Microbiology's Air Force
By John Bohannon
ScienceNOW Daily News
20 December 2006

Air is filthy with microbes, at least in the city. That's the conclusion from a genetic study of airborne bacteria in two U.S. cities that suggests the atmosphere may be a more important part of global microbial ecology than was assumed. It also provides the first baseline for monitoring the air for bioterrorist attacks.
Because airborne bacteria are exposed to extremes of temperature, dryness, and radiation, they are thought to be far less diverse and abundant than their peers down on the ground. It has been difficult to test that idea. The traditional method of surveying microbial populations--growing colonies in the lab--doesn't work well for studying the atmosphere's flora. Not only are airborne populations relatively sparse, but the cells are often also in a quiescent state, requiring special conditions to start growing. Finding better methods would be useful, not only for studying basic microbial ecology but also for improving a 3-year-old U.S. government effort called BioWatch, which aims to put sniffing machines in hundreds of public places to sound the alarm in case of a bioterrorism attack.

To get a better fix on flying microbes, a team led by Gary Andersen, a microbial ecologist at Lawrence Berkeley National Laboratory in Berkeley, California, used a recently developed microbe-detector called the Phylochip. Rather than relying on microbes to grow into visible colonies, the device detects individual cells by grabbing their ribosomal RNA (rRNA) genes out of a solution of broken-up cells. Fluorescent dye then gloms onto the microbial rRNA. To see who's who, the rRNA is then washed over a target array of more than 8000 different matching rRNA strands that represent the 121 taxonomic orders of prokaryotic microbes. A computer records positive hits by checking for bright spots on the array.

For their atmospheric samples, the researchers used three sites each in San Antonio and Austin, Texas, both part of the BioWatch monitoring network. The team pumped air samples through fine-meshed filters at the rate of 10 liters per hour and collected the filters weekly for 17 weeks in the summer of 2003.

A surprising discovery was that several nonpathogenic microbes closely related to bioterror weapons of choice, including anthrax and tularemia, were common in city air, which may explain some of BioWatch's false alarms in recent years. Another surprise was the sheer diversity of the airborne microbes, which included 1800 types of bacteria, as diverse an assemblage as typically found in soil, the team reports online today in Proceedings of the National Academies of Science. The diversity and concentration varied dramatically from week to week, with much of the variation explained by weather conditions.

The bottom line? "We humans are embedded in a microbial world that we barely acknowledge, and this study is one that is beginning to shed light on what kinds of organisms are out there in the environment," says microbiologist Norman Pace of the University of Colorado at Boulder. "The only problem I see is that the numbers of samples and locales are very limited. We need a lot more of this in a lot of environments."