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Aircraft surveys for air eDNA: probing biodiversity in the sky - PubMed

️Sun Jan 01 2023

Aircraft surveys for air eDNA: probing biodiversity in the sky

Kimberly L Métris et al. PeerJ. 2023.

Abstract

Air is a medium for dispersal of environmental DNA (eDNA) carried in bioaerosols, yet the atmosphere is mostly unexplored as a source of genetic material encompassing all domains of life. In this study, we designed and deployed a robust, sterilizable hardware system for airborne nucleic acid capture featuring active filtration of a quantifiable, controllable volume of air and a high-integrity chamber to protect the sample from loss or contamination. We used our hardware system on an aircraft across multiple height transects over major aerosolization sources to collect air eDNA, coupled with high-throughput amplicon sequencing using multiple DNA metabarcoding markers targeting bacteria, plants, and vertebrates to test the hypothesis of large-scale genetic presence of these bioaerosols throughout the planetary boundary layer in the lower troposphere. Here, we demonstrate that the multi-taxa DNA assemblages inventoried up to 2,500 m using our airplane-mounted hardware system are reflective of major aerosolization sources in the survey area and show previously unreported airborne species detections (i.e., Allium sativum L). We also pioneer an aerial survey flight grid standardized for atmospheric sampling of genetic material and aeroallergens using a light aircraft and limited resources. Our results show that air eDNA from terrestrial bacteria, plants, and vertebrates is detectable up to high altitude using our airborne air sampler and demonstrate the usefulness of light aircraft in monitoring campaigns. However, our work also underscores the need for improved marker choices and reference databases for species in the air column, particularly eukaryotes. Taken together, our findings reveal strong connectivity or mixing of terrestrial-associated eDNA from ground level aerosolization sources and the atmosphere, and we recommend that parameters and indices considering lifting action, atmospheric instability, and potential for convection be incorporated in future surveys for air eDNA. Overall, this work establishes a foundation for light aircraft campaigns to comprehensively and economically inventory bioaerosol emissions and impacts at scale, enabling transformative future opportunities in airborne DNA technology.

Keywords: Aerial survey; Aeroallergen; Air filtration; Air sampler; Atmospheric survey; Bioaerosol; Biodefense; Biomonitoring; Environmental DNA; Environmental genetics; Metabarcoding.

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Conflict of interest statement

Kimberly L Métris and Jérémy Métris are co-founders of Airborne Science, the company that designed and built the high integrity probe and supporting system used in this work. A patent application has been filed for the high-integrity capture system. The authors and company did not receive financial support or compensation for this study.

Figures

**Figure 1. A schematic drawing of our high-integrity probe and supporting system for air eDNA sampling.**

**Figure 2. Our portable high integrity sampler in action on a genetic aerial survey.**
Image credit: the authors.

**Figure 3. Genetic aerial survey grid perimeter (top panel). Genetic aerial surveys in the southeast United States (bottom panel).**
Top panel: The sides of each square measure 18.52 km (10 nautical miles). The area represents 18.52 km² or 1,852 hectares (4,576.39 acres). Map credit: © ForeFlight^®. Bottom panel, clockwise from left: (A) view of study area from highest altitude sampled above the PBL at 2,500 m above ground level (8,500 ft mean sea level) and (B) from 1,200 m (4,500 ft MSL) with haze visible on horizon; view at 300 m (1,800 ft MSL) over (C) a poultry facility and (D) cattle on agricultural land; (E) view on a June survey flight with visible moisture as clouds. Photo credit: the authors.

**Figure 4. GPS flight path tracks for genetic aerial surveys.**
Flight path tracks for genetic surveys at 300 m (yellow), 1,200 m (orange), and 2,500 m (pink) on (A) 9 May and (B) 4 June. Flight patterns are based on GPS telemetry data recorded from ForeFlight^®. Ten nautical mile legs were flown. Scale bar in lower right of each track represents four nautical miles. Test flight tracks in Data S1. Map credit: © Google Landsat/Copernicus.

**Figure 5. Heatmap of taxonomic matrices representing presence/absence of each biological group (vertebrates, plants, bacteria) at and above the PBL.**
Taxa are represented at the family or closest taxonomic level. Quick-reference coloured circles at left represent detection at that altitude. The three samples marked s were inconclusive by metabarcoding but confirmed through Sanger sequencing.

**Figure 6. Taxonomic composition and relative abundance of bacteria, plant, and vertebrate airborne DNA detected by aircraft surveys at 300, 1,200, and 2,500 m.**
Taxonomy across biological entities is shown at the family level.

**Figure 7. Taxonomic composition and relative abundance of bacteria, plant, and vertebrate airborne DNA on six research survey flights.**
Taxonomy shown at the level of genus except for vertebrates (family).

**Figure 8. Kinematic back trajectories modelling air mass transport histories for flights in May and June.**
Representation of backward 72 h forecast trajectories from the survey area grid location of 34.32 N, −83.01 W at 300, 1,200, and 2,500 m above ground level using HYSPLIT and GDAS (Global Data Assimilation System) meteorological data. The representation is superimposed on a physical map and displayed as a schematic for three flights per day at different altitudes. Map credit: © NOAA.

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Aircraft surveys for air eDNA: probing biodiversity in the sky - PubMed