Fig. 1: Earthworm dung: the activity of the earthworms are fundamental for the fertility of our forest soils. Photo: B. Frey

Fig. 2: Rhizobia in roots of legumes are able to fix atmospherically derived nitrogen. Photo: B. Frey

Fig. 3: Soil bacteria: soil microbial communities mediate many processes such as nitrification, denitrification, and methanogenesis that regulate ecosystem functioning and also feed back to influence atmospheric chemistry. Photo: B. Frey

Fig. 4: Fungal spores are thick-walled and contain interesting features on the surface which are crucial for the taxonomic identification. Photo: B. Frey

Soil microorganisms mediate many processes such as nitrification, denitrification, and methanogenesis that regulate ecosystem functioning and also feed back to influence atmospheric chemistry. These processes are of particular interest in terrestrial ecosystems where nutrient cycling is highly responsive to anthropogenic perturbations and soil gas releases may be sensitive to climate warming.

Motivation for Microbial Research

• Biodiversity: Soils contain by far the greatest diversity of organisms, with estimates that one gram of soil can contain several thousand genotypes. Micro-organisms are essential for the functioning and sustainability of natural ecosystems but are frequently ignored due to their small size and consequent methodological difficulties in detecting cells and assessing their activity. However, we do not know which of these organisms are active, what their functional role is and whether they respond to changing environmental conditions.

• Climate Change: Climate change is a major driving force behind changes in fire regimes, plant community distributions, glacier retreat, and permafrost melt. Understanding ecosystem biogeochemical response to global climate change requires a special emphasis of the linkages between the aboveground and belowground (e.g. fungal and bacterial) biotic communities. Alterations in the composition and function of soil microbial communities affect the biogeochemical cycling of elements, resulting in positive and negative feedbacks to aboveground biota and trace gas fluxes.

• Air Pollution: Heavy metals are emitted in the atmosphere by industrial activities, transported through long distances, they deposit and accumulate in terrestrial ecosystems. Increased accumulation of Cd, Hg and Pb from anthropogenic and geogenic sources in soils especially of forest soils has led to exceedances of the current guide values defined by the environmental legislation. Heavy metals are highly persistent in the environment and are known to alter soil ecosystem diversity, structure and function. Especially, Hg as a global pollutant is of high ecotoxicological concern. However, little information is available on rates of atmospheric deposition, distribution, mobility of Hg compounds (methylmercury) in soils and their transfer functions in the biosphere (bioaccumulation).

Goals of Microbial Ecology

The general goal of microbial research has been to understand how microbial groups respond to changing environmental conditions. This includes work on the interactions among environmental controls over process rates, environmental constraints on microbial activities and community composition, and changes in processes at the ecosystem level. Finding ways to link process-based and biochemical or gene-based assays is becoming increasingly important as we intend to get a better mechanistic understanding of the response of forest ecosystems to current and future anthropogenic perturbations.

Current projects

Heavy metals

Critical Limits and Effect Based Approaches for Heavy Metals

Soil compaction

Characterization of different compacted wheel tracks by means of microbial properties in a forested site

Glacier forefield

Microbial colonization and its effects on mineral weathering (CCES-Big Link)

Litter decomposition

Decomposition of litter and fine roots, microbial biomass and activity on LWF-plots

Carbohydrate metabolism of roots

Influence of above-ground stress on the metabolism of non-structural carbohydrates in poplar roots

Methods

Nucleic-acid-based methods and high-throughput genetic profiling tools are used to follow population changes of rhizosphere microbial communities under particular conditions (soil pollution, soil compaction and climatic factors). The taxonomic variability of microbial communities will be linked with the analysis of functional genes and activity measurements to obtain an understanding of the functional roles of natural microbial communities in soil. New approaches such as stable isotope probing and functional gene arrays will lead to a better insight into biogeochemical processes.

Facilities

Our institute is well equipped to conduct the studies described above, including the following equipment and instrumentation.

Fully equipped Molecular Microbial Ecology Laboratory (in house):

• ABI 7500 Fast real-time PCR
• ABI Genescan 310 and 3100, capillary electrophoresis for sequencing and genetic profiling (T-RFLP)
• Agilent Bioanalyzer
• Thermocyclers
• DGGE/TGGE gel electrophoresis apparatus, Gel Doc 2000 photodocumentation and D-Code systems
• Gel electrophoresis, Elchrom, Metaphor
• Nanodrop Spectrophotometer for DNA, RNA quantification
• UV-Vis, fluorescence, luminescence microplate reader
• Low temperature scanning electron microscope combined with energy-dispersive X-ray microanalysis (SEM-EDX)
• Freeze drier
• Bead beater
• Miscellaneous equipment and supplies: sonicator/sample disruptor, minicentrifuges, Eppendorf high speed refrigerated centrifuge, high speed centrifuges, incubators, -20 and -80 freezers, vacuum filtration manifold, fume hoods, biosafety lab

Central Laboratory (in house):

• GC-IRMS with gas-bench
• AAS, ICP-MS
• Total C and N analyzer
• Ion chromatography

Recent publications

• Ernst G., Zimmermann S., Christie P., Frey B. (2008) Mercury, cadmium and lead concentrations in different ecophysiological groups of earthworms in forest soils. Environmental Pollution (in press).
• Frey B., Pesaro M., Rüdt A., Widmer F. (2008a) Dynamics of bacterial communities in bulk and poplar rhizosphere soil contaminated with heavy-metals. Environmental Microbiology (in press: doi: 10.1111/j.1462-2920.2007.01556.x).
• Lazzaro A., Widmer F., Sperisen C., Frey B. (2008) Identification of dominant phylotypes in a cadmium-treated forest soil. FEMS Microbiology Ecology 63:143-155.
• Novak C., Schaub M., Fuhrer J., Skelly JM., Frey B., Kräuchi N. (2008) Ozone effects on visible foliar injury and growth of Fagus sylvatica and Viburnum lantana seedlings grown in monoculture or in mixture. Environmental and Experimental Botany 62:212-220.
• Brunner I., Luster J., Gûnthardt-Goerg M., Frey B. (2007) Heavy metal accumulation and phytostabilisation potential of tree fine roots in a contaminated soil. Environ Pollut (in press: doi:10.1016/j.envpol.2007.07.006).
• Ernst G., Frey B. (2007) The effect of feeding behaviour on Hg accumulation in the ecophysiologically different earthworms Lumbricus terrestris and Octolaseon cyaneum: a microcosm experiment. Soil Biology and Biochemistry 39:386-390.
• Nötzli K., Böll A., Frey B., Graf F., Holdenrieder O. (2007) Release of iron from bonding nails in torrent control check dams and its effect on wood decomposition by Fomitopsis pinicola. Wood research 52:1-14.
• Frey B., Stemmer M., Widmer F., Luster J., Sperisen C. (2006) Microbial characterization of a heavy metal-contaminated soil in a model forest ecosystem. Soil Biology and Biochemistry 38:1745-1756.
• Frey B., Hagedorn F., Giudici F. (2006) Effect of girdling on soil respiration and root composition in a sweet chestnut forest. Forest, Ecology and Management 225:271-277.
• Novak B., Rais D., Frey B., Menon M., Schulin R., Günthardt-Goerg M., Luster J. (2006) Influence of heavy metal contamination on soil parameters in a lysimeter experiment designed to evaluate phytostabilization by afforestation. For. Snow Landsc. Res. 80:201–211.
• Lazzaro A., Hartmann M., Blaser P., Widmer F., Schulin R., Frey B. (2006a) Bacterial community structure and activity in different Cd-treated forest soils. FEMS Microbiology Ecology 58:278-292.
• Lazzaro A., Schulin R., Widmer F., Frey B. (2006b) Changes in lead availability affect bacterial community structure but not basal respiration. Science of Total Environment 371:110-124.
• Rigling D., Günthardt-Goerg M., Blauenstein H., Frey B. (2006). Absorption of heavy metals into Armillaria rhizomorphs from contaminated soils. For. Snow Landsc. Res. 80:213–220.
• Widmer F., Hartmann M., Frey B., Koelliker R. (2006) A novel strategy to extract specific phylogenetic sequence information from community T-RFLP. Journal of Microbiological Methods 66:512-520.
• Cosio, C., DeSantis L., Frey B., Diallo S., Keller C. (2005) Cadmium distribution in leaves of Thlaspi caerulescens. Journal of Experimental Botany 56:765-775.
• Hartmann M., Frey B., Kölliker R., Widmer F. (2005) Semi-automated genetic analyses of soil microbial communities: comparison of T-RFLP and RISA based on descriptive and discriminative statistical spproaches. Journal of Microbiological Methods 61:349-360.
• Heim A., Frey B. (2004) Predicting litter decomposition rates for Swiss forests. Biogeochemistry 70:301-315.
• Jung C, Maeder V, Funk F, Frey B, Sticher H, Frossard E (2003) Release of phenols from Lupinus albus L. roots exposed to Cu and their possible role in Cu detoxification. Plant and Soil 252:301-312.
• Schwab B, Mathur J, Saedler R, Schwarz H, Frey B, Scheidegger C, Hülskamp M (2003) Regulation of cell expansion by the distorted genes in Arabidopsis thaliana: Action controls the spatial organization of microtubules. Molecular Genetics and Genomics 269:350-360.
• Ringli C., Baumberger N., Diet A., Frey B, Keller B. (2002) ACTIN2 is essential for bulge site selection and tip growth during root hair development of Arabidopsis. Plant Physiology 129: 1464-1472.
• Zimmermann S., Frey B. (2002). Soil respiration and microbial properties in an acid forest soil: the effects of wood ash. Soil Biology and Biochemistry 34:1727-1737.
• Heim A., Brunner I., Frey B., Frossard E., Luster J. (2001) Root exudation, organic acids, and element distribution in roots of Norway spruce seedlings treated with aluminum in hydroponics. J Plant Nutr Soil Sci 164:519-526.
• Frey B., Keller C., Zierold K., Schulin R (2000) Distribution of Zn in functionally different leaf epidermal cells of the hyperaccumulator Thlaspi caerulescens. Plant Cell and Environment, 23: 675-687.
• Frey B., Zierold K., Brunner I (2000) Extracellular complexation of Cd in the Hartig net and cytosolic Zn sequestration in the fungal mantle of Picea abies – Hebeloma crustuliniforme ectomycorrhizas. Plant, Cell and Environment 23: 1257-1265.
• Brunner I., Frey B. (2000). Detection and localization of aluminium and heavy metals in ectomycorrhizal Norway spruce seedlings. Environmental Pollution 108: 121-128.
  

Contact

• Beat Frey