Guillaume LENTENDU
My research is focus on terrestrial eukaryotes biogeography and macroecology.
My main project focus on island biogeography along elevation gradients, and aim to understand the main drivers of protists island endemicity and phylogeography. Using Illumina MiSeq sequencing of the V4 region, we first demonstrate the increase resolution of protist communities when soil samples are first filtered and let sedimented prior to eDNA extraction (Lentendu et al. 2023). We have shown the elevation gradients could be properly describe by adding more elevation replicate than replicates at the same elevation (Huang et al., 2023). And we showed a limited impact of seasons on microbial eukaryotic communities when investigating biodiversity in such elevation gradients (Bruni et al., 2024).
In a second project, I am developing new molecular techniques to characterize the diversity of springtails and mites in Switzerland. Long sequencing barcoding targeting the 28SrRNA or the full rRNA operon is done on morphologically identified specimens using the Nanopore sequencing technology. These sequences serve to create a new reference database which is then used to identified soil eDNA metabarcodes generated by newly design primers targeting a fragment of 28S rRNA and Illumin MiSeq sequencing. This project highlight the importance of taxonomist work in conjunction with molecular approaches.
My last project aims at disclosing potential effect of warming on the soil microbial loop, and particularly on heterotrophic protist impact on nutrient cycles in forest soils.
My work is is highly dependent on bioinformatic analyses, and brings me to develop multiple bioinformatic tools which make use of computational power offered by HPC. I developped for example a pipeline for the analyses of eDNA HTS datasets for metabarcode based diversity assessments (DeltaMP), tools for in-silico PCR and barcode raw data analyses (see in barcode_toolkit), network analyses (NetworkNulHPC) and R packages (e.g. EukFunc for functional assignment of terrestrial eukaryotes).
Finally, I am involved in international collaborations for global analyses of Ciliates diversity (with Micah Dunthorn), the characterization of the grit crust biodiversity in Atacama desert (Patrick Jung) and for functional placement of terrestrial eukaryotes (with Stefan Geisen, sabine Agatha, David Singer and Enrique Lara).
Research Projects
Biodiversity and biogeography of soil protists in continental and oceanic islands – SNSF funded to Prof. Edward Mitchell – 2019-2023 – project number 182531
Inventaire national des collemboles et acariens et développement du metabarcoding pour le monitoring de la biodiversité des sols – OFEV funded to Prof. Edward Mitchell, Dr. Guillaume Lentendu, Sylvain Lanz (horizon a) and Loïc Bulliard (horizon a) – 2021-2024
Heterotrophic protists impact on forest soil prokaryotes and nutrients cycles in a global warming context – Bois Chamblard Foundation funded to Dr. Guillaume Lentendu – 2023-2025
Education History
2010 – 2014
Ph.D. Microbial Ecology, University of Leipzig and UFZ Halle (Saale), Germany
“High-throughput single cell and molecular methods to analyse soil eukaryotic microbes and their long term changes in response to soil fertilisation”
2007 – 2009
M.Sc. Ecology, Paul Sabatier University, Toulouse, France
2006 – 2007
B.Sc. (third year) Biology of Organism, Population and Ecosystem, Paul Sabatier University, Toulouse, France
2004 – 2006
B.Sc. Biology, Paul Verlaine University, Metz, France
Employment History
2019 – present
Post-Doctorate, Protist and testate amoebae biogeography, University of Neuchâtel, Switzwerland
2016 – 2019
Post-Doctorate, Protist biogeography and macroecology, University of Kaiserslautern, Germany
2014 – 2016
Post-Doctorate, GFBio project, Helmholtz Centre for Environmental Research-UFZ Halle (Saale), Germany
2013 -2014
Research assistant in bioinformatic, Helmholtz Centre for Environmental Research-UFZ Halle (Saale), Germany
Publications
Lentendu, G., Singer, D., Agatha, S., Bahram, M., Hannula, S. E., Helder, J., Tedersoo, L., Traunspurger, W., Geisen, S., & Lara, E. (2025). EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes. Molecular Ecology Resources, in press, e14118. https://doi.org/10.1111/1755-0998.14118 – [PDF Accepted Version]
Bruni, E. P., Lorite, J., Peñas, J., Mulot, M., Fournier, B., Vittoz, P., Mitchell, E. A. D., & Lentendu, G. (2024). Higher spatial than seasonal beta diversity of soil protists along elevation gradients. Frontiers of Biogeography, 17, 1–17. https://doi.org/10.21425/fob.17.132637
Jung, P., Brand, R., Briegel-Williams, L., Werner, L., Jost, E., Lentendu, G., Singer, D., Athavale, R., Nürnberg, D. J., Alfaro, F. D., Büdel, B., & Lakatos, M. (2024). The symbiotic alga Trebouxia fuels a coherent soil ecosystem on the landscape scale in the Atacama Desert. Environmental Microbiome, 19(1), 59. https://doi.org/10.1186/s40793-024-00601-5
Huang, S., Lentendu, G., Fujinuma, J., Shiono, T., Kubota, Y., & Mitchell, E. A. D. Soil Micro-eukaryotic Diversity Patterns Along Elevation Gradient Are Best Estimated by Increasing the Number of Elevation Steps Rather than Within Elevation Band Replication. Microbial Ecology
Lentendu, G., Bruni, E., Ah-Peng, C., Fujinuma, J., Kubota, Y., Lorite, … Mitchell, E.A.D. Soil filtration-sedimentation improves shelled protist recovery in eukaryotic eDNA surveys. Molecular Ecology Ressources, 23(6), 1361–1371
Lentendu, G., Lara, E., & Geisen, S. Metabarcoding Approaches for Soil Eukaryotes, Protists, and Microfauna. In F. Martin & S. Uroz (Eds.), Microbial Environmental Genomics (MEG) (pp. 1–16). Springer US.
Gulin Beljak, V., Kulaš, A., Lentendu, G., Vlaičević, B., Gligora Udovič, M., Sertić Perić, … Matoničkin Kepčija, R. Changes in Phylogenetic and Functional Diversity of Ciliates along the Course of a Mediterranean Karstic River. Microorganisms, 10(12), Article 12.
Jung, P., Lehnert, L. W., Bendix, J., Lentendu, G., Grube, M., Alfaro, F. D., … Lakatos, M. The grit crust: A poly-extremotolerant microbial community from the Atacama Desert as a model for astrobiology. Frontiers in Astronomy and Space Sciences, 9.
Lansac-Tôha, F. M., Buosi, P. R. B., … , Dunthorn, M., Lentendu, G., Lansac-Tôha, F. A., & Velho, L. F. M. Molecular insight reveals broad-scale spatial patterns in floodplain ciliate communities, while morphology reflects local environmental controls. Freshwater Science, 41(2).
Francioli, D., Lentendu, G., Lewin, S., & Kolb, S. DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions. Microorganisms, 9(2), 361.
Kulaš, A., Gulin, V., Matoničkin Kepčija, R., Žutinić, P., Sertić Perić, M., Orlić, S., Kajan, K., Stoeck, T., Lentendu, G., Čanjevac, I., Martinić, I., & Gligora Udovič, M. (2021). Ciliates (Alveolata, Ciliophora) as bioindicators of environmental pressure: A karstic river case. Ecological Indicators, 124, 107430.
Lentendu, G., & Dunthorn, M. Phylogenetic relatedness drives protist assembly in marine and terrestrial environments. Global Ecology and Biogeography, 30(7), 1532–1544.
Singer, D., Seppey, C. V. W., Lentendu, G., Dunthorn, M., Bass, D., Belbahri, L., …. Lara, E. Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems. Environment International, 146, 106262.
Forster, D., Lentendu, G., Wilson, M., Mahé, F., Leese, F., Andersen, T., Khomich, M., & Dunthorn, M. Evaluating geographic variation within molecular operational taxonomic units (OTUs) using network analyses in Scandinavian lakes. BioRxiv, 2020.08.06.240267.
Frühe, L., Cordier, T., Dully, V., Breiner, H.-W., Lentendu, G., Pawlowski, J., Martins, C., Wilding, T. A., & Stoeck, T. Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes. Molecular Ecology, 30(13), 2988–3006.
Theodorou, P., Radzevičiūtė, R., Lentendu, G., Kahnt, B., Husemann, M., Bleidorn, C., … Paxton, R. J. Urban areas as hotspots for bees and pollination but not a panacea for all insects. Nature Communications, 11(1), 1–13.
Lentendu, G., Buosi, P. R. B., Cabral, A. F., Segovia, B. T., Meira, B. R. de, Lansac-Toha, F. M., … Dunthorn, M., Protist Biodiversity and Biogeography in Lakes From Four Brazilian River–Floodplain Systems. Journal of Eukaryotic Microbiology, 66(4), 592-599
Forster, D., Lentendu, G., Filker, S., Dubois, E., Wilding, T.A., Stoeck, T.,, Improving eDNA-based protist diversity assessments using networks of amplicon sequence variants. Environmental Microbiology
Lentendu, G., Mahé, F., Bass, D., Rueckert, S., Stoeck, T., & Dunthorn, M., Consistent patterns of high alpha and low beta diversity in tropical parasitic and free-living protists. Molecular Ecology, 27(13), 2846–2857
Banos, S., Lentendu, G., Kopf, A., Wubet, T., Glöckner, F. O., & Reich, M., A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms. BMC Microbiology, 18(1), 190
Purahong, W., Wubet, T., Kahl, T., Arnstadt, T., Hoppe, B., Lentendu, G., … Buscot, F., Increasing N deposition impacts neither diversity nor functions of deadwood-inhabiting fungal communities, but adaptation and functional redundancy warrants ecosystem function. Environmental Microbiology, 20(5), 1693–1710
Purahong, W., Wubet, T., Lentendu, G., Hoppe, B., Jariyavidyanont, K., Arnstadt, T., … Buscot, F., Determinants of deadwood-inhabiting fungal communities in temperate forests: molecular evidence from a large scale deadwood decomposition experiment. Frontiers in Microbiology, 9
Schöps, R., Goldmann, K., Herz, K., Lentendu, G., Schöning, I., Bruelheide, H., … Buscot, F., Land-Use Intensity Rather Than Plant Functional Identity Shapes Bacterial and Fungal Rhizosphere Communities. Frontiers in Microbiology, 9.
Weißbecker, C., Wubet, T., Lentendu, G., Kühn, P., Scholten, T., Bruelheide, H., & Buscot, F., Experimental Evidence of Functional Group-Dependent Effects of Tree Diversity on Soil Fungi in Subtropical Forests. Frontiers in Microbiology, 9.
Mahé, F., de Vargas, C., Bass, D., Czech, L., Stamatakis, A., Lara, E., … Lentendu, G., … Dunthorn, M., Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests. Nature Ecology & Evolution 1, 0091.
Morawe, M., Hoeke, H., Wissenbach, D. K., Lentendu, G., Wubet, T., Kröber, E., & Kolb, S., Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil. Frontiers in Microbiology, 8.
Purahong, W., Pietsch, K., Lentendu, G., Schöps, R., Bruelheide, H., Wirth, C., … Wubet, T. et al., Characterization of unexplored deadwood mycobiome in highly diverse subtropical forests using culture-independent molecular technique. Frontiers in Microbiology 8: 574.
Francioli, D., Schulz, E., Lentendu G., Wubet, T., Buscot, F., & Reitz, T., Mineral vs. Organic Amendments: Microbial Community Structure, Activity and Abundance of Agriculturally Relevant Microbes Are Driven by Long-Term Fertilization Strategies. Frontiers in Microbiology, 7, 1446.
Purahong W, Wubet T, Lentendu G., … Buscot D., Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition. Molecular Ecology 25 (16), 4059-4074
Ramirez K. S., Döring M., Eisenhauer N., Gardi C., Ladau J., Leff J. W., Lentendu G., … Wall D. H. (2015) Towards a global platform for linking soil biodiversity data, Frontiers in Ecology and Evolution, 3: 91
Purahong W., Stempfhuber B., Lentendu G., Francioli D., Reitz T., Buscot F., Schloter M., Krüger D. (2015) Influence of Commonly Used Primer Systems on Automated Ribosomal Intergenic Spacer Analysis of Bacterial Communities in Environmental Samples, PLoS One, doi: 10.1371/journal.pone.0118967
Lentendu G., Chatzinotas A., Wubet T., Buscot F., Wilhelm C., Schlegel M. (2014) Effects of long term differential fertilization on eukaryotic microbial community of an arable soil: a multiple barcoding approach. Molecular Ecology, 23(13): 3341-3355
Lentendu G., Hübschmann T., Müller S., Dunker S., Buscot F., Wilhelm C. (2013) Recovery of soil unicellular eukaryotes: an efficiency and activity analysis on the single cell level. Journal of Microbiological Methods, 95: 463-469
Lentendu G., Zinger L., Manel S., Coissac E., Choler P., Geremia R., Melodelima C. (2011) Assessment of soil fungal diversity in different alpine tundra habitats by means of pyrosequencing. Fungal Diversity, 49(1): 113-123
Acta Oecologia, Applied Soil Ecology, Biology & Fertility of Soil, Cytometry Part A, Environmental Microbiology Reports, FEMS Microbiology Ecology, Microbial Ecology, Molecular Ecology, Molecular Ecology Resources, Research in Microbiology, Revista Ambiente & Água, Science of The Total Environment, Scientific Reports, Systematics and Biodiversity
2019/20
Bioinformatics and statistics for metabarcoding studies in environmental microbiology and ecology, practical course, joint course of CUSO Doctoral Program in Ecology and Evolution and Interuniversity Doctoral Program in Organismal Biology, University of Neuchâtel, Switzerland (16h)
2018/19
Introducing DeltaMP, an automatic metabarcoding bioinformatic pipeline for HPC, practical course, Ecology Dept., University of Kaiserslautern, Germany (8 h)
Bioinformatic and statistics in microbial community ecology, master Ecology and Microbial Biodiversity, practical course, University of Kaiserslautern, Allemagne (16 h)
2017/18
Ecology and diversity of aquatic microbial eukaryotes, practical course, master Ecology and Microbial Biodiversity, University of Kaiserslautern, Allemagne (16 h)
Bioinformatic and statistics in microbial community ecology, lecture, master Ecology and Microbial Biodiversity, University of Kaiserslautern, Allemagne (16 h)
2016/17
Bioinformatic and statistics in microbial community ecology, practical course, master Ecology and Microbial Biodiversity, University of Kaiserslautern, Allemagne (16 h)
2015/16
Assessing microbial diversity and interactions in soil with NGS, practical course, master Evolution and Ecology, University of Leipzig, Germany (4 h)
Submission of raw amplicon sequences and their associated metadata to Short Read Archives databases, practical course, HIGRADE graduate school, UFZ Halle/Salle, Allemagne (8 h)
2011/12
Introduction to unix bash language, OBITools and virtual In silico PCR, practical course, HIGRADE graduate school, UFZ Halle/Salle, Allemagne (8 h)
2019- present
E. Bruni, PhD thesis, Biodiversity And Biogeography of Euglyphida (Rhizaria) in Continental and Oceanic Islands, University of Neuchâtel
2018/19
I. Simeth, B.Sc., Einfluss der Artensubstitution und Änderungen des Artenreichtums auf marine Protisten entlang des LDG, University of Kaiserslautern
2017/18
V. Immel, B.Sc., Parametric vs. Non-parametric estimation of Neotropical soil protist diversity, University of Kaiserslautern
V. Dully, M.Sc., Inferring Indicator Values from ciliate eDNA metabarcodes for ecological status assessment of salmon farms, University of Kaiserslautern
M. Wilson, B.Sc., Protist intra-OTU biogeographic patterns in Norvegian Lakes, University of Kaiserslautern
2016/2017
N. Faulhaber, M.Sc., Latitudinal Diversity Gradient of protistan plankton, University of Kaiserslautern
2015/16
C. Porges, M.Sc., Changes in rhizosphere microbial community association with different parental types of Arabidospsis thaliana MAGIC lines, University of Leipzig
2012
S. Gerstl, B.Sc., Response of soil ciliates diversity to fertilization, University of Leipzig
2019
Metabarcoding soil protists for macroecology studies: insight into bioinformatic and use cases, Lab. Biodiversity & Conservation Biogeography , University of the Ryukyus, Okiinawa, Japan, September 4th
2016
Microbial diversity and interactions in cultivated soils, Ecology Dept. seminar, University of Kaiserslautern, Germany, January 16th
2015
High-throughput single cell and molecular methods to analyse soil eukaryotic microbes and their long term changes in response to soil fertilisation, Ecological Symposium, University of Cologne, Germany, February 14th
2014
Metagenomics and amplicon sequencing for species and phylogenetic diversity assessment of complex communities, workshop iSEQ, iDiv Leipzig, Germany, Novembre 13th to 14th
2013
Effect of long term differential fertilization on the soil microbial eukaryotic community, Laboratoire Ampère, Ecole Centrale de Lyon, France, Octobre 14th
Effect of long term differential fertilization on the soil microbial eukaryotic community, Molecular Systématic group seminar, université de Genève, Switzerland, Octobre 15th
2019
Biogeography of protists in Neotropical rainforest soils and in the oceans, workshop Protists diversity and ecology in aquatic and terrestrial ecosystems, University of Neuchâtel, Swotzerland
2018
Latitudinal diversity gradient of protistan plankton in the Atlantic ocean, The 5th joint meeting of the Phycological Society of America & International Society of Protistologists, Vancouver, Canada
Phylogenetically Close Protists Co-occur: Assembly Patterns in Two Large Scale Environmental Sequencing Surveys, MACRO 2018, Birmensdorf, Switzerland
2017
Persistent biogeographic patterns of tropical free-living and parasitic protists, 15th international congress of protistology, Prague, Czech Republic
Persistent patterns of protist biogeography in three Neotropical rainforest, 37th annual meeting of the German Society for Protozoology, Meißen, Germany
2014
Effects of long term differential fertilization on microbial eukaryotic community of an arable soil: a multiple barcoding approach, 33rd annual meeting of the German Society for Protozoology, Essen, Germany
2013
Soil eukaryotic unicellular microorganisms facing crop fertilization: a metagenomic approach, Annual Conference of the Association for General and Applied Microbiology (VAAM), Bremen, Germany
Soil eukaryotic unicellular microorganisms facing crop fertilization, BioSyst.EU 2013 Global systematics!, Vienna, Austria
2011
High-throughput analysis of soil eukaryotic unicellular microorganisms: from cytometry to pyrosequencing, 5th International Conference on Analysis of Microbial Cells at the Single Cell Level, Marseille, France
2018
Holz-Conner award from the International Society of Protozoology to Vancouver, Canada
2017
from the International Research Coordination Network for Biodiversity of Ciliates to Meißen, Germany
Holz-Conner award from ISOP to Prague, Czech Republic
2016
from the International Research Coordination Network for Biodiversity of Ciliates to Lyon, Fance
2016
Lentendu G., Mahé F., Dunthorn M., Biogeography of predatory protists in Neotropical forest soils, 17ème Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Lyon, France
2015
Lentendu G., Schmidt J., Schultz E., Buscot F., Wubet T., Alfalfa root symbionts under soil nutrient pressure: cooperation or competition?, Ecology Of Soil Microorganism, Prague, Czech Republic
Lentendu G., Schmidt J., Schultz E., Buscot F., Wubet T., Alfalfa root symbionts under soil nutrient pressure: cooperation or competition?, 13th Symposium on Bacterial Genetics and Ecology, Milan, Italy
2014
Lentendu G., Schmidt J., Schultz E., Buscot F., Wubet T.,”How do crop fertilization affect the soil microbiome on a long-term basis?”, The First Global Soil Biodiversity Conference, Dijon, France
2013
Lentendu G., Wubet T., Chatzinotas A., Wilhelm C., Schlegel M., Buscot F.,Effect of long term differential fertilization on the soil microbial eukaryotic community, 2nd Thünen Symposium on Soil Metagenomics, Brunswick, Allemagne
Lentendu G., Wubet T., Hübschmann T., Müller S., Schlegel M., Wilhelm C., Buscot F.,Soil unicellular eukaryotic community analyzed at the single cell level: coupling flow cytometry and metagenomics, the 5th Congress of European Microbiologist, Leipzig, Allemagne
2011
Lentendu G., Müller S., Hübschmann T., Wubet T., Buscot F., Schlegel M., Wilhelm C.,”High-throughput analysis of soil eukaryotic unicellular microorganisms: from cytometry to pyrosequencing”, Workshop of the GfÖ Soil Ecology Group, Berlin, Allemagne