Click here for a list of things to prepare for your lab space.

1) Biomarker evaluation/search:

• Probe check: ProbeBase ; ProbeCheck ; MathFISH ; RDP probe base ; Silva probe base ; Silva primer base ; NCBI blast.
• Evaluation of restriction enzymes: MiCA ; TRF-cut.
• Universal PCR Primers: Blackwood et al., 2005, AEM ;  Baker et al., 2003, J Microbiol Methods ; Klindworth et al 2012;
• Improved pyrosequencing procedure: Berry et al., 2011, AEM, 77:7846.

2) Cloning and Screening (e.g. T-RFLP):

• TOPO TA Cloning Kit pCR 2.1 TOPO-Vektor product number #45-0641 Invitrogen/Life Technologies.
• Preparation of clones.
• M13 PCR for control of insert size.
• Screening of clones with restriction enzymes and T-RFLP.

3) Culture Collections

• ATTC/LGC.
• DSMZ.
• World Federation of Culture Collections.

4) FISH:

• Standard fixation of prokaryotes.
• Coating of microscope slides for FISH.
• Standard FISH and DOPE FISH.
• Tables for FISH experiments.
• CARD-FISH. Check the VAAM 2013 proceedings for new improvement of the CARD FISH protocol (Canosa et al).
• FISH for bioremediation - in preparation.
• Silva weblink about FISH.
• Where to order primers and probes: Biomers.

• Faust et al. 2012.
• Fuhrman 2012. 
• Tempterton et al 2012. 
• Wikipedia link about metagenomics.
• The fourth domaine - Zakaib 2011.
• Current Biotechnology issue on single cell biology and -omics.

• General links about microbial growth: Wikipedia ; Abedon at Ohio State University ; Equations (by H. Smith) ; Wikipedia r/K strategists ; VBNC concept.
• Microbial evolution DeLong 2012 ; Denef et al 2012.
• Microbial olympics Youle et al 2012 ; Bacterial records.
• A molecular view on biodiversity. Pace 1997.
• The unseen majority Whitman et al 1998.
• What determines cell size? Marshall et al 2012.
• Microbial numbers.

7) Microbial media:

• Nutrient rich media: CASO/TSB ;  LB ; HD ; NA.

• Nutrient poor media: R2A ; Mineral medium.

• List of various media: ATCC/LGC ; DSMZ

• General surveys and media for various prokaryotic groups:
  • Bergey´s Manual Springer Verlag.
  • Handbook of microbiological media ASM.
  • Methods for General and Molecular Microbiology and ASM Press
  • MicrobeWiki
  • The Prokaryotes Springer Verlag.

• Supplementary reagents for media:
  • Antifungal reagents.

• Media for dilution of samples with microbes:
  • 0,9 % NaCl (dissolved either in distilled water or in a suitable buffer, e.g. 20 mM HEPES, pH 7).
  • 0,9 % NaCl with 0,1 % tween 80 and 10 µM Na-pyrophosphate (dissolved either in distilled water or in a suitable buffer, e.g. 20 mM HEPES, pH 7).

• Specific media for different bacterial groups (below some examples, please consult further literature for more info):
  • Denitrifying bacteria: (Heylen et al 2006 AEM).
  • Fe/Mn precipitating bacteria: Leptothrix/Sphaerotilus DSMZ 803.
  • Fe (neutrophilic)/Mn oxidizing bacteria: Emerson et al, 2005 Methods in Enzymology Elsevier.
  • Fe(III)/heavy metal/radionuclide reducing bacteria (e.g. Anaeromyxobacter DSM; Geobacter DSMZ; Straub et al 2005, Methods in Enzymology Elsevier).
  • Fungi (Malt media SIGMA ; Plant Pathology WSU ; FMB Lab, USA; Bioworld commercial media).
  • Lytic Chloroflexi species: Herpetosiphon (e.g. WAT medium, VY2A medium).
  • Methanogens: DSMZ ;  R. Wolfe 2011, Methods in Enzymology.
  • Mineral precipitating bacteria: De Muynck et al 2010, Ecological Engineering.
  • Nitrifying bacteria: Research on Nitrification and Related Processes A/B 2011 Methods in Enzymology Elsevier.
  • Reductively dechlorinating systems: Löffler et al, 2005, Methods in Enzymology Elsevier ; DCB-1 medium from the Löffler lab UTK, USA ; TSB for anaerobes from the Löffler lab, UTK USA.

• CMEIAS.
• Cypionka´s Microbiological Garden.
• DAIME.
• Fungi.
• Kunkel Science Photography. 
• Picolay.
• Protists - movies.
• Sciencephoto.
• Zeiss browser for Zeiss images (select download, then Axiovision or LSM 5).

• BAC-DIVE.
• BLAST-NCBI.
• EMBL.
• FunGene.
• GEBA.
• Genome News Network.
• Geographic blast (silva tool).
• INSCD. 
• JGI.
• Living tree project.
• Ez taxon.
• NCBI.
• RDP.
• SILVA-ARB

• MOBIO extraction kits: (e.g. Power Biofilm, Power Soil, Power Water).
• MP biomedical: bead beater, extraction kits, lysing matrix.
• Quick DNA/RNA extraction protocol according to Griffiths et al, 2000.
• General DNA/RNA extraction protocol.
• DNA and RNA extraction from groundwater Ritalahti et al. 2010 a, b: In K. N. Timmis (ed.), Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds. Springer Berlin.
• Invisorb Forensic kit Stratec.
• Whole genome amplification kit Quiagen.
• Plasmid extraction kit Easy Prep Pro Biozyme (product number #390055).
• Standard plasmid extraction protocol.
• Phaselock gel.
• Evaluation of nucleic acid extractions, see General DNA/RNA extraction protocol.
• Wikipedia link about nucleic acid extraction.

• General PCR conditions for Bacteria. 
• Gel electrophoresis procedure.
• PCR reaction table.
• Gel electrophoresis table.
• Calculation of  OligoCalc.
• Tm for PCR (link from Promega).
• Measurement of concentration of PCR amplificate, see General DNA/RNA extraction protocol.
• Purification of PCR amplificates, Quiagen (product number #28108).
• Wikipedia link about PCR.
• Wikipedia link about gel electrophoresis.

• Wikipedia about bioinformatics.
• Wikipedia about phylogenetics.
• Phylogenetic Backbone &Taxonomic Framework for Procaryotic Systematics 2001 Bergey´s Manual of Bacteriology.
• SOPPI.
• Tree of Life.
• Uniting the classification of archae and bacteria 2014 et al

13) Preservation of cells:

• Long term storage of cells at -80 Degrees C preparation of standard glycerol stock cultures.
• General review on long term preservation of cells (Day and Stacey, 2007).

14) Sequencing (filing of data, concentration, volumes, shipping, evaluation):

• Single reads at GATC (e.g. of PCR amplificates, plasmids). CHECK for updates! 
• GATC sample table (check for update on GATC website)
• General procedure and evaluation.
• Free softwares for visualizing sequence chromatograms.
• Proper description of sequence data (contextual data by SILVA)

15) Software for bioinformatics:

• Arb.
• Dendroscope.
• Mothur.

16) Stains:

• Activity stains (review by Joux and Lebaron, 2000).
• DAPI stain (see page 15 in Standard FISH and DOPE FISH).
• Gram stain.
• Molecular stains.
• Quick Gram test (based on KOH).
• Slideshow about how stains work.
• Stains for activated sludge according to D. Jenkins et al. (includes stains for PHB, volutins (Neisser,) Crystal violet sheath, Sulfur oxidation).
• SYBR Green/Gold stain (see page 15 in Standard FISH and DOPE FISH).

17) Taxonomy:

• Wikipedia about classification. 
• Wikipedia about taxonomy.
• Silva taxonomy browser.
• NCBI taxonomy.
• RDP taxonomy.
• Ez taxon.
• LPSN.
• MicrobeWiki.
• Names for Life.  
• A Place for DNA-DNA Reassociation and16s rRNA Analysis in the Present Species Definition i Stackebrandt et al 1994.
• Ad hoc committe on the reevaluation of the species definition Stackebrandt et al 2002.
• The bacterial species in the genomic era Konstantidis et al 2006.
• The bacterial species challenge Fraser et al 2009.
• On the fitness of microbial taxonomy Tamames and Rossello-Mora 2012.
• Species exploration.

• Scientific organisations - examples (for grant proposal, meetings, etc): AGU; Alexander von der Humboldt Foundation; ASM; BAGECO; Batelle; C-DEBI; DAAD; DFG; EANA; FEMS; Goldschmidt; ICGR;  ISME; ISSOL; ISSM; IUMS; IWA; REMTEC; Tardigrada; UIS; VAAM; WFCC.

Comment on the above listed protocols:  Please regard all information critically. We hope that the protocols and links listed above are correct, yet we cannot guarantee that they are free from occassional, unintended errors. If you have questions about the contents on this website, please contact nlee<at>environmental-microbiology.de.