Dr. Stefan Geisen

Expertise

Protistology, Protozoology, Oomycetes, Fungi, Taxonomy, Phylogeny, Cultivation, qPCR, Cloning, High-throughput amplicon sequencing, Metatranscriptomics, Range-expanding plants, Plant pathogens

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

Geisen S (2016) The bacterial-fungal energy channel concept challenged by enormous functional versatility of soil protists Soil Biol Biochem 102, 22-25

Wilschut RA, Geisen S, ten Hooven FC, van der Putten WH (2016) Interspecific differences in nematode control between range-expanding plant species and their congeneric natives. Soil Biol Biochem 100, 233-241

Geisen S (2016) Thorough high-throughput sequencing analyses unravels huge diversities of soil parasitic protists. Environ Microbiol 18, 1669–1672

Griffiths BS, Römbke J, Schmelz RM, Scheffczyk A, Faber JH, Bloem J, Pérès G, Cluzeau D, Chabbi A, Suhadolc M, Sousa JP, Martins da Silva P , Carvalho F, Mendes S, Morais P, Francisco R, Pereira C, Bonkowski M, Geisen S, Bardgett RD, deVries FT, Bolger T, Dirilgen T, Schmidt O, Winding A, Hendriksen NB, Johansen A, Philippot L, Plassart P, Bru D, Thomson B, Griffiths RI, Bailey MJ, Keith A, Rutgers M, Mulder C, Hannula SE, Creamer R, Stone D (2016) Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function. Ecol Indic 69, 213-223

Bass D, Silberman JD, Brown MW, Tice AK, Jousset A, Geisen S, 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. Environ Microbiol 18: 1604–1619

Geisen S, Koller R Hünninghaus M, Dumack K, Urich T, Bonkowski M (2016). The soil food web revisited: Diverse and widespread mycophagous soil protists. Soil Biol Biochem 94, 10-18

Imparato V, Santos SS, Johansen A, Geisen S, Winding A (2016). Stimulation of bacteria and protists in rhizosphere of glyphosate-treated barley. Appl Soil Ecol 98, 47-55

Stone D, Blomkvist P, Hendriksen NB, Bonkowski M, Jørgensen HB, Carvalho F, Dunbar MB, Gardi C, Geisen S, et al. (2016). A method of establishing a transect for biodiversity and ecosystem function monitoring across Europe." Appl Soil Ecol 97: 3-11

Andriuzzi W, Ngo PT, Geisen S, Keith A, Dumack K, Bolger T. Bonkowski M, Brussaard L, Faber JH, Chabbi A, Rumpel C, Schmidt O (2016). Organic matter composition and the protist and nematode communities around anecic earthworm burrows. Biol Fert Soils 52: 91-100

Geisen S, Rosengarten J, Koller R, Urich T, Mulder C, Bonkowski M (2015). Pack hunting by a common soil amoeba on nematodes. Environ Microbiol 17: 4538-46

Geisen S, Bonkowski M, Zhang J, De Jonckheere JF (2015). Heterogeneity in the genus Allovahlkampfia and the description of the new genus Parafumarolamoeba (Vahlkampfiidae; Heterolobosea). Eur J Protistol 51: 335-349

Geisen S, Laros I, Vizcaíno A, Bonkowski M, de Groot GA (2015). Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa. Mol Ecol 24: 4556–4569