VENI laureat; Junior Group Leader

Current research 

From January 2018 on I will start my three year VENI project. It aims at disentangling whether soil biodiversity affects plant performance, both of crop plant species and even more of natural (early- and mid-successional) plant species. I will focus on soil protists and a diversity gradient of up to 100 species, a diversity that to date has never been touched in diversity-functioning experiments. 

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In line, in collaboration with Alex Jousset from Utrecht University I have been granted an NWO project that aims at applying soil protists to increase plant performance for applied purposes.

To disentangle the importance of protists within the soil microbiome and to get a better understanding of soil biodiversity in general I will coollaborate with other scientists at the NIOO including Wim van der Putten, Paolina Gerbeva, Eiko Kuramae in diverse projects.

However, I am also directly interested in other soil organisms, their diversity and ecological functioning and therefore directly include bacteria, fungi and nematodes in my studies using both classical cultivation based as well as molecular (qPCR, sequencing) approaches.

 

Previous work

ERC work on plant range expansion

Between April 2014 and end 2017 I was working both at the NIOO and for a 8 months period at Wageningen University in Wim van der Puttens ERC project SPECIALS. In this project we tried to determine mechanistic abiotic and biotic drivers that help plants expand their range northwards in the course of climate warming. My role was to investigate the diversity and role of fungal and fungal like oomycete organisms associated with range-expanding and related native plants (e.g. Geisen et al. Frontiers in Microbiology 2017)

Furthermore, I was involved in molecular analyses of bacteria, fungi and nematodes the plant's rhizosphere along a transect throughout Europe (from Greece to the Netherlands). My focus was to design mitochondrial and chloroplast blocking primers to allow higher coverage of bacteria inside roots and design a high-throughput sequencing methodology to study nematodes.

I was collaborating with several partners within that project to disentangle belowground processed that determine range-expansion (e.g. Wilschut, Geisen et al. 2016 SBB)

 

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. 

 

Protist work

Starting from my PhD and continuing thereafter, my major focus is on soil protists, and I am interested in many aspects including their diversity and their ecological functioning. 

I am trying to raise awareness of the importance of soil protists in the scientific community; for instance I started the soil protist initiative where more than a 100 scientists are involved in which also resulted in a large opinion paper with 47 authors. This initiative is in close link to the global soil biodiversity initiative. Furthermore, I am involved as a steering committee member in the global UniEuk project that aims at providing a universal taxonomic framework to better study and understand protists with help of all scientists working on protists. More details at the webpage and Berney at al. Journal of Eukaryotic Microbiology 2017. By standardizing and optimizing methods to study soil protists (Geisen & Bonkowski 2017), I hope to help a wider range of scientists to include protists in their studies.

 

My entire interest on protists started with my PhD 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. 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, ), such as new species of beautiful Cochliopodium (Figure 2). Other taxonomic and phylogenetic work on protists emerging from my PhD efforts descriptions Bass et al. 2016, Tice et al. 2016, Smirnov et al. 2017 showing that classical cultivation based work is fruitful but even more that a lot of this work is needed to get a better understanding of soil (protist) biodiversity!

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Figure 2: Light microscopic pictures of the newly described species Cochliopodium plurinucleolum

 

I also 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 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