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ABSTRACT: 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.
Canadian Journal of Microbiology 05/2010; 56(5):380-8. · 1.36 Impact Factor
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ABSTRACT: 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 x 10(9) 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.
The ISME Journal 07/2009; 3(10):1218-21. · 7.38 Impact Factor
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ABSTRACT: 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.Keywords: wood-inhabiting bacteria, phylogeny, white-rot, basidiomycetes, interactions, wood degradation
The ISME Journal 06/2009; 3(10):1218-1221. · 7.38 Impact Factor
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ABSTRACT: 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.
FEMS Microbiology Ecology 03/2008; 63(2):181-91. · 3.41 Impact Factor
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ABSTRACT: In Western Europe, arable lands have been abandoned to increase the area of nature, such as Calluna vulgaris–dominated heathlands. However, the growth conditions, e.g., nutrient availability and lack of a phenolics-rich organic layer, on ex-arable sandy soils differ markedly from those of heathland and will favor fast-growing plant species. Succession toward Calluna-dominated heathland is expected to take decades unless intensive restoration management is applied. Here, we report a possible mechanism to explain the occurrence of Calluna patches (0.7–2.0 m diameter) in a 10-year abandoned agricultural field within a dominant vegetation of grasses and forbs. All roots sampled from the Calluna patches were colonized by ericoid mycorrhizal (ERM) and other endomycorrhizal fungi. Both nitrogen mineralization of soil organic N and potential nitrogen mineralization (arginine ammonification) were much lower in soil under Calluna patches than in the rest of the ex-arable soil, although other soil characteristics did not differ. The nitrogen to phosphorus ratio in Calluna shoots was much greater than that in shoots of grasses and forbs, indicating that the latter were more N limited. The results indicate that the association with ERM fungi is probably providing the host competitive superiority for nitrogen even in a soil with low organic matter content. Our results suggest that the conversion from arable land into heathland may be accomplished by the immediate establishment of Calluna seedlings and ERM inoculum when agricultural activities are stopped. This needs to be tested in controlled experiments.
Restoration Ecology 01/2008; 17(2):308 - 313. · 1.68 Impact Factor
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ABSTRACT: 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.
FEMS Microbiology Ecology 02/2007; 59(1):177-85. · 3.41 Impact Factor
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ABSTRACT: 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 isolates, which were found in 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 C(16 : 0), C(16 : 1)omega7c and C(18 : 1)omega7c. DNA G+C contents were 57-62 mol%. Analysis of nearly full-length 16S rDNA sequences showed that the isolates were related closely to each other (>98.6 % sequence similarity) and could be assigned to the beta-Proteobacteria, family 'Oxalobacteraceae', order 'Burkholderiales'. The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, exhibiting 95.9-96.7 % (Herbaspirillum species) and 94.3-95.6 % (Janthinobacterium species) 16S rDNA sequence similarity to the isolates. Several physiological and biochemical properties indicated that the isolates could be distinguished clearly from both of these genera. Therefore, it is proposed that the isolates described in this study are representatives of 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 four subclusters. The name Collimonas fungivorans gen. nov., sp. nov. has been given to one subcluster (four isolates) that appears to be in the centre of the novel genus; isolates in the other subclusters have been tentatively named Collimonas sp. The type strain of Collimonas fungivorans gen. nov., sp. nov. is Ter6(T) (=NCCB 100033(T)=LMG 21973(T)).
International journal of systematic and evolutionary microbiology 06/2004; 54(Pt 3):857-64. · 2.27 Impact Factor
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ABSTRACT: Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.
Applied and Environmental Microbiology 03/2003; 69(2):835-44. · 3.83 Impact Factor
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ABSTRACT: The relative importance of specific plant properties versus soil characteristics in shaping the bacterial community structure of the rhizosphere is a topic of considerable debate. Here, we report the results of a study on the bacterial composition of the rhizosphere of the wild plant Carex arenaria (sand sedge) growing at 10 natural sites in The Netherlands. The soil properties of the sandy soils at these sites were highly disparate, most notably in pH, chloride and organic matter content. Rhizosphere and bulk soil bacterial communities were examined by culture-independent means, namely, 16S rDNA-directed PCR-DGGE profiling. Large differences were observed between the bacterial communities of the different sites for both bulk and rhizosphere soil. Cluster analysis of bacterial profiles revealed that the rhizosphere community of each site was generally more closely related to the bulk soil community of that site rather than to rhizosphere communities of other sites. Hence, bacterial community structure within the rhizosphere of C. arenaria appeared to be determined to a large extent by the bulk soil community composition. This conclusion was supported by a reciprocal planting experiment, where C. arenaria shoots of different sites yielded highly similar rhizosphere communities when planted in the same soil.
Soil Biology and Biochemistry.
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ABSTRACT: 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.
Soil Biology and Biochemistry.
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ABSTRACT: It has frequently been reported that chitinolytic soil bacteria, in particular biocontrol strains, can lyse living fungal hyphae, thereby releasing potential growth substrate. However, the conditions used in such assays (high bacterial density, rich media, fragmented hyphae) make it difficult to determine whether mycolytic activity is actually of importance for the growth and survival of chitinolytic bacteria in soils. An unidentified group of β-subclass Proteobacteria (CβPs) was most dominant among the culturable nonfilamentous chitinolytic bacteria isolated from Dutch sand dune soils. Here we demonstrate that the CβPs grew at the expense of extending fungal mycelium of three dune soil fungi (Chaetomium globosum, Fusarium culmorum, and Mucor hiemalis) under nutrient-limiting, soil-like conditions. Aggregates of CβPs were also often found attached to fungal hyphae. The growth of a control group of dominant nonchitinolytic dune soil bacteria (β- and γ-subclass Proteobacteria) was not stimulated in the mycelial zone, indicating that growth-supporting materials were not independently released in appreciable amounts by the extending hyphae. Therefore, mycolytic activities of CβPs have apparently been involved in allowing them to grow after exposure to living hyphae. The chitinase inhibitor allosamidin did not, in the case of Mucor, or only partially, in the cases of Chaetomium and Fusarium, repress mycolytic growth of the CβPs, indicating that chitinase activity alone could not explain the extent of bacterial proliferation. Chitinolytic Stenotrophomonas-like and Cytophaga-like bacteria, isolated from the same dune soils, were only slightly stimulated by exposure to fungal hyphae.
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ABSTRACT: Anti-fungal properties of chitinolytic soil bacteria may enable them to compete successfully for chitin with fungi. Additionally, the production of chitinase may be part of a lytic system that enables the bacteria to use living hyphae rather than chitin as the actual growth substrate, since chitin is an important constituent of most fungal cell walls. Lysis of living fungal hyphae by chitinolytic bacteria has been reported frequently; however, these reports nearly always deal with bacteria that had been selected because of their mycolytic properties. Our main objective was to get a better understanding of the relationship between chitinolytic and anti-fungal properties of bacteria that occur naturally in soils, i.e. without artificial selection. Three inner dune sites, two of which were lime-poor and one lime-rich, along the Dutch coast were selected for this study. Bacteria that were able to degrade colloidal chitin in water–agar comprised 0.2–5.7% of the total amount of culturable bacteria of these dune sites. Pseudomonas spp. were the most abundant culturable, chitin-degrading bacteria at the lime-poor sites, whereas Xanthomonas spp. and Cytophaga spp. were important at the lime-rich site. Chitinolytic actinomycetes were relatively abundant at all three sites. Chitinolytic and non-chitinolytic bacteria were randomly selected and tested for the possession of antagonistic activities against fungal dune strains [Chaetomium globosum, Fusarium culmorum, F. oxysporum, Idriella (Microdochium) bolleyi, Mucor hiemalis, Phoma exigua, Ulocladium sp.]. The tests were done using water–agar to simulate the energy-limiting conditions that bacteria will encounter in dune soils. The percentage of bacterial isolates that were antagonistic against these fungi was considerably higher for chitinolytic strains than for non-chitinolytic ones. Therefore, the possible involvement of chitinase with respect to the inhibition of fungal growth was studied in more detail. It appeared that in many cases the inhibition of fungal growth was not accompanied by bacterial chitinase production. There was also no clear relationship between the activity of other cell wall degrading enzymes (β-1,3-glucanase and protease) and antagonism. Chitinolytic bacteria had selective rather than general anti-fungal properties, which were not necessarily related to differences in general susceptibility of the fungi towards antagonism. These results may indicate that antibiotics were involved in the antagonistic activities of chitinolytic bacteria against fungi. Only growing fungi were antagonized by the chitinolytic bacteria; none of the chitinolytic bacteria were able to lyse existing mycelium of any of the fungi. The relevance of the results for the ecology of chitinolytic soil bacteria is discussed.
Soil Biology and Biochemistry.
