Author Interview: Aircraft surveys for air eDNA: probing biodiversity in the sky

PeerJ talks to Dr. Kimberly L. Metris about the recently published PeerJ Life & Environment article Aircraft surveys for air eDNA: probing biodiversity in the sky.

Can you tell us a bit about yourself?

I am a molecular ecologist and commercial pilot. I feel at home in the lab and flying airplanes. My research program is multidisciplinary and currently focuses on aerobiology using environmental DNA/RNA and metagenomics. Species I have studied range from bacteria to African buffalo.  I hold a MSc in Zoology from the University of Pretoria, and a Ph.D. in Genetics from Clemson University.

Can you briefly explain the research you published in PeerJ?

We use aircraft surveys for air environmental nucleic acids, including eDNA. In this study, we create a durable, sterilizable probe and supporting system to capture airborne nucleic acids with full-flow filtration and a high-integrity chamber. We introduce aerial mapping of genetic material (such as DNA or RNA) and a standardized flight pattern that is scalable using light aircraft.

Our aim was to collect bioaerosols, or aerosolized genetic material, from multiple taxa by airplane, at various altitudes over major emissions sources. In this paper, we targeted bacteria, plant, and vertebrate DNA with metagenomics to show our system’s operability against rigorous controls and test the hypothesis that organismal DNA is detectable thousands of meters into the planetary boundary layer.

What did you discover and where?

Using our sampling probe and multi-taxa metagenomics, we discovered widespread presence of prokaryotic and eukaryotic DNA in the atmosphere thousands of meters into the planetary boundary layer.

In the southeastern US, we detected chicken, cow, and human DNA at all altitudes flown, including 8,500 feet above ground level! We also identified various plant operational taxonomic units (OTUs), including hardwoods and grasses, and over 50 bacterial OTUs. DNA from aerobic and anaerobic bacteria, spore-forming and non-spore forming bacteria, and bacterial species that use atmospheric components as nutrient sources was detected. Our study also identified bacteria with potential uses in bioprospecting, including reducing environmental contamination, degrading toxic compounds, providing plant tolerance to heavy metals, or serving as sources of natural pigments.

What was significant about your findings? Do you have any recommendations for the scientific community?

Our sterilizable sampling probe successfully filters genetic material directly from air in a reliable manner and limits sample loss and contamination. Our aerial survey technique allows us to map genetic material like environmental nucleic acids from potentially all species using light aircraft using our sampling probe and tie these aerobiome profiles to ground level processes, with applications in biodiversity, wildlife ecology and population genomics, biodefense, and pathogen and allergen monitoring.

High throughput amplicon sequencing of DNA from bacteria, vertebrates, and plants indicates that bioaerosols can arise from both natural ecosystem processes, such as wind-induced pollination in forests, as well as human activities, including poultry production, farming, wastewater treatment, and hospital waste decontamination. Both natural and anthropogenic sources likely contribute to these bioaerosols in the air.

Airborne DNA profiles we detected in the atmosphere reflect ground emissions, allergens, and potential ice and cloud condensation nuclei. Aerosolization efficacy likely modulates the air DNA profiles detected at altitude, and we suggest indices of lift and air mass characteristics be incorporated into air eDNA survey standardization. We also recommend standardized reporting of real-time, empirical flow rates, total air volumes, and sampler type(s) used, as they have critically different operating airflow requirements.

How did you first hear about PeerJ, and what persuaded you to submit to us?

PeerJ was featured in a recent paper addressing journal turnaround times and impact (Runde 2021). A multidisciplinary scope, open access, and opportunities for dissemination through various types of media were important factors in our decision to publish in PeerJ Life and Environment.

Reference:  Runde BJ (2021) Time to publish? Turnaround times, acceptance rates, and impact factors of journals in fisheries science. PLoS ONE 16(9): e0257841.

How was your experience publishing an article?

The experience was very positive and efficient. The academic editor who handled our submission, Dr. Eric Ward, was swift, helpful, and fair. Communications with senior staff editor Dr. Stephen Johnson were also very helpful. All reviewers’ comments were thorough, well-considered, and appreciated. It was clear the academic editor and all reviewers spent time on our article and supporting materials and valued our contribution.

Smoke on research flight

You can find more PeerJ author interviews here.

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