Methods in the Kirchman Lab

Here are a few of the methods used in the Kirchman lab. Click on the method to get a cookbook description.

• Preparing samples for direct counts of prokaryotes and our handy Excel macro.

• Microcentrifuge method for thymidine or leucine incorporation.

• Counting microbes in phylogenetic groups using fluorescence in situ hybridization (FISH) or CARD-FISH with our Microbe Counter software for ImagePro Plus.

• Extracting DNA and RNA from microbes collected on filters.

• Single-cell analysis of microbial activity using Micro-FISH with PowerPoint figures.

• Preparing fresh 20% paraformaldehyde used in FISH and Micro-FISH.

• Collection and isolation of DNA for cloning into fosmids, using agarose noodle or without noodles.

• Counting aerobic anoxygenic phototrophic (AAP) bacteria by IR epifluorescence microscopy.

• Estimating gene copy numbers by quantitative PCR (QPCR) using the Rotogene or the ABI instruments

• Measuring bacterial biovolumes using SYPRO Ruby protein stain

• Counting bacteria in sediments

• Sampling protocols for MO monthly trips

Kirchman's Home Page

MOPE home page

 

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Updated: 14 June 2011