Publications

@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}

}

@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}

}

@article{nokey,

title = {Can We Accurately Predict the Distribution of Soil Microorganism Presence and Relative Abundance?},

author = {Valentin Verdon and Lucie Malard and Flavien Collart and Antoine Adde and Erika Yashiro and Enrique Lara Pandi and Heidi Mod and David Singer and Hélène Niculita-Hirzel and Nicolas Guex and Antoine Guisan},

url = {https://doi.org/10.1111/ecog.07086, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Verdon_2024_Can_we_accurately_predict_the_distribution_of_soil_microorganism_presence_and_relative_abundance.pdf, PDF},

issn = {0906-7590},

year  = {2025},

date = {2025-01-01},

urldate = {2025-01-01},

journal = {Ecography},

volume = {2025},

number = {3},

pages = {e07086},

publisher = {John Wiley & Sons, Ltd},

abstract = {Soil microbes play a key role in shaping terrestrial ecosystems. It is therefore essential to understand what drives their distribution. While multivariate analyses have been used to characterise microbial communities and drivers of their spatial patterns, few studies have focused on predicting the distribution of amplicon sequence variants (ASVs). Here, we evaluate the potential of species distribution models (SDMs) to predict the presence-absence and relative abundance distribution of bacteria, archaea, fungi, and protist ASVs in the western Swiss Alps. Advanced automated selection of abiotic covariates was used to circumvent the lack of knowledge on the ecology of each ASV. Presence-absence SDMs could be fitted for most ASVs, yielding better predictions than null models. Relative abundance SDMs performed less well, with low fit and predictive power overall, but displayed a good capacity to differentiate between sites with high and low relative abundance of the modelled ASV. SDMs for bacteria and archaea displayed better predictive power than for fungi and protists, suggesting a closer link of the former with the abiotic covariates used. Microorganism distributions were mostly related to edaphic covariates. In particular, pH was the most selected covariate across models. The study shows the potential of using SDM frameworks to predict the distribution of ASVs obtained from topsoil DNA. It also highlights the need for further development of precise edaphic mapping and scenario modelling to enhances prediction of microorganism distributions in the future.},

keywords = {Diversity, Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{nokey,

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

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

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

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

issn = {0377-8398},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Marine Micropaleontology},

volume = {188},

pages = {102353},

abstract = {Assessing the distribution of species in natural environments is essential for their use in environmental surveys. Here, we investigate the distribution of three pseudo-cryptic species formerly lumped in the morphospecies \textit{Ammonia tepida} (Cushman, 1926), commonly found on estuarine mudflats along the European coasts: \textit{Ammonia veneta} Schultze, 1854 (T1), \textit{Ammonia aberdoveyensis} Haynes, 1973 (T2) and \textit{Ammonia confertitesta} Zheng, 1978 (T6). We studied their distribution at 51 sites located in seven estuaries of the French North Atlantic coast (Elorn, Aulne, Odet, Crac'h, Auray, Vilaine, Vie), using both morphological and molecular identification methods. \textit{Ammonia veneta} was detected by both approaches at most of the stations. While \textit{A. aberdoveyensis} was frequently identified by the morphological method but not detected with metabarcoding, the presence of \textit{A. confertitesta} in the eDNA data often contrasted with its absence in the morphological analysis. The absence of \textit{A. aberdoveyensis} in eDNA of sites where it was identified morphologically could be the consequence of its relative scarcity, and eventually a patchy distribution. Concerning \textit{A. confertitesta}, we hypothesise that these contradictory results can be explained by the supposedly invasive character of this species. Despite the widespread presence of \textit{A. confertitesta} genetic material (including adults, juveniles and propagules), a mature population has not yet fully developed everywhere. The seven investigated estuaries seem to represent different stages of replacement of the autochthonous species \textit{A. veneta} and \textit{A. aberdoveyensis} by \textit{A. confertitesta}. Our study demonstrates that the combination of visual observations and molecular approaches is ideal for monitoring the progressive spreading of exotic species.},

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

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@article{nokey,

title = {Discrepancies between Prokaryotes and Eukaryotes Need to Be Considered in Soil DNA-based Studies},

author = {Enrique Lara and David Singer and Stefan Geisen},

url = {https://doi.org/10.1111/1462-2920.16019, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Lara_2022_Discrepancies_between_prokaryotes_and_eukaryotes_need_to_be_considered_in_soil.pdf, PDF},

issn = {1462-2912},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Environmental Microbiology},

volume = {24},

issue = {9},

pages = {3829-3839},

publisher = {John Wiley & Sons, Ltd},

abstract = {Summary Metabarcoding approaches are exponentially increasing our understanding of soil biodiversity, with a major focus on the bacterial part of the microbiome. Part of the soil diversity are also eukaryotes that include fungi, algae, protists and Metazoa. Nowadays, soil eukaryotes are targeted with the same approaches developed for bacteria and archaea (prokaryotes). However, fundamental differences exist between domains. After providing a short historical overview of the developments of metabarcoding applied to environmental microbiology, we compile the most important differences between domains that prevent direct method transfers between prokaryotic and eukaryotic soil metabarcoding approaches, currently dominated by short-read sequencing. These include the existence of divergent diversity concepts and the variations in eukaryotic morphology that affect sampling and DNA extraction. Furthermore, eukaryotes experienced much more variable evolutionary rates than prokaryotes, which prevent capturing the entire eukaryotic diversity in a soil with a single amplification protocol fit for short-read sequencing. In the final part we focus on future potentials for optimization of eukaryotic metabarcoding that include superior possibility of functionally characterizing eukaryotes and to extend the current information obtained, such as by adding a real quantitative component. This review should optimize future metabarcoding approaches targeting soil eukaryotes and kickstart this promising research direction.},

keywords = {Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Protist Taxonomic and Functional Diversity in Soil, Freshwater and Marine Ecosystems},

author = {David Singer and Christophe V. W. Seppey and Guillaume Lentendu and Micah Dunthorn and David Bass and Lassâad Belbahri and Quentin Blandenier and Didier Debroas and G. Arjen Groot and Colomban Vargas and Isabelle Domaizon and Clément Duckert and Irina Izaguirre and Isabelle Koenig and Gabriela Mataloni and M. Romina Schiaffino and Edward A. D. Mitchell and Stefan Geisen and Enrique Lara},

url = {https://doi.org/10.1016/j.envint.2020.106262, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_and_Seppey_2021_Protist_taxonomic_and_functional_diversity_in_soil_freshwater_and_marine_ecosystems.pdf, PDF},

issn = {0160-4120},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Environment International},

volume = {146},

pages = {106262},

abstract = {Protists dominate eukaryotic diversity and play key functional roles in all ecosystems, particularly by catalyzing carbon and nutrient cycling. To date, however, a comparative analysis of their taxonomic and functional diversity that compares the major ecosystems on Earth (soil, freshwater and marine systems) is missing. Here, we present a comparison of protist diversity based on standardized high throughput 18S rRNA gene sequencing of soil, freshwater and marine environmental DNA. Soil and freshwater protist communities were more similar to each other than to marine protist communities, with virtually no overlap of Operational Taxonomic Units (OTUs) between terrestrial and marine habitats. Soil protists showed higher γ diversity than aquatic samples. Differences in taxonomic composition of the communities led to changes in a functional diversity among ecosystems, as expressed in relative abundance of consumers, phototrophs and parasites. Phototrophs (eukaryotic algae) dominated freshwater systems (49% of the sequences) and consumers soil and marine ecosystems (59% and 48%, respectively). The individual functional groups were composed of ecosystem- specific taxonomic groups. Parasites were equally common in all ecosystems, yet, terrestrial systems hosted more OTUs assigned to parasites of macro-organisms while aquatic systems contained mostly microbial parasitoids. Together, we show biogeographic patterns of protist diversity across major ecosystems on Earth, preparing the way for more focused studies that will help understanding the multiple roles of protists in the biosphere.},

keywords = {Diversity, First-Last-Author, Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@article{nokey,

title = {Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes},

author = {Ismael Velasco-González and Abel Sanchez-Jimenez and David Singer and Antonio Murciano and Sergio Díez-Hermano and Enrique Lara and Mercedes Martín-Cereceda},

url = {https://doi.org/10.1007/s00248-019-01463-y, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Velasco_Gonzalez_2019_Rain_Fed_Granite_Rock_basins_accumulate_a_high_diversity_of_dormant_microbial_eukaryote.pdf, PDF

},

issn = {1432-184X},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Microbial Ecology},

volume = {79},

number = {4},

pages = {882–897},

abstract = {Rain fed granite rock basins are ancient geological landforms of worldwide distribution and structural simplicity. They support habitats that can switch quickly from terrestrial to aquatic along the year. Diversity of animals and plants, and the connexion between communities in different basins have been widely explored in these habitats, but hardly any research has been carried out on microorganisms. The aim of this study is to provide the first insights on the diversity of eukaryotic microbial communities from these environments. Due to the ephemeral nature of these aquatic environments, we predict that the granitic basins should host a high proportion of dormant microeukaryotes. Based on an environmental DNA diversity survey, we reveal diverse communities with representatives of all major eukaryotic taxonomic supergroups, mainly composed of a diverse pool of low abundance OTUs. Basin communities were very distinctive, with alpha and beta diversity patterns non-related to basin size or spatial distance respectively. Dissimilarity between basins was mainly characterised by turnover of OTUs. The strong microbial eukaryotic heterogeneity observed among the basins may be explained by a complex combination of deterministic factors (diverging environment in the basins), spatial constraints, and randomness including founder effects. Most interestingly, communities contain organisms that cannot coexist at the same time because of incompatible metabolic requirements, thus suggesting the existence of a pool of dormant organisms whose activity varies along with the changing environment. These organisms accumulate in the pools, which turns granitic rock into high biodiversity microbial islands whose conservation and study deserve further attention.},

note = {5},

keywords = {Diversity, Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{nokey,

title = {Contrasted Micro-Eukaryotic Diversity Associated with \textit{Sphagnum} Mosses in Tropical, Subtropical and Temperate Climatic Zones},

author = {David Singer and Sebastian Metz and Fernando Unrein and Satoshi Shimano and Yuri Mazei and Edward A. D. Mitchell and Enrique Lara},

url = {https://doi.org/10.1007/s00248-019-01325-7, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_2019_Contrasted_Micro_Eukaryotic_Diversity_Associated_with_Sphagnum.pdf, PDF},

issn = {0095-3628},

year  = {2019},

date = {2019-01-01},

urldate = {2019-01-01},

journal = {Microbial Ecology},

volume = {78},

number = {3},

pages = {714–724},

abstract = {\textit{Sphagnum}-dominated ecosystem plays major roles as carbon sinks at the global level. Associated microbial communities, in particular, eukaryotes, play significant roles in nutrient fixation and turnover. In order to understand better the ecological processes driven by these organisms, the first step is to characterise these associated organisms. We characterised the taxonomic diversity, and from this, inferred the functional diversity of microeukaryotes in \textit{Sphagnum} mosses in tropical, subtropical and temperate climatic zones through an environmental DNA diversity metabarcoding survey of the V9 region of the gene coding for the RNA of the small subunit of the ribosomes (SSU rRNA). As microbial processes are strongly driven by temperatures, we hypothesised that saprotrophy would be highest in warm regions, whereas mixotrophy, an optimal strategy in oligotrophic environments, would peak under colder climates. Phylotype richness was higher in tropical and subtropical climatic zones than in the temperate region, mostly due to a higher diversity of animal parasites (i.e. Apicomplexa). Decomposers, and especially opportunistic yeasts and moulds, were more abundant under warmer climates, while mixotrophic organisms were more abundant under temperate climates. The dominance of decomposers, suggesting a higher heterotrophic activity under warmer climates, is coherent with the generally observed faster nutrient cycling at lower latitudes; this phenomenon is likely enhanced by higher inputs of nutrients most probably brought in the system by Metazoa, such as arthropods.},

keywords = {Biogeography, First-Last-Author, Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

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

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

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

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

issn = {1462-2912},

year  = {2019},

date = {2019-01-01},

urldate = {2019-01-01},

journal = {Environmental microbiology},

volume = {21},

number = {10},

pages = {3885–3895},

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

keywords = {Biogeography, Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

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

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

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

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

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {FEMS Microbiology Reviews},

volume = {42},

number = {3},

pages = {293–323},

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

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

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Comparative Analysis of Bones, Mites, Soil Chemistry, Nematodes and Soil Micro-Eukaryotes from a Suspected Homicide to Estimate the Post-Mortem Interval},

author = {Ildikó Szelecz and Sandra Lösch and Christophe V. W. Seppey and Enrique Lara and David Singer and Franziska Sorge and Joelle Tschui and M. Alejandra Perotti and Edward A. D. Mitchell},

url = {https://doi.org/10.1038/s41598-017-18179-z, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Szelecz_2018_Comparative_analysis_of_bones_mites_soil_chemistry_nematodes_and_soil_microeukaryotes_from_a_suspected_homicide_to_estimate_the_post_mortem_interval.pdf, PDF},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {Scientific Reports},

volume = {8},

number = {1},

pages = {25},

abstract = {Criminal investigations of suspected murder cases require estimating the post-mortem interval (PMI, or time after death) which is challenging for long PMIs. Here we present the case of human remains found in a Swiss forest. We have used a multidisciplinary approach involving the analysis of bones and soil samples collected beneath the remains of the head, upper and lower body and “control” samples taken a few meters away. We analysed soil chemical characteristics, mites and nematodes (by microscopy) and micro-eukaryotes (by Illumina high throughput sequencing). The PMI estimate on hair ¹⁴C-data via bomb peak radiocarbon dating gave a time range of 1 to 3 years before the discovery of the remains. Cluster analyses for soil chemical constituents, nematodes, mites and micro-eukaryotes revealed two clusters 1) head and upper body and 2) lower body and controls. From mite evidence, we conclude that the body was probably brought to the site after death. However, chemical analyses, nematode community analyses and the analyses of micro-eukaryotes indicate that decomposition took place at least partly on site. This study illustrates the usefulness of combining several lines of evidence for the study of homicide cases to better calibrate PMI inference tools.},

keywords = {Diversity, Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Parasites Dominate Hyperdiverse Soil Protist Communities in Neotropical Rainforests},

author = {Frédéric Mahé and Colomban Vargas and David Bass and Lucas Czech and Alexandros Stamatakis and Enrique Lara and David Singer and Jordan Mayor and John Bunge and Sarah Sernaker and Tobias Siemensmeyer and Isabelle Trautmann and Sarah Romac and Cédric Berney and Alexey Kozlov and Edward A. D. Mitchell and Christophe V. W. Seppey and Elianne Egge and Guillaume Lentendu and Rainer Wirth and Gabriel Trueba and Micah Dunthorn},

url = {https://doi.org/10.1038/s41559-017-0091, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Mahe_2017_Parasites_dominate_hyperdiverse_soil_protist_communities_in_Neotropical_rainforests.pdf, PDF},

issn = {2397-334X},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {Nature Ecology & Evolution},

volume = {1},

number = {4},

pages = {0091},

abstract = {High animal and plant richness in tropical rainforest communities has long intrigued naturalists. It is unknown if similar hyperdiversity patterns are reflected at the microbial scale with unicellular eukaryotes (protists). Here we show, using environmental metabarcoding of soil samples and a phylogeny-aware cleaning step, that protist communities in Neotropical rainforests are hyperdiverse and dominated by the parasitic Apicomplexa, which infect arthropods and other animals. These host-specific parasites potentially contribute to the high animal diversity in the forests by reducing population growth in a density-dependent manner. By contrast, too few operational taxonomic units (OTUs) of Oomycota were found to broadly drive high tropical tree diversity in a host-specific manner under the Janzen-Connell model. Extremely high OTU diversity and high heterogeneity between samples within the same forests suggest that protists, not arthropods, are the most diverse eukaryotes in tropical rainforests. Our data show that protists play a large role in tropical terrestrial ecosystems long viewed as being dominated by macroorganisms.},

keywords = {Diversity, Metabarcoding, Protists},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{nokey,

title = {Soil Protistology Rebooted: 30 Fundamental Questions to Start With},

author = {Stefan Geisen and Edward A. D. Mitchell and David M. Wilkinson and Sina Adl and Michael Bonkowski and Matthew W. Brown and Anna Maria Fiore-Donno and Thierry J. Heger and Vincent E. J. Jassey and Valentyna Krashevska and Daniel J. G. Lahr and Katarzyna Marcisz and Matthieu Mulot and Richard Payne and David Singer and O. Roger Anderson and Dan J. Charman and Flemming Ekelund and Bryan S. Griffiths and Regin Rønn and Alexey Smirnov and David Bass and Lassaâd Belbahri and Cédric Berney and Quentin Blandenier and Antonis Chatzinotas and Marianne Clarholm and Micah Dunthorn and Alan Feest and Leonardo D. Fernández and Wilhelm Foissner and Bertrand Fournier and Eleni Gentekaki and Michal Hájek and Johannes Helder and Alexandre Jousset and Robert Koller and Santosh Kumar and Antonietta La Terza and Mariusz Lamentowicz and Yuri Mazei and Susana S. Santos and Christophe V. W. Seppey and Frederick W. Spiegel and Julia Walochnik and Anne Winding and Enrique Lara},

url = {https://doi.org/10.1016/j.soilbio.2017.04.001, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Geisen_2017_Soil_protistology_rebooted_30_fundamental_questions_to_start_with.pdf, PDF},

issn = {0038-0717},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {Soil Biology and Biochemistry},

volume = {111},

pages = {94–103},

abstract = {Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this, protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in soil studies. Recent methodological advances, particularly in molecular biology techniques, have made the study of soil protists more accessible, and have created a resurgence of interest in soil protistology. This ongoing revolution now enables comprehensive investigations of the structure and functioning of soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive review, we provide a synthesis of research gaps that should be prioritized in future studies of soil protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics that will establish soil protistology as a hub discipline connecting different fundamental and applied fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers in biology.},

keywords = {Protists},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {\textit{Mycamoeba Gemmipara} Nov. Gen., Nov. Sp., the First Cultured Member of the Environmental Dermamoebidae Clade LKM74 and Its Unusual Life Cycle},

author = {Quentin Blandenier and Christophe V. W. Seppey and David Singer and Michèle Vlimant and Anaële Simon and Clément Duckert and Enrique Lara},

url = {https://doi.org/10.1111/jeu.12357, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Blandenier_2016_Mycamoeba_gemmipara_nov_gen_nov_sp_the_First_Cultured_Member_of_the_Environmental_Dermamoebidae_Clade_LKM74_and_its_Unusual_Life_Cycle.pdf, PDF},

issn = {1066-5234},

year  = {2017},

date = {2017-01-01},

urldate = {2017-01-01},

journal = {Journal of Eukaryotic Microbiology},

volume = {64},

number = {2},

pages = {257–265},

abstract = {Since the first environmental DNA surveys, entire groups of sequences called "environmental clades" did not have any cultured representative. LKM74 is an amoebozoan clade affiliated to Dermamoebidae, whose presence is pervasively reported in soil and freshwater. We obtained an isolate from soil that we assigned to LKM74 by molecular phylogeny, close related to freshwater clones. We described \textit{Mycamoeba gemmipara} based on observations made with light- and transmission electron microscopy. It is an extremely small amoeba with typical lingulate shape. Unlike other Dermamoebidae, it lacked ornamentation on its cell membrane, and condensed chromatin formed characteristic patterns in the nucleus. \textit{M. gemmipara} displayed a unique life cycle: trophozoites formed walled coccoid stages which grew through successive buddings and developed into branched structures holding cysts. These structures, measuring hundreds of micrometres, are built as the exclusive product of osmotrophic feeding. To demonstrate that \textit{M. gemmipara} is a genuine soil inhabitant, we screened its presence in an environmental soil DNA diversity survey performed on an experimental setup where pig cadavers were left to decompose in soils to follow changes in eukaryotic communities. \textit{Mycamoeba gemmipara} was present in all samples, although related reads were uncommon underneath the cadaver.},

keywords = {Diversity, Protists},

pubstate = {published},

tppubtype = {article}

}