Bacterial census of Texas air reveals microbial diversity

Novel microarray detects 1,800 microbial species in the air above Austin and San Antonio

Dec 19, 2006
Jeffrey M. Perkel
A bacterial census of the air above two Texas cities reveals striking microbial diversity, according to a report to be published this week by the Proceedings of the National Academy of Sciences Early Edition. Gary Andersen, a staff scientist at Lawrence Berkeley National Laboratory, and colleagues used a novel microarray to detect some 1,800 different bacterial species -- including relatives of bioterror pathogens -- in the skies above San Antonio and Austin, Texas, revealing a level of diversity approaching that found in soil. According to Andersen, the study arose out of the Department of Homeland Security's BioWatch program, an effort to monitor the skies over urban areas for signs of bioterrorism. After three years of monitoring, he said, DHS had detected nothing, despite several false-positives. "They wondered, what is the microbial background, and how does that background affect monitoring?" Andersen explained.He and his team developed a novel microarray called the PhyloChip, which contains about 500,000 probes to detect the 16S ribosomal RNA signatures from 8,741 bacteria and archaea. They probed the chip with amplified 16S rRNA samples taken weekly from air filtration systems in both Austin and San Antonio, which are about 80 miles (128 km) apart, and found between 1,500 and 1,800 bacterial species above each city. Statistical analysis of the microbial populations showed that they varied with meteorological conditions like temperature, wind speed, and air pressure. "The basic conclusion is that the air had a very diverse population of different organisms, from different groups and phyla, with extremely different properties," Andersen said. "Most studies up to now have relied on culturing, and the level of diversity has been much less, so we're really seeing for the first time the real diversity of the air." That diversity, he said, includes relatives of bacteria found in hot springs, deep sea vents, and activated sewage sludge, as well as pathogenic organisms like Francisella tularensis and Bacillus anthracis, a finding that could explain some of the DHS' false positives. "We humans are embedded with bacteria; we are surrounded by them," said Norman Pace, professor of molecular, cellular, and developmental biology at the University of Colorado, Boulder, who was not involved with the study. "You take a deep breath, and you pull in a thousand bacteria. You take a shower and you aerosolize bacteria that you suck in. When you flush the toilet, you generate an aerosol that you then breathe in. We're surrounded by bacteria, and they are not necessarily friendly." The vast majority of these microbes cannot be cultured, however, so until recently it was difficult to identify and study them. The report provides "an entirely new perspective on the organisms in the air," Pace said. "I think it's a wonderful experiment...It's too limited, but that's not their fault. There's not much money for this sort of thing."According to Pace, Andersen's array-based method "is not as precise as sequencing, but it is cheaper. It's a reasonable first-order survey method.... Their question was, what's the diversity? That's a loose question, and loose answers fill the bill."If anything, Andersen could be underestimating the microbial diversity, said J. Craig Venter whose, eponymous Institute is sequencing the metagenome of the air above New York City. "When you base things on 16S ribosomal RNAs, what the environmental genomics show is that each 16S rRNA corresponds to hundreds or thousands of different organisms. So the diversity they show is just a fraction of the real diversity in the air." Either way, these findings "represent something that is critical and needed now," said Andersen. "As weather patterns change, different things go up into the air. We could be changing what's in the air, and unless we know what's in the air now, we'll never know how it changes. It points to a real need for a microbial census." Andersen said he would like to study the air above other major cities. In the meantime, he is using the PhyloChip technology to take microbial censuses of other environments, including a recently published "crustal biome" from 2.8 kilometers beneath the earth's surface. Jeffrey M. Perkel jperkel@the-scientist.comLinks within this article:Proceedings of the National Academy of Sciences Early Edition Andersen Delude, "Swimming with the mycobacteria," The Scientist, June 6, 2005 Hutchison III et al., "The New Biological Synthesis," The Scientist, Jan. 1, 2006 Perkel, "The big picture in microbial genomics," The Scientist, 20[7]:59, July 2006. Lin et al., "Long-term sustainability of a high-energy, low-diversity crustal biome," Science, 314:479 -82, Oct. 20, 2006.