Analyzing airborne environmental DNA: A comparison of extraction methods, primer type, and trap type on the ability to detect airborne eDNA from terrestrial plant communities

Abstract

Airborne environmental DNA (eDNA) research has typically focused on the detection of pollen from anemophilous terrestrial plant species; however, recent findings have expanded the definition of airborne eDNA to include a variety of eDNA sources, such as leaf and flower fragments. While methods for capturing pollen are well studied, there is less known about how to best analyze and capture more broadly defined bulk airborne eDNA samples. Therefore, this study aimed to identify efficient techniques for the extraction and amplification of airborne eDNA and how best to capture these samples. First, we collected samples using Big Spring Number Eight dust traps and quantified the influence of three different extraction methods (cetrimonium bromide‐chloroform, DNeasy Plant Maxi Kit, and DNeasy PowerPlant Pro DNA Isolation Kit) and two global plant primer sets (targeting the trnL and ITS2 genes) on quantitative polymerase chain reaction (qPCR)‐based terrestrial plant detection. Additionally, we examined how best to capture airborne eDNA by comparing the performance of three difference passive dust collectors (Big Spring Number Eight, Modified Wilson and Cooke, and Marble dust collectors). We found that the detection of airborne eDNA was significantly influenced by both the extraction methods employed and choice of qPCR primer. Additionally, we found that all three traps preformed similarly but the Big Spring Number Eight dust traps trended as consistently one of the most effective, shedding light on the nonhomogeneous nature of airborne eDNA. This study represents the first methodology paper focusing on airborne eDNA as a bulk environmental sample containing more than just pollen. In the future, additional research should examine more about the ecology of airborne eDNA (origin, state, transport, fate), explore active dust collectors compared to the passive traps used here, and develop the application of metabarcoding for airborne eDNA analysis.

Airborne eDNA Reflects Human Activity and Seasonal Changes on a Landscape Scale

“…Within each sampling location, three Big Spring Number Eight (BSNE) passive dust traps were deployed. Johnson et al (2019b) demonstrated that BSNE traps performed well compared to other passive dust traps. The BSNE traps (Figure 2) consisted of two triangular traps 0.914 and 0.406 m above the ground.…”

Environmental DNA and RNA as Records of Human Exposome, Including Biotic/Abiotic Exposures and Its Implications in the Assessment of the Role of Environment in Chronic Diseases

“…Despite being an emerging new environmental monitoring technique, the enormous potential of eDNA application in biological monitoring has already been widely recognized and established [ 32 ]. Methods in eDNA research—particularly, sampling and handling of samples, DNA extraction, DNA half-life in aquatic, terrestrial and air samples, contamination, low abundance of DNA from higher organisms—have been extensively reviewed [ 32 , 33 , 34 , 35 , 36 , 37 , 38 ]. Therefore, herein we have not discussed these topics and related issues.…”

eDNAir: proof of concept that animal DNA can be collected from air sampling

“…What is surprising is that no active attempts to collect terrestrial biodiversity from air have been reported, even though reviews on the current state and future direction of eDNA metabarcoding (e.g., Ruppert, Kline & Rahman, 2019 ) mention the next area of interest being airborne DNA mostly in the context of microbes, pollen, and fungi. Early PCR-based studies were used to identify pollen ( West et al, 2008 ; Longhi et al, 2009 ; Folloni et al, 2012 ; Mohanty, Buchheim & Levetin, 2017 ) and a small number of metabarcoding studies of airborne particles have identified anemophilous plants (e.g., Johnson, Cox & Barnes, 2019a ; Johnson, Cox & Barnes, 2019b ), pathogenic microbes ( Nicolaisen et al, 2017 ; Núñez et al, 2017 ) and allergenic pollen ( Kraaijeveld et al, 2015 ; Korpelainen & Pietilainen, 2017 ; Núñez et al, 2017 ; Leontidou et al, 2018 ; Brennan et al, 2019 ), with a focus on human and crop health ( Yoo et al, 2017 ). Similarly, Abrego et al (2018) successfully conducted a fungal biodiversity survey by DNA barcoding fungal spores across Finland, and biodiversity assessments of seasonal plant and fungal diversity have been demonstrated as viable ( Banchi et al, 2020 ).…”