Microbiology and Molecular Ecology studies in Bemidji, MN
Our collaborators: Barbara Bekins, Isabelle Cozzarelli
A crude oil spill from an underground tank in a remote area resulted in a unique opportunity to study the response of the endemic bacterial community.
This site has been intensively studied, and much data is available. To obtain an overview, visit the Bemidji home page listed in the links section below.
The role of the molecular ecology group at Bemidji has been to compare abundance estimates obtained using pcr (polymerase chain reaction) based methods of detection with more traditional techniques (mpn), culture-based techniques.
Methods traditionally used to estimate abundance of functional groups of organisms have relied on the use on culturing for enumeration. These methods are inadequate to allow for identification of the species present in microbial communities, and may be biased toward culturable organisms. The development of molecular technology has presented new possibilities which are not dependent on cultivation, such as comparative rRNAsequencing. These techniques are useful tools which help to increase our understanding of microbial communities and their role in contaminated environments without the biases imposed by traditional culturing methods.
The "most probable number" (mpn) of organisms is obtained by culturing replicate dilutions and measuring microbial activity (such as methanogenesis). For molecular techniques, DNA from the sediment is amplified by pcr, and functional genes for methanogenesis are detected. Phylogenetic groups (i.e. Eubacteria and Archaea) can also be enumerated. And individual species can be identified by cloning and sequencing 16SrDNA region of the chromosome.
This graph (at right) shows preliminary data (Kim Fry Martz, Masters Thesis) comparing molecular enumeration with mpn data collected by Bekins and coworkers in and adjacent to the oil plume at Bemidji, MN.
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Links
Bemidjimicrobiology of the oil plume
