Kirchman Lab Methods

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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David Kirchman

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Maxwell P. and Mildred H. Harrington Professor Marine Biosciences


CEOE School & Departments

School of Marine Science & Policy

Advancing the understanding, stewardship, and conservation of estuarine, coastal, and ocean environments.

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Department of Geological Sciences

Discovering how geological processes have operated over various time scales to create and influence the planet’s surface environments.

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Department of Geography

Investigating the interactions between people and the environment and the processes that explain the location of human and natural phenomena.

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