From air to insight: the evolution of airborne DNA sequencing technologies

Abstract

Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.

Keywords: air; eDNA; metabarcoding; metagenomics; microbiome; next-generation sequencing (NGS).

Fig. 1.. Pictorial representation of applications and challenges of air sampling for eDNA analysis.

Fig. 2.. Airborne eDNA analysis pipelines typically comprise four stages: sample collection, DNA extraction and isolation, amplification and sequencing and bioinformatics. Each stage includes several steps with different options depending on the study’s research objectives.

Fig. 3.. Stages in bioinformatic analysis for sequence data generated from air samples. On the right of each row is listed a selection of commonly used tools. Further details of the tools can be found in Table 2.