By Jesse H. Ausubel and Vice Admiral Paul Gaffney II. (Ret.), appeared in The Hill 05/07/20
Front. Mar. Sci., 05 May 2020 | https://doi.org/10.3389/fmars.2020.00226
Improved Environmental DNA Reference Library Detects Overlooked Marine Fishes in New Jersey, United States
Mark Y. Stoeckle*, Mithun Das Mishu and Zachary Charlop-Powers
- Program for the Human Environment, The Rockefeller University, New York, NY, United States
An accurate, comprehensive reference sequence library maximizes information gained from environmental DNA (eDNA) metabarcoding of marine fishes. Here, we used a regional checklist and early results from an ongoing eDNA time series to target mid-Atlantic U.S. coastal fishes lacking reference sequences. We obtained 60 specimens representing 31 species from NOAA trawl surveys and institutional collections, and analyzed 12S and COI barcode regions, the latter to confirm specimen identification. Combined with existing GenBank accessions, the enhanced 12S dataset covered most (74%) of 341 fishes on New Jersey State checklist including 95% of those categorized abundant or common. For eDNA time series, we collected water samples approximately twice monthly for 24 months at an ocean and a bay site in New Jersey. Metabarcoding was performed using separate 12S primer sets targeting bony and cartilaginous fishes. Bioinformatic analysis of Illumina MiSeq fastq files with the augmented library yielded exact matches for 90% of the 104 fish amplicon sequence variants generated from field samples. Newly obtained reference sequences revealed two southern U.S. species as relatively common warm season migrants: Gulf kingfish (Menticirrhus littoralis) and Brazilian cownose ray (Rhinoptera brasiliensis). A beach wrack specimen corroborated the local presence of Brazilian cownose ray. Our results highlight the value of strengthening reference libraries and demonstrate that eDNA can help detect range shifts including those of species overlooked by traditional surveys.
Jesse evokes the decade just ended with a verbal time machine.
The kombucha cheeseball airballed flyover states.
A flashmob of microbiomes pinged frenemies with fake news about emojis.
Bestie truthers in gender dysphoria friended crunchy snowflakes with selfies.
Muggles on staycation clickbaited eco grief with chai latte before Brexit.
Digerati on hoverboards vaped Bibimbop while cloud computing their carbon credits.
Locavore hashtags unfriended ringtones.
Bling ransomware exfoliated the deep state over net neutrality.
Sriracha fitbits f-bombed safe spaces with froyo in go-cups.
Uber & Lyft doxx’d bougie Anthropocene woo-woo.
The worstest guac onboarded vegan qubits.
Buzzy connectomes face-palmed oppo memes.
Unplugged vulture capitalists binge-watched paywalls.
Micro-aggressions woke the Alt-right in airplane mode.
Anti-vax traumatology misgendered #MeToo.
Sounds like a plan. OMG LOL fuhgeddaboudit.
Jesse H. Ausubel 8 May 2020
PHE Guest Investigator David Thaler co-published a letter in Nature “Coronavirus: sampling now for future analysis”
We all continue healthy and working long hours and hard, though mostly from our homes. We are catching up on lots of writing and editing but also trying to seize immediate, unique opportunities.
For example, COVID-19 may have created the reduction of additions of human noise that we dreamed about for the International Quiet Ocean Experiment. IQOE welcomes ideas about how the present quieting of the world economy may advance research in marine sound. High-quality observations of the ocean soundscape, as well as possibly related behavior of marine life during this period, may offer unique opportunities of exceptional value.
Resuming our interest in Serious Games, we are also please to encourage a team at the Indian Institute of Technology in Tirupati that is developing SurviveCovid-19 — A Game for Improving Awareness of Social Distancing and Health Measures for Covid-19 Pandemic
Jesse has also written a foreword for Simon Mitton’s forthcoming history of deep carbon science, From Crust to Core, to be published by Cambridge U. Press. https://www.cambridge.org/core/books/from-crust-to-core/E0E2E8FC30B4C784B0FB268AC4AA8371
Dating back to the Ordovician period about 450 million years ago, Bryozoa are small aquatic invertebrates with exoskeletons that typically sieve food particles out of the water with a crown of tentacles. The individual zooids live in colonies forming fans, bushes, and sheets.
Dennis P. Gordon, distinguished taxonomist at New Zealand’s National Institute of Water & Atmospheric Research, has described “New Hippothoidae (Bryozoa) from Australasia” in the journal Zootaxa.
Dennis and Jesse Ausubel worked together in the Census of Marine Life 2000-2010. Dennis has named a new genus of Hippothoidae Bryozoans the Jessethoa and the first species Jessethoa ausubeli.
This brings the total of described hippothoid genera to nine (plus two fossil) and species to 83 recent (plus 15 fossil).
On behalf of the entire Census of Marine Life, Jesse is greatly honored to be permanently associated with this fascinating taxon. Thank, Dennis Gordon!
The lively mind and pen of Robert Bryce have authored the new book, A Question of Power: Electricity and the Wealth of Nations. We were happy to talk with Robert about subjects in the book, for example, vertical cities. ‘Ausubel continued, “Basically, height is electrical.”‘ (p. 24)
Journalist Eric Niler publishes a good feature in Wired magazine on eDNA that includes coverage of the work of PHE’s Mark Stoeckle:
‘Environmental DNA’ Lets Scientists Probe Underwater Life
With the help of a new kind of drone, marine biologists can sequence DNA found in the ocean to reveal what’s living in an ecosystem—and what’s missing.
PHE researcher Iddo Wernick published a short essay ‘The Big Data Mindset” in Issues in Science and Technology
We post Leonardo DNA Project: Strategy, goals and aspirations. A bridge across science and art. This is the chapter from Leonardo da Vinci, The Faces of Genius, the superb 2019 book edited by Christian Galvez.