The Microbial Clock: Diverse Airborne Microbiota Follow A Diel Cycle

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The world is teeming with microorganisms in the soil, water, and even air. However, the study of the atmospheric microbial ecosystem has long been outshone by research into the Earth’s diverse terrestrial, aquatic, and human microbiomes. At the Singapore Center for Environmental Life Sciences Engineering at Nanyang Technological University, researchers discovered an ecosystem of microorganisms in Singapore’s tropical air that rivals the diversity and complexity of the Earth’s other ecosystems.

The next-generation sequencing (NGS) revolution, which began in 2005, demonstrated the ease of directly sequencing DNA from the environment without the need for cloning or growing it in a lab. Stephan Schuster, a professor at Nanyang Technological University, was an early pioneer of next-generation sequencing at Pennsylvania State University. “With next-generation sequencing, it suddenly became possible to produce genomic data so cheaply and so quickly that you could do…projects that were unthinkable before,” Schuster said.

Before NGS, scientists could only sequence the DNA of a miniscule fraction of the microbial world that could be cultivated in a laboratory. NGS opened up the microbial world for study by allowing direct DNA sequencing from the environment, but the atmosphere was still out of reach. Only with an industry-sized air sampler, massive amounts of air, and months of analysis could scientists attempt to analyze the genome of a single cell in the atmosphere. To increase efficiency and reduce unintended bacteria growth on biomass filters, Schuster and his colleagues developed an approach that could reduce the air sampling time from months to days, and ultimately to fifteen minutes. In this study, the researchers took air samples every two hours for five days in a row—this was frequency and precision of sampling that had never before been possible. They called their new approach the “ultra-low biomass pipeline.”

After analyzing 795 metagenomes from the atmosphere, the scientists discovered something incredible. During each 24-hour period, the atmosphere cycled through numerous different species and numbers of microorganisms. Microbe communities remained stable over weeks and months, but during the span of a day, they fluctuated significantly. Schuster and his colleagues found that they could isolate a microbial community and predict with strong accuracy the exact time of day the sample had been taken. The differences in microbial communities changed even more drastically between day and night. “If you want to put your finger on the pulse, the heart rate, of the planet, you can do this by sequencing the organisms that are in the air. This rhythm— the pulse—that’s the diel cycle,” Schuster said.

Researchers found that microbial communities responded to environmental factors as well, including carbon dioxide, temperature, and humidity levels. Schuster believes that these communities could have applications as biological sensors; for example, researchers could find carbon dioxide levels in the past through microbial archives in sediments and geological layers.

The temporal study of the atmosphere was just the first step. Schuster is now in the process of studying the variation of microbial communities with more breadth and depth: how will microbial communities change over different climates and atmospheric levels? “Whatever work has been done over the two decades in the ocean in trying to find out how the marine microbial systems are organized, we are doing the same for the air. Because of the throughput in technology and the level of automation, we can do this much faster than what has been done in the ocean,” Schuster said.

This potential for efficient data collection and analysis has exciting implications, particularly for respiratory health. For instance, concentrations of mold in buildings prevalent with sick building syndrome can be more accurately examined and quantified. Air quality standards for industrial law can begin to encompass the biological content of air (e.g. microorganisms and bioaerosols) in addition to its physical and chemical characteristics. Currently, the researchers are working with infectious disease hospitals in China to monitor the spread of the airborne coronavirus pathogen. Monitoring the safety of the air in hospitals or isolation wards is vital to keeping medical personnel safe from the disease.

All in all, examining the living organisms in our atmosphere is crucial to maintaining healthy and breathable air. “You have a choice not to drink water, you have a choice not to eat, but you do not have a choice to breathe,” Schuster said.