Here are a few of the methods used in the Kirchman lab. Click on the method to get a 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 (email Matt Cottrell to request).
Extracting DNA and RNA from microbes collected on filters.
Single-cell analysis of microbial activity using MAR-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 small boat sampling
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