Wietse de Boer  is senior researcher at the department of Microbial Ecology (NIOO-KNAW). Since 1 March 2012 he is also connected as special Professor  in Microbial Soil Ecology  to the Wageningen University, department of Soil Quality.

Other professional activities

Editor of FEMS Micobial Ecology
Editorial Board of Pedobiologia
Advising Member  - Dutch Centre for Soil Ecology
Member of national and international PhD thesis evaluation committees
Member of national and international grant evaluation committees
Co-organizer of international PhD course Microbial Ecology (Research School PE&RC)
Invited lecturer at national and international MSc and PhD courses
Key-note speaker at national and international scientific symposia

Nederlandstalige info over het onderzoeksgebied: inaugurele rede  en bijdrage aan cahier Leve(n)de Bodem

 

Review articles with further details on the research interests in fungal-bacterial interactions: 

 De Boer et al (2005) FEMS Microbiol. Rev. 29, 795-811 ( doi:10.1016/j.femsre.2004.11.005)

 Garbeva et al (2011) Soil Biol. Biochem. 43, 469-477 ( doi:10.1016/j.soilbio.2010.11.020)

 Van der Wal et al (2013) FEMS Microbiol. Rev. 37, 477-494 (doi:10.1111/1574-6976.12001)

 De Boer (2017) Curr. Opin. Microbiol. 37, 25-41 ( doi:10.1016/j.mib.2017.03.007)

 

 

1. Application of fungal-bacterial interactions

My current research is mostly focused on the possibility to apply results obtained in basic scientific projects on fungal-bacterial interactions which are described below (2. to 5.).

The real world is far more complex than the model-systems in which we often study interactions. So the challenge is to translate insights from model studies to real ecosystems and to use this to develop strategies to steer microbiomes in a desired direction (De Boer (2017) Curr.Opin. Microbiol. 37, 25-41;  doi:10.1016/j.mib.2017.03.007).

 


Multiple Interactions in Model Systems: One Step Closer to Reality

 
Stimulating antagonistic interactions between fungi and bacteria to enhance natural bioncontrol of soil-borne pathogens

Saprofeed-project:  In this project we use insights on competitive interactions between organotrophic (saprotrophic)  fungi and bacteria as basis for application. From our basic research projects (see 5.) we know that enhanced fungal competition for root-exudates can increase the frequency of rhizosphere bacteria with antifungal properties. This results in better natural protection against root-infecting fungal pathogens. To use this principle in agricultural soils, the abundance of saprotrophic fungi should be stimulated. In intensively managed agriculture soils the abundance of fungi is mostly very low. The saprofeed project is examining how fungi can be stimulated in such soils and  if this is indeed resulting in a better protection against soil-borne fungal diseases. Saprofeed is funded by The Netherlands Organisation of Scientific Research (NWO-TTW).

 


Saprofeed Hypothesis

 

Insectloop-project:  In this project we examine if waste (moulting skins, manure) of insect growing companies can be used for biocontrol and fertilisation purposes. Moulting skins contain chitin and may therefore be an interesting source to stimulate chitinolytic soil microbes with biocontrol properties. Another aspect of the project is to examine whether mixing of insect waste with other organic fertilizers is enhancing the nutritional value.

Insectloop is a collaborative project between Wageningen University and NIOO and is coordinated by Prof. Marcel Dicke (WUR, Lab. of  Entomology ). Next to the aspects mentioned here also effects of insect waste on control of harmful insects (Lab. of  Entomology) and economic feasibility of using insect waste (WUR, Subdivision of Business Economics, Prof. Alfons Oude Lansink) is studied. Insectloop is funded by The Netherlands Organisation of Scientific Research (NWO-Circular Economy).

 


Bacteria Occurring on Decaying Insect Skins

 

Stimulating microbial inhibition of a parasitic weed

Promise-project 10A: Possibilities to use volatile-producing and signal-degrading microbes to suppress infection of cereals by Striga.

This project is part of the discovery programme PROMISE (Promoting Root Microbes for Integrated Striga Eradication) which is led by the Netherlands Institute of Ecology (NIOO-KNAW; coordinator Prof. Jos Raaijmakers) and funded by the Bill & Melinda Gates Foundation.  Promise Website

The overall goal of PROMISE is to engineer soil and plant microbiomes for enhanced crop productivity in Sub-Saharan Africa. In the sub-project the focus is on microbial-mediated effects on Striga-seed germination and on infection of Sorghum-roots by Striga. The emphasis will be (1) on microbes producing volatiles which either stimulate (without presence of the host) or inhibit Striga seed germination and (2) on microbes that degrade signals that are essential for Striga to recognize the host plant Sorghum.

Discovery of new antibiotics & enzymes

No current projects are dealing with this. However, our research on fungal-bacterial interactions has revealed several possibilities for discovery of novel metabolites that are now being explored by other research groups.

For example, a project on “mining of Streptacidiphilus species as a potential source of novel bioactive natural products” is running at the research group of Prof. Gilles van Wezel of the Leiden university. These Streptacidiphilus  strains have been isolated from decaying wood in a project on interactions between wood-decay fungi and bacteria (see. 4.)

Another example, is the exploration of the collection of we isolated from decaying wood for application in biofuel production at the microlifesolutions company (http://www.microlifesolutions.nl/).

Within the department of Microbial Ecology investigation of interaction-mediated production of secondary metabolites is an important topic in the research of the group of Dr. Paolina Garbeva

 


Bacterium with Antifungal Activity

 

2. Feeding of bacteria on living fungi (mycophagy)

Withdrawal of organic nutrients form living fungi is a strategy developed by some soil bacteria in the struggle to obtain energy resources. We discovered this strategy  for a group of soil bacterial isolates that have been grouped in the genus Collimonas (De Boer et al (2004)  Int. J. Syst. Evol. Microbiol. 54, 857-864; doi:10.1099/ijs.0.02920-0). This genus, and in particular the species Collimonas fungivorans, is now being studied in our department as a model organism for bacterial mycophagy. Research ranges from mechanisms of mycophagous feeding ( e.g. Mela et al (2011) ISME J 5: 1494-1504; doi:10.1038/ismej.2011.29) by collimonads to the role of mycophagous bacteria in microbial community dynamics, soil food webs and soil ecosystem functioning (e.g. Höppener-Ogawa et al (2009) Environ. Microbiol 11, 1444-1452; doi:10.1111/j.1462-2920.2009.01872.x)

 

                
       Collimonas fungivorans                         Enjoying a fungal meal

Further research (Ph.D thesis Max-Bernhard Rudnick (now Ballhausen); http://edepot.wur.nl/330215 ) has indicated that mycophagous feeding is not restricted to Collimonas bacteria, but is in fact widespread among bacteria occurring in the rhizosphere. Together with the fact that several studies have shown prominent uptake of root-exudates by saprotrophic fungi in several ecosystems this has led to the sapro-rhizosphere concept: the flow of root-derived carbon via fungi to bacteria ( Ballhausen and de Boer (2016) Soil Biol. Biochem. 102, 14-17) (doi:10.1016/j.soilbio.2016.06.014)

Recent findings related to bacterial mycophagy research:

- Comparative genomics analysis based on whole-genome sequencing of six Collimonas strains representing 3 recognized species. Song et al (2015) BMC Genomics 16 (doi:10.1186/s12864-015-2289-3).

- Bacteria that are strongly associated with a zygomycete fungus.Schulz-Bohm (2016) Fung. Genet. Biol. 102, 38-48 (doi:10.1016/j.fgb.2016.07.011)

Reviews on bacterial mycophagy: Leveau et al (2010) Environ. Microbiol. 12, 281-292.(http://leveau.ucdavis.edu/wp-content/uploads/sites/220/2015/05/Leveau201...).

 

3. Suppression of fungi in soils (Fungistasis)

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis which was firstly described by Dobbs and Hinson in 1953. Many studies on fungistasis have been done in the sixties and seventies of the former century. These studies have indicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of anti-fungal compounds (antibiosis hypothesis).

We have shown that microbial community composition and interactions therein are important for fungistasis (De Boer et al (2003) Appl. Environ. Microbiol. 69, 835-844, doi:10.1128/AEM.69.2.835-844.2003 ; De Boer et al (2007) FEMS Microbiol. Ecol. 59, 177-185, doi:10.1111/j.1574-6941.2006.00197.x) and used this as an argument to support the antibiosis hypothesis (see also Garbeva group page; https://nioo.knaw.nl/nl/node/3651).

With the increasing interest in sustainable agriculture also a revival of interest in fungistasis is seen. This is because fungistasis is the first buffer in soil against soil-borne fungal diseases. Hence, it is expected that agricultural measurements which increase fungistasis will also enhance the natural protection of crops against soil-borne fungal diseases. Basic knowledge on the factors that cause microbes to produce fungistatic compounds is needed to indicate which management strategies should be taken to stimulate fungistasis and disease suppression.

Currently we are giving much attention to the contribution of bacterial volatiles to fungistasis and disease suppression.

 


Exploration of Soil by Fungal Hyhae of Wood-decay Fungi

 

Recent findings related to fungistasis research:

- Low abundant soil bacterial species have an important contribution to the production of antifungal volatiles (Hol et al (2015) Ecology 96, 2042-2048). (doi:10.1890/14-2359.1)

- Strong impact of soil management (anaerobic disinfestation) on bacterial communities and production of pathogen suppressing volatiles (Van Agtmaal et al (2015) Front. Microbiol.

(doi:10.3389/fmicb.2015.00701)

- Wide-spread occurrence of pathogen-suppressing volatiles in agricultural soils (Van Agtmaal et al (2018) Soil Biol. Biochem. 117, 164-17). (doi:10.1016/j.soilbio.2017.11.015)

Review on fungistasis:

Garbeva et al (2011) Soil Biol. Biochem. 43, 469-477 (doi:10.1016/j.soilbio.2010.11.020)

Review on microbial volatiles:

Schmidt et al (2015) ISME J. (doi:10.1038/ismej.2015.42)

 

4. Interactions between wood-rot fungi and bacteria

 

Decomposition of woody materials in terrestrial ecosystems is mainly accomplished by specialized fungi, called wood-rot fungi. Wood-polymers (cellulose, hemi-cellulose and lignin) are attacked by enzymes and mediators that are exuded by these fungi. The soluble, low-weight compounds that are released by the fungal enzymes are the actual growth substrates for the fungi. Although bacteria are not well able to grow directly on the wood-polymers they can grow on the compounds released by the fungal enzymes i.e. they can profit from the decaying activities of fungi.

 


Wood-rot Fungus in Action

                                                         

Our research has focused on two aspects of wood decomposers :

(1) Assembly of fungal communities in decaying wood

The research on community assembly of wood rot fungi has been initiated and coordinated by Dr. Annemieke van der Wal. This research was connected to a long-term field experiment on decomposition of logs, named LogLife (doi:10.1007/s13280-012-0304-3). After the leave of Annemieke in 2017, the research is being continued by Dr. Mariet Hefting, Utrecht University.

(2) Composition of bacteria in decaying wood and their interactions with wood-rot fungi

Research on bacteria in wood decayed by fungi was started as wood-rot fungi create an extreme environment (low pH, reactive oxygen species, inhibitors) (De Boer et al (2010) Can. J. Microbiol. 56, 380-388; doi:10.1139/W10-023). These conditions  have a strong selective effect on the composition of bacteria (Valášková et al (2009) ISME J 3, 218-221; doi:10.1038/ismej.2009.64). This makes decaying wood also attractive to discover new bacterial genera (Methylovirgula) and species (Acidicapsa ligni)  (Vorob'ev et al (2009) Int. J. Syst. Evol. Microbiol. 59, 2538-2545[doi:10.1099/ijs.0.010074-0] ; Kulichevskaya et al (2012) Int. J. Syst. Evol. Microbiol. 62, 1512-1520 [doi:10.1099/ijs.0.034819-0] ). Since wood-inhabiting bacteria must have special properties they are of particular interest for applications (see: 1.)

 


Methylvirgula: A Bacterial Genus Occurring in Decaying Wood

 

Current research on interactions between wood-decomposing fungi and bacteria has shifted towards the application of woody materials as fungus-stimulating materials in agricultural soils ( see 1., saprofeed project).

Recent findings related to research on fungal-bacterial interactions in wood:

- Fungal community composition in decaying wood is an important factor in explaining wood decay (Van der Wal. et al (2015) Ecology 96, 124-133 (  http://www.esajournals.org/doi/abs/10.1890/14-0242.1).

- Fungal community assembly during in initial decomposition of logs (Van der Wal et al. (2016) Ecosphere7, 1393) (10.1002/ecs2.1393).

- Impact of logs on compostion of fungi in the forest floor (Van der Wal et al. (2017) Fungal Ecology, 30, 132-134. (doi:10.1016/j.funeco.2017.08.006).

- Tree pathogens in decaying logs (Van der Wal et al. (2017) Forest Ecology and Management, 406, 266-273). (doi:10.1016/j.foreco.2017.08.018).

Reviews on wood decomposer ecology:

De Boer & Van der Wal (2008) Interactions between saprotrophic basidiomycetes and bacteria, British Mycological Society Symposia Series, Volume 28 (pp. 141-151). Amsterdam: Elsevier.

Van der Wal et al (2013) FEMS Microbiol. Rev. 37, 477-494 (doi:10.1111/1574-6976.12001).

 

5. Interactions between saprotrophic fungi and bacteria in the rhizosphere

Roots provide soil micro-organisms with energy substrates by exuding simple soluble compounds (such as sugars, organic acids and amino acids) and more complex compounds (such as slime and sloughed-off cells). The soil zone surrounding roots that becomes enriched with these compounds is called the rhizosphere. It has been generally assumed that simple root exudates are mainly decomposed by bacteria which occur in high densities in the rhizosphere. However, 13C-CO2 labelling of plants indicated that saprotrophic fungi can be prominent users of root exudates even in intensive agricultural soils, which are bacteria-dominated (Hannula et al (2012) New Phytol.  194, 784-799; doi:10.1111/j.1469-8137.2012.04089.x). In addition, fungi growing on soil organic matter fractions can also use root exudates as energy resource when their hyphae extend into the rhizosphere. The  presence and activity of saprotrophic fungi in the rhizosphere can extert a a selective effect on the taxonomical and functional composition of rhizopshere bacteria (De Boer et al (2008) Soil Biol Biochem 40, 1542-1544; doi:10.1016/j.soilbio.2007.12.030).

 


Taking Samples from the Rhizosphere

 

Recent findings related to interactions between saprotrophic fungi and bacteria in the rhizosphere:

- Chitinases of fast-growing soil bacteria seem to be involved in antagonistic activities against fungi rather than in degradation of chitin resources (Bai et al (2016) Environmental Microbiology, 18(1), 38-49. (doi:10.1111/1462-2920.12545).

- Ability for mycophagous feeding is taxonomically widespread among rhizosphere bacteria ( Ballhausen and de Boer (2016) Soil Biol. Biochem. 102, 14-17) (doi:10.1016/j.soilbio.2016.06.014)

- Antifungal rhizosphere bacteria can increase as response to the presence of saprotrophic fungi. (De Boer et al. (2015) PLoS One, 10(9), [e0137988]. (doi:10.1371/journal.pone.0137988).

- Importance of fungi as consumers of root exudates increases with time of land abandonment (Hannula et al. (2017) ISME J.11, 2294-2304) (doi:10.1038/ismej.2017.90).

Reviews on interactions between saprotrophic fungi and bacteria in the rhizosphere: 

Buee et al (2009) Plant and Soil 321, 189-212 (doi:10.1007/s11104-009-9991-3)

Van der Wal et al (2013) FEMS Microbiol. Rev. 37, 477-494 (doi:10.1111/1574-6976.12001).

Publications at: http://www.narcis.nl/personpub/id/105/Language/en/uquery/Boer/RecordID/PRS1258931