I call Barb a "molecular detective" because she studies bacteria associated with the Alvinella pompejana worm. She is trying to culture a community of bacteria to see what kinds of biochemical pathways the bacteria use to live in the hydrothermal vent environments.

So far, she hasn't been able to culture these bacteria, but that's not unusual. Over 99% of the bacteria in the environment cannot be cultured because it's very difficult to provide the right conditions for bacteria to grow. Many bacteria live off the by-products of other bacteria within the community, and when they are cultured (grown in an artificial environment), it's very hard to reproduce exactly the right growing environment. There are so many factors to take into account (temperature, pH, and the culturing medium) that it's really a matter of trial and error.

Bacteria are not solitary organisms; they live in communities. Barb wants to look at these communities and see what kinds of biochemical pathways they use to live in these extremely hot conditions. She has two big questions about these communities that she'd like to answer:

1. What kind of bacteria are found around and on the Alvinella pompejana worm?

2. What are they doing there, and why are they there?

Since it's next to impossible to culture these bacteria, Barb uses molecular techniques to figure out what types of pathways are present in these bacterial communities and which of those pathways are used. There are pathways involved in sulfur and nitrogen metabolism (both of which are used rather than oxygen for bacterial respiration and growth). Add to that the extreme temperature range that the bacteria live in, and she has a pretty perplexing problem to solve.

Barb examines these bacterial communities by extracting the nucleic acids (DNA and RNA) from the entire community. She then "chops" the nucleic acids up into little pieces, and clones them so that she has lots of different random clones. The average size of a piece is between 1,000 and 3,000 base pairs. Bacterial genes are not very big. They are usually made up of about 1,000 base pairs. She then sequences these pieces. The sequence tell you whether or not you have the potential for a gene (not every sequence yields a gene). This information is archived as a "shotgun library."

The "shotgun library" is an archive of information that Barb has been collecting about the bacteria. She can take her sequence, "blast it," and then compare it to other sequences of bacteria housed in a public data base of bacterial sequences at the National Institutes of Health in Washington, DC.

After examining these results, she's found that genes are involved in denitrification (nitrogen cycle), sulfur metabolism, and the carbon cycle in the bacterial communities found on the worms. All of these are used for the purposes of growth.

Barb doesn't know if she's been successful in cultivating the bacteria she's collected. She's hoping for the best, but is philosophical about the outcome.

Note: All of this work is being done in Dr. Craig Cary's lab in conjunction with Bob Feldman and Amir Ghadiri at Amersham Biosciences.