Rockefeller University

Program for the Human Environment

Area of Research: Oceans

AI & Energy foreseen in 2019

In 2019 the CEO of the electric company AEP asked Jesse to address his leadership. Jesse’s talk on Climate and Power included the following prescient words:

A more fascinating and important question is how IT and AI will alter demand.  Siri and Alexa are hungry goddesses.  I mentioned illuminated skylines of cities but consider that a square foot of a data center guzzles more than 100 times the electricity of a square foot of a skyscraper.  More than 1500 skyscrapers of more than 40 stories now define the world’s cities, but the population of enterprise-class date centers now exceeds 5000.  The Switch Corporation’s Citadel data center in Northern Nevada will be 7.2 m square feet, 0.25 square miles, and more than twice the area of the world’s largest office building, the Burj al Khalifa in Dubai.  It will consume 650 MW around the clock.  In round numbers, one million square feet of a new data center demand about 100 MW to live, a density of about 1000 watts per square meter.  The world’s most powerful computer, the Summit Supercomputer in Oak Ridge, demands per square foot about 20 times a conventional data center.  While efficiency gains continuously, the cloud is nevertheless a glowing cloud of electrons.

Connecting the clouds and all the devices that rely on the clouds also uses a lot of electricity.  Per unit of data transported, wireless systems use about ten times the juice of a wired system.  Each smart phone finally uses about the same electricity as a high-efficiency household refrigerator.  The global population of smart phones may pass five billion in 2019.  Meanwhile, Amazon has already sold an additional 100 million digital assistants such as Alexa.  We are creating a world with hundreds or thousands of radios per person.  The system now operates at 4G, which involves about 20 base stations per square km, globally about four million cell towers.  Present information networking uses about 200-300 TW hours per year, about $20 billion worth. 

5G, one hundred times faster and needed for high resolution streaming, virtual reality, and autonomous devices, may employ as many as 2000 base stations per sq km, and the Global Small Cell Forum of the telecom industry anticipates for 2025 some 70 million base stations and networking demand for $90 bn worth of electricity.   All this will come before autonomous vehicles and indeed is the prerequisite for the sensors and AI that will make autonomy safe and effective.

Whether or not the autonomous vehicles (AVs) use batteries or hydrogen for propulsion, they will use electricity to process their zettabytes and yottabytes of data.  In effect each AV will be a high-level server.  A fully connected car is expected to generate 25 GB of data per hour.  If the car is used 2 hours each day, 60 such cars would generate a petabyte in a year, 60,000 cars an exabyte, and 60,000,000 cars a zettabyte.  The present global annual market for servers is about 10 million units.  Motor vehicle sales globally are an order of magnitude larger, about 100 million.  No wonder software and hardware companies now read Car and Driver.  Powering a global stock of one billion servers that also happen to be autos will be a good business, even apart from propulsion.  IT can drive a new wave of global electrification, including for mobility.  Keep an eye on energy use patterns in Northern Virginia, which hosts the world’s largest concentration of large data centers.

DNA of New York City’s East River

Mark Y. Stoeckle and Jesse H. Ausubel

Animals shed environmental DNA (eDNA) into the environment. Sources include cells sloughed from body surfaces, body wastes, and tissue remnants following predation, death, or injury.  eDNA is a bit like dandruff.  DNA of course consists of long strands of four chemical compounds: cytosine (C), adenine (A), guanine (G), and thymine (T). Researchers use strands of about 100 “letters” from variable parts of the genome, like a long telephone number, to identify the species of animal from which the DNA comes. Acidity, heat, and light can speed eDNA degradation, and bacteria eat eDNA. A rule of thumb is that eDNA sufficient for reliable identification lasts about 24 hours and thus gives a good current portrait of life in a water body.

As seen in these 5 slides, the PHE’s Mark Stoeckle regularly collects a half liter of water from the East River adjacent to the Rockefeller campus (slide 1) with a bucket on a string, filters the water, extracts the DNA from the sediment on the filter using special chemicals called primers to grab only the DNA that came from vertebrates, sequences these pieces of eDNA, and matches the sequences against genetic libraries. The number of copies for each species corresponds well to the recent abundance of that animal in the East River.

Our vertebrate eDNA studies show that that the East River abounds in fishes (slide 2), with tautog most common but also herring, bass, and eel.  The presence of water from sewage treatment plants and rains that wash city streets also brings DNA of urban wildlife into the East River.  A cup of water from the East River reports the abundance of rats, pigeons, dogs, and cats (slide 3).  It also reports the presence in the River or nearby of additional wildlife ranging from deer and beaver to seal and dolphin (slide 4).  Finally, the eDNA in the East River neatly tracks the diet of humans of New York (slide 5).  The fractions of aquatic eDNA of commonly consumed meats such as chicken and cow match nicely with national data on meat consumption.  An exception is sea bass (branzino), widely served in New York City restaurants and thus common in East River water samples but a tiny proportion of the national fish diet.

eDNA revolutionizes the ability for people to know, affordably, what animals live in or use the waters near them. eDNA will be a routine component of fish stock assessment, detection of invasive species, and monitoring effects of coastal storms and climate change.  Genomics enables a cup of water to tell the natural history of the East River.

New paper on eDNA as way to define marine regions

PLOS One publishes our new paper demonstrating the use of eDNA to define marine biogeography.  This graphic summarizes key findings of the paper.  The paper builds on our earlier work proving that loose DNA in seawater reveals both diversity AND abundance of marine life, in particular, fishes.  Full title and abstract are below.

A potential tool for marine biogeography: eDNA-dominant fish species differ among coastal habitats and by season concordant with gear-based assessments Mark Y. Stoeckle , Jesse H. Ausubel, Greg Hinks, Stacy M. VanMorter Published: November 11, 2024 https://doi.org/10.1371/journal.pone.0313170

Abstract Effective ocean management asks for up-to-date knowledge of marine biogeography. Here we compare eDNA and gear-based assessments of marine fish populations using an approach that focuses on the commonest species. The protocol takes advantage of the “hollow curve” of species abundance distributions, with a minority of species comprising the great majority of individuals or biomass. We analyzed new and published teleost eDNA metabarcoding surveys from three neighboring northwest Atlantic coastal locations representing sandy, rocky, or estuary habitat. Fish eDNA followed a hollow curve species abundance distribution at each location—the 10 commonest taxa accounted for more than 90% of eDNA copies. Top ten taxa were designated eDNA-dominant species (eDDS) and categorized as habitat-associated (top 10 in one study) or as shared. eDDS by category were similarly abundant in concurrent bottom trawl and seine surveys. eDDS habitat category profiles correctly classified most (94%-100%) individual eDNA and capture measurements within surveys and recognized estuarine sites in other regional eDNA and seine studies. Using a category metric like that for habitats, eDDS demonstrated strong seasonal turnover concordant with trawl catch weights. eDNA seasonal profiles applied to historical trawl and seine records highlighted known long-term trends in mid-Atlantic fish populations. This study provides evidence that eDNA-abundant fish species differ among coastal habitats and by season consistent with gear-based assessments. Grouping abundant species by category facilitated comparisons among habitats and integration with established surveys. eDNA metabarcoding of dominant fish species potentially offers a useful tool for marine biogeography and ocean monitoring.

Short video about passive acoustic monitoring for ocean life

The International Quiet Ocean Experiment (IQOE) in 2023 gave birth to World Ocean Passive Acoustic Monitoring (WOPAM) Day.  The excellent 2024 WOPAM Day video can be seen at https://x.com/GLUBS1/status/1798995048522277190.   The full soundtrack for WOPAM Day 2024 is at: https://www.wo-pam.com/wopam-2024 (scroll down and see the link).  Congratulations to Miles Parsons and other team members on extending the 2024 monitoring to about 400 sites around the world!

Jesse & Mark NOAA ‘Omics Webinar on eDNA-dominant fish species

NOAA has posted the video of their ‘Omics Seminar Series: eDNA-Dominant Marine Fish Species Characterize Coastal Habitats presented on 28 February, 2024 by Mark Stoeckle and Jesse Ausubel. The 1-hour seminar is full of new results and ideas about using eDNA data to characterize marine regions and features Mark’s excellent graphics.

Title: eDNA-Dominant Marine Fish Species Characterize Coastal Habitats: an eDNA-Based Classifier Approach to Aid Marine Biogeography and Ocean Monitoring by Mark Stoeckle & Jesse Ausubel

Abstract: A small minority of species typically account for the great majority of individuals or biomass. Here we characterize marine coastal habitats based on abundance of marine fish environmental DNA. We designate the ten most eDNA-abundant fish species in each habitat as eDNA-dominant species. eDNA-dominant species are similar within but differ among habitats and seasons and accord with abundance by traditional survey methods. “Classifiers” based on eDNA-dominant fish species could help map marine fish habitats and monitor changing oceans. Advantages include relatively low sampling requirements, a single technology applicable to diverse habitats, and ease of application to multiple datasets.

eDNA of Newtown Creek, industrial waterway separating Queens & Brooklyn

RockEDU summer students Priyam Shah and Michael Epelman, who just completed high school, teamed with mentor extraordinaire Mark Stoeckle to study the fishes of an NYC Superfund Site, Newtown Creek.  Their excellent poster shows that eDNA detected a surprising diversity of fish in Newtown Creek, despite ongoing pollution and sewage overflow. The number and relative abundance of fish species differed among sites consistent with species habitat preference and pollution tolerance. Our data support eDNA as a cost-effective, non-destructive method for monitoring fish populations and assessing habitat restoration efforts in Newtown Creek and other Superfund sites

Quiet Ocean news

IQOE Newsletter #11  reports on the IQOE Science Committee meeting and Global Library on Underwater Sounds (GLUBS) workshop in Woods Hole in April in which Jesse participated, as well as  the first World Ocean Passive Acoustic Monitoring Day in June. The newsletter also provides updates on the global hydrophone metadatabase, low-cost hydrophones, and effects of the COVID-19 pandemic on ocean sound.