Curriculum Vitae
Dr. Wietse de Boer (1957) graduated from the University of Groningen in 1983 with principal subject Microbial Ecology and subsidiary subjects Plant Ecology, Molecular Genetics and Biochemistry. He got his PhD degree in 1989 at the Agricultural University of Wageningen, promotores Prof. Alex Zehnder and Prof. Wim Harder, on a study of nitrification in acid heathland soils, which he had performed at the department of Soil Biology at the former Instituteof Ecology(now NIOO-KNAW-CTO) during the period 1985-1989. As a Post Doc he continued research on nitrification in acid soils at the department of Soil Biology as part of the Durch Priority Programme on Acidification. In 1992 the Netherlands Organization for Scientific Research (NWO) awarded him a NATO-fellowship for a research stay of 12 months at the Department of Biological Sciences, University of Calgary, Canada. During this stay at the Soil Ecology group of Prof. Dennis Parkinson he studied the possibility of biotic causes of spatial variability of nitrification. In 1993, he got a position as senior researcher at the newly formed department of Plant Microorganism Interactions. In this group he started projects on interactions between bacteria and fungi in soils with emphasis on fungal-eating (mycophagous) bacteria, fungal-associated bacteria and competitive interactions (fungistasis). From 2004 to 2008 he was head of the Project group FBI (Fungal Bacterial Interactions) in which researchers of the KNAW institutes NIOO and CBS collaborate. Occassionally he is replacing the head of the department ME.
Expertise
Fungal Bacterial Interactions
The study of interrelationships between bacteria and fungi is a fascinating area of Microbial Ecology that has received increasing attention during the last decade. The importance of studying interactions between fungi and bacteria can be best illustrated by comparing aquatic and terrestrial environments. During life`s history bacteria have been and still are the dominant decomposers in water and sediments. Fungi, however, have obtained a prominent position as decomposers in soil. The soil is fundamentally different from sediments in that three phases are present (air, water, solids) instead of two (water, solids). The unicellular form of bacteria is well suited to move in water, but not to bridge air-filled soil pores. For this purpose, fungal hyphae are very appropriate. During evolution of land life, fungi have been able to monopolize two important niches in terrestrial ecosystems, namely mycorrhizal associations and decomposition of ligno-cellulose. This has given them a pivotal role in the functioning of terrestrial ecosystems. The important role of fungi in the development of terrestrial ecosystems must also have had a strong impact on the evolution of terrestrial bacteria. Bacteria have been outstripped by fungi with respect to ligno-cellulose decomposition, whereas they have been able to keep a prominent position in the degradation of simple substrates. The presence of fungi has, however, not only resulted in loss of potential niches for bacteria, but has also created new ones e.g. fungal-exudate consumers, fungal-eating bacteria (mycophagy) and endo-symbionts. Confrontation of bacteria with fungi is ongoing and from studying the current interactions we can learn about the impact that fungi have (had) on bacterial ecology and evolution.
Bacteria on fungal hyphae
The study of fungal-bacterial interactions in soils is not only interesting from a basic point of view but is also yielding findings of societal and economical relevance. This can be illustrated by the application of bacteria for biocontrol of fungal plant diseases, growing of mushrooms and stimulation of mycorrhizal infection. Bacteria that are harmful to fungi may in potential also form a source of new antibiotics with therapeutic value. A better basic understanding of the in situ interactions between such bacteria and fungi will result in much more straightforward approaches to screen for new antibiotics.
An article from our group with further details on the research interests: De Boer et al (2005) FEMS Microbiol. Rev. 29, 795-811
Projects
Mycophagy
The dominant chitinolytic bacteria in acid dune soils appeared to be able to grow at the expense of living hyphae of several dune soil fungi (see selected publications). At first, we thought that the bacteria were pseudomonads (bases on FAME-analysis), but sequencing of 16S rDNA revealed that it belonged to a new bacterial genus, Collimonas, in the ß-proteobacteria.
Collimonas fungivorans is now being studied in our department as a model organism for bacterial mycophagy in soils. The genome of one strain has been completely sequenced.
 
Collimonas fungivorans Enjoying a fungal meal
Some of the articles of our group dealing with this topic: De Boer et al (2004) Int. J. Syst. Evol. Microbiol. 54, 857-864; Höppener-Ogawa et al (2007) Appl. Environm. Microbiol. 73, 4191-4197; Fritsche et al (2008) FEMS Microbiol. Ecol. 66, 123-135; Leveau & Preston (2009) New Phytol 177, 859-876; Höppener-Ogawa et al (2009) Environ. Microbiol 11, 1444-1452; Leveau et al (2010) Environ. Microbiol. 12, 281-292.
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 and used this as an argument to support the antibiosis hypothesis (see selected publications and personal page of Paolina Garbeva).
With the increasing interest in sustainable agriculture also a revival of interest in fungistasis is apparent. 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. Basic knowledge on fungistasis is needed to indicate which management strategies should be taken to stimulate fungistasis.
Articles of our group dealing with this topic: De Boer et al (2003) Appl. Environ. Microbiol. 69, 835-844; De Boer et al (2007) FEMS Microbiol. Ecol. 59, 177-185; Garbeva & De Boer (2009) Microbiol Ecol 58, 36-46; Garbeva et al (2011) Soil Biol. Biochem. 43, 469-477
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 eactual 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. In our research group we want to get more insight in the way wood-rot fungi deal with potentially competing wood-inhabiting bacteria.
Wood-rot fungus in action
Articles of our group dealing with this topic: Van der Wal et al. (2007) Plant & Soil 301, 189-201; Folman et al (2008) FEMS Microbiol Ecol 63, 181-191; De Boer & Van der Wal (2008) In: Ecology of Saprotrophic Basidiomycetes (L. Boddy, J. Frankland & P. van West, eds.),Academic Press, pp. 142-151; Valaskova et al (2009) ISME J 3, 218-221; De Boer et al (2010) Can. J. Microbiol. 56, 380-388
Interactions between fungi and bacteria in the rhizosphere
Roots exude compounds like sugars, organic acids and amino acids. The soil zone surrounding roots that becomes enriched with these compounds is called the rhizosphere. The root exudates are mainly decomposed by bacteria which occur in high densities in the rhizosphere. Although saprotrophic fungi seem to play a minor role in the decomposition of root exudates, they may have a selective effect on the taxonomical and functional composition of rhizopshere bacteria.
Articles of our group dealing with this topic: De Boer et al. (2006) New Phytol 170, 3-6; De Boer et al (2008) Soil Biol Biochem 40, 1542-1544
Co-Operation
National collaboration
Jaap Bloem (WUR), Jos Raaijmakers (WUR), Jan Dijksterhuis (CBS-KNAW) Dick van Elzas (RUG), Aad Termorshuizen (BLGG)
International Collaboration
Lynne Boddy (Cardiff), Petr Baldrian (Prague), Pascale Frey-Klett & Stephane Uroz (Dijon), Björn Lindahl (Uppsala), Svetlana Dedysh (Moscow)
Selected Publications
Fransesca Mela, Katrhrin Fritsche, Wietse de Boer, Johannes A. van Veen, Leo H. de Graaff, Marlies van den Berg, Johan H. J. Leveau(2011) Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger ISME J. 5, 1494-1504.
Interactions between bacteria and fungi cover a wide range of incentives, mechanisms and outcomes. The genus Collimonas consists of soil bacteria that are known for their antifungal activity and ability to grow at the expense of living fungi. In non-contact confrontation assays with the fungus Aspergillus niger, Collimonas fungivorans showed accumulation of biomass concomitant with inhibition of hyphal spread. Through microarray analysis of bacterial and fungal mRNA from the confrontation arena, we gained new insights into the mechanisms underlying the fungistatic effect and mycophagous phenotype of collimonads. Collimonas responded to the fungus by activating genes for the utilization of fungal-derived compounds and for production of a putative antifungal compound. In A. niger, differentially expressed genes included those involved in lipid and cell wall metabolism and cell defense, which correlated well with the hyphal deformations that were observed microscopically. Transcriptional profiles revealed distress in both partners: downregulation of ribosomal proteins and upregulation of mobile genetic elements in the bacteria and expression of endoplasmic reticulum stress and conidia-related genes in the fungus. Both partners experienced nitrogen shortage in each other's presence. Overall, our results indicate that the Collimonas/Aspergillus interaction is a complex interplay between trophism, antibiosis and competition for nutrients.
Paolina Garbeva, Mark W. Silby, Jos M. Raaijmakers, Stuart B. Levy, Wietse de Boer (2011) Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors. ISME J. 5, 973-985.
The ability of soil bacteria to successfully compete with a range of other microbial species is crucial for their growth and survival in the nutrient-limited soil environment. In the present work, we studied the behavior and transcriptional responses of soil-inhabiting Pseudomonas fluorescens strain Pf0-1 on nutrient-poor agar to confrontation with strains of three phylogenetically different bacterial genera, that is, Bacillus, Brevundimonas and Pedobacter. Competition for nutrients was apparent as all three bacterial genera had a negative effect on the density of P. fluorescens Pf0-1; this effect was most strong during the interaction with Bacillus. Microarray-based analyses indicated strong differences in the transcriptional responses of Pf0-1 to the different competitors. There was higher similarity in the gene expression response of P. fluorescens Pf0-1 to the Gram-negative bacteria as compared with the Gram-positive strain. The Gram-negative strains did also trigger the production of an unknown broad-spectrum antibiotic in Pf0-1. More detailed analysis indicated that expression of specific Pf0-1 genes involved in signal transduction and secondary metabolite production was strongly affected by the competitors’ identity, suggesting that Pf0-1 can distinguish among different competitors and fine-tune its competitive strategies. The results presented here demonstrate that P. fluorescens Pf0-1 shows a species-specific transcriptional and metabolic response to bacterial competitors and provide new leads in the identification of specific cues in bacteria–bacteria interactions and of novel competitive strategies, antimicrobial traits and genes.
Paolina Garbeva, W.H. Gera Hol, Aad J. Termorshuizen, George A. Kowalchuk, Wietse de Boer (2011) Fungistasis and general soil biostasis - A new synthesis. Soil Biol. Biochem. 43, 469-477.
In most soils, fungal propagules are restricted to a certain extent in their ability to grow or germinate. This phenomenon, known as soil fungistasis, has received considerable attention for more than five decades, mostly due to its association with the general suppression of soil-borne fungal diseases. Here, we review major breakthroughs in understanding the mechanisms of fungistasis. Integration of older fungistasis research and more recent findings from different biological and chemical disciplines has lead to the consensus opinion that fungistasis is most likely caused by a combination of microbial activities, namely withdrawal of nutrients from fungal propagules and production of fungistatic compounds. In addition, recent findings indicate that there is mechanistic link between these activities leading towards an integrated theory of fungistasis. Among the potentially fungistatic compounds volatiles have received particular attention. Whereas it has long been assumed that fungistasis is the result of the metabolic activity of the total soil microbial biomass, more recent research points at the importance of activities of specific components of the microbial community. These insights into fungistasis have also formed the basis for strategies to increase general soil suppression. Besides these basic and practical aspects of fungistasis, its impact on fungal ecology, in particular on fungal exploration strategies, is discussed. Finally, we take a closer look at plant–soil feedback experiments to demonstrate the occurrence of fungistasis-like phenomena and to suggest that fungistasis may be part of a much wider phenomenon: general soil biostasis
S. Emilia Hannula, Wietse de Boer, Johannes A. van Veen (2010) In situ dynamics of soil fungal communities under different genotypes of potato, including a genetically modified cultivar. Soil Biol. Biochem. 42, 2211-2223.
Fungi are key to the functioning of soil ecosystems, and exhibit a range of interactions with plants. Given their close associations with plants, and importance in ecosystem functioning, soil-borne fungi have been proposed as potential biological indicators of disturbance and useful agents in monitoring strategies, including those following the introduction of genetically modified (GM) crops. Here we report on the impact of potato crop varieties, including a cultivar that was genetically modified for its starch quality, on the community composition of the main phyla of fungi in soils, i.e. Ascomycota, Basidiomycota and Glomeromycota in rhizosphere and bulk soil. Samples were collected at two field sites before sowing, at three growth stages during crop development and after the harvest of the plants, and the effects of field site, plant growth stage and plant cultivar (genotype) on fungal community composition assessed using three phylum-specific T-RFLP profiling strategies and multivariate statistical analysis (NMDS ordinations with ANOSIM test). In addition, fungal biomass, arbuscular mycorrhizal colonization of roots and activities of extracellular fungal enzymes (laccases, Mn-peroxidases and cellulases) involved in degradation of lignocelluloses-rich organic matter were determined. Fungal community compositions, densities and activities were observed to differ significantly between the rhizosphere and bulk soil. The most important factors determining fungal community composition and functioning were plant growth stage for the rhizosphere communities and location and soil properties for the bulk soil communities. The basidiomycetes were the most numerous fungal group in the bulk soils and in the rhizosphere of young plants, with a shift toward greater ascomycete numbers in the rhizosphere at later growth stages. There were no detectable differences between the GM cultivar and its parental cultivar in terms of influence on fungal community structure of function. Fungal community structure and functioning of both GM- and parental cultivars fell within the range of other cultivars at most sampling moments.
Wietse de Boer, Larissa B. Folman, Paulien J.A. Klein Gunnewiek, Teresia Svensson, David Bastviken, Gunilla Oberg, Jose C. del Rio, Lynne Boddy (2010) Mechanism of antibacterial activity of the white-rot fungus Hypholoma fasciculare colonizing wood. Can. J. Microbiol. 56, 380-388
In a previous study it was shown that the number of wood-inhabiting bacteria was drastically reduced after colonization of beech (Fagus sylvatica) wood blocks by the white-rot fungus Hypholoma fasciculare, or sulfur tuft (Folman et al. 2008). Here we report on the mechanisms of this fungal-induced antibacterial activity. Hypholoma fasciculare was allowed to invade beech and pine (Pinus sylvestris) wood blocks that had been precolonized by microorganisms from forest soil. The changes in the number of bacteria, fungal biomass. and fungal-related wood properties were followed for 23 weeks. Colonization by the fungus resulted in a rapid and large reduction in the number of bacteria (colony-forming units), which was already apparent after 4 weeks of incubation. The reduction in the number of bacteria coincided with fungal-induced acidification in both beech and pine wood blocks. No evidence was found for the involvement of toxic secondary metabolites or reactive oxygen species in the reduction of the number of bacteria. Additional experiments showed that the dominant bacteria present in the wood blocks were not able to grow under the acidic conditions (pH 3.5) created by the fungus. Hence our research pointed at rapid acidification as the major factor causing reduction of wood-inhabiting bacteria upon colonization of wood by H. fasciculare.
Johan H.J. Leveau, Stephane Uroz, Wietse de Boer (2010) The bacterial genus Collimonas: mycophagy, weathering and other adaptive solutions to life in oligotrophic soil environments. Environ. Microbiol. 12, 281-292
This minireview provides a synopsis of past and present research on the biology and ecology of members of the bacterial genus Collimonas. From the distribution, abundance and functional behaviours of these so-called collimonads emerges a general picture of bacterial adaptation to low-nutrient soil environments. Among these adaptations is the ability to extract nutrients from living fungi (mycophagy) and from rocks and minerals (weathering). This unique combination of properties will be discussed in the context of other interactions that collimonads have with their biotic and abiotic surroundings, such as the ability to inhibit fungal growth (fungistasis), protect plant roots from fungal disease (biocontrol), and degrade natural polymers and synthetic pollutants (biodegradation). Future research on Collimonas is expected to take advantage of the genomic tools and resources that are becoming available to uncover and describe the genes and gene functions that distinguish this group of bacteria and are the basis for its phenotypes. Potential applications of collimonads include the control of unwanted fungi, for example in agriculture, their use as biological indicators of soil quality and fertility, and as a source of bioactive compounds.
Paolina Garbeva, Wietse de Boer (2009) Inter-specific interactions between carbon-limited soil bacteria affect behavior and gene expression. Microbial Ecol. 58, 36-46.
Recent publications indicate that inter-specific interactions between soil bacteria may strongly affect the behavior of the strains involved, e.g., by increased production
of antibiotics or extracellular enzymes. This may point at an enhanced competitive ability due to inter-specific triggering of gene expression. However, it is not known if
such inter-specific interactions also occur during competition for carbon which is the normal situation in soil. Here, we report on competitive interactions between two taxonomically non-related bacterial strains, Pseudomonas sp. A21 and Pedobacter sp. V48, that were isolated from a dune soil. The strains showed strong effects on each other’s behavior and gene expression patterns when growing together under carbon-limited conditions on agar. The most pronounced observed visual changes in mixed cultures as compared to monocultures were (1) strong inhibition of a bioindicator fungus, suggesting the production of a broadspectrum antibiotic, and (2) the occurrence of gliding-like movement of Pedobacter cells. Two independent techniques, namely random arbitrary primed-PCR (RAP-PCR) and suppressive subtractive hybridization (SSH), identified in total 24 genes that had higher expression in mixed cultures compared to monocultures. Microbial interactions were clearly bidirectional, as differentially expressed genes were detected for both bacteria in mixed cultures. Sequence analysis of the differentially expressed genes indicated that several of them were most related to genes involved in motility and chemotaxis, secondary metabolite production and two-component signal transduction systems. The gene expression patterns suggest an interference competition strategy by the Pseudomonas strain and an escape/explorative strategy by the Pedobacter strain during confrontation with each other. Our results show that the bacterial strains can distinguish between intra- and inter-specific carbon competition.
Sachie Höppener-Ogawa, Johan H.J. Leveau, Maria Hundscheid, Johannes A. van Veen, Wietse de Boer. 2009. Impact of Collimonas bacteria on community
composition of soil fungi. Environ. Microbiol. 11, 1444-1452
The genus Collimonas consists of soil bacteria that have the potential to grow at the expense of living fungal hyphae. However, the consequences of this mycophagous ability for soil fungi are unknown. Here we report on the development of fungal communities after introduction of collimonads in a soil that had a low abundance of indigenous collimonads. Development of fungal communities was stimulated by addition of cellulose or by introducing plants (Plantago lanceolata). Community composition of total fungi in
soil and rhizosphere and of arbuscular mycorrhizal fungi in roots was examined by PCR-DGGE. The introduction of collimonads altered the composition of all fungal communities studied but had no effects on fungal biomass increase, cellulose degrading activity or plant performance. The most likely explanation for these results is that differences in sensitivity of fungal species to the presence of collimonads result in competitive replacement of species. The lab and greenhouse experiments were complemented with a
field experiment. Mesh bags containing sterile sand with or without collimonads were buried in an ex-arable field and a forest. The presence of collimonads had an effect on the composition of fungi invading these bags in the ex-arable site but not in the forest site.
Sachie Höppener-Ogawa, Johan H.J. Leveau, Johannes A. van Veen, Wietse de Boer. 2009. Mycophagous growth of Collimonas bacteria in natural soils, impact on fungal
biomass turnover and interactions with mycophagous Trichoderma fungi. ISME J. 3, 190-198.
Bacteria of the genus Collimonas are widely distributed in soils, although at low densities. In the laboratory, they were shown to be mycophagous, that is, they are able to grow at the expense of
living hyphae. However, so far the importance of mycophagy for growth and survival of collimonads in natural soil habitats is unknown. Using a Collimonas-specific real-time PCR assay, we show here that the invasion of field soils by fungal hyphae (Absidia sp.) resulted in a short-term, significant increase (average fourfold) of indigenous collimonads. No such responses were observed for other soil bacteria studied (Pseudomonas, Burkholderia, PCR-denaturing gradient gel electrophoresis patterns of total bacteria and Burkholderia). Hence, it appears that the stimulation of growth of Collimonas bacteria by fungal hyphae is not common among other soil bacteria. In the same field soils, Trichoderma, a fungal genus known for mycophagous (mycoparasitic) growth, increased
upon introduction of Absidia hyphae. Hence, mycophagous growth by Collimonas and Trichoderma can occur in the same soils. However, in controlled xperiments (sand microcosms), collimonads appeared to have a negative effect on mycophagous growth of a Trichoderma strain. The effect of mycophagous growth of collimonads on fungal biomass dynamics was studied in sand microcosms using the same Absidia sp. as a test fungus. The growth of collimonads did not cause a significant reduction in the Absidia biomass. Overall, the study indicates that mycophagous nutrition may be important for collimonads in natural soils, but the impact on fungal biomass turnover is likely to be minor.
Vendula Valaskova, Wietse de Boer, Paulien J. A. Klein Gunnewiek, Martin Pospisek, Petr Baldrian. 2009. Phylogenetic composition and properties of bacteria coexisting with the fungus Hypholoma fasciculare in wood. ISME J. 3, 1218-1221.
White-rot fungi are major degraders of woody materials in terrestrial environments because of their ability to decompose lignin. However, little is known on the possible associations of white-rot fungi with other microorganisms during wood decay. We investigated the numbers, community composition and functional traits of bacteria present in natural wood samples under advanced decay by the white-rot basidiomycete Hypholoma fasciculare. The wood samples contained high numbers of cultivable bacteria (0.2–8_109 colony forming units (CFU) per g of dry wood). Most cultivable bacteria belonged to Proteobacteria and Acidobacteria (75% and 23% of sequences, respectively). The same phyla were also found to be dominant (59% and 23%, respectively) using a non-culturable quantification technique, namely, direct cloning and sequencing of 16sRNA genes extracted from wood. Bacteria that could be subcultured consisted of acid-tolerant strains that seemed to rely on substrates released by lignocellulolytic enzyme activities of the fungus. There were no indications for antagonism (antibiosis) of the bacteria against the fungus.
Wietse de Boer, Annelies S. de Ridder-Duine, Paulien J.A. Klein Gunnewiek, Wiecher Smant, Johannes A. van Veen. 2008. Rhizosphere bacteria from sites with higher fungal densities exhibit greater levels of potential antifungal properties. Soil Biol. Biochem. 40, 1542-1544.
A field study was performed to examine whether an increased density of saprotrophic fungi in the rhizosphere selects for bacteria with traits advantageous to living in a fungal-rich environment. Fast-growing bacteria were isolated from the rhizosphere of Carex arenaria (sand sedge) plants growing in fungal-poor (sand drifts) and fungal-rich (forest) sites in the Netherlands and screened for several potential antifungal properties, namely in vitro antagonism and the production of siderophores, cyanide and lytic enzymes. A higher incidence of putatively antifungal traits was generally found in bacteria isolated from fungal-rich soils, thus supporting the hypothesis that high fungal densities can impose a selection pressure on rhizosphere bacteria.
Larissa B. Folman, Paulien J.A. Klein Gunnewiek, Lynne Boddy, Wietse de Boer. 2008. Impact of white-rot fungi on numbers and community composition
of bacteria colonizing beech wood from forest soil. FEMS Microbiol. Ecol. 63, 181-191.
White-rot fungi are important wood-decomposing organisms in forest ecosystems. Their ability to colonize and decompose woody resources may be strongly influenced by wood-inhabiting bacteria that grow on easily utilizable compounds e.g. oligomers of wood-polymers released by fungal enzymes. However, so far, it is not known how white-rot fungi deal with the presence of potential competing bacteria. Here, the effects of two white-rot fungi, Hypholoma fasciculare and Resinicium bicolor, on the numbers and composition of bacteria colonizing sterile beech wood blocks from forest soil are reported. Both total numbers (microscopic counts) and the numbers of cultivable wood-inhabiting bacteria were considerably lower in wood blocks that became colonized by the white-rot fungi than in control blocks. This points to the fungi out-competing the opportunistic bacteria. The presence of white-rot fungi resulted in a change in the relative abundance of families of cultivable bacteria in wood and also in a change of denaturing gradient gel electrophoresis patterns of directly amplified 16S rRNA gene fragments. Analysis of the bacterial community structure in soil adhering to exploratory
mycelium (cords) indicated that fungal species-specific effects on bacterial community composition were also apparent in this fungal growth phase.
Annemieke van de Wal, Wietse de Boer, Wiecher Smant, Johannes A. van Veen. 2007. Initial decay of woody fragments in soils is influenced by size, vertical position, nitrogen availability and soil origin. Plant & Soil 301, 189-201.
Fast-growing bacteria and fungi are expected to cause the initial stage of decomposition of woodyfragments in and on soils, i.e. the respiration of sugars, organic acids, pectin and easily accessible cellulose and hemi-cellulose. However, little is known about the factors regulating initial wood decomposition. We examined the effect of wood fragment size, vertical position, nitrogen addition and soil origin on initial wood decay and on the relative importance of fungi and bacteria therein. Two fractions of birch wood were used
in microcosm experiments, namely wood blocks (dimensions: 3×0.5×0.5 cm) and sawdust (dimensions: 0.5–2 mm). The woody fragments were enclosed in nylon bags and placed on top of- or buried in an abandoned arable soil and in a heathland soil. After 15, 25 and 40 weeks of incubation, fungal biomass was quantified (as ergosterol and chitin content) and bacterial numbers were determined. The results indicated that initial wood decay was mostly caused by fungi; bacteria were only contributing in sawdust in/on
abandoned arable soil. Larger fragment size, burial of fragments and nitrogen addition positively influenced fungal biomass and activity. Fungal biomass and decay activities were much lower in woody fragments incubated in/on heathland soil than in those incubated in/on abandoned arable soil, indicating that soil origin is also an important factor determining initial wood decay.
Wietse de Boer, Anne-Marieke Wagenaar, Paulien J.A. Klein Gunnewiek, Johannes A. van Veen. 2007. In vitro suppression of fungi caused by combinations of apparently non-antagonistic soil bacteria. FEMS Mircobiol. Ecol. 59, 177-185
We hypothesized that apparently non-antagonistic soil bacteria may contribute to suppression of fungi during competitive interactions with other bacteria. Four soil
bacteria (Brevundimonas sp., Luteibacter sp., Pedobacter sp. and Pseudomonas sp.) that exhibited little or no visible antifungal activity on different agar media were
prescribed. Single and mixed strains of these species were tested for antagonism on a nutrient-poor agar medium against the plant pathogenic fungi Fusarium
culmorum and Rhizoctonia solani and the saprotrophic fungus Trichoderma harzianum. Single bacterial strains caused little to moderate growth reduction of
fungi (quantified as ergosterol), most probably due to nutrient withdrawal from the media. Growth reduction of fungi by the bacterial mixture was much stronger
than that by the single strains. This appeared to be mostly due to competitive interactions between the Pseudomonas and Pedobacter strains. We argue that
cohabitation of these strains triggered antibiotic production via interspecific interactions and that the growth reduction of fungi was a side-effect caused by
the sensitivity of the fungi to bacterial secondary metabolites. Induction of gliding behavior in the Pedobacter strain by other strains was also observed. Our results
indicate that apparently non-antagonistic soil bacteria may be important contributors to soil suppressiveness and fungistasis when in a community context.
Wietse de Boer, Larissa B. Folman, Richard C. Summerbell, Lynne Boddy. 2005 . Living in a fungal world: impact of fungi on soil bacterial niche development FEMS Microbiol. Rev. 29, 795-811
The colonization of land by plants appears to have coincided with the appearance of mycorrhiza-like fungi. Over evolutionary time, fungi have maintained their prominent role in the formation of mycorrhizal associations. In addition, however, they have been able to occupy other terrestrial niches of which the decomposition of recalcitrant organic matter is perhaps the most remarkable. This implies that, in contrast to that of aquatic organic matter decomposition, bacteria have not been able to monopolize decomposition processes in terrestrial ecosystems. The emergence of fungi in terrestrial ecosystems must have had a strong impact on the evolution of terrestrial bacteria. On the one hand potential decomposition niches, e.g. lignin degradation, have been lost for bacteria, whereas on the other hand the presence of fungi has itself created new bacterial niches. Confrontation between bacteria and fungi is ongoing, and from studying contemporary interactions we can learn about the impact that fungi now have, and have had in the past, on the ecology and evolution of terrestrial bacteria. In the first part of the review, the focus is on niche differentiation between soil bacteria and fungi involved in the decomposition of plant-derived organic matter. Bacteria and fungi are seen to compete for simple plant-derived substrates and have developed antagonistic strategies. For more recalcitrant organic substrates, e.g. cellulose and lignin, both competitive and mutualistic strategies appear to have evolved. In the second part of the review, bacterial niches with respect to the utilization of fungal-derived substrates are considered. Here, several lines of development can be recognized, ranging from mutualistic exudate-consuming bacteria that are associated with fungal surfaces to endosymbiotic and mycophagous bacteria. In some cases there are indications of fungal specific selection of fungus-associated bacteria, and possible mechanisms for such selection are discussed.
Wietse de Boer, Johan H. J. Leveau, George A. Kowalchuk, Paulien J. A. Klein Gunnewiek, Edwin C. A. Abeln, Marian J. Figge, Klaas Sjollema, Jaap D. Janse and Johannes A. van Veen. 2004. Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae
Int. J. Syst. Evol. Microbiol. 54: 857-864
A polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. These bacteria, which were isolated from slightly acidic dune soils in the Netherlands, were strictly aerobic, gram-negative rods. Cells grown in liquid cultures were flagellated and possessed pili.A wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and trisaccharides could not be used as substrates. The major cellular fatty acids were 16:0, 16:1 w7cis and 18:1 w7cis. DNA base composition varied between 57 and 62 mol% G+C. Analysis of nearly full length 16S rDNA sequences showed that the isolates were closely related to each other (> 98.6% sequence identity) and could be assigned to the ß-subclass of the class Proteobacteriain the family Oxalobacteraceae of the order Burkholderiales.The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, and exhibited 95.9 – 96.7 % (Herbaspirillum species) and 94.3 – 95.6% (Janthinobacterium species) sequence identity. Several physiological and biochemical properties indicated that the isolates could be clearly distinguished from either of these genera. Therefore, we propose to assign the isolates described in this study to a novel genus Collimonas gen. nov. Genomic fingerprinting (BOX-PCR), detailed analysis of 16S rDNA patterns and physiological characterization (BIOLOG) of the isolates revealed the existence of 4 subclusters. The new species name Collimonas fungivorans gen. nov., sp. nov. is given to one of these subclusters (4 isolates) that appears to be in the centre of the new genus, whereas isolates in the other subclusters are tentatively named Collimonas sp. The type strain of Collimonas fungivorans gen. nov., sp. nov. is Ter6T (= NCCB 100033T = LMG 21973T).
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