Air microbiome provides answers to climate change
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Microbiome | DNA Kits

Air microbiome provides answers to climate change
Dr. Darren Chooneea scrutinizes the molecular details of almost everything, including the incredible biodiversity of air, to gain insights on how the world is changing and to prepare for events related to climate change.

Dr. Darren Chooneea briskly walks through the National 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.”

What can changes of the invisible microbiome in air tell us? Dr. Darren Chooneea, of the London Natural History Museum, explains how he sequences various cells found in air to answer questions regarding climate change and evolution. 
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It's quite important to monitor the changes in diversity in various areas such as in agriculture. Climate change might cause certain pathogens to proliferate and destroy important crops.
Dr. Darren Chooneea, Research Scientist, London Natural History Museum

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 a 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.

Air microbiome provides answers to climate change
Dr. Darren Chooneea enjoys method development and pushing the limits of technology with the most challenging of samples. He currently works at the Molecular Laboratories of the Natural History Museum (NHM), and has been involved in numerous projects including researching FFPE samples, various tissues, hair, blood, human stool, and animal samples, and most recently sequencing air.
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We are working with such a wide range of organisms in the air ranging from bacterial to fungal spores, and some cells are harder to break than others.
Dr. Darren Chooneea, Research Scientist, London Natural History Museum

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.”

Air microbiome provides answers to climate change
Environmental DNA - genetic material directly obtained from environmental samples such as soil, water, sediment - coupled with DNA sequencing technology can be used to monitor earth's biodiversity. The hope is that eDNA will enable us to make informed conservation decisions by allowing us to monitor biodiversity at an ecosystem level. 
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We developed a method to collect and sequence what's in air, and it's basically getting data from nothing.
Dr. Darren Chooneea, Research Scientist, London Natural History Museum

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.

Air microbiome provides answers to climate change
Darren Chooneea is part of a group of researchers working on sequencing every living organism in the U.K. The project will analyze what they can collect today but also compare it to what has been collected in the past. This "Darwin Tree of Life" project will focus on sequencing thousands of specimens, and potentially identify new species scientists anticipate – as well as explore the evolution of organisms as they adapted to changing environmental conditions and identify the genes that have helped these organisms to survive.
Extracting environmental DNA from challenging samples?
For the isolation of microbial genomic DNA from diverse sample types, explore QIAGEN’s broad kit portfolio.
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