Technology News - August 18, 2004

A nationwide census of airborne bacteria

Scientists at Lawrence Berkeley National Labs (LBNL) are using microarrays to compile a national database of airborne bacteria, which could be a boon for environmental researchers. Immediately after the September 11 attacks, American security officials began planning for a possible chemical or biological attack, and the Department of Homeland Security set up detection systems in major cities. But the detectors have to be calibrated to ignore background noise or, in the case of a biological attack, ambient airborne bacteria.

“The problem is that we really had to create the technology to do this,” says Gary Andersen of the Center for Environmental Biotechnology at LBNL in Berkeley, Ca. “Nobody else has ever done this before.” Created with the aid of gene-chip company Affymetrix, the current generation microarray chip now holds 500,000 probes for over 9000 taxa.

“You end up with a table of what’s present and their relative abundance,” says LBNL research associate Todd DeSantis. “So you can see from the sample when a taxa is declining or if it’s on the rise.” This is the first work that shows microarrays can detect not just the presence but also the quantity of taxa. The findings will be published this fall in the journal Environmental Microbiology.

While the above drawing shows a microarray with binding sites that are only a six bases in length, the airborne bacteria study uses binding sites that are 25 bases long. This is the first microarray to broadly sample for different taxa.

The microarray chips uses 25 DNA-base long probes to bind selected sections of 16s ribosomal DNA. The ribosomal DNA is probed because it has sufficient variability to serve as a marker of biological taxa. DeSantis says designing the first chip for broad environmental sampling was difficult, because microarrays were developed for gene- expression work. “We initially wanted to handle this with off-the-shelf technology, using microarray techniques for expression analysis,” he says. “We found that this just wasn’t working.”

After almost two years of work, the lab has already evaluated thousands of samples and is now awash in data. The researchers now have to figure out what to do with it all. DeSantis says they have just enlisted the help of a statistician and are building a website so that scientists can ask questions with different parameters. For instance, a wildlife biologist in Louisiana studying avian disease might want to identify which bacteria are present in the local environment, while an epidemiologist at a hospital in Minnesota might want to know the seasonal fluctuations of bacteria in a nearby city.

“We’re just squirreling away a lot of data and trying to put together an ftp site so that people can select cities and download information,” he says.

The LBNL researchers recently analyzed data collected during the summer of 2003 from two cities in Texas. Separated by only 80 miles, Austin and San Antonio show some significant differences in their bacterial biota. Both cities have airborne bacteria from the genera Pirellula, Pseudomonas, Rickettsia, Clostridium, and Bacillus. But San Antonio has a much greater diversity of bacteria and also supports Denitrovibrio, Legionella, and Actinomyces. It is not known why two cities so close geographically differ so dramatically in their bacteria. “There must be some local reservoirs for the bacteria,” speculates Andersen. “We’re looking at weather patterns to see if that might explain it.”

Although the sampling phase of the project will end in the summer of 2005, analysis of the data could take years. In the future, the research might be expanded, according to Pete Pesenti, a project officer with the Science and Technology Directorate at the Department of Homeland Security. “We’ll take a look at the project next year and then decide if we might need to look at other things in the air like viruses and fungi,” he says. —PAUL D. THACKER