Environmental & Geomicrobiology

Introduction: A major limitation for understanding the microbiology in the environment is our limited knowledge of the micro-organisms and their activities, because the majority of these organisms has not yet been cultured. During the last decades, a plethora of different techniques based on molecular and radioactive markers have become available that provide increased possi-bilities to detect microorganisms that have not yet been cultured and trace their activities in situ. This international course aims to teach and discuss current state-of the art in situ detection techniques and future developments for innovative applications in different types of microbiological samples.

Next FISH courses in 2015 and 2016: Please contact Natuschka Lee nlee<at>microbial-systems-ecology.de.

Background and layout of course: Since the development of the fluorescence in situ hybridization (FISH) technique based on rRNA-targeted nucleic acid probes in the 1980-90s, cultivation-independent identification and quantification of microbial cells in the environment have provided powerful possibilities for advanced ecological in situ studies (see e.g. Wagner and Haider, 2012 in Current Opinion in Biotechnology; and by Lee et al, 2011, in Encyclopedia of Geobiology, Springer Verlag). However, several difficulties have been encountered when applying these techniques on different organisms and environmental systems. To circumvent these problems, the standard FISH technique has either been combined with other methods, such as cell-sorting, microautoradiography, electron microscopy, RAMAN spectroscopy or nano SIMS; or further developed and refined with respect to signal detection or probe chemistry, such as CARD-FISH, clone-FISH, LNA-FISH, mRNA-FISH, PNA-FISH, polynucleotide probes, RING-FISH or DOPE-FISH. The aim of this course is to give a theoretical overview of different kinds of FISH techniques and applications, and some lab experiences on a selected amount of these techniques:

The course is normally organised at the department of microbiology, TUM, in Freising (outside Munich, Germany). However, the course can also be leased to other institutes.

History:

This course has been organised regularly since 2006, for undergraduates,graduates and senior researchers, from different academic research fields and industry (aquatic biology, astrobiology, bioremedation, biotechnology, environmental microbiology, food microbiology, geobiology, medical microbiology, microbial ecology, soil ecology) and nearly 40 different countries in Europe, North America, South America, Middle East, Russia, China, India and Japan. Upon wish and availability, we also invite special guest lectures to our courses, e.g.:

AdvanDx PNA-FISH technology (USA);
Ametek/CAMECA (nanoSIMS technology, Germany);
Dr. Gesche Braker (Max Planck Institute Marburg, Germany);
Dr. Martin Elsner (Environmental Isotope Chemistry, Groundwater Ecology, Helmholtz Center, Germany)
Dr. Johannes Fried (Eukaryote microbiology,TUM, Germany);
Dr. Bernhard Fuchs (Molecular Microbiology, Max Planck Institute Bremen, Germany);
Prof. Dr Frank O. Glöckner (Metagenomics and bioinformatics (the SILVA tool, Max Planck Institute Bremen, Germany);
Dr. Christian Griebler (Microbial Ecology, Groundwater Ecology, Helmholtz Center, Germany);
Dr. Harald Meier (arb bioinformatics group TUM, Germany);
Prof. Dr. Frank E. Loeffler (Bioremediation, UTK, Knoville TN (former Georgia Institute of Technology, Atlanta, GA, USA);
Implen GmbH (Munich, Germany);
Dr. Wolfgang Ludwig (Microbiology/arb bioinformatics TUM, Germany);
Dr. Tillmann Lüders (Molecular Ecology, GGroundwater Ecology, Helmholtz Center, Germany);
Dr. Michael Rothballer (Helmholtz Zenter Munich Plant-microbe interactions, Germany);
Dr. Michael Schmid (Helmholtz Zenter Munich Plant-microbe interactions,Germany);
Zeiss Microimaging GmbH.