PHE’s marine eDNA expert Mark Stoeckle comments on new papers on airborne eDNA in the video Scientists ID Dozens of Plants, Animals from Free-Floating DNA. In a trio of studies, researchers report capturing and analyzing airborne prepared for the magazine and website The Scientist. The report is spurred by widely reported terrific new papers measuring airborne DNA around zoos.
While presented as a first, this study of airborne DNA began in 2005 under the auspices of the Alfred P. Sloan Foundation. Paula Olsiewski and Jesse Ausubel recruited and managed a series of grants to explore the potential for airborne DNA studies. The largest grant went to the Venter Institute, which pioneered the techniques:
Among resulting publications: A metagenomic framework for the study of airborne microbial communities …, J Glass, MD Adams, R Friedman, JC Venter – PloS one, 2013 – journals.plos.org Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic …
Among other findings, while focusing on microbial aspects, the Venter team found more rat DNA circulating in the air of NY than human DNA.
We test modifications to lab components of an eDNA metabarcoding protocol for marine finfish. Higher-read (more abundant) species were amplified more reproducibly and with less variation in read number than were lower-read (less abundant) species. Our results support the unofficial standard collection volume of one liter for eDNA assessment of commonly encountered marine fish species. We conclude that eDNA rarity poses the main challenge to current methods.
For its 2021 Annual Review, the Andrew W. Marshall Foundation presented an hour-long seminar in which Jesse Ausubel speaks briefly on experimentation, Melissa Flagg on intellectual courage, and Dan Patt on mentorship, followed by Q&A. IGood session. Jesse’s 5 minutes of remarks, titled Don’t Do Anything for the First Time, begin 15 minutes into the session following Jaymie Durnan’s opening review.
Thanks to Tracy Gill and Katharine Egan, Mark Stoeckle and Jesse Ausubel gave a NOAA-wide “Omics” seminar. 29 October 2021. Title and abstract are below. View the recording of the webinar via Adobe Connect, here: https://noaabroadcast.adobeconnect.com/pnnos0mcsh3z/ Thanks to the attendees for lotss of great questions and the lively to-and-fro in the Chat Box.
Abstract: Measuring quantities of eDNA is fast becoming a preferred method of learning the presence and abundance of fish and other aquatic species. But how much water need one filter and how much DNA need one process to obtain a reasonably complete and reproducible answer? Tests of an eDNA metabarcoding protocol for marine bony fish show more water, more species of fish up to levels tested. Amplifying decreasing amounts of extracted DNA yields progressively fewer species. Species represented by more copies (reads) of their DNA are detected more reproducibly and with less variation than lower-read species. Findings are consistent with Poisson distribution of rarer eDNA. We also vary PCR cycles, sequencing depth, primer concentrations, and primers. Our findings have multiple practical implications, including for survey strategies for both common and rare species, and identify some limits of knowledge and research directions for aquatic eDNA science.
PHE’s Mark Stoeckle shared our work on marine eDNA at Parsons School of Design, New School University on October 22, 2021. The online series invites artists and scientists to share perspectives on what they see when they look at a glass of water.