Dr. Stefan Geisen
Researcher
Terrestrial Ecology
- Profiel
- CV
- Projecten
- Belangrijkste publicaties
- Peer-reviewed publicaties
- Niet-wetenschappelijke publicaties
Current research
My task is to evaluate the impact of plant-pathogenic organisms on range-expanding plants within the ERC-advanced grant of Wim van der Putten. Questions addressed are whether pathogens are causative agents of range expansion and how they shape competition between range expanding plants and closely related congeneric species.
This work includes a survey of a range of range-expanding and congeneric plants along a transect through Europe, roughly equivalent with the route on which plants expanded their range. We will apply a number of sequencing approaches to study root associated bacteria, fungi and protists, all of which include plant-pathogenic taxa.
Figure 1: Summary scheme showing my current work; due to global climate change, plants expand their range towards the north, which might relax them from pathogens in their native area. This favors their performance in their expanded range.
Subsequent greenhouse experiments will be established to focus more specifically on the effects of pathogens on range-expanding and congeneric plants. These aim at investigating whether plant pathogens from expanded ranges are less harmful to range expanding plants than native pathogens and whether this release of pathogens provides range expanders with an advantage in a competitive interaction with native plants.
However, I am still interested in my former topic, i.e. protists (see below) and keep working on these organisms. One experiments established together with Rutger Wilschut includes treatments with a little studied group of nematophagous protists and aims at identifying whether these protists can reduce the impact plant-parasitic nematodes exert on both range-expanding and native plants. Do they maybe even have direct effects on the performance of different plants?
Protist work
My PhD thesis entitled “Soil Protists - Diversity, Distribution and Ecological Functioning” aimed at increasing the knowledge on soil protists across different European soils and were embedded in the EU project EcoFINDERS (http://ecofinders.dmu.dk/) and performed in the terrestrial ecology department at the University of Cologne, Germany (http://www.uni-koeln.de/math-nat-fak/zoologie/oekologie/agbonkowski/inde...). To approach this vast topic on soil protists I used a wide range of tools to investigate protist taxonomy, community composition, diversity and species-specific functioning.
The taxonomic (and phylogenetic) work resulted in the description of several new species and genera of soil protists and modifications of current phylogeny of many groups of protists (Geisen et al. 2014a, Geisen et al. 2014b, Berney, Geisen et al. 2015, Geisen et al. 2015c, Bass et al. 2016), such as new species of beautiful Cochliopodium (Figure 2).
Figure 2: Light microscopic pictures of the newly described species Cochliopodium plurinucleolum
I applied a range of techniques to study the diversity and community structure of protists in soils and terrestrial environments ranging from microscope-based enrichment cultivation (Geisen et al. 2015) to a combination of cultivation and sequencing (Geisen et al. 2014c), to high-throughput sequencing approaches (Geisen et al. 2015a, Andriuzzi, Phuong-Thi, Geisen et al. 2016, Bass et al. 2016, Geisen et al. 2015b)
All methods revealed that the diversity of soil protists is much higher than previously suggested as, in addition to the identification of several new protist taxa mentioned above, the diversity of soil protists in each investigated sample was high.
In my major research focus are ecological functioning of soil protists. Starting in my PhD work and continuing after, I could show that protists are much more than merely bacterivorous; I could show that mycophagous taxa (those that feed on fungi) are common (Geisen et al. 2016b) and that common soil protists can even feed on larger nematodes (Geisen et al. 2016c; Figure 3). Many soil protists seem to feed on different food sources and are therefore omnivores, which contradicts the classical perception of clearly separated and simple bacterial- and fungal energy channels in soils (Geisen et al. 2016d).
I could also elaborate that parasites are common among soil protists (Geisen et al. 2015) and that many of those inhabit larger soil organisms like mites and earthworms (Geisen et al. 2015b; Geisen et al. 2016e)
Figure 3: Time series of soil amoebae feeding on a nematode
These results lead to propose a conceptual revision of the soil food web (Figure 4, Geisen et al. 2016d).
Figure 4: Conceptual model of soil food webs focusing on the diverse nodes occupied by protists
Stefan Geisen
Bretagnesingel 138, 6666XX Heteren, NL
Phone: +31 (0)636526706; Email: s.geisen@nioo.knaw.nl
WORK EXPERIENCE AND EDUCATION
04/16 – 11/16 Post-doctoral fellow; Wageningen University, Wageningen, NL
Aim: Opimizing and calibrating molecular tools to study soil nematodes
04/14 – 03/16 Post-doctoral fellow; Netherland Institute for Ecology (NIOO), Wageningen, NL,
Aim: characterizing soil communities associated with range-expanding plants focusing on protists and plant pathogenic organisms
04/11 – 03/14 PhD thesis; University of Cologne, Germany (Grade: Summa cum laude)
Title: “Soil Protists: Diversity, Distribution and Ecological Functioning”
- Teaching and co-supervision of diverse internships and bachelor students
- Lab safety advisor
10/10 – 02/11 Supply teacher for biology and mathematics; Elly-Heuss-Knapp Realschule,
Cologne, Germany
10/08 – 09/10 Master of Science in „General Biology“; University of Cologne (Grade: 1.3)
Master thesis in the faculty of Terrestrial Ecology in collaboration with the Netherlands
Institute of Ecology, the Netherlands; title: “Soil amoebae (Acanthamoeba castellanii)
alter plant competition between Plantago lanceolata and Rumex acetosella in
presence of mycophagous Collimonas bacteria" (Grade: 1.1; supervisor: Prof. Dr.
Michael Bonkowski)
01/05 – 07-08 Bachelor of Science in Biology (Grade: 2.0)
01/05 – 05/06 University of Maryland, College Park, USA (full scholarship)
10/06 – 07/08 University of Cologne
Bachelor thesis at Bayer CropScience AG (Frankfurt, Germany)
Translated title: Studies on the impact and degradation of a new sulphonylurea
herbicide under varying environmental parameters
05/03 – 06/04 Voluntary Year of Social Services; Federal sports association of Rhineland-
Palatinate; trainer education; diverse club affairs; event organizations
06/94 – 03/03 Abitur certificate; Johannes-Gymnasium, Lahnstein, Germany
RESEARCH EXPERIENCE AND INTERNSHIPS
02/15 – ongoing Initiator and manager of the Soil Protist Initiative in a joint effort with the Global Soil
Biodiversity Initiative (http://www.globalsoilbiodiversity.org/)
Designing and managing a webpage (https://soilprotists.wordpress.com/) and organize joint projects (e.g. sessions at conferences, design of flyers)
01/14 Research stay; Natural history museum, London; Great Britain
Planning and discussing collaborative projects, instructions and analyses of
metagenomic datasets; supervisor: David Bass
02/13 Research stay; INRA Dijon, France
Method development for the quantification of soil protists supervisor: Laurent Philippot
06/12 -07/12 Research stay; St. Petersburg State University, Russia
Taxonomy and methodology of amoebae; supervisor: Alexey Smirnov
08/09 -12/09 Erasmus-Semester; Lund University, Sweden
Performing a weed establishment experiment evaluating different land-use intensities;
microscopical analyses of nematode populations & determination of soil microbes
(PLFA analyses); supervisor: Prof. Dr. Katharina Hedlund
01/09 - 07/09 Student helper in the faculty of Terrestrial Ecology at the University of Cologne;
supervisor: Prof. Dr. Michael Bonkowski
03/09 – 04/09 Internship at the Federal Institute for Hydrology (BfG), Koblenz, Germany
Sampling and analysing river water samples from (Elbe, Mosel, Rhine)
06/08 – 07/08 Internship at Teagasc Research Station, Wexford, Irland
Evaluating different agricultural land use on the abundance and composition of
nematodes and determining soil volatiles using gas chromatography
08/07 – 09/07 Internship at Bayer CropScience AG, Frankfurt-Höchst
Profiling of Herbicides for plant protection; performing an experiment to evaluate plant
performance after herbicide application
ADDITIONAL PROFESSIONAL ACTIVITIES AND SKILLS
Active participation at workshops and conferences (Name; location; contribution)
10/16 COST workshop KEYSOME on role of soil fauna in decomposition; Coimbra, Portugal
07/16 Wageningen soil network kick-off meeting; Wageningen, NL, Talk
05/16 UniEuk kick-off & first implementation meeting; Paris, France; Talk and permanent member of
the steering committee
03/16 Workshop “Soil food webs: Linking structure, energy flux and function”; Berlin, Germany; Talk
02/16 German society for Protozoology; Saignelégier, Switzerland; Talk
02/16 Netherlands Annual Ecology Meeting, Lunteren, Netherlands; Convening a Session and Talk
11/15 Meeting of the working group soil organisms and pathogens; Wageningen, Netherlands; Talk
09/15 Joint conference of the International Society of Protistology and the European Congresses of Protistology; Sevilla, Spain; Convening a Session and Talk
06/15 Rhizosphere4 conference, Maastricht, The Netherlands; Talk
02/15 Netherlands Annual Ecology Meeting, Lunteren, Netherlands; Poster
12/14 Final meeting of EU-Project EcoFINDERS and Global Soil Biodiversity (GSBI) conference, Dijon, France; Poster
10/14 Metagenomic course; Wageningen, Netherlands
04/14 Instructor for morphological and molecular work on soil protists as part of the PhD workshop „Selecting Indicators for Monitoring Soil Biodiversity and Ecosystem Services“; Wexford, Irland
02/14 Annual meeting of the EU-project EcoFINDERS; Manchester, Great Britain; Talk
10/13 Post-graduate course “Soil processes”; Jena, Germany
09/13 Next generation sequencing workshop; Nancy, France
07/13 Free living amoebae meeting; Vienna, Austria; Talk
06/13 Linking microbial ecology & evolution; Berlin, Germany
03/12 Moving from lab to field; Jülich, Germany; Talk
02/13 German society for Protozoology; Kartause-Ittingen, Switzerland; Talk
11/12 Post-Grad course “Soil, Biodiversity and Life” preceeding the annular meeting of the EU-project
EcoFINDERS; Wageningen, the Netherlands
11/12 Current Themes in Ecology conference “Soil, Biodiversity and Life: The contribution of soil to
sustainability of life”; Wageningen, The Netherlands; Poster
09/12 DBG Kommission III, „Habitat: soil “; Hohenheim, Germany; Talk
03/12 German society for Protozoology; Wuppertal, Germany; Poster + Talk
03/12 Multitrophic Interactions; Göttingen, Germany; Talk
02/12 Crossroads in Biology; Cologne, Germany; Poster
11/11 Annual meeting of the EU-project EcoFINDERS; Coimbra, Portugal
10/11 Science for the Environment; Aarhus, Denmark; Talk
10/11 Symposium on “agro-biodiversity in Germany”; Bonn, Germany
06/11 Functions and Services of Biodiversity; Göttingen, Germany; Poster
06/11 “Professional discussion on soil biodiversity”; Dessau, Germany
04/11 Next-generation sequencing and transcriptomics; Göttingen, Germany
02/11 Kick-off meeting EU-Projekt EcoFINDERS; Dijon, France
Invited presentations
12/15 Seminar at the Department of Animal Ecology, University of Göttingen; Germany; Invited by
Prof. Stefan Scheu
11/15 Seminar at the Department of Nematology, Wageningen University Netherlands; Invited by
Prof. Johannes Helder
12/13 Seminar at the department of Soil Quality, Wageningen University; Netherlands; Invited by Prof.
Lijbert Brussard
Additional professional training courses
10/15 Entrepreneurship in and outside of Science
11/13 Creative idea generation
11/13 Advanced training for lab safety officers
09/13 Leadership seminar in Science
08/13 Debate moderation
06/13 Scientific writing
06/13 Basics of moderation
04/12 Advanced Scientific Writing
04/12 Designing and presenting a Poster
02/12 Introduction in patent issues with practical exercises
09/11 Advanced training for project management and agent for biological safety §15 and GenTSV
Book chapter
- de Groot GA, Laros I, Geisen S (2016). Molecular Identification of Soil Eukaryotes and Focused Approaches Targeting Protist and Faunal Groups Using High-Throughput Metabarcoding. Methods in molecular biology (Clifton, N.J.), 1399, 125-140.
Peer-Reviewed articles for
- Ecol Lett; ISME J; Nature Ecol Evol; New Phytol; Environ Microbiol; Mol Ecol; Mol Ecol Res; Soil Biol Biochem; Divers Distrib; Plos One; Res Microbiol; Protist; BMC Research Notes; Diversity; Pedobiologia; Biomed Res Int; Science of Nature; Appl Environ Microbiol; Folia Parasitol; Appl Soil Ecol; Rep Parasitol; Sci Total Environ; FEMS Microbiol Ecol; J Eukaryot Microbiol; Oikos; Eur J Protistol; J Biogeogr; Pedosphere; Polar Biol; Acta Protozool
Ongoing External Collaborations
- Prof. Dr. Edward Mitchell and Dr. Enrique Lara; Université de Neuchâtel, Switzerland
- Dr. David Bass; Natural History Museum, London, UK
- Dr. Cédric Berney; Station Biologique De Roscoff, France
- Prof. Dr. Bryan Griffiths; Scotland’s Rural College, Edinburgh, UK
- Assistant Prof. Dr. Alexandre Jousset; Utrecht University, The Netherlands
- Jiayi Qin and Dr. Paul Henning Krough; Aarhus University, Silkeborg, Denmark
- Susana Santos and Dr. Anne Winding; Aarhus University, Roskilde, Denmark
- Dr. Robert Griffiths; Centre for Ecology & Hydrology, Wallingford, UK
- Dr. Arjen de Groot; Alterra, Wageningen, The Netherlands
- Prof. Dr. Michael Bonkowski and Dr. Gernot Glöckner; University of Cologne, Germany
- Dr. Alexey Smirnov and Dr. Alexander Kudryavtsev; Saint Petersburg State University, Russia
- Prof. Dr. Tim Urich; University of Greifswald, Germany
Teaching
06/16 Seminar Soil microbiome; Utrecht University
10/15 Practical instructor; Wageningen University
Supervision of 10 Bachelor students during their thesis, 2 Master students during their internships
Co-promotor of 3 PhD students
OTHER SKILLS
Language English: business fluent
Swedish, French, Dutch: Basic knowledge
Computer MS Office: Word, Excel, PowerPoint, Access
Bioinformatic programs: Seaview, MrBayes, RAxML, Megan, R
Statistical software: SPSS, R, Past
ACTIVITIES/ENGAGEMENT/HOBBIES
Teaching Course leader at the Junior-University in Wuppertal (2011-2014)
Course leader at Children Universities organised by the Kreissparkasse Köln (2010-2014)
Course leader of the German Junioracademy NRW (2008-2011)
Sports Climbing coach in the climbing forest Sayn (2008-2009)
Competitive swimming, e.g. German junior-champion 2003
Other sports especially endurance sports (cycling, running)
2016: Post-doc at WUR to establish molecular methods to study the community structure of soil nematodes
2014 - 2016 Post-doc investigating soil-bourne plant-pathogenic organisms in the framework of an ERC advanced grant of Wim van der Putten
2011 - 2014 EU project EcoFINDERS (http://ecofinders.dmu.dk), investigating distribution, community structure and ecological functioning of soil protists
Geisen S*, Schultz-Böhm K*, Wubs JER, Song C, de Boer W, Garbeva P (in press) The prey’s scent – volatile mediated interactions between soil bacteria and their protist predators ISME J
- Berney, C., Ciuprina, A., Bender, S., Brodie, J., Edgcomb, V., Kim, E.,... de Vargas, C. (2017). UniEuk: Time to Speak a Common Language in Protistology! Journal of Eukaryotic Microbiology, 64(3), 407-411. doi:10.1111/jeu.12414
- Geisen, S., Mitchell, E. A., Wilkinson, D. M., Adl, S., Bonkowski, M., Brown, M. W.,... Lara, E. (2017). Soil protistology rebooted: 30 fundamental questions to start with. Soil Biology and Biochemistry, 111, 94-103. doi:10.1016/j.soilbio.2017.04.001
- Geisen, S., & Bonkowski, M. (2017). Methodological advances to study the diversity of soil protists and their functioning in soil food webs. Applied Soil Ecology, in press, -. doi:10.1016/j.apsoil.2017.05.021
- Morriën, E., Hannula, S. E., Snoek, B., Helmsing, N. R., Zweers, H., De Hollander, M.,... van der Putten, W. H. (2017). Soil networks become more connected and take up more carbon as nature restoration progresses. Nature Communications, in press, [14349]. doi:10.1038/ncomms14349
- Schulz-Bohm, K., Geisen, S., Wubs, E. R. J., Song, C., De Boer, W., & Garbeva, P. V. (2017). The prey’s scent – volatile organic compound mediated interactions between soil bacteria and their protist predators. ISME Journal, 11, 817-820. doi:10.1038/ismej.2016.144
- Andriuzzi, W. S., Ngo, P-T., Geisen, S., Keith, A. M., Dumack, K., Bolger, T.,... Schmidt, O. (2016). Organic matter composition and the protist and nematode communities around anecic earthworm burrows. Biology and Fertility of Soils, 52(1), 91-100. doi:10.1007/s00374-015-1056-6
- Bass, D., Silberman, J. D., Brown, M. W., Pearce, R. A., Tice, A. K., Jousset, A.,... Hartikainen, H. (2016). Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists. Environmental Microbiology, 18(5), 1604-1619. doi:10.1111/1462-2920.13235
- Geisen, S., Koller, R., Huenninghaus, M., Dumack, K., Urich, T., & Bonkowski, M. (2016). The soil food web revisited: Diverse and widespread mycophagous soil protists. Soil Biology & Biochemistry, 94, 10-18. doi:10.1016/j.soilbio.2015.11.010
- Geisen, S. (2016). Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists. Environmental Microbiology, 18(6), 1669-1672. doi:10.1111/1462-2920.13309
- Geisen, S. (2016). The bacterial-fungal energy channel concept challenged by enormous functional versatility of soil protists. Soil Biology & Biochemistry, 102(November), 22-25. doi:10.1016/j.soilbio.2016.06.013
- Griffiths, B., Römbke, J., Schmelz, R., Scheffczyk, A., Faber, J., Bloem, J.,... Stone, D. (2016). Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function. Ecological Indicators, 69, 213-223. doi:10.1016/j.ecolind.2016.04.023
- Tice, A. K., Shadwick, L. L., Fiore-Donno, A. M., Geisen, S., Kang, S., Schuler, G. A.,... Brown, M. W. (2016). Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group. 11(1), [69]. doi:10.1186/s13062-016-0171-0
- Wilschut, R. A., Geisen, S., Ten Hooven, F. C., & van der Putten, W. H. (2016). Interspecific differences in nematode control between range-expanding plant species and their congeneric natives. Soil Biology & Biochemistry, 100, 233-241. doi:10.1016/j.soilbio.2016.06.025
- Geisen, S., Laros, I., Vizcaíno, A., Bonkowski, M., & de Groot, G. A. (2015). Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa. Molecular Ecology, 24(17), 4556-4569. doi:10.1111/mec.13238
- Geisen, S., Bonkowski, M., Zhang, J., & De Jonckheere, J. F. (2015). Heterogeneity in the genus Allovahlkampfia and the description of the new genus Parafumarolamoeba (Vahlkampfiidae; Heterolobosea). European Journal of Protistology, 51(4), 335-349. doi:10.1016/j.ejop.2015.05.003
- Geisen, S., Tveit, A. T., Clark, I. M., Richter, A., Svenning, M. M., Bonkowski, M., & Urich, T. (2015). Metatranscriptomic census of active protists in soils. ISME Journal, 9(10), 2178-2190. doi:10.1038/ismej.2015.30
- Geisen, S., Rosengarten, J., Koller, R., Mulder, C., Urich, T., & Bonkowski, M. (2015). Pack hunting by a common soil amoeba on nematodes. Environmental Microbiology, 17(11), 4538-4546. doi:10.1111/1462-2920.12949
