Prof. dr. Wietse de Boer

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).

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).

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).

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.

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

2. Feeding of bacteria on living fungi (mycophagy)

                

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.

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

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.)

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).

 

 

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).