Rapid pan-biodiversity lifeform and genomic diversity detection from shotgun sequencing of air eDNA

Rapid pan-biodiversity lifeform and genomic diversity detection from shotgun sequencing of air eDNA | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Rapid pan-biodiversity lifeform and genomic diversity detection from shotgun sequencing of air eDNA David J. Duffy, Mark McCauley, Orestis Nousias, Maximilian R. Stammnitz, and 7 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5953812/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Biodiversity and its associated genetic diversity are being lost at an unprecedented rate. Simultaneously, the distributions of flora, fauna, fungi, microbes and pathogens are rapidly changing. Novel ways to capture and record genetic diversity before it is lost, and to measure population shifts and pathogen distributions are urgently required. Here we report the rapid application of shotgun long-read environmental DNA (eDNA) analysis for non-invasive biodiversity, genetic diversity and pathogen assessments from air. We also compared air eDNA with water and soil eDNA. Coupling long-read sequencing with established cloud-based biodiversity pipelines enabled a two-day turnaround from airborne sample collection to completed analysis, by a single investigator. To determine the full utility of airborne eDNA, we also conducted a local bioinformatic analysis and deep short-read shotgun sequencing. From outdoor air eDNA alone, comprehensive genetic analysis was performed including population genetics (phylogenetic placement) of a charismatic mammal (bobcat, Lynx rufus ), and a venomous spider (golden silk orb weaver, Trichonephila clavipes ), and haplotyping humans ( Homo sapiens ), from natural complex community settings, such as sub-tropical forests and temperate locations. The rich datasets also enabled deeper analysis of specific species and genomic regions of interest, including viral variant calling, human variant analysis, and antimicrobial resistance gene surveillance from airborne DNA. Our results highlight the speed, versatility, and specificity of pan-biodiversity monitoring via non-invasive eDNA sampling using current benchtop/portable and cloud-based approaches. Furthermore, they reveal the future feasibility of scaling down (equipment and temporally) these approaches for near real-time analysis. Together these approaches can enable rapid lifeform and genetic diversity detection from air, water, and sediment samples for unbiased non-targeted information-rich genomics-empowered i) biodiversity monitoring, ii) population genetics, iii) pathogen and disease vector genomic surveillance, iv) allergen and narcotic surveillance, v) antimicrobial resistance surveillance and vi) bioprospecting. Epigenetics & Genomics Conservation Biology Bioinformatics Population Genetics Molecular Biology Molecular Epidemiology Terrestrial Ecology Wildlife Biology Medical Genetics Evolutionary Genetics metagenomics wholge genome sequencing population genetics airborne DNA environmental DNA human exome enrichment qPCR Full Text Additional Declarations The authors declare no competing interests. Supplementary Files SuppFigs.pdf Supplemental Figures 1-7 ExtendedDataTable1.pdf Extended Data Table 1 1.SupplementalTable1Seqsampledetailsv12.2.xlsx 1.SupplementalTable2v4.1.xlsx 1.Supp.Table3v2.0.xlsx Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-5953812","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":410754442,"identity":"095392cf-6425-4d3f-9d3a-2090a6fd4f06","order_by":0,"name":"David J. 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