Edmonds Lab

Ecosystem Ecology


Research  tools

Here are some of the methodological approaches we use to answer questions regarding the role of microbial community structure/function in biogeochemical cycling.

Research Tools

Bottle incubations of sediment give rates of  aerobic and anaerobic respiration by monitoring the production of metabolic end products, including CO2, CH4, N2O, Fe (II), and H2S.

Denitrification Assays

T-RFLPs involve amplification of a gene of interest (16S rRNA, nirK, mcrA, etc.) followed by a restriction enzyme digest to generate a sample with varying size fragments. The fragments can then be evaluated as a measure of community composition. Terminal Restriction Fragment Length Polymorphisms (T-RFLP)


qPCR allows the researcher to quantify the number of copies of a gene of interest in a sample, relating microbial activity to gene expression by a particular species, genera, or class of prokaryotes.

Quantitative Polymerase Chain Reaction (qPCR)

For samples where large (>1,000) numbers of sequences are needed to evaluate the biodiversity (16S rRNA) or gene expression suite (metagenomic sample) of the microbial community, high-throughput sequencing with  pyrosequencing has been used.  We are now moving to use of Illumina platforms for increased coverage and reduced cost.

High-throughput Sequencing

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Measurements of diel changes in dissolved oxygen in the surface stream can be used to model rates of oxygen consumption (respiration) and production (photosynthetic activity) on a whole-system basis, taking into account at once both water column and benthic production.

Organic Matter Complexity

Whole-stream metabolism

Heterotrophic microbial activity is often regulated more heavily by the composition of the organic matter supplied, rather than the quantity.  Excitation-emission matrices (EEMs) help us determine where and when organic matter chemical composition is changing.