Air microbiome provides answers to climate change

Dr. Darren Chooneea briskly walks through the Natural History Museum’s garden in his prominent lace-up boots. Armed with a Ph.D. in the field of Infectious Diseases and Microbiology, he works as a scientist in one of London’s most venerable museums with nearly 150 years of history. He carries a mysterious box with telescopic legs, and with the ease that comes from frequent repetition, he unfolds the device and positions it in front of him. On a quest to capture, sequence, and identify the diverse range of life that exists in the air we breathe, Darren Chooneea is hunting for environmental DNA (eDNA) in the city’s air. 

“The air is an untouched ecosystem that we are only tapping into now,” says Chooneea, and with any ecosystem, biodiversity can change over time with changes in the environment. A change in air ecology can bring with it new pathogens, fungal spores, or invasive insects, for example. 

Finding traces of life in the air is no easy task. “In the air there are hundreds of different types of organisms,” explains Chooneea. “It is only in the last five to six years that advances in technology enable us to explore such unique areas.”

Capturing micro-organisms

In order to capture air samples, his device collects samples onto a filter at predetermined intervals, catching microorganisms and biological material, which he then prepares for sequencing. “The initial results were very surprising. We were able to DNA sequence not only fungal and bacterial microorganisms, but also identify various plants, insects and even human DNA.” he says.

The ultimate goal is tracking changes seen in the air over time: Linking collection data to environmental differences over time could have applications with mitigating the impacts of climate change, influence agriculture, public health, and even apply to food biosecurity.  Chooneea’s research project has become a fundamental step in documenting the biodiversity contained within the air’s ecosystem. “Nature is always in a state of flux. There is constant change above and around us. Seasonally, we see changes.  In spring and summer, there’s more plant material and pollen kicking around, and when it gets wet, you can pick up more fungi spores. Also, various locations and environments have different background profiles.”

Studying the changes in air ecology over time will allow us to identify and understand its typical components. This information would be particularly useful for the agriculture industry. “With consistent sampling you would pick up, for example, a certain fungal pathogen capable of destroying soybeans. An early detection system could warn farmers that a pathogen is coming, enabling them to prepare a targeted treatment method saving them time and money while also saving the crop.”  This same air sampling technology also has applications with food security, public health, and detecting bioterrorism threats.

Getting data from nothing

It is no surprise that extremely small amounts of biological material exist in these invisible samples and the team must ensure the lysis method is adequate to recover sufficient DNA. “We have tried various products and a wide range of methods to break up cells, identifying which products work best for our area of application. The QIAGEN PowerSoil Pro Kit is best at breaking really tough cells like Cryptosporidium. We know if we are able to break those down, the softer cells will be broken. It's got the harder beads, and also there's pollutants in the air that can cause inhibition downstream when we do whole genome amplification. Knowing that the kit has Inhibitor Removal Technology (IRT) is quite reassuring. Because we work with such small samples, we use the REPLI-g UltraFast Kit which gives us a few hundred nanograms in 90 minutes, rather than using whole genome kits that can take 16 hours to recover sufficient amounts of DNA. Once the DNA is recovered, we go into sequencing using the Oxford Nanopore GridION sequencer.”

eDNA Key to the Future

Enthusiastically walking through the doors each morning, Chooneea enjoys the tranquillity of the quiet hallways. “Those peaceful moments prep me for the day, and there is limitless knowledge hidden within these walls that remains to be discovered.” 

Chooneea’s search for eDNA in the air and participation in the Darwin Tree of Life project could uncover several hundred new species. With the assistance of QIAGEN, sequencing all life that exists today along with the information gained by exploring the museum collection could shed light on how species cope with environmental changes.