Equipment of the Micorbial Ecology group

The list is organized into methodological capabilities, with a list of equipment related to each capability below it. (H. Bürgmann, K. Beck, March 12, 2013)

• Pipeline for extraction and purification of Nucleic Acids (DNA, RNA) from cultures and environmental samples using various kits and in house extraction protocols:
  
  • Filtration devices for sampling bacteria in water
  • FastPrep 24 “Bead Beater“ for cell disruption, 24 samples in parallel
  • Bead beating adaptors for vortex mixers, for use with MoBio extraction kits (24*2 ml, 4* 15 ml, 2* 50 ml tubes)
  • SpeedVac / vacuum concentrator (Eppendorf concentrator 5301)
  • Cooling centrifuges Eppendorf (5804 R, 5415 R), for various tube sizes and microplates
  • Ultracentrifuge (gradient centrifugation, e.g. for stable isotope probing)
  • Various gel electrophoresis chambers, for horizontal agarose gel electrophoresis (different formats available)
    
    

• DNA quantification, enzyme assays, and other spectrophotometric applications:
  
  • NanoDrop ND-1000, micro-spectrophotometer (DNA quantification, spectrophotometer for 1 µl samples)
  • Synergy HT plate reader: Spectrophotometer with fluorescence and luminescence detection for microplates: E.g. DNA quantification with fluorophores, enzyme assays, kinetics, BIOLOG, spectrophotometric measurements.
    
    

• PCR based methods: standard PCR and qPCR for detection, quantification, and downstream analysis of various functional genes, 16S rDNA amplification of specific phylogenetic groups or general bacteria or archaea communities. ARISA and t-RFLP community fingerprinting on capillary sequencer hardware. Gel-based DGGE fingerprinting. Next generation sequencing (454), sequence analysis (MOTHUR pipeline). Cloning and plasmid preparation for Sanger sequencing.
  
  • Eppendorf shaker / incubator (for eppendorf tubes)
  • PCR workstations with air particle filtration
  • Touchgene PCR thermocyclers and gradient thermocyclers for regular PCR and gradient PCR
  • AB 7500 FAST real time PCR for quantitative real time PCR methods (SYBR-green, TaqMan)
  • ABI 3130xl 16 capillary sequencer (ARISA and t-RFLP analysis, Sanger sequencing)
  • BioRad DCode mutation detection system for DGGE gel analysis.
    
    

• Gel electrophoresis, blotting and imaging:
  
  • FUSION FX7 imaging system: Gel documentation, fluorescence and chemoluminescence imaging (blots, etc.) and image analysis
  • Various electrophoresis chambers for horizontal agarose gel electrophoresis, different formats and sizes available.
  • Dot- and slot-blot equipment
    
    

• Microscopy, including FISH and CARD-FISH analysis for specific detection and quantification of bacterial cells in environmental samples:
  
  • Hybridization oven
  • Temperature regulated water baths
  • Zeiss Axioskop 2, Equipped with various filters e.g. for DAPI, Cy3, Autofluorescence
  • Leica DMI 6000B inverted fluorescence microscope, fitted with various fluorescence filters, with image acquisition and analysis software
    
    

• Flow Cytometry for cells and phytoplankton detection and quantification:
  
  • BD Accuri C6 flow cytometer, equipped with autosampler
    
    

• Cultivation:
  
  • Anaerobic glove box
  • Biological safety workbench
  • Various incubators and shakers
  • Tabletop and full-scale autoclaves