RESEARCH GROUPS

 

General Soil Microbiology

Research projects

 

The Ecology and Physiology of the Mycorrhizal Symbioses

Research projects

 

Fungal-host interactions in terrestrial ecosystems - ecological significance and evolution of genomic diversity

Research projects

 

EXAMINATIONS

Ph.D. dissertations

 

PUBLICATIONS

Scientific articles

• Interactions between wood-decomposing basidiomycetes and the soil environment (KT with Stefan Olsson, KVA Copenhagen)
  The extracellular lignin-degrading enzymes of wood decomposing fungi degrade a wide variety of resistant organic pollutants, but the effect on the surrounding environment in soil is relatively unknown. In this project we have studied the colonization of wood-decomposing fungi on soil contaminated by aromatic wastes. When colonizing the soil, the composition of the bacterial community changes depending on the species of fungi penetrating the soil. We now examine if these changes are related to the activity of extracellular enzymes secreted by the fungi. The effects on fungal colonization on other biotic (e g mycorrhiza) and abiotic (e g PAH) factors in the soil are also of interest.
• Bacterial growth rates in the rhizosphere (KS, EB)
  From the soil organisms point of view the most important effect of the root is the input of energy through exudation to the normally starving microbial community, with the subsequent increase in activity and biomass. The former has sofar been very difficult to assess, and since activity (as for example growth rate) is the microbial variable that initially are affected by all changes in the environment, the lack of direct measurements of activities has been a major draw back in understanding rhizosphere effects in soil. We therefor apply new techniques, that earlier have been used to measure bacterial growth rates in natural environments (water, soil), to study factors affecting microbial activity in the rhizosphere.
• Factors affecting rates of changes in soil bacterial communites (MP, EB)
  This project focus on the effects that different environmental disturbance / stress situations will have on the activity of soil organisms. Different parts of the microbial community will react differently to a stress situation or a pertubation, i.e. will have a variable selection pressure. This will eventually lead to an altered community composition. This can be detected using specific techniques, indicating community tolerance to the stress factor, as well as more unspecific methods like the PLFA technique. We are particularely interested in the importance of the community turn-over rate on the rate of these changes.
• Bacterial and fungal activities in soil (EB)
  This project focus on the effects that different environmental disturbances/stress situations will have on the activity of soil organisms. Different parts of the microbial community will react differently to a stress situation or a pertubation, i.e. we will have a variable selection pressure. This will be seen as different activities within different groups of microorganisms (fungi-bacteria, sensitive-tolerant bacteria, mesophilic- thermophilic bacteria, large-small bacteria etc.), eventually leading to an altered community composition.
• Pollution effects (mainly heavy metals) on the soil microbial community (EB)
  Ecotoxicological studies of pollution effects on microorganisms in soil have been centered either around effects on processes (like carbon and nitrogen transformations) or on studies of single species or groups of organisms. Community composition has only seldom been used as a test parameter. Due to adaptation of the community, changes in the microbial community composition may occur at contamination levels at which no effects on ecosystem processes are seen. We have analyzed the phospholipid fatty acid (PLFA) pattern of soil organisms as a fast indicator of environ- mental disturbance. Another indirect way of assessing pollution effects on communities without identifying individual species is to measure community tolerance.
• Carbon and Nitrogen effects on soil microorganisms (FD, EB)
  There are two fundamental approaches to characterize organic matter (OM) in soil. Either one relies on different chemical methods to characterize the organic matter, or one tries to draw conclusions about availability (OM) for the microorganisms. The latter approach relies on the use of the microorganisms themselves as bioindicators of their invironment. We will use techniques based on this approach to study (i) availability of dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) for microbial growth, (ii) limiting factors for microbial growth in soil with different availability of C and N, (iii) effects of C/N ratios on microbial biomass, activity and community structure, where especially the effect of C/N on the fungal/bacterial ratio will be emphazised.

• Influence of nitrogen availability on growth of ectomycorrhiza external mycelium in the field (HW, LON)
  Growth of ectomycorrhizal mycelium has in laboratory experimental systems been shown to be regulated by nitrogen availability. In this project we test how nitrogen availability in natural ecosystems influences growth of ectomycorrhizal mycelia. This is tested with ingrowth bags that are colonized by fungal mycelia. We are investigating nitrogen fertilized spruce forests in southern Sweden, natural nutrient gradients in northern Sweden and nitrogen gradients from Halland to Öland in southern Sweden.
• How will liming, nitrogen addition and an increased biofuel harvest affect the ectomycorrhizal community structure and function? (DH, SE, SM, HW)
  Different forest management practices have the potential to influence the ectomycorrhizal community in forest soil. Wood ash granules amended to forest soil, to counteract acidification, are colonised by specific ectomycorrhizal fungi. The abundance of these species is increasing as a result of the wood ash fertilisation. The potential of these fungi to solubilise nutrients from the ash is currently tested in the laboratory.
• Ectomycorrhiza and soil weathering processes (DH, HW)
  In the laboratory it has been found that certain ectomycorrhizal (EM) fungi can stimulate the weathering of minerals such as apatite and biotite. The rate of weathering was correlated to the production of organic acid by the fungus. In the field it has been found that the addition of wood ash and minerals such as apatite and biotite will stimulate the growth of EM mycelia. The importance of EM fungi, soil bacteria and abiotic factors for the weathering processes in the field is currently being tested.
• Spatial and functional aspects of ectomycorrhizal community structure (SE)
  The extramatrical mycelium of ectomycorrhizal fungi is central to carbon and nutrient cycling in the Boreal forest ecosystems. The diversity, both species and functional, of the ectomycorrhizal fungi colonising roots is large. Changes in community structure of ectomycorrhizal species in relation to pollution and forest practise have been show in several investigations. The continous development of molecular methods provide possibilities to study the spatial and temporal dynamics of these mycelia in situ. Key species can be pin pointed and further studied in the laboratory.
• Carbon allocation strategies in arbuscular mycorrhizal fungi (PAO, MG, AN, JR)
  The arbuscular mycorrhizal fungi forage through symbiotic colonization characterized by a P-flow from aungus to plant and a C-flow from plant to fungus. An individual mycelium is connected to several plant roots and the optimal foraging for carbon energy will consequently depend on the plant roots that are colonized. The colonization and growth strategies of the AM fungi are studied in systems where several hosts can be colonized simultaneously. These hosts can be of different plant species as well as of different light and nutrient status. The strategies of the fungi are studied by using signature fatty acids for detection of mycelium proliferation and allocation to energy storage in roots and soil Quantitative studies of C-flow involve ¹³C labeling of plant assimilates and subsequent estimation of incorporation into fungal specific molecules by GC-MS.
• Importance of the arbuscular mycorrhiza for the availability of organically bound P in different biotopes (IA, PAO)
  Most non-woody plants form mycorrhizas called arbuscular vesicular mycorrhiza. The fungi involved in this symbiosis cannot be grown in pure culture. Consequently, we know little about their physiologi. In this project we are interested in studying the fungal phosphatases and their activity in releasing phosphorus from soil organic material. We also study the possible effects of the fungus on plants in soils with different pH values.

• The ectomycorrhizal symbiosis: characterization of symbiosis related genes and assessment of functional diversity (TJ, DA, ALeQ, PS, EF, BS, AT)
  The understanding of how ectomycorrhizal (ECM) fungi infect their hosts, including the mechanisms of host recognition, development of infection structures and of nutrient and carbon exchange is very limited. To examine the molecular background to the ECM interaction, we have generated a database constisting of ca 10.000 transcripts (ESTs) from the ectomycorrhizal association between Paxillus involutus and Betula pendula (birch). A unique set of transcripts has been used for making cDNA arrays, that are utilized in a number of different experiments to identify the "marker" genes and pathways that are involved in the development and physiological activities in of the P. involutus and birch associations. Finally, methods are developed to extract and analyse the expression of such markers in soil microcosms. The specific aims of this project are: (1) To identify differentially expressed genes or regulons that correlate temporally and spatially to the development of the ectomycorrhizal symbiosis and to assign their functional and metabolic roles; (2) By comparative analyses identify the genes/regulons that are commonly expressed in different ectomycorrhizal associations.
• Uptake and transport of nutrients by the mycorrhizal fungus Paxillus involutus in soil (DW, EF, MS, BS, AT)
  Uptake of nutrients by mycorrhizal fungi occurs via the extraradical mycelium, which is the part of the fungus that develops outside the infected root tips. These hyphae form the connection between the mycorrhizal roots and soil and provide the pathways for the uptake and transport of nutrients. In the last few years research has shown that carbon from the plant can support extensive growth of the extraradical mycelium and that this mycelium comprises a significant part of the total microbial biomass in soils. The goal of this project is to identify genes and metabolic pathways that are involved in the fungal uptake and translocation of nutrients from soils to the host plant. The studies will be conducted using the fungus Paxillus involutus ("pluggskivling") and various host plants including birch. We are using DNA microarays to follow the growth and functional aactivity of the mycelium when growing and colonizing various nutrient patches in a soil microcosm.
• Genomic diversity and plasticity in Paxillus involutus: implications for understanding the evolution of symbiosis in ectomycorrhihzal fungi (ALeQ, TJ, AS, SE, AT)
  There are several thousands of species of fungi that can form ectomycorrhizal associations with plants. The species are found in many taxonomic groups and phylogenetic studies have shown that the symbiotic life-style has evolved repeatedly from non-symbiotic (free-living) fungi. The transition is most probably an ongoing process and the outcome depends on the benefits of growing as a symbiont and saprophyte. The objective of this research program is to characterize the genomic diversity of various populations of the ectomycorrhizal fungus Paxillus involutus and to relate this variation to the adaptation to symbiotic and vegetative growth. The genomic variation of the fungus are examined using DNA microarrays and the adaptation to various environments are studied both in field and laboratory experiments
• The area of interaction between the mycorrhizal fungi and the plant roots (PS, MS, BS)
  The mycorrhizal fungi are unique in that they may colonize host plants and within the plant roots establish specific morphological structures. These structures are important in the nutrient exchange between the symbiotic partners: carbohydrates are transferred from the plant to the fungus and other nutrients from the fungus to the host. We are interested in describing this plant-fungal interface, both from an morphological and physiological basis.
• Evolution of genomic diversity in parasitic fungi (DA, ML, AT)
  Molecular phylogenetic studies have shown that parasitic fungi are found in all major taxonomic groups of fungi and that the parasitic habit has evolved multiple times in distantly related groups. The evolution of parasitism in fungi is closely linked to the development of infection structures. Most parasitic fungi, including those infecting plants and animals, can grow both as saprophytes and parasites. The transition from the saprophytic to parasitic growth involves the development of specific morphological structures. We are examining mechanisms for the evolution of fungal parasitism using the nematode trapping fungi and nematodes including the model organism Caenorhabditis elegans. Despite the fact that the nematode-trapping fungi display a large variation in the morphology of infection structures (nets, knobs, contricting rings etc.) they represent a group of closely related species. We are trying to identify genes and pathways controlling the development of infection structures in nematode-trapping fungi using instertional mutagenesis and transcriptional analyses (expressed sequenced tags, ESTs and microarray).
• How to kill a nematode? Analyses of genes expressed during fungal infection of nematodes (MT, CF, EF, AT)
  Parasitic nematodes have substantial impact on human welfare, through crop damage and diseases of both humans and domestic animals. Such nematodes are most often controlled by various chemicals and drugs. Environmental and health concerns about these methods have introduced a sense of urgency into the search for alternative methods for nematode control. One source for isolating new nematicides/anthelmintics is from microbial anatagonsists that parasitize nematodes. Among them, are the nematophagous fungi that has a unique ability to infect and kill nematodes. The specific aims of this program are: (1) To identify and characterize genes and metabolic pathways that are active during fungal infection of the nematode C. elegans; (2) To identify possible targets in nematodes that can be used for killing nematodes; (3) To establish the use of C. elegans as a model for studying fungal pathogenesis

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Last updated: 2003-06-24