Rockefeller University

Program for the Human Environment

Area of Research: DNA Barcoding

Airborne DNA

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:

After Mapping the Human Genome, Analyzing the City’s Air Mar 7, 2005 — Dr J Craig Venter will study New York City’s air by installing filter system atop one of Midtown-Manhattan’s skyscrapers and studying its …  

  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.

Journal of Marine Science publishes our latest on eDNA protocols

Current laboratory protocols for detecting fish species with environmental DNA optimize sensitivity and reproducibility, especially for more abundant populations by Mark Y Stoeckle, Jason Adolf, Jesse H Ausubel, Zach Charlop-Powers, Keith J Dunton, Greg Hinks appears in ICES Journal of Marine Science, fsab273, 11 January 2022.

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.

The paper is a sequel to our December 2020 entry: Fish abundance survey by eDNA published

Thanks to our partners at Monmouth University, the New Jersey Bureau of Marine Fisheries, and the National Oceanic and Atmospheric Administration.

Mark and Jesse give NOAA ‘Omics seminar on “Fishing for DNA”

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.

Title: Fishing for DNA: how much water to catch and other questions

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.

NOAA Science Seminar page

NOAA ‘Omics Website

Mark Stoeckle looks at a glass of water

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. 

LOOKING AT WATER: Conversations with artists and scientists
Observational Practices Lab @ Parsons
The New School University, New York City

Podcast with Jesse Ausubel

Jesse reflects on decarbonization, dematerialization, land-sparing, industrial ecology, industrialization of the oceans, biological traces of fishes and of Leonardo Da Vinci, and the Seven Deadly Sins in an 83″ podcast with Robert Bryce, author of Smaller Faster Lighter Denser Cheaper: and A Question of Power: Electricity and the Wealth of Nations.

The Podcast is also on YouTube where you get to see who sings Take Me Out to the Ballgame.

eDNA book chapter by Alan Curry and Jesse Ausubel

We post the book chapter by Alan Curry and Jesse H. Ausubel, Biological information for the new blue economy and the emerging role of eDNA, in the comprehensive new book by Liesl Hotaling and Richard W. Spinrad (eds), Preparing a Workforce for the New Blue Economy: People, Products, and Policies Elsevier, 2021.  Rick is now the Administrator of the National Oceanic and Atmospheric Administration.

A short version of the chapter appeared on 1 March in the magazine Maritime Executive as Biological information for the new blue economy and the emerging role of eDNA.

Archive Sewage!

PHE Guest Investigator David Thaler and RU colleague Tom Sakmar publish open access in BMC Infectious Diseases 21, Article #601 (2021) ‘Archiving time series sewage samples as biological records of built environments.”  The idea for the article arose during our 2020 twice-weekly PHE Zooms.  It is rooted in part in Paula Olsiewski’s completed Sloan Foundation program on the Microbiology of the Built Environment, to which David contributed.  It also links to the Leonardo Da Vinci DNA Project, to which both David and Tom belong, and which searches for biological relics from times past and also explores how better to preserve recent traces of DNA and RNA.

Abstract

This commentary encourages the regular archiving of nucleic-acid-stabilized serial samples of wastewaters and/or sewage. Stabilized samples would facilitate retrospective reconstitution of built environments’ biological fluids. Biological time capsules would allow retrospective searches for nucleic acids from viruses such as SARS-CoV-2. Current resources for testing need not be diverted if samples are saved in case they become important in the future. Systematic storage would facilitate investigation into the origin and prevalence of viruses and other agents. Comparison of prevalence data from individual and clinical samplings with community wastewater would allow valuable comparison, contrast and correlation among different testing modalities. Current interest is focused on SARS-CoV-2, but archived samples could become valuable in many contexts including surveys for other infectious and chemical agents whose identity is not currently known. Archived time series of wastewater will take their place alongside other biological repositories and records including those from medical facilities, museums, eDNA, living cell and tissue collections. Together these will prove invaluable records of the evolving Anthropocene.

PHE student earns 1st place in science fair

Ossining NY high school sophomore Samara Davis, with guidance from PHE’s Mark Stoeckle, earned 1st place in the Somers/Westlake Science Fair for her project Environmental DNA Analysis to Determine Population Characteristics of Elusive Ephemeral Pool-Breeding Mole Salamanders, in Relation to the Effects of Climate Change. Congratulations to Samara! Thanks, Mark!