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Despite their small size, protozoa represent the highest biomass of all animals in the soil, next to earthworms. Due to their rapid generation times and high, and selective feeding pressure on bacteria, protozoa account for about 70% of the total respiration of soil animals and contribute to 14-66% of the total carbon and 20-40% of the nitrogen turnover in the soil (“microbial loop”). Protozoa thus form the basis of the heterotrophic food web that directs energy and nutrients from bacteria to higher trophic levels in the soil food web.

Based on their mode of locomotion, there are traditionally three groups: Amoebae, Flagellates and Ciliates. In fact, protozoa are an extremely diverse group taxonomically. “Amoebae” and “flagellates” represent life form types that in many cases have evolved in quite different phylogenetic lineages.

Despite their functional importance, the diversity of soil protozoa is largely unknown. It is not known which taxa of flagellates and shell-less amoebae dominate in soil, or how different soil types and land use affect protozoan abundance, biomass or diversity. Even the biogeographical distribution of protozoa in soil is hardly known.


In two cooperating projects at the University of Cologne, the abundance, biomass and diversity of functional key groups of soil protozoa, the amoebae (WG Bonkowski), as well as flagellates and partly ciliates (WG Arndt) are being studied along land use gradients on forest and grassland sites within the framework of the Biodiversity Exploratories.


  • Protozoa are a dominant group of soil fauna in terms of number and biomass.
  • As the most important consumers of bacteria in the soil, protozoa form the basis of the bacterial-fed food web.
  • Morphotypes and genetic diversity, abundance and biomass of protozoa differ along land use gradients and on a small scale with respect to soil type and resource distribution in the soil, especially in the rhizosphere of plants.

  • Determination of microbial biomass (CFE method)
  • Determination of the abundance of protozoa in soil and litter
  • Isolation and cultivation of dominant protozoan species from soil
  • Sequencing of the 18S rRNA genes of the protozoan community in soil using specific primers

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Interaktionen von Protozoen (Acanthamoeba sp.), Mykorrhiza und endophytischen Pilzen auf das Wachstum von Weidelgras (Lolium perenne)
Becker C.(2009): Interaktionen von Protozoen (Acanthamoeba sp.), Mykorrhiza und endophytischen Pilzen auf das Wachstum von Weidelgras (Lolium perenne). Bachelor thesis, University Cologne
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Brabender M., Kiss A. K., Domonell A., Nitsche F., Arndt H. (2012): Phylogenetic and Morphological Diversity of Novel Soil Cercomonad Species with a Description of Two New Genera (Nucleocercomonas and Metabolomonas). Protist 163, 495–528. doi: 10.1016/j.protis.2012.02.002
More information:  doi.org
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Diversität von Protisten im Totholz: Eine molekularbiologische Untersuchung von Schleimpilzen
Clissmann F., Fiore-Donno A. M., Hoppe B., Krüger D., Kahl T., Unterseher M., Schnittler M. (2015): First insight into dead wood protistan diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime-moulds) in decaying beech logs. FEMS Microbiology Ecology 91 (6): fiv050. doi: 10.1093/femsec/fiv050
More information:  doi.org
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Hochauflösende Analysen der lokalen und globalen Protisten Gemeinschaftsstruktur des Bodens unter Verwendung von morphologischen uund molekularen Methoden
Domonell A. (2013): High resolution analysis of local and global protistan soil community structures using morphological and modern molecular techniques. Dissertation, University Cologne
More information:  kups.ub.uni-koeln.de
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Einzeller im Boden von Grünland zeigen eine bisher ungeahnte Diversität
Domonell A., Brabender M., Nitsche F., Bonkowski M., Arndt A.(2013): Community Structure of Cultivable Protists in Different Grassland and Forest Soils of Thuringia. Pedobiologia 56 (1), 1–7. doi: 10.1016/j.pedobi.2012.07.001
More information:  doi.org
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Fiore-Donno A. M., Rixen C., Rippin M., Glaser K., Samolov E., Karsten U., Becker B., Bonkowski M. (2018): New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts. Molecular Ecology Resources 18 (2), 229-239. doi: 10.1111/1755-0998.12729
More information:  doi.org
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Die Vielfalt von Amöben in Grünlandböden
Fiore-Donno A. M., Weinert J., Wubet T., Bonkowski M. (2016): Metacommunity analysis of amoeboid protists in grassland soils. Scientific Reports 6: 19068. doi: 10.1038/srep19068
More information:  doi.org
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Soil amoebae (Acanthamoeba castellanii) alter plant competition between Plantago lanceolata and Rumex acetosellain presence of mycophagous Collimonasbacteria
Geisen S. (2010): Soil amoebae (Acanthamoeba castellanii) alter plant competition between Plantago lanceolata and Rumex acetosellain presence of mycophagous Collimonasbacteria. Master thesis, University Cologne.
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Bodenprotisten Diversität, Verteilung und ökologische Bedeutung
Geisen S. (2014): Soil Protists - Diversity, Distribution and Ecological Functioning. Dissertation, Universität zu Köln
More information:  kups.ub.uni-koeln.de
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Neubeschreibung und Wiederentdeckung von Amoeben
Geisen S., Weinert J., Kudryavtsev A., Glotova A., Bonkowski M., Smirnov A. (2014): Two new species of the genus Stenamoeba (Discosea, Longamoebia): Cytoplasmic MTOC is present in one more amoebae lineage. European Journal of Protistology 50 (2), 153–165. doi: 10.1016/j.ejop.2014.01.007
More information:  doi.org
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Diversity and function of amoebae (Protozoa) from woodland soils of Biodiversity Exploratories
Diversität und Funktion von Amöben (Protozoa) aus Waldböden der Biodiversitäts-Exploratorien.
Husmann H.(2010): Diversity and function of amoebae (Protozoa) from woodland soils of Biodiversity Exploratories. Thesis, University Cologne
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Das Protistanmikrobiom der deutschen Grünlandböden
Venter P. C. (2018): The protistan microbiome of German grassland soils. Dissertation, Universität zu Köln
More information:  kups.ub.uni-koeln.de
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Die verborgene Vielfalt von begeißelten Protisten im Boden
Venter P. C., Nitsche F., Arndt H. (2018): The hidden diversity of flagellated protists in soil. Protist 169 (3), 432-449. doi: 10.1016/j.protis.2018.04.007
More information:  doi.org
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Das Mikrobiom der Protisten in Grünland-Boden: Mesoskala-Diversität
Venter P. C., Nitsche F., Domonell A., Heger P., Arndt H. (2017): The protistan microbiome of grassland soil: diversity in the mesoscale. Protist 168 (5), 546-564. doi: 10.1016/j.protis.2017.03.005
More information:  doi.org
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Diskrepanzen zwischen molekularen und morphologischen Datenbanken von Boden-Ciliaten aus gemäßigten Klimazonen des Mitteleuropäischen Grünlands
Venter P. C., Nitsche F., Scherwass A., Arndt H. (2018): Discrepancies between molecular and morphological databases of soil ciliates studied for temperate grasslands of central Europe. Protist 169 (4), 521-538. doi: 10.1016/j.protis.2018.04.001
More information:  doi.org

Scientific assistants

Prof. Dr. Hartmut Arndt
Project manager
Prof. Dr. Hartmut Arndt
Prof. Dr. Michael Bonkowski
Project manager
Prof. Dr. Michael Bonkowski
Universität zu Köln
Dr. Anna-Maria Fiore-Donno
Project manager
Dr. Anna-Maria Fiore-Donno
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