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Researchers Describe the Troposphere Microbiome

NEW YORK (GenomeWeb News) – By getting airmass samples from a DC-8 flown high above land and the ocean, researchers led by Konstantinos Konstantinidis, an assistant professor at the Georgia Institute of Technology, reported in the Proceedings of the National Academy of Sciences today that a significant portion of particles found in the troposphere are bacteria.

Those bacteria may aid in cloud and ice formation and precipitation, as well as possibly serving as a means for bacterial dispersal, including of pathogenic bacteria, the study authors said.

The airmass samples, taken between four and six miles above the Earth's surface, were analyzed using microscopic and genomic techniques to get a better understanding of what bacteria live in the middle to upper troposphere and how they arrived there. About 20 percent of the particles isolated in the 0.25 micrometer to 1 micrometer diameter range were bacteria. Additionally, samples taken over land tended to include bacteria of a terrestrial origin while those take over the ocean included more marine bacteria.

The researchers further noted that there appeared to be a core troposphere microbiome consisting of 17 operational taxonomic units, including the Methylobacteriaceae and Oxalobacteraceae families.

"We did not expect to find so many microorganisms in the troposphere, which is considered a difficult environment for life," Konstantinidis, the paper's senior author, said in a statement. "There seems to be quite a diversity of species, but not all bacteria make it into the upper troposphere."

The air samples were collected aboard a DC-8 during the 2010 National Aeronautics and Space Administration's Genesis and Rapid Intensification Processes campaign, which was studying high- and low-altitude air masses in relation to tropical storms. The samples were collected during the course of seven flights over the mainland US as well as over the Atlantic Ocean, Caribbean Sea, and Gulf of Mexico under cloudy and sunny conditions as well as before, during, and after two hurricanes.

Using qPCR and microscopy approaches, Konstantinidis and his colleagues quantified the concentration of bacterial and fungal cells in their samples, finding that bacterial cells outnumbered fungal cells by about two orders of magnitude. The microscopic analysis of the cells also found that most, between 60 percent and 100 percent, of the cells were viable, a finding that indicates that the bacteria are able to live at such high altitudes.

Based on Roche/454 pyrosequencing of bacterial SSU rRNA genes, the researchers identified 317 operational taxonomic units in their samples most of which belonged to the Alphaproteobacteria and Betaproteobacteria classes.

Samples taken at similar times or from similar spots were made up of similar bacterial communities, though if a hurricane had swept through, the communities present "were dramatically different," the researchers reported.

"These results suggest that hurricanes have a major impact on the composition of the tropospheric communities based apparently on the large number of new microbial cells that they aerosolize and the precipitation scavenging of preexisting cells," they added.

Overall, though, a set of 17 OTUs were common to all samples, no matter where they were taken from, though they were present at various abundance levels. Two of those OTUs were the bacterial families Methylobacteriaceae and Oxalobacteraceae, which, the researchers pointed out, are known to be able to metabolize oxalic acid. Oxalic acid is a byproduct of cloud chemistry and suggests a possible way for the bacteria to be metabolically active in the troposphere.

Bacteria likely follow the same route as dust and other particles to the troposphere. "When sea spray is generated, it can carry bacteria because there are a lot of bacteria and organic materials on the surface of the ocean," Athanasios Nenes, a professor at Georgia Tech, said.

The researchers also searched through the GreenGenes database to trace the origins of these lofted bacteria. From this, they found that the bacteria present in their samples were derived from nearly every habitat on Earth, though the hurricane samples included more marine-origin bacteria. Additionally, they noted that the hurricane samples were the only ones to contain bacteria usually associated with human or animal feces, a likely consequence, they said, of the hurricanes passing over populated areas.

Some bacteria, like those that can metabolize oxalic acid, may be better suited to life in the clouds than others. "For these organisms, perhaps, the conditions may not be that harsh," said Konstantinidis. "I wouldn't be surprised if there is active life and growth in clouds, but this is something we cannot say for sure now."