Wietse de Boer

Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms

A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems. Indeed, above-ground plant communities have long been assumed to drive below-ground microbial diversity, but to date very little is known as to how plant species composition and diversity influence the community composition of micro-organisms in the soil. We examined this relationship in fields subjected to different above-ground biodiversity treatments and in field experiments designed to examine the influence of plant species on soil-borne microbial communities. Culture-independent strategies were applied to examine the role of wild or native plant species composition on bacterial diversity and community structure in bulk soil and in the rhizosphere. In comparing the influence of Cynoglossum officinale (hounds tongue) and Cirsium vulgare (spear thistle) on soil-borne bacterial communities, detectable differences in microbial community structure were confined to the rhizosphere. The colonisation of the rhizosphere of both plants was highly reproducible, and maintained throughout the growing season. In a separate experiment, effects of plant diversity on bacterial community profiles were also only observed for the rhizosphere. Rhizosphere soil from experimental plots with lower macrophyte diversity showed lower diversity, and bacterial diversity was generally lower in the rhizosphere than in bulk soil. These results demonstrate that the level of coupling between above-ground macrophyte communities and below-ground microbial communities is related to the tightness of the interactions involved. Although plant species composition and community structure appear to have little discernible effect on microbial communities inhabiting bulk soil, clear and reproducible changes in microbial community structure and diversity are observed in the rhizosphere.

Soil networks become more connected and take up more carbon as nature restoration progresses

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.

Anti-fungal properties of chitinolytic dune soil bacteria

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.

Microbial Community Composition Affects Soil Fungistasis

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.

A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes

Filamentous fungi are critical to the decomposition of terrestrial organic matter and, consequently, in the global carbon cycle. In particular, their contribution to degradation of recalcitrant lignocellulose complexes has been widely studied. In this review, we focus on the functioning of terrestrial fungal decomposers and examine the factors that affect their activities and community dynamics. In relation to this, impacts of global warming and increased N deposition are discussed. We also address the contribution of fungal decomposer studies to the development of general community ecological concepts such as diversity-functioning relationships, succession, priority effects and home-field advantage. Finally, we indicate several research directions that will lead to a more complete understanding of the ecological roles of terrestrial decomposer fungi such as their importance in turnover of rhizodeposits, the consequences of interactions with other organisms and niche differentiation.

Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors

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.

Ectomycorrhizal Cortinarius species participate in enzymatic oxidation of humus in northern forest ecosystems.

In northern forests, belowground sequestration of nitrogen (N) in complex organic pools restricts nutrient availability to plants. Oxidative extracellular enzymes produced by ectomycorrhizal fungi may aid plant N acquisition by providing access to N in macromolecular complexes. We test the hypotheses that ectomycorrhizal Cortinarius species produce Mn-dependent peroxidases, and that the activity of these enzymes declines at elevated concentrations of inorganic N. In a boreal pine forest and a sub-arctic birch forest, Cortinarius DNA was assessed by 454-sequencing of ITS amplicons and related to Mn-peroxidase activity in humus samples with- and without previous N amendment. Transcription of Cortinarius Mn-peroxidase genes was investigated in field samples. Phylogenetic analyses of Cortinarius peroxidase amplicons and genome sequences were performed. We found a significant co-localization of high peroxidase activity and DNA from Cortinarius species. Peroxidase activity was reduced by high ammonium concentrations. Amplification of mRNA sequences indicated transcription of Cortinarius Mn-peroxidase genes under field conditions. The Cortinarius glaucopus genome encodes 11 peroxidases - a number comparable to many white-rot wood decomposers. These results support the hypothesis that some ectomycorrhizal fungi--Cortinarius species in particular--may play an important role in decomposition of complex organic matter, linked to their mobilization of organically bound N.

Volatile affairs in microbial interactions

Microorganisms are important factors in shaping our environment. One key characteristic that has been neglected for a long time is the ability of microorganisms to release chemically diverse volatile compounds. At present, it is clear that the blend of volatiles released by microorganisms can be very complex and often includes many unknown compounds for which the chemical structures remain to be elucidated. The biggest challenge now is to unravel the biological and ecological functions of these microbial volatiles. There is increasing evidence that microbial volatiles can act as infochemicals in interactions among microbes and between microbes and their eukaryotic hosts. Here, we review and discuss recent advances in understanding the natural roles of volatiles in microbe–microbe interactions. Specific emphasis will be given to the antimicrobial activities of microbial volatiles and their effects on bacterial quorum sensing, motility, gene expression and antibiotic resistance.

The bacterial genus Collimonas mycophagy, weathering, and other adaptive solutions to life in oligotrophic soil environments

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.

Impact of white-rot fungi on numbers and community composition of bacteria colonizing beech wood from forest soil

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.