Microbe Atlas

New Research Details Which Microbes Live Where
May 6, 2015

People tend to have a climate that works for them.
 
As a native New Englander, growing up in the summer meant running around outside all day with impunity and sleeping soundly at night as the temperature dropped to the 60s. Here in North Carolina, summer means avoiding physical activity like the plague between the hours of 10AM and 8PM because I cannot take the heat and humidity.
 
And that goes both ways. I went to college on Lake Ontario, and the northerners always had a good chuckle when our friends from Florida or southern California donned their heavy winter parkas at the first flurries in late October, never dreaming that the temperature might not top freezing for a few weeks at a time, and two feet of snow could fall in a day.
 
As it turns out, the bacteria and fungi that float through the air are the same way, according to a new study from the University of Colorado at Boulder and NC State University.
 
Biologist Rob Dunn and his colleagues analyzed samples of more than 110,000 species of bacteria and 55,000 species of fungus from across the country and constructed the first ever nationwide atlas of airborne microbes. The maps show that different species of airborne microbes tend to thrive in different climates.
 
Twelve hundred citizen scientists from all 50 states took swabs of dust from their front door trim and sent the swabs to Dunn and his colleagues. The standard technique for determining the microbe species present in each swab would be to allow those species to grow in a culture and identify them based on their colonies. Instead, Dunn and his colleagues used a genetic technique called PCR — short for polymerase chain reaction — that replicates the microbes’ DNA, allowing scientists to identify each species genetically.
 
While cultures generally only show a few species, PCR revealed that each swab contained 4,700 species of bacteria and 1,400 species of fungi on average!
 
After all the bacteria and fungi were identified, a few patterns emerged. For us, average temperature tends to separate Minnesotans from Texans, but microbes are pickier about other things. The acidity of soil, for example, correlates very well with the distribution of different bacteria. Different fungi, on the other hand, seem to be choosier about the amount of yearly rainfall — some favoring more rain and others less.
 
Airborne BacteriaOn a larger scale, the maps show that the microbial populations on the coast are more similar to each other than to those in the interior; that is Rhode Island microbes have more in common with Florida, California and Oregon microbes than they do with Missouri or Nebraska microbes.
 
Also, it turns out that microbes have their own version of “city folk.” The example Dunn gave in a press release was that Raleigh microbes are more similar to New York City microbes than they are to Cary or Pittsboro microbes. That data agrees with an urban ecology phenomenon called homogenization, which is a fancy word describing why every city in America has squirrels and pigeons regardless of what sorts of animals live around that city.
 
This microbe atlas, now published in the Proceedings of the National Academy of Sciences, have a number of uses. Every breath we take may contain a few microbes that find their way into our lungs, and most of the time that story ends with our bodies disposing of them with ease. But sometimes they can make us sick or cause an allergic reaction. With these new maps, a person with a serious fungal allergy could learn which places have the highest concentrations of their allergen.
 
This work also has applications in forensics. The same researchers published a paper in the journal PLOS ONE in April of 2015 describing a method for predicting where something came from based on the population of fungi in a dust sample. The researchers chose fungi because of their large regional variability — 72.4% of all the fungal species were found in less than 1% of the dust swabs.
 
Dust PredictionRight now, their algorithm cannot assign a dust sample a street address of origin based on the fungus present. In 900 tests of their method, the average error was about 140 miles. So if you gave them a sample from Asheville, the algorithm might say it came from Winston-Salem or, as the study showed, a sample the algorithm says is from Columbia, South Carolina might actually be from Raleigh (pictured left). The researchers acknowledge that this method is not perfect yet, but it could point an investigator in the general direction.
 
Also, this method can be refined by including data from future fungal swabs, pollen (commonly used in forensics to determine the origin of dust samples), bacteria, and insects. DNA from all of these sources shows up in dust and can potentially be used to locate the origin of that dust.
 
Dunn and his colleagues are still crunching the data from all the dust swabs but you can learn more about this project and his other citizen science projects here.

— Daniel Lane
 
Daniel Lane covers science, engineering, medicine and the environment in North Carolina.

GSK