Rockefeller University

Program for the Human Environment

Area of Research: The Microbial Environment

Our paper on eDNA as bioassay of Anthropocene published

The new journal based in China, The Innovation, has published the Thaler-Ausubel-Stoeckle paper on Human and domesticated animal environmental DNA as bioassays of the Anthropocene in their “Out of the Box” category, where we like to be. We also post the pdf.

We thank Song Sun and Ke Chen for editorial assistance.

Summary: Human and domesticated animal sequences, commonly detected in environmental DNA (eDNA) metabarcoding studies, are routinely excluded from analysis. Here we suggest that reporting human and domesticated animal eDNA results might open new lines of investigation. For example, the relative abundance of human and domesticated animal eDNA as compared to that of wild vertebrate species might provide an index of human impact on local biota. Such an index could be applied to sites ranging from urban harbors to remote villages, and possibly to analyze historical samples. Various potential sources of contamination complicate the picture, but it should be possible to develop procedures that minimize risk of DNA introduction during collection and processing. Our near-term recommendation is to encourage inclusion of human and domesticated animal data in eDNA publications as an incentive for discovery, to lift quality controls, and to collectively contribute to new vistas that eDNA science might open.

Thaler memo on “Distinguishing contamination from authentic human eDNA”

PHE guest investigator David Thaler summarizes “Ways in which contamination might be distinguished from authentic human eDNA” in a useful draft memo. Meeting this challenge matters greatly for using human eDNA as an assay of the Anthropocene, a subject of a forthcoming paper by Thaler, Ausubel, and Stoeckle.

eDNA degradation; 2nd National Workshop

PHE’s guest investigator David Thaler offers some stimulating ideas in a memo about ways of understanding and learning from degradation of aquatic eDNA. The title: How long has each particular species’ eDNA been outside the organism from which it came? Some thoughts on the possibility to obtain more information from eDNA analysis of water samples

Meanwhile, Jesse Ausubel and Mark Stoeckle are involved in the program for the 2nd US National Workshop on eDNA, 12-15 September in Southern California. PHE hosted the 1st US national meeting in 2018.

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.

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.

Plant and animal diversity is declining, but what about microbial diversity?

Spurred by PHE Guest Investigator and microbiologist David Thaler’s publication, “Is global microbial biodiversity increasing, decreasing, or staying the same?” , David and Jesse Ausubel co-author a 900-word essay raising the question of what’s happening to microbes in RealClear Science.

As plant and animal diversity wanes, is microbial life changing too?

PHE Guest Investigator and microbiologist David Thaler has published the paper, “Is global microbial biodiversity increasing, decreasing, or staying the same?” in Frontiers in Ecology and Evolution.  The answer is, we do not know.

The paper arose from Zoom discussions PHE began holding every Tuesday and Thursday noon during COVID lockdown of our NYC group members with colleagues in California, Israel, Switzerland, and elsewhere.  Bravo to David for asking a bold question and putting it onto the research agenda.  Thanks to Gary Borisy (Forsyth Institute) and Jessica Mark Welch (Marine Biological Laboratory) for sharing images.  A Press Release from the journal summarize the paper.

The Guardian, Microbes are ‘unknown unknowns’ despite being vital to all life, says study (another excellent article from Guardian science reporters!)

Agencia EFE, Spain, Un estudio resalta la “profunda ignorancia” de la biodiversidad de microbiosAargauer Zeitung, Switzerland, Biologie – Gilt das Artensterben auch für die Mikroben?

IndoAsian News Service, India Is microbial life, including viruses, changing too?
COSMOS Magazine, Australia The great unknown of global microbial diversity

Mongabay, ‘Profound ignorance’: Microbes, a missing piece in the biodiversity puzzle by Ian Morse on 26 April 2021