a16, 2021.
Abstract | PDF/Link | Tags: Diversity, Protists, Testate-amoebae
@article{nokey,
title = {\textit{Erugomicula}, a New Genus of Arcellinida (Testate Lobose Amoebae)},
author = {A. Nasser Nawaf and R. B. Gregory Braden and David Singer and R. Timothy Patterson and Helen M. Roe},
url = {https://doi.org/10.26879/807, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Nasser_2021_Erugomicula_a_new_genus_of_Arcellinida.pdf, PDF
},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Palaeontologia Electronica},
volume = {24(1)},
issue = {a16},
abstract = {Testate lobose amoebae of the order Arcellinida are a diverse, cosmopolitan group of shelled protists found in many environments, including freshwater habitats, peatlands, and soils. Their decay-resistant tests make them an important fossil group for reconstructing Quaternary environments. Within the family Difflugidae Stein, 1859 more than 300 species and 200 sub-species have been attributed to the genus Difflugia Leclerc, 1815. Although carried out on only a few taxa, molecular evidence has demonstrated that test morphology is more important than test composition in categorizing distinct taxa within the Arcellinida. The type species of \textit{Difflugia, D. proteiformis} Lamarck, 1816, is characterized by a terminal aperture and an elongate acuminate test. The morphology of \textit{D. proteiformis} is vastly different from most species assigned to \textit{Difflugia}, explaining its polyphyletic status. We reclassify \textit{Difflugia bidens} Penard, 1902 as type species of \textit{Erugomicula}, a new genus within the Difflugidae, which is distinguished from other taxa within \textit{Difflugia} by its broad, ovoid test, and distinct compression. Based on the compressed morphology of the test, which is not a characteristic of the Difflugiidae, we tentatively assign \textit{Erugomicula} to the family Hyalospheniidae.},
keywords = {Diversity, Protists, Testate-amoebae},
pubstate = {published},
tppubtype = {article}
}
Testate lobose amoebae of the order Arcellinida are a diverse, cosmopolitan group of shelled protists found in many environments, including freshwater habitats, peatlands, and soils. Their decay-resistant tests make them an important fossil group for reconstructing Quaternary environments. Within the family Difflugidae Stein, 1859 more than 300 species and 200 sub-species have been attributed to the genus Difflugia Leclerc, 1815. Although carried out on only a few taxa, molecular evidence has demonstrated that test morphology is more important than test composition in categorizing distinct taxa within the Arcellinida. The type species of Difflugia, D. proteiformis Lamarck, 1816, is characterized by a terminal aperture and an elongate acuminate test. The morphology of D. proteiformis is vastly different from most species assigned to Difflugia, explaining its polyphyletic status. We reclassify Difflugia bidens Penard, 1902 as type species of Erugomicula, a new genus within the Difflugidae, which is distinguished from other taxa within Difflugia by its broad, ovoid test, and distinct compression. Based on the compressed morphology of the test, which is not a characteristic of the Difflugiidae, we tentatively assign Erugomicula to the family Hyalospheniidae.
2020
Marcisz, Katarzyna; Jassey, Vincent E. J.; Kosakyan, Anush; Krashevska, Valentyna; Lahr, Daniel J. G.; Lara, Enrique; Lamentowicz, Łukasz; Lamentowicz, Mariusz; Macumber, Andrew; Mazei, Yuri; Mitchell, Edward A. D.; Nasser, Nawaf A.; Patterson, R. Timothy; Roe, Helen M.; Singer, David; Tsyganov, Andrey N.; Fournier, Bertrand
Testate Amoeba Functional Traits and Their Use in Paleoecology Journal Article
In: Frontiers in Ecology and Evolution, vol. 8, pp. 340, 2020, ISSN: 2296-701X, (3).
Abstract | PDF/Link | Tags: Peatland, Testate-amoebae
@article{nokey,
title = {Testate Amoeba Functional Traits and Their Use in Paleoecology},
author = {Katarzyna Marcisz and Vincent E. J. Jassey and Anush Kosakyan and Valentyna Krashevska and Daniel J. G. Lahr and Enrique Lara and Łukasz Lamentowicz and Mariusz Lamentowicz and Andrew Macumber and Yuri Mazei and Edward A. D. Mitchell and Nawaf A. Nasser and R. Timothy Patterson and Helen M. Roe and David Singer and Andrey N. Tsyganov and Bertrand Fournier},
url = {https://doi.org/10.3389/fevo.2020.575966, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Marcisz_et_al_2020_Testate-amoeba_functional_traits_and_their_use_in_paleoecology.pdf, PDF
},
issn = {2296-701X},
year = {2020},
date = {2020-01-01},
urldate = {2020-01-01},
journal = {Frontiers in Ecology and Evolution},
volume = {8},
pages = {340},
abstract = {This review provides a synthesis of current knowledge on the morphological and functional traits of testate amoebae, a polyphyletic group of protists commonly used as proxies of past hydrological changes in paleoecological investigations from peatland, lake sediment and soil archives. A trait-based approach to understanding testate amoebae ecology and paleoecology has gained in popularity in recent years, with research showing that morphological characteristics provide complementary information to the commonly used environmental inferences based on testate amoeba (morpho-)species data. We provide a broad overview of testate amoeba morphological and functional traits and trait-environment relationships in the context of ecology, evolution, genetics, biogeography, and paleoecology. As examples we report upon previous ecological and paleoecological studies that used trait-based approaches, and describe key testate amoebae traits that can be used to improve the interpretation of environmental studies. We also highlight knowledge gaps and speculate on potential future directions for the application of trait-based approaches in testate amoeba research.},
note = {3},
keywords = {Peatland, Testate-amoebae},
pubstate = {published},
tppubtype = {article}
}
This review provides a synthesis of current knowledge on the morphological and functional traits of testate amoebae, a polyphyletic group of protists commonly used as proxies of past hydrological changes in paleoecological investigations from peatland, lake sediment and soil archives. A trait-based approach to understanding testate amoebae ecology and paleoecology has gained in popularity in recent years, with research showing that morphological characteristics provide complementary information to the commonly used environmental inferences based on testate amoeba (morpho-)species data. We provide a broad overview of testate amoeba morphological and functional traits and trait-environment relationships in the context of ecology, evolution, genetics, biogeography, and paleoecology. As examples we report upon previous ecological and paleoecological studies that used trait-based approaches, and describe key testate amoebae traits that can be used to improve the interpretation of environmental studies. We also highlight knowledge gaps and speculate on potential future directions for the application of trait-based approaches in testate amoeba research.
2019
Singer, David; Mitchell, Edward A. D.; Payne, Richard J.; Blandenier, Quentin; Duckert, Clément; Fernández, Leonardo D.; Fournier, Bertrand; Hernández, Cristián E.; Granath, Gustaf; Rydin, Håkan; Bragazza, Luca; Koronatova, Natalia G.; Goia, Irina; Harris, Lorna I.; Kajukało, Katarzyna; Kosakyan, Anush; Lamentowicz, Mariusz; Kosykh, Natalia P.; Vellak, Kai; Lara, Enrique
Dispersal Limitations and Historical Factors Determine the Biogeography of Specialized Terrestrial Protists Journal Article
In: Molecular Ecology, iss. ja, 2019, ISSN: 0962-1083.
Abstract | PDF/Link | Tags: Biogeography, First-Last-Author, Peatland, Testate-amoebae
@article{nokey,
title = {Dispersal Limitations and Historical Factors Determine the Biogeography of Specialized Terrestrial Protists},
author = {David Singer and Edward A. D. Mitchell and Richard J. Payne and Quentin Blandenier and Clément Duckert and Leonardo D. Fernández and Bertrand Fournier and Cristián E. Hernández and Gustaf Granath and Håkan Rydin and Luca Bragazza and Natalia G. Koronatova and Irina Goia and Lorna I. Harris and Katarzyna Kajukało and Anush Kosakyan and Mariusz Lamentowicz and Natalia P. Kosykh and Kai Vellak and Enrique Lara},
url = {https://doi.org/10.1111/mec.15117, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_2019_Dispersal_limitations_and_historical_factors_determine_the_biogeography_of_specialized_terrestrial_protists.pdf, PDF
},
issn = {0962-1083},
year = {2019},
date = {2019-01-01},
urldate = {2019-01-01},
journal = {Molecular Ecology},
issue = {ja},
abstract = {Recent studies show that soil eukaryotic diversity is immense and dominated by microorganisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to microorganisms. Major diversification events in multicellular organisms have often been attributed to long-term climatic and geological processes, but the impact of such processes on protist diversity has received much less attention as their distribution has often been believed to be largely cosmopolitan. Here, we quantified phylogeographic patterns in \textit{Hyalosphenia papilio}, a large testate amoeba restricted to Holarctic \textit{Sphagnum}-dominated peatlands, to test if the current distribution of its genetic diversity can be explained by historical factors or by the current distribution of suitable habitat. Phylogenetic diversity was higher in Western North America, corresponding to the inferred geographical origin of the \textit{H. papilio} complex, and was lower in Eurasia despite extensive suitable habitat. These results suggest that patterns of phylogenetic diversity and distribution can be explained by the history of Holarctic \textit{Sphagnum} peatland range expansions and contractions in response to Quaternary glaciations that promoted cladogenetic range evolution, rather than the contemporary distribution of suitable habitats. Species distributions were positively correlated with climatic niche breadth, suggesting that climatic tolerance is key to dispersal ability in \textit{H. papilio}. This implies that, at least for large and specialized terrestrial microorganisms, propagule dispersal is slow enough that historical processes may contribute to their diversification and phylogeographic patterns and may partly explain their very high overall diversity.},
keywords = {Biogeography, First-Last-Author, Peatland, Testate-amoebae},
pubstate = {published},
tppubtype = {article}
}
Recent studies show that soil eukaryotic diversity is immense and dominated by microorganisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to microorganisms. Major diversification events in multicellular organisms have often been attributed to long-term climatic and geological processes, but the impact of such processes on protist diversity has received much less attention as their distribution has often been believed to be largely cosmopolitan. Here, we quantified phylogeographic patterns in Hyalosphenia papilio, a large testate amoeba restricted to Holarctic Sphagnum-dominated peatlands, to test if the current distribution of its genetic diversity can be explained by historical factors or by the current distribution of suitable habitat. Phylogenetic diversity was higher in Western North America, corresponding to the inferred geographical origin of the H. papilio complex, and was lower in Eurasia despite extensive suitable habitat. These results suggest that patterns of phylogenetic diversity and distribution can be explained by the history of Holarctic Sphagnum peatland range expansions and contractions in response to Quaternary glaciations that promoted cladogenetic range evolution, rather than the contemporary distribution of suitable habitats. Species distributions were positively correlated with climatic niche breadth, suggesting that climatic tolerance is key to dispersal ability in H. papilio. This implies that, at least for large and specialized terrestrial microorganisms, propagule dispersal is slow enough that historical processes may contribute to their diversification and phylogeographic patterns and may partly explain their very high overall diversity.
2018
Singer, David; Kosakyan, Anush; Seppey, Christophe V. W.; Pillonel, Amandine; Fernández, Leonardo D.; Fontaneto, Diego; Mitchell, Edward A. D.; Lara, Enrique
Environmental Filtering and Phylogenetic Clustering Correlate with the Distribution Patterns of Cryptic Protist Species Journal Article
In: Ecology, vol. 99, no. 4, pp. 904–914, 2018, ISSN: 1939-9170.
Abstract | PDF/Link | Tags: Diversity, Ecology, First-Last-Author, Peatland, Testate-amoebae
@article{nokey,
title = {Environmental Filtering and Phylogenetic Clustering Correlate with the Distribution Patterns of Cryptic Protist Species},
author = {David Singer and Anush Kosakyan and Christophe V. W. Seppey and Amandine Pillonel and Leonardo D. Fernández and Diego Fontaneto and Edward A. D. Mitchell and Enrique Lara},
url = {https://doi.org/10.1002/ecy.2161, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_2018_Environmental_filtering_and_phylogenetic_clustering_correlate_with_the_distribution_patterns_of_cryptic_protist_species.pdf, PDF
},
issn = {1939-9170},
year = {2018},
date = {2018-12-01},
urldate = {2018-12-01},
journal = {Ecology},
volume = {99},
number = {4},
pages = {904–914},
abstract = {The community composition of any group of organisms should theoretically be determined by a combination of assembly processes including resource partitioning, competition, environmental filtering, and phylogenetic legacy. Environmental DNA studies have revealed a huge diversity of protists in all environments, raising questions about the ecological significance of such diversity and the degree to which they obey to the same rules as macroscopic organisms. The fast-growing cultivable protist species on which hypotheses are usually experimentally tested represent only a minority of the protist diversity. Addressing these questions for the lesser known majority can only be inferred through observational studies. We conducted an environmental DNA survey of the genus \textit{Nebela}, a group of closely related testate (shelled) amoeba species, in different habitats within \textit{Sphagnum}-dominated peatlands. Identification based on the mitochondrial cytochrome c oxidase 1 gene, allowed species-level resolution as well as phylogenetic reconstruction. Community composition varied strongly across habitats and associated environmental gradients. Species showed little overlap in their realized niche, suggesting resource partitioning, and a strong influence of environmental filtering driving community composition. Furthermore, phylogenetic clustering was observed in the most nitrogen-poor samples, supporting phylogenetic inheritance of adaptations in the group of \textit{N. guttata}. This study showed that the studied free-living unicellular eukaryotes follow to community assembly rules similar to those known to determine plant and animal communities; the same may be true for much of the huge functional and taxonomic diversity of protists.},
keywords = {Diversity, Ecology, First-Last-Author, Peatland, Testate-amoebae},
pubstate = {published},
tppubtype = {article}
}
The community composition of any group of organisms should theoretically be determined by a combination of assembly processes including resource partitioning, competition, environmental filtering, and phylogenetic legacy. Environmental DNA studies have revealed a huge diversity of protists in all environments, raising questions about the ecological significance of such diversity and the degree to which they obey to the same rules as macroscopic organisms. The fast-growing cultivable protist species on which hypotheses are usually experimentally tested represent only a minority of the protist diversity. Addressing these questions for the lesser known majority can only be inferred through observational studies. We conducted an environmental DNA survey of the genus Nebela, a group of closely related testate (shelled) amoeba species, in different habitats within Sphagnum-dominated peatlands. Identification based on the mitochondrial cytochrome c oxidase 1 gene, allowed species-level resolution as well as phylogenetic reconstruction. Community composition varied strongly across habitats and associated environmental gradients. Species showed little overlap in their realized niche, suggesting resource partitioning, and a strong influence of environmental filtering driving community composition. Furthermore, phylogenetic clustering was observed in the most nitrogen-poor samples, supporting phylogenetic inheritance of adaptations in the group of N. guttata. This study showed that the studied free-living unicellular eukaryotes follow to community assembly rules similar to those known to determine plant and animal communities; the same may be true for much of the huge functional and taxonomic diversity of protists.
Duckert, Clément; Blandenier, Quentin; Kupferschmid, Fanny A. L.; Kosakyan, Anush; Mitchell, Edward A. D.; Lara, Enrique; Singer, David
En Garde! Redefinition of Nebela Militaris (Arcellinida, Hyalospheniidae) and Erection of Alabasta Gen. Nov. Journal Article
In: European Journal of Protistology, vol. 66, pp. 156–165, 2018.
Abstract | PDF/Link | Tags: Diversity, First-Last-Author, Peatland, Testate-amoebae
@article{nokey,
title = {En Garde! Redefinition of \textit{Nebela} \textit{Militaris} (Arcellinida, Hyalospheniidae) and Erection of \textit{Alabasta} Gen. Nov.},
author = {Clément Duckert and Quentin Blandenier and Fanny A. L. Kupferschmid and Anush Kosakyan and Edward A. D. Mitchell and Enrique Lara and David Singer},
url = {https://doi.org/10.1016/j.ejop.2018.08.005, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Duckert_Blandenier_2018_En_garde_Redefinition_of_Nebela_militaris_Arcellinida_Hyalospheniidae_and_erection_of_Alabasta_gen_nov.pdf, PDF},
year = {2018},
date = {2018-11-01},
urldate = {2018-11-01},
journal = {European Journal of Protistology},
volume = {66},
pages = {156–165},
abstract = {Molecular data have considerably contributed to building the taxonomy of protists. Recently, the systematics of Hyalospheniidae (Amoebozoa; Tubulinea; Arcellinida) has been widely revised, with implications extending to ecological, biogeographical and evolutionary investigations. Certain taxa, however, still have an uncertain phylogenetic position, including the common and conspicuous species \textit{Nebela militaris}. A phylogenetic reconstruction of the Hyalospheniidae using partial sequences of the mitochondrial Cytochrome Oxidase Subunit 1 (COI) gene shows that \textit{N. militaris} does not belong to genus \textit{Nebela}, but should be placed in its own genus. The morphological singularities (strongly curved pseudostome and a marked notch in lateral view) and phylogenetic placement of our isolates motivated the creation of a new genus: \textit{Alabasta} gen. nov. Based on their morphology, we include in this genus \textit{Nebela kivuense} and \textit{Nebela longicollis}. We discuss the position of genus \textit{Alabasta} within Hyalospheniidae, and the species that could integrate this new genus based on their morphological characteristics.},
keywords = {Diversity, First-Last-Author, Peatland, Testate-amoebae},
pubstate = {published},
tppubtype = {article}
}
Molecular data have considerably contributed to building the taxonomy of protists. Recently, the systematics of Hyalospheniidae (Amoebozoa; Tubulinea; Arcellinida) has been widely revised, with implications extending to ecological, biogeographical and evolutionary investigations. Certain taxa, however, still have an uncertain phylogenetic position, including the common and conspicuous species Nebela militaris. A phylogenetic reconstruction of the Hyalospheniidae using partial sequences of the mitochondrial Cytochrome Oxidase Subunit 1 (COI) gene shows that N. militaris does not belong to genus Nebela, but should be placed in its own genus. The morphological singularities (strongly curved pseudostome and a marked notch in lateral view) and phylogenetic placement of our isolates motivated the creation of a new genus: Alabasta gen. nov. Based on their morphology, we include in this genus Nebela kivuense and Nebela longicollis. We discuss the position of genus Alabasta within Hyalospheniidae, and the species that could integrate this new genus based on their morphological characteristics.
2015
Singer, David; Kosakyan, Anush; Pillonel, Amandine; Mitchell, Edward A. D.; Lara, Enrique
Eight Species in the Nebela Collaris Complex: Nebela Gimlii (Arcellinida, Hyalospheniidae), a New Species Described from a Swiss Raised Bog Journal Article
In: European Journal of Protistology, vol. 51, no. 1, pp. 79–85, 2015, ISSN: 0932-4739.
Abstract | PDF/Link | Tags: Diversity, First-Last-Author, Peatland, Testate-amoebae
@article{nokey,
title = {Eight Species in the \textit{Nebela} \textit{Collaris} Complex: \textit{Nebela} \textit{Gimlii} (Arcellinida, Hyalospheniidae), a New Species Described from a Swiss Raised Bog},
author = {David Singer and Anush Kosakyan and Amandine Pillonel and Edward A. D. Mitchell and Enrique Lara},
url = {https://doi.org/10.1016/j.ejop.2014.11.004, Link
https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_2015_Eight_species_in_the_Nebela_collaris_complex_Nebela_gimlii_Arcellinida_Hyalospheniidae_a_new_species_described_from_a_Swiss_raised_bog.pdf, PDF},
issn = {0932-4739},
year = {2015},
date = {2015-01-01},
urldate = {2015-01-01},
journal = {European Journal of Protistology},
volume = {51},
number = {1},
pages = {79–85},
abstract = {We describe here a new species of sphagnicolous testate amoeba found abundantly in the forested part of the Le Cachot peatland (Jura Mountains, Neuchâtel, Switzerland) based on microscopical observations (LM, SEM). The new species, called \textit{Nebela gimlii} was placed in a phylogenetic tree based on mitochondrial cytochrome oxidase sequences (COI), and branched robustly within the \textit{N. collaris} complex next to the morphologically similar \textit{N. guttata} and \textit{N. tincta}. It is however genetically clearly distinct from these two species, and differs morphologically from them by its smaller size and stouter shape of the shell. This new species completes the phylogeny of the \textit{Nebela collaris} species complex, with now eight species described, mostly from peatlands and acidic forest litter, and further demonstrates the existence of an unknown diversity within testate amoebae. Improving the taxonomy of testate amoebae in peatlands and clarifying the ecology of newly discovered species should make these organisms even more valuable as bioindicator and for palaeoecological reconstruction.},
keywords = {Diversity, First-Last-Author, Peatland, Testate-amoebae},
pubstate = {published},
tppubtype = {article}
}
We describe here a new species of sphagnicolous testate amoeba found abundantly in the forested part of the Le Cachot peatland (Jura Mountains, Neuchâtel, Switzerland) based on microscopical observations (LM, SEM). The new species, called Nebela gimlii was placed in a phylogenetic tree based on mitochondrial cytochrome oxidase sequences (COI), and branched robustly within the N. collaris complex next to the morphologically similar N. guttata and N. tincta. It is however genetically clearly distinct from these two species, and differs morphologically from them by its smaller size and stouter shape of the shell. This new species completes the phylogeny of the Nebela collaris species complex, with now eight species described, mostly from peatlands and acidic forest litter, and further demonstrates the existence of an unknown diversity within testate amoebae. Improving the taxonomy of testate amoebae in peatlands and clarifying the ecology of newly discovered species should make these organisms even more valuable as bioindicator and for palaeoecological reconstruction.