|
|||||||||
|
|||||||||
|
|
|
|
|
|
|
|||
Projects
| Ectomycorrhizal fungi - molecular mechanisms of plant infection and nutrient acquisition
and sequestering of carbon |
||
| Anders Tunlid, Tomas Johansson, Francois Rineau, Magnus Ellström & Håkan Wallander | ||
|
Ectomycorrhizal (EM) fungi forms mutualistic relationships with the roots of woody plants. During the symbiosis the two organisms exchange carbon (C) and nutrients. The plant-derived C supports the growth of a large fungal mycelium that colonizes the soil. This translocation provides a dominant pathway by which C enters the pool of organic mater matter in forest soils. The plant C supports the growth of an extensive external mycelium in the soil. When encountering a patch of organic nutrients, the mycelium proliferates extensively and the finely branched hyphae secrete a wide range of hydrolytic enzymes that degrade the organic material. The released nutrients particularly nitrogen (N) and phosphorous (P) are taken up by the fungus and transferred to the plant. When the nutrients have been withdrawn from the patch, the fungal mycelium dies, and the plant re-allocated the C to more actively growing parts of the fungal mycelium. The aims of this project are: (i) To characterize the molecular mechanisms including enzymes and biochemical pathways that are expressed during the degradation of organic material by EM fungi. (ii) To examine how the biodegradability of organic material is changing as a consequence of growth and senescence of EM fungi (iii) To develop molecular markers that can be used to follow the processes of nutrient acquisition and C sequestration by EM fungi in forest soils. (iv) To examine how the abundance and expression of such functional genes are responding to changes in the environment like increased N deposition. The studies are done using the EM fungus Paxillus involutus as a model (Figure). Expression of enzymes, proteins and metabolites are analyzed by transcriptome sequencing, DNA microarrays and mass spectrometry
|
Key references |
| The role of ectomycorrhizal fungi for carbon accumulation in forest soils
|
||
| Håkan Wallander, Adam Bahr & Magnus Ellström (in collaboration with Cecilia Akselsson (INES - Lund University)) | ||
Carbon stocks in soil exceed those in vegetation by 5:1 in boreal forests. A better understanding of how carbon accumulates in forest soil is essential in order to predict how a future changing climate, increased nitrogen deposition and changed land use will influence forest carbon stocks. Ectomycorrhizal (EM) fungi contribute significantly to carbon flux from trees to soil in boreal forests. It has been estimated that 10-50% of the carbon fixed by photosynthesis is allocated belowground to the symbiotic EM fungi. The amount of EM-associated carbon that contributes to soil organic matter (SOM) formation on a longer time scale is thus potentially vary large but the most poorly understood flux in the terrestrial carbon cycle. To obtain new knowledge in this area we perform comparative studies of production of EM fungal biomass and accumulation of EM derived SOM in chronosequences in northern Sweden where it is possible to follow the influence of EM fungi on SOM formation over longer time periods (up to 8000 years). In addition we estimate the contribution of EM biomass production and formation of EM derived SOM to net ecosystem exchange (NEE) which is followed by eddy-covariance measurements in two stands in central Sweden. The information obtained will be useful for understanding to what extent forests in the future may change from being carbon sinks to carbon sources. |
Key references |
|
| What is the role of ectomycorrhizal fungi in apatite weathering in forest soils?
|
||
| Håkan Wallander, Anders Tunlid, Tomas Johansson & Christoffer Berner (in collaboration with Per Persson & Reiner Gielser (Umeå University)) | ||
Certain species of ectomycorrhizal (EM) fungi can stimulate weathering of apatite to obtain P and Ca from mineral sources in laboratory systems as well as younger field conditions. In the present project we take a more multidisciplinary approach to include experts in microbial ecology, surface chemistry, and molecular ecology to investigate this process in more detail. The weathering process will be investigated both in experimental systems in the laboratory where P availability can be varied and in the field with more complex communities of EM fungi in forest with different P status. One of our aims is to identify species of EM fungi with especially high potential to weather apatite. Another aim is to identify metabolic responses (using gene expression analyses) of a model E; fungus (P. involutus) that can be related to chemical changes of apatite surfaces during weathering (Estimated by XPS and FTIR spectroscopy analysis). The outcome of the project will give us information about how EM fungi respond to P deficiency and detailed information about the mechanisms of EM induced mineral weathering, This will have consequences for predicting long-term productivity of forest ecosystems, especially in areas with high N deposition since P can be expected to become growth limiting in these forests in the future. |
Key references |
|
| Genome evolution of symbiotic fungi
|
||
| Anders Tunlid, Dag Ahrén & Tomas Johansson (in collaboration with Björn Canbäck (Björn Canbäck Bioinformatics)) | ||
At least 6,000 species of fungi form ectomycorrhiza (EM). Analyses of DNA-based phylogenies have shown that the ancestors of the EM species were free-living and that the symbiotic habit has evolved repeatedly from saprophytic (i.e. free-living) precursors. On the genome level, there are three, compatible, mechanisms: changes in gene content, structural differences in gene products, and quantitative differences in gene expression. Insights into these mechanisms were recently obtained by analyzing the genome of Laccaria bicolor which was the first species of an EM fungus to be fully sequenced. The project was funded by the Joint Genome Institute (JGI) at the Department of Energy (DOE) in the US. As part of an international consortium, we showed that L. bicolor has a relatively large genome, and that the large genome size is partly due to an expansion of gene family sizes. Among the largest gene families are protein kinases and RAS small GTPases, which are key components of signal transduction pathways. Presently, we are involved in a project comparing the genome architecture of L. bicolor with that of other basidiomycetes including Coprinopsis cinerea (with Jason Stajich, University of California, USA) We are coordinating another JGI-DOE sequencing project of an EM fungus, Paxillus involutus. L. bicolor and P. involutus belong to different evolutionary lineages within the basidiomycetes, but their morphological and physiological responses observed during EM formation are very similar. Comparative genome analyses will provide insights into common as well as unique mechanisms underlying the evolution of mutualism in these two lineages of basidiomycetes. We will also compare the genome structure and trancriptome of P. involutus strains that differ in host preferences. Using cDNA microarrays and DNA sequencing, we have previously shown that variation in host preferences can be related to changes in gene expression patterns, gene content and gene sequences. |
Key references |
|
| Nematode trapping fungi – genome evolution and mechanisms of infection |
||
| Dag Ahrén, Anders Tunlid, Tejashwari Meerupati, Karl-Magnus Andersson, Eva Friman & Tomas Johansson | ||
Nematode-trapping fungi are parasites on nematodes. They are commonly found in soils and enter the parasitic stage by developing specific morphological structures called traps. The traps develop from hyphal branches and they can be formed either spontaneously or be induced in response to signals from the environment, including peptides and other compounds secreted by the host nematode. There is large variation in the morphology of trapping structures, even between closely related species (Figure). Despite this variation, phylogenies inferred from molecular data have shown that a majority of nematode-trapping fungi belong to a monophyletic group placed in the family of Orbiliaceae, Ascomycota. These studies have shown that the trapping mechanisms have evolved along two major lineages, one leading to the constricting rings, and the other into adhesive traps. Among species with adhesive traps, those with adhesive networks separated early from the species with adhesive knobs and branches (Figure). To get a more detailed understanding of the genomic mechanisms that could account for the evolution of parasitism in nematode-trapping fungi, we are sequencing the genomes of two nematode-trapping fungi, Arthrobotrys oligospora and Monacrosporium haptotylum. We are also examining the mechanisms by which nematode-trapping fungi kill (paralyze) captured nematodes. Previous studies have shown that A. oligospora produce subtilisins with nematotoxic activites. More recently, we have used DNA microarrays to identify a large number of fungal genes that are specifically expressed during killing of the nematode Caenorhabditis elegans. The functions of a majority of these genes are not known and they appear to be specific for nematode-trapping fungi. The aim of the project is to characterize the peptides encoded by these genes. Based on bioinformatic analyses, a few candidates will be selected for heterologous expression in Pichia pastoris. The nematicidal activity of these peptides and their mode of action will be examined using C. elegans as a model.
Figure. A cladistic tree showing the relationship between various nematode-trapping fungi and other ascomycetes based on 18S ribosomal DNA sequences. Only branches with bootstrap support values above 50 are shown. Note that the nematode-trapping fungi form a monophyletic clade among an unresolved cluster of apothecial ascomycetes. The phylogenetic pattern within the clade of nematode-trapping fungi is concordant with the morphology of the traps. The tree is redrawn from Ahrén et al. (1998). The pictures are reproduced from Nordbring-Hertz et al. (1995), courtesy of Birgit Nordbring-Hertz and IWF, Göttingen. |
Key references
|
|
Interaction between fungi and bacteria in soil |
||
Johannes Rousk & Erland Bååth (in collaboration with Gema Bárcenas Moreno (University of Alicante, Spain)) |
||
Fungi and bacteria comprise more than 90% of the soil microbial biomass and are the main agents for decomposition of organic matter in soil. Until recently it was thought that these two organism groups could be lumped in this respect and often total microbial biomass or total activity (respiration) are the only variables included in soil microbiology studies of decomposition and soil organic matter turn-over. However, there is increasing evidence that if decomposition is performed by bacteria or fungi, and thus energy is channelled through the bacterial or fungal food web, this can have profound effects on the ecosystem. Such effects can be direct, including effects on higher trophic levels in the food web, but also indirect, including effects on nutrient mineralization rates and nutrient transfer in soil, and even decisively influence the rate of carbon sequestration in the soil. We have devised methods that specifically measure bacterial (using thymidine or leucine incorporation) or fungal (acetate incorporation into ergosterol) growth in soil. We also use phospholipid fatty acids (PLFA) as a way of detecting shifts in the microbial community, where the addition of 13C-labelled substrate can be used to trace decomposition through different microbial groups. We apply these techniques to study how different environmental variables affect the balance of fungal and bacterial decomposition in soil, e.g. effects of pH, different substrates, freezing/thawing, drying/rewetting, limiting factors. We are especially interested in possible interaction between these decomposer groups, including antagonism, competition and facilitation. |
Key references |
|
| Effect of environmental factors, especially temperature, on fungal and bacterial growth in soil
|
||
| Stephanie Reischke, Johannes Rousk & Erland Bååth (in collaboration with Riikka Rinnan (Copenhagen University)) | ||
The anthropogenic increase in CO2 emission and the consequent increased concentrations in the atmosphere will result in increased temperatures on earth, affecting all biota. The temperature sensitivity of soil microbial activity has been a topic of considerable interest and debate, especially soil respiration due to its potential feedback effects on climate change. The extent of temperature adaptation of the soil microbial community is also a topic with divergent results. Recent studies have suggested either adaptation or no response to altered temperature regimes. There is also no consensus in what way temperature affects the balance between fungal and bacterial growth in soil. We aim to attack these problems by measuring bacterial and fungal growth in natural habitats under different temperature regimes. Earlier studies by us showed that respiration rate, bacterial and fungal growth follow the square root relationship with changes in temperature, a model well proven and used within microbiology. Thus, below optimum temperature for growth, a plot of the square root of the growth or activity against temperature) will result in a linear relationship, with Tmin indicated by the intercept with the x-axis (Figure, lower panel, where arrows indicate Tmin, lowest in AI (Antarctic samples) and highest in Swedish samples). This model can thus be used to differentiate between direct temperature effects and community adaptation. In this project we will determine the effect of increasing temperature on the temperature relationship of bacterial activity in soil, including possible community adaptation. We will also compare the effect of temperature on fungal and bacterial growth adaptation and study if temperature will affect the balance between fungal and bacterial decomposition. Last, we will study how fungi and bacteria are affected by natural, reoccurring perturbations that are supposed to increase in future global change scenarios.
|
Key references
|
|
| Pollution effects on soil microorganisms
|
||
Erland Bååth, David Fernández-Calviño (Spain) & Susann Milenkovski (Lund) |
||
Most ecotoxicological tests in soil that rely on community or flux studies and not single organisms are problematic. First, they can be affected by most other environmental factors such as nutrient conditions. This will be especially problematic when very different soils are studied or when organic pollutants, that can be metabolized and thus be a nutrient source for the microorganisms, are studied. Second, they can not be used to detect which pollutant that is the most toxic in a multiple pollution situation, a situation which very often is the case in nature. One way of circumventing these problems are to use the microorganisms themselves as indicator of their environment, since the level of tolerance of the community will increase if a toxic substance is applied, and thus the degree of tolerance can be seen as a measure of the level of toxicity. This is the theoretical basis behind the concept of Pollution Induced Community Tolerance (PICT). We have pioneered the use of growth based techniques to measure PICT for bacteria in soil to study effects of heavy metals, phenols and antibiotics using leucine and thymidine incorporation techniques. We have contrasted different methods to estimate PICT in soil and proven that the leucine / thymidine incorporation endpoint is of superior efficiency and sensitivity. PICT has also been used to directly study the often elusive concept of co-tolerance. We are now using the PICT concept, together with direct measurements of bacterial growth to study different types of pollution in soils and sediments. |
Key references |
|
Identifying the carbon drivers and microbial agents of soil respiration |
||
| Johannes Rousk* (in collaboration with Davey L. Jones (School of the Environment, Natural Resources & Geography, Bangor University, UK)) | ||
The aim of this project is to elucidate the link between soil respiration, via its microbial agents, and the carbon (C) compounds derived from the soil organic matter (SOM) that are respired. To achieve this, I first aspire to identify the carbon (C) compounds of the SOM that primarily contribute to respiration and subsequently investigate which microbial groups that dominate this process. This will be accomplished through four parallel research efforts:
*supported by A Swedish Research Council Postdoctoral Fellowship |
Key references
|
|
| Microbial communities – structure and dynamics
|
||
| Anders Tunlid & Björn Canbäck (in collaboration with Per Lundberg & Mikael Pontarp (Section of Theoretical Ecology, Lund University), Åke Hagström, Johanna Sjöstedt & Lars Riemann & (Kalmar University)) | ||
The most common approach to estimate microbial diversity is based on the analysis of DNA sequences of specific target genes including ribosomal genes. Analysis of such sequences have revealed an immense genetic diversity of microorganisms, most of which is not yet characterized. In this project, the structure and dynamics of communities of marine bacterioplankton are studied. Because of their small size, great abundance and easy dispersal, it is often assumed that these bacteria have a ubiquitous distribution that prevents any structured assembly into local communities. However, we have shown that marine bacterioplankton communities display distinct patterns of diversity and structure that include a clear latitudinal gradient of species richness, a high degree of endemism, and few cosmopolitan species. We are now conducting experimental studies on bacterial communities from the Baltic Sea and the North Sea, which allows detailed comparative studies of community dynamics and the phylogenetic contingencies of community structure. In this way, we can advance our understanding of how the current environmental condition together with evolutionary history shapes bacterial communities. The most common approach to estimate microbial diversity based on the ribosomal genes is to cluster sequences into operational taxonomic units (OTUs) based on genetic distance (sequence similarity). This method may fail to adequately identify clusters of evolutionary related sequences and it provides no information on the phylogenetic structure of the community. We have developed an ease-of-use web application RAMI which clusters related nodes in a phylogenetic tree based on the patristic distance (genetic change). RAMI and can be run or downloaded from http://130.235.46.10/rami.html. |
Key references |
|
| The role of archaea in soil carbon and nitrogen turnover
|
||
| Per Bengtson, Tomas Johansson & Anna Karlsson | ||
Despite the fact that archaea was recognized as a separate kingdom some 30 years ago, virtually nothing is know about their activities in most ecosystems. Recently, a few high profile publications have acknowledged their importance in C and N turnover in marine environments, and their dominant role in ammonium oxidation in terrestrial environments. C and N turnover are some of the most extensively studied processes in forest soils. Knowledge about the factors determining the rate of these processes has implications for our understanding of plant productivity, carbon sequestration, nitrogen leakage, greenhouse gas production, etc. Still, the involvement of archaea in these processes in terrestrial environments is to a large extent unknown. The apparent lack of attention might partly be explained by methodological constrains. The project will relief these constrains and aims to give a first insight into the life and activities of archaea in soil environments. The interaction between and relative importance of archaea and bacteria for soil C and N turnover will be determined. This will be achieved by exploiting the unique physiology of the archaeal cell-membrane to measure 13/14C incorporation into specific biomarkers, as well as DNA/RNA. These techniques in combination with quantification of abundance and expression of relevant functional genes provide an excellent but largely unexplored opportunity to study the virtually unknown activities of this group of microorganisms. |
Key references
|
|
| Metabolic architecture of the wheat pathogen Stagonospora nodorum
|
||
| Dag Ahrén (in collaboration with Richard Oliver, Murdoch University & Peter Solomon, The Australian National University) | ||
Stagonospora nodorum SN15 is a filamentous ascomycete that is a major pathogen of wheat and related cereals. The sexual stage is important in the field and the teleomorph is called Phaeosphaeria nodorum. S. nodorum causes major losses in wheat crops. In Australia, losses of $57M pa are considered typical. Almost all these losses are concentrated in the Western Australian wheat belt. It is a major pathogen in most other wheat growing regions. In some areas, such as parts of eastern, it renders wheat an uneconomic crop. Stagonospora is a member of the Dothideomycetes, a class of fungi that includes many important plant pathogens such as Leptosphaeria, Ascochyta, Pyrenophora, Cochliobolus, Alternaria and Mycosphaerella. It is the first Dothideomycete genome sequence to be publicly released. We are reconstructing the metabolic pathways of S. nodorum to identify the biochemical capabilities of the pathogen. By integrating the biochemical architecture with gene expression and metabolomics data during infection we can identify key metabolic enzymes involved in pathogenicity. Metabolic reconstruction requires sophisticated bioinformatics tools such as the Pathway Tools software. This allows us to reconstruct organism specific metabolic databases from metabolites, proteins, enzymatic activities and generating metabolic maps. |
Key references |
|
Microbial Ecology, The Ecology Building, Lund University, SE-223 62 Lund, Sweden
Last updated
2010-10-26
