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 = {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}

}

@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 = {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 = {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 = {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 = {Effect of Dry-Rewetting Stress on Response Pattern of Soil Prokaryotic Communities in Alpine Meadow Soil},

author = {Petr Heděnec and David Singer and Jiabao Li and Minjie Yao and Qiang Lin and Huan Li and Jaroslav Kukla and Tomáš Cajthaml and Jan Frouzc and Junpeng Rui and Xiangzhen Li},

url = {https://doi.org/10.1016/j.apsoil.2018.02.015, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Hedenec_2018_Effect_of_dry_rewetting_stress_on_response_pattern_of_soil_prokaryotic_communities_in_alpine_meadow_soil.pdf, PDF},

doi = {Applied Soil Ecology},

year  = {2018},

date = {2018-01-01},

urldate = {2018-01-01},

journal = {Applied Soil Ecology},

volume = {126},

pages = {98–106},

abstract = {Soil microorganisms are recognized as key players in all biogeochemical cycles. However, little effort has been paid to incorporate them in predictive models for future climate change. Here, we investigated the variation of prokaryotic community composition in alpine meadow soil from the Qinghai-Tibet Plateau under dry-rewetting stress using MiSeq sequencing approach. We incubated soils treated by various frequencies of rewetting and durations of desiccation. Emission rates of methane, carbon dioxide and nitrous oxide were measured every week during five months of incubation, and soil samples were taken each month for community composition analysis. Our results revealed that soil prokaryotic community showed different response patterns to dry-wetting cycles. Diversity indices significantly increased in soils under short-term drought and soils rewetted after long-term drought. Higher niche partitioning was promoted by higher frequencies of disturbance and rapid physiological activation of inactive microbial communities during desiccation, allowing colonization by a diverse array of organisms. Null model percentage of NTI revealed a strong phylogenetic relatedness of soil prokaryotic communities across all treatments and incubation times, suggesting that desiccation and rewetting events were strong biological filters shaping community assemblies. Our results also indicated different responses of various genera belonging to same phylum. These results suggest that prokaryotes that are well adapted to extremely stressful conditions such as long-term desiccation may release more greenhouse gasses in a positive feedback loop and that this prospect should be considered when modeling climate change.},

keywords = {Metabarcoding},

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 = {High-Throughput Sequencing Reveals Diverse Oomycete Communities in Oligotrophic Peat Bog Micro-Habitat},

author = {David Singer and Enrique Lara and Mónica M. Steciow and Christophe V. W. Seppey and Noelia Paredes and Amandine Pillonel and Tomasz Oszako and Lassâad Belbahri},

url = {https://doi.org/10.1016/j.funeco.2016.05.009, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Singer_2016_High_throughput_sequencing_reveals_diverse_oomycete_communities_in_oligotrophic_peat_bog_micro-habitat.pdf, PDF},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Fungal Ecology},

volume = {23},

pages = {42–47},

abstract = {Oomycete diversity has been generally underestimated, despite their ecological and economic importance. Surveying unexplored natural ecosystems with up-to-date molecular diversity tools can reveal the existence of unsuspected organisms. Here, we have explored the molecular diversity of five microhabitats located in five different oligotrophic peat bogs in the Jura Mountains using a high-throughput sequencing approach (Illumina HiSeq 2500). We found a total of 34 different phylotypes distributed in all major oomycete clades, and comprising sequences affiliated to both well-known phylotypes and members of undescribed, basal clades. Parasitic species, including obligate forms were well-represented, and phylotypes related to highly damaging invasive pathogens ( \textit{Aphanomyces astaci}: X1100 and \textit{Saprolegnia parasitica}: X1602) were retrieved. Microhabitats differed significantly in their community composition, and many phylotypes were strongly affiliated to free water habitats (pools). Our approach proved effective in screening oomycete diversity in the studied habitat, and could be applied systematically to other environments and other fungal and fungal-like groups.},

keywords = {Diversity, Ecology, First-Last-Author, Metabarcoding, Peatland},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Microbial Eukaryote Communities Exhibit Robust Biogeographical Patterns along a Gradient of Patagonian and Antarctic Lakes},

author = {M. Romina Schiaffino and Enrique Lara and Leonardo D. Fernández and Vanessa Balagué and David Singer and Christophe V. W. Seppey and Ramon Massana and Irina Izaguirre},

url = {https://doi.org/10.1111/1462-2920.13566, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Schiaffino_2016_Microbial_eukaryote_communities_exhibit_robust_biogeographical_patterns_along_a_gradient_of_Patagonian_and_Antarctic_lakes.pdf, PDF},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Environmental microbiology},

volume = {18},

number = {12},

pages = {5249–5264},

abstract = {Microbial eukaryotes play important roles in aquatic ecosystem functioning. Unravelling their distribution patterns and biogeography provides important baseline information to infer the underlying mechanisms that regulate the biodiversity and complexity of ecosystems. We studied the distribution patterns and factors driving diversity gradients in microeukaryote communities (total, abundant, uncommon and rare community composition) along a latitudinal gradient of lakes distributed from Argentinean Patagonia to Maritime Antarctica using both denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (Illumina HiSeq). DGGE and abundant Illumina operational taxonomic units (OTUs) showed both decreasing richness with latitude and significant differences between Patagonian and Antarctic lakes communities. In contrast, total richness did not change significantly across the latitudinal gradient, although evenness and diversity indices were significantly higher in Patagonian lakes. Beta-diversity was characterized by a high species turnover, influenced by both environmental and geographical descriptors, although this pattern faded in the rare community. Our results suggest the co-existence of a ‘core biosphere’ containing reduced number of abundant/dominant OTUs on which classical ecological rules apply, together with a much larger seedbank of rare OTUs driven by stochastic and reduced dispersal processes. These findings shed new light on the biogeographical patterns and forces structuring inland microeukaryote composition across broad spatial scales.},

keywords = {Biogeography, Diversity, Metabarcoding},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Planktonic Eukaryote Molecular Diversity: Discrimination of Minerotrophic and Ombrotrophic Peatland Pools in Tierra Del Fuego (Argentina)},

author = {Enrique Lara and Christophe V. W. Seppey and Gabriela González Garraza and David Singer and Maria Victoria Quiroga and Gabriela Mataloni},

url = {https://doi.org/10.1093/plankt/fbv016, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Lara_2015_Planktonic_eukaryote_molecular_diversity_discrimination_of_minerotrophic_and_ombrotrophic_peatland_pools_in_Tierra_del_Fuego_Argentina.pdf, PDF},

year  = {2015},

date = {2015-01-01},

urldate = {2015-01-01},

journal = {Journal of Plankton Research},

volume = {37},

number = {3},

pages = {645–655},

abstract = {We investigated the composition of the smallest size fraction (<3 µm) of eukaryotic plankton communities of five pools located in the Rancho Hambre peat bog in Argentinean Tierra del Fuego with an IlluminaHiSeq massive sequencing approach applied to the v9 region of the eukaryotic SSU rRNA gene. Communities were generally dominated by chrysophytes, with a good representation of Perkinsea and Cercozoa clade NC-10. A community composition analysis performed using GUniFraC separated minerotrophic and ombrotrophic sites, reflecting perfectly the classification of the sites based on environmental data. However, this separation disappeared when more weight was given to abundant phylotypes, suggesting that subordinate phylotypes were responsible for site discrimination. The 5% best indicators for, respectively, minerotrophic and ombrotrophic environments were searched using an IndVal analysis. Among these, autotrophic taxa were more common in minerotrophic environments, whereas mixotrophic taxa represented best ombrotrophic water bodies. However, the ecological traits of many taxa have still not been determined, and still needs to be investigated for a better understanding of freshwater systems ecology.},

keywords = {Diversity, Ecology, Metabarcoding},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Response of Forest Soil Euglyphid Testate Amoebae (Rhizaria: Cercozoa) to Pig Cadavers Assessed by High-Throughput Sequencing},

author = {Christophe V. W. Seppey and Bertrand Fournier and Ildikò Szelecz and David Singer and Edward A. D. Mitchell and Enrique Lara},

url = {https://link.springer.com/article/10.1007/s00414-015-1149-7, Link

https://david-singer-biologist.com/wp-content/uploads/2026/03/Seppey_2015_Response_of_forest_soil_euglyphid_testate_amoebae_Rhizaria_Cercozoa_to_pig_cadavers_assessed_by_high_throughput_sequencing.pdf, PDF},

issn = {0937-9827},

year  = {2015},

date = {2015-01-01},

urldate = {2015-01-01},

journal = {International Journal of Legal Medicine},

volume = {130},

number = {2},

pages = {551–562},

abstract = {Decomposing cadavers modify the soil environment, but the effect on soil organisms and especially on soil protists is still poorly documented. We conducted a 35-month experiment in a deciduous forest where soil samples were taken under pig cadavers, control plots and fake pigs (bags of similar volume as the pigs). We extracted total soil DNA, amplified the SSU ribosomal RNA (rRNA) gene V9 region and sequenced it by Illumina technology and analysed the data for euglyphid testate amoebae (Rhizaria: Euglyphida), a common group of protozoa known to respond to micro-environmental changes. We found 51 euglyphid operational taxonomic units (OTUs), 45 of which did not match any known sequence. Most OTUs decreased in abundance underneath cadavers between days 0 and 309, but some responded positively after a time lag. We sequenced the full-length SSU rRNA gene of two common OTUs that responded positively to cadavers; a phylogenetic analysis showed that they did not belong to any known euglyphid family. This study confirmed the existence of an unknown diversity of euglyphids and that they react to cadavers. Results suggest that metabarcoding of soil euglyphids could be used as a forensic tool to estimate the post-mortem interval (PMI) particularly for long-term (>2 months) PMI, for which no reliable tool exists.},

keywords = {Diversity, Ecology, Metabarcoding},

pubstate = {published},

tppubtype = {article}

}