Unknown direction and pace of change in microbial — including viral — biodiversity may have deep consequences for all life on Earth

With alarms sounding about the declining diversity of plants and animals, a related concern with equally profound implications is posed: is the variety of microbial life, including viruses, changing too — and if so, in which direction and how fast?

In a new paper published by Frontiers in Ecology and Evolution (here), David S. Thaler of the University of Basel, Switzerland, and Guest Investigator at The Rockefeller University’s Programme for the Human Environment (PHE), notes the well-documented, “clearly downwards” trajectory of plant and animal diversity, constituting “a key issue of the Anthropocene.”

Whether change is underway also in the world of microbes — the tiniest cogs in planetary functioning — is “a complete unknown. We have no idea whether global microbial diversity is increasing, decreasing, or staying the same,” says Dr. Thaler.

“Most scientific papers tell us new facts. This is a different kind of paper; it does not answer anything but asks a new question,” says Dr. Thaler.

“Socrates called ignorance of what we do not know ‘profound ignorance.’ This kind of ignorance was also famously termed ‘unknown unknowns’ (youtu.be/GiPe1OiKQuk) by former US Defence Secretary Donald Rumsfeld. Today’s paper identifies what is (or was, as of now) a biological ‘unknown unknown’.”

Dr. Thaler points out that assessing plant and animal biodiversity involves counting different species within a given timeframe, and then comparing a subsequent count. By doing so, we learned that some species have recently become extinct, and many exist in fewer numbers, with an estimated one million at risk of extinction within decades.

The same approach has been used to monitor, for example, changes in microbial diversity in an intestine due to dietary changes.

Unfortunately, says Dr Thaler, it may be impossible to “count everything at different times” to figure out the direction of change in global microbial biodiversity because:

• The extent of current microbial biodiversity is unknown, and a large fraction of the microbial world may exist in hard-to-access, rare, or extreme environments — the deeper the depth, the less we know. Previous research has theorized that the deep hot biosphere may contain the majority of our planet’s microbial biodiversity. Resolving this problem might require 20 years before there is a sufficient understanding of the deep biosphere and other hard-to-access environments.
• A possible ‘chicken and egg’ paradox may prove hard to resolve: Establishing a baseline sequence library may never be finished because new diversity is generated more rapidly than it is measured. If some or all parts of microbial diversity are rapidly increasing, then survey approaches may never catch up to this dynamic process.

Says Dr. Thaler: The world is finding hundreds of variants of the SARS-CoV-2 virus that causes COVID-19, one of a very roughly estimated 10 billion different kinds of microbes each evolving in its own ways.

(Dr. Thaler cites a Harvard Medical School video, at https://youtu.be/plVk4NVIUh8, documenting how quickly bacteria can mutate to overcome increasing higher concentrations of antibiotics. Meanwhile, a recent study (bit.ly/IPBESpandemics) also estimates that there are more than 1 million animal viruses, about half of them potentially infectious to humans.)

“Microbial evolution is not always toward greater diversity, microbes can also become extinct, smallpox virus being an example,” he adds. “Countless other viruses and bacteria probably have also come and gone without our ever having known of their existence. Some microbes are specific in their associations with certain animals and plants. As these plants and animals become extinct, it seems likely that specialized microbes associated with them have also vanished.”

“The key point is that with plants and animals we know that the current overall trajectory of Earth’s biosphere is toward fewer species, but there is no comparable understanding of the overall trajectory or detailed fine-structure trajectories of microbial evolution.”

Possible implications in the trajectory of microbial evolution are not limited to the evolution of pathogens that attack humans or the few species we depend on for our food.

Changes in non-pathogenic microbial life might also have major implications for the biosphere. The importance of these complex communities of microorganisms — with estimates of up to 10 billion types of microbes alone — is hard to overstate: They maintain Earth’s habitability.

(In 2011, scientists estimated that Earth’s plant and animal species (or “macrobes”) numbered almost 10 million, meaning therefore that for every “macrobe” species there are 1,000 kinds of microbes, with the same macrobe/microbe ratio applicable to both terrestrial and marine species.)

Humanity depends on the ecological services performed by bacteria, archaea, fungi and protists, which recycle nutrients, nurture plant growth, purify water, make cheese and wine, and decompose wastes. And, by turning atmospheric carbon dioxide back into carbon to be stored in soils or the ocean depths (and doing likewise with nitrogen, sulfur, iron, manganese and more), microbes are key to Earth’s atmosphere and climate.

Globally today, heritable DNA sequence information “is probably dominated by microbes, including viruses,” Dr. Thaler says. “The intriguing possibility is that macroscopically visible animals and plants may constitute an ever-shrinking proportion of the biosphere’s heritable information. We really don’t know.”

“We probably ought to know if we are on the losing end of a biological information race, however, and might even want to take practical steps to increase the information content of ‘our team.’ There is also a purely intellectual interest to learn more about our place in the universe of biological information, perhaps analogous to our place in an expanding physical universe.”

This is a hard question but hard does not mean impossible, he adds, “what approaches at least begin to address it?”

DNA technologies are an obvious place to look. How might current technologies be applied and how might future developments help?

Two approaches suggest themselves, says Dr. Thaler.

One is to focus on “modulators and vectors” of microbial evolution such as bacterial sex. Other new approaches that might be harnessed include single molecule or single cell (DNA) sequencing.

DNA barcodes and other sequence-based methods used to identify species of plants and animals and to assess the amount of variation within species “invite comparison to measures of microbial biodiversity,” Dr Thaler says.

“The clustering pattern seen in macroscopic life seems in a general way also a property of microscopic forms of life. The details of comparison are of interest. There might be quantitative general principles behind the truism that ‘life is lumpy’.”

In both the microbial and the macroscopic world of visible plants and animals, a ‘species’ may be considered a cluster “in sequence space,” which can be thought of in terms of stars and galaxies, where individuals are stars and species are galaxies.

Concludes Jesse Ausubel, Director of The Rockefeller University’s PHE, a sponsor of the study: “Linnaeus started his Systema Naturae in 1735, almost 300 years ago, and we still do not have a complete list of the species of plants and animals that he started to catalogue. It will not be easy to do something similar with probably 1,000 times as many microbes, and measure the changes!”

Visual images from the laboratories of Gary Borisy (Forsyth Institute) and Jessica Mark Welch (Marine Biological Laboratory) show the difficulty of direct counts. A few tens of micrometers, the width of a human hair, span entire diverse, populous communities of microbes.

Dr. Thaler says this paper does not offer “protocols to solve the problem,” but tries “to frame the rate of change of microbial biodiversity as an interesting and possibly important question on which progress is possible. I hope that someone reading this paper is stimulated to think of new approaches better than the ones suggested in it.”

Adds Mr. Ausubel: “There is no agency yet monitoring the state of the microbial world, and no World Wildlife Fund, no Nature Conservancy for microbes. Perhaps one day soon we will realize and rectify our neglect and lift our respect for the diversity of microbial life.”

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About

Biozentrum, University of Basel
https://bit.ly/3d32Cdn

Programme for Human Environment, The Rockefeller University
https://bit.ly/3dJwgU5

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Media coverage highlights

The Guardian, UK: Microbes are ‘unknown unknowns’ despite being vital to all life, says study

RealClear Science, United States: Plant and Animal Diversity Is Declining, But What About Microbial Diversity?

Agencia EFE, Spain: Un estudio resalta la “profunda ignorancia” de la biodiversidad de microbios

Aargauer Zeitung, Switzerland: Biologie – Gilt das Artensterben auch für die Mikroben?

IndoAsian News Service, India: Is microbial life, including viruses, changing too?

Jioforme, India: Dangerous “serious ignorance” – are microbial life changing as plant / animal diversity declines?

COSMOS Magazine, Australia: The great unknown of global microbial diversity

Technology Networks, United Kingdom: Is Microbial Diversity Decreasing Like Animals and Plants?

Scientias, Netherlands: We hebben geen flauw idee hoe virussen en bacteriën er op dit moment voorstaan

The Science Times, United States: Study Seeks to Track Changes in Microbial Diversity, Indicates Difficulties

News 24, France: Le monde microbien, y compris les virus, change-t-il aussi?

South Africa Today, South Africa: Microbes, a missing piece in the biodiversity puzzle

Anygator, Italy: Microbi, perché è importante imparare a conoscerli

Mongabay News, United States: ‘Profound ignorance’: Microbes, a missing piece in the biodiversity puzzle

Radio Ecoshock, Canada (104 radio stations): Is the micro world in trouble too?

News release in full, click here

Full coverage summary, click here

New tool will help census oceans, monitor fish, track shifting marine life; “eDNA makes the ocean a sea of biological information”

• DNA bits in seawater samples drawn during New Jersey government fish trawls reveals relative abundance of fish with a 70% match between the two sampling methods;
• In addition to great concordance, study finds that each method yields information missed by the other
• Research advances novel, inexpensive way to census oceans from surface to seafloor, help monitor fisheries, assess shifts in marine life due to climate change, around coral reefs, aquaculture or wind farms, oil rigs, and more
• Message in a bottle: DNA in 1 litre of seawater = a trawl sweep of 66 million litres, enough to fill a sports stadium to top of goalposts
• Proposed “Great American Fish Count,” involving citizen scientists collecting waters samples, could set stage for 2nd global Census of Marine Life during upcoming UN Oceans Decade

Humanity is a step closer to answering one of the most ancient of questions — “how many fish in the sea?” — thanks to newly-published proof that the amount of fish DNA collected in a water sample closely corresponds to kilos of fish captured in a trawl with nets.

In a breakthrough study, scientists report that floating bits of DNA found in small water samples reveal the relative biomass of fish in the sea roughly as well as a “gold standard” US state government trawl with nets.

The researchers drew seawater samples during New Jersey government fish trawls and tested the water for fish DNA. Analysis of the water was able to reveal the relative abundance of fish with a 70% match in results between the two sampling methods. In addition to the great concordance between methods, the study found that each sampling method yielded information missed by the other.

While environmental DNA (“eDNA”) has been proven before as a reliable way to determine the variety of fish in an area of water, the new study is the first to show that bits of eDNA floating in seawater also disclose the relative abundance of the species swimming through it.

Published by the prestigious ICES Journal of Marine Science, the paper certifies “fishing for DNA” as an inexpensive, harmless complement to nets, acoustics and other established ways to monitor the health of fish stocks and/or the shifting diversity, distribution and abundance of aquatic life.

The paper, a collaboration between The Rockefeller University, Monmouth University, and the New Jersey Bureau of Marine Fisheries, says the information about the diversity and relative abundance of fish available in a one-litre sample is comparable to a 66 million litre trawl sweep, enough seawater to fill a football stadium to the top of the goalposts.

During four voyages by the New Jersey Ocean Trawl Survey in 2019 aboard the research vessel “Sea Wolf,” scientists led by Dr. Mark Stoeckle, Senior Research Associate at The Rockefeller University Program for the Human Environment, drew one-litre pop-bottle sized water samples from various depths just before the trawler’s nets were lowered.

The finding has profound implications for improving global fisheries management and has led to early proposals for a “Great American Fish Count” in rivers and coastal waters, aided by millions of citizen scientists, comparable to Audubon’s Great Backyard Bird Counts.

Fish and other organisms shed DNA like dandruff, Dr. Stoeckle explains, leaving an invisible trail wherever they swim. This environmental DNA can be skin cells, droppings, urine, eggs, and other biological residues that last in the ocean for a few days.

One year of eDNA sampling, out-of-pocket costs: $12,000

The eDNA process is straightforward and extremely inexpensive compared with traditional marine life monitoring methods, which involve ships with large crews and hand counts.

Co-author Zachary Charlop-Powers at The Rockefeller University, lead developer of the software used in the DNA analyses, explains that eDNA testing involves collecting and filtering a water sample, extracting and sequencing the DNA in a laboratory, then matching the results found in an online DNA reference library.

“The bioinformatic tools used by the team are the same ‘barcode’ analysis pipelines commonly used by microbiologists but were adapted for the study of marine vertebrates.”

He notes too that the year of sampling and DNA extraction required an investment of just $12,000, exclusive of salaries.

“The applications of environmental DNA in the marine realm are vast,” says Dr. Stoeckle, a Harvard-educated MD who helped pioneer DNA “barcoding,” the identification of species from a small region of the animal’s DNA sequence.

“eDNA offers a low-cost way to monitor the effectiveness of a marine protected area, for example, or whether efforts to restore a coral reef are succeeding. It could reveal the ecological effects of marine industrial activities, including offshore wind farms, oil and gas rigs, and commercial and recreational fishing.”

Adds Dr. Stoeckle: To put this in perspective, if we thought of a trawl as a full medical CAT or MRI scan, then eDNA can be thought of as a pocket ultrasound–it can be carried and used anywhere in the hospital, without the time and expense of scheduling a full-scale exam. And eDNA surveys will become better and more informative every year as the technique improves and the DNA reference library grows.

Says co-author Dr. Jason Adolf, Endowed Associate Professor of Marine Science, Monmouth University: “eDNA could also be used to identify life in ocean regions hard to access with trawls, such as very rocky areas, or places too deep or too shallow.”

Monmouth co-author Dr. Keith J. Dunton, an expert on endangered fish species, notes that the results are promising for rare as well as common fish species.

“eDNA along with other technologies like acoustic telemetry offers a sensitive, non-extractive way to monitor declines and revivals of rare, threatened, and endangered species,” he says. “We do not have to put them through stressful capturing to know that they are there.”

Trawl surveys, the main tool used to monitor fish populations, have carefully established protocols and yield rich information but are costly, time-consuming, and require special equipment and fish identification experts. Due to the crew size needed, such trawls have been limited recently by COVID-19.

The New Jersey surveys every season involve deploying a bottom trawl, similar to that used in commercial fishing, behind a vessel over a predetermined pattern. The catches in the nets are hauled up and sorted on tables where the weight of each identified species is recorded. Between 30 and 40 trawls are done about every three months.

To compare the trawl survey to the eDNA survey, one-litre water samples were collected at the surface and at depth before the trawls were done. However, samples were only taken before every fourth trawl. When the data from the two surveys were analyzed, the eDNA survey found most of the same fish species, and also found species not captured in the trawl. And it did so with only one-quarter of the samples taken and a fraction of the effort involved.

The paper says most (70% to 87%) species detected by trawl in a given month were also detected by eDNA, and vice versa, including nearly all (92% to 100%) abundant species. Conversely, most dropouts were relatively rare taxa.

Trawl and eDNA peak seasonal abundance agreed for about 70% of fish species.

In other comparisons, monthly eDNA species “reads” correlated with the monthly weight, or biomass, of that species recovered in the trawl.

The eDNA reporting “largely concorded with monthly trawl estimates of marine fish species richness, composition, seasonality, and relative abundance,” the paper says.

“It’s important to understand that the results of both methods are true, and complementary,” noted Stoeckle. “They catch a lot of overlapping, concordant information as well as some information unique to each method.”

Gregory Hinks of the New Jersey Department of Environmental Protection, who co-authored the paper with Bureau of Marine Fisheries colleague Stacy M. VanMorter, adds: “During times like COVID when it is unsafe to conduct surveys with large crews, the eDNA method might allow us still to maintain some continuity in our surveys. In any case, piggybacking eDNA onto an existing survey may eventually provide an affordable way to improve marine fish stock assessment.”

The new paper lays out further research required, such as better calibration of eDNA “reads” to fish body mass — how much DNA is shed by 1,000 anchovies weighing 1 kilo, for example, compared with a one kilo sized sea bass? — and how to account for eDNA reads that may be the result of injury due to a predator attack.

Since collecting water for eDNA is so quick and easy to do, research or oceanographic vessels and commercial and recreational vessels can collect samples as they travel from place to place. Even drones could be deployed to collect water samples.

And with the benefit of additional studies in marine and freshwaters, estimates of animal numbers using eDNA will continue to improve as well as the DNA reference data banks that allow reliable identification of aquatic species.

eDNA opens the way to surveys of unprecedented value, quality, and affordability, says Jesse Ausubel, Director of The Rockefeller University’s Program for the Human Environment, who developed and helped oversee the first international Census of Marine Life, a decadal (2000-2010) collaboration of about 2,700 scientists in 80 countries.

“eDNA makes the ocean a sea of biological information,” he says. “In the USA we could organize a Great American Fish Count in which millions of citizen scientists might collect water for eDNA testing spanning all our waters. Globally, the incipient UN Decade of the Oceans could include a Great Global Fish Count sampling from sea floor to sea surface and near shore to mid-ocean all during a single day or week.”

Tony MacDonald, Director of the Monmouth University Urban Coast Institute, says “Our institute and scientists were excited to support this innovative work, one of several partnerships in recent years between UCI and The Rockefeller University Program for the Human Environment.”

“We hope to have the opportunity to continue and expand our collaboration with New Jersey’s Department of Environmental Protection Marine Fisheries and the National Oceanic and Atmospheric Administration on future fish trawls to further advance eDNA research.”

Comments Tim Gallaudet, Ph.D., Rear Admiral, U.S. Navy (Ret.) Assistant Secretary of Commerce for Oceans and Atmosphere and Deputy NOAA Administrator: “NOAA is rapidly advancing ‘omics technologies, including eDNA, to improve our ability to monitor and understand biological communities in our oceans and the Great Lakes.”

“Important applications include monitoring endangered and invasive species, assessing biodiversity for ecosystem health, tracking aquaculture pathogens, and augmenting fisheries surveys.”

“Through the NOAA ‘Omics Strategy‘ and our forthcoming Implementation Plan, we have defined goals and actionable steps to integrate modern ‘omics technologies to help meet our mission. Collaboration with Rockefeller University and other partners will allow us to expand and advance ‘omics research and eDNA in direct support of the American Blue Economy.”

(‘Omics refers to a suite of advanced methods used to analyze material such as DNA, RNA, proteins, or metabolites.)

Marine eDNA’s potential applications include

• Exploration: discovering species previously unknown in certain ranges
• Discovering rare species and others unknown to science (or absent from genome databases)
• Sampling remote, difficult-to-reach, and intriguing places
• Assessment of the size of fish stocks
• Identifying the range of marine animals
• Determining the effect of protected area designation on fish and other marine animal populations and other forms of ecological restoration
• Monitoring the effect on native species of fish farming operations, offshore oil and gas operations, or wind farms
• Determining the effects of artificial reefs, of severe storms and other disturbances to marine ecosystems including harmful algal blooms
• Monitoring vulnerable, threatened or endangered species, invasive species, or the presence of species dangerous to swimmers
• Gauging the impacts of climate variability
• Mapping marine animal diversity, distribution, migration and abundance, including invasive species, and species popular with sport fishers

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Coverage highlights

Science Magazine, United States, Fisheries in a flask? Loose DNA in seawater offers a new measure of marine populations, click here

Agencia EFE, Spain, El análisis del ADN ambiental permite saber el número de peces de los océanos, click here

Inside Science, United States, DNA Floating in Ocean Water Reveals Fish Abundance, click here , via ABC News, USA, click here

New Indian Express, India, Experts find trick to count fish in sea, click here

Coverage summary, click here

News release in full, click here

DNA scientists sampling the New Jersey shore bottle the changing ranges of marine life predicted a decade ago; Fishing DNA from seawater: a harmless, economical way to study marine animals’ movements, diversity, distribution … and perhaps abundance

DNA scientists investigating new marine life migration patterns in the Atlantic Ocean surfaced the genetic traces of species far from their usual southern homes.

A species of ray — the Brazilian cownose ray, Rhinoptera brasiliensis, and the Gulf kingfish, Menticirrhus littoralis, have been turning up when the weather turns warm in New Jersey’s Barnegat Inlet, about a two hour drive south of New York City.

The ray has never before been recorded in the US north of the Gulf of Mexico; the perch-like Gulf kingfish has never before been recorded north of Chesapeake Bay, Virginia, about 250 miles (400 km) to the south.

Led by Mark Stoeckle of The Rockefeller University and published in the journal Frontiers in Marine Science, the study involved drawing seawater twice monthly for two years and testing it for genetic material — DNA contained in cells sloughed off the slimy, gelatinous outer coating of a fish as it swims, for example, in its excretions, in tissue fragments shed in combat with a predator, or after death or injury.

Dr. Stoeckle explains that DNA degrades and disperses within a few days of an animal’s departure, but lingers in the water, despite currents and tides, long enough to detect a species’ passing presence.

Over two years, from spring 2017 to spring 2019, sampling was conducted at a pair of Barnegat Inlet, NJ sites within a few miles of each other — an outer shore to sample Atlantic Ocean waters, and inside a sheltered bay.

In 2010, a Census of Marine Life program, the Future of Marine Animal Populations (FMAP), forecast changes in diversity of marine species based on available habitat and anticipated changes in water temperature.

Jesse Ausubel, Director of the Program for the Human Environment at The Rockefeller University, and CoML’s co-founder, says the Brazilian cownose ray or Gulf kingfish far north of its known range fits FMAP’s prediction, while noting that other explanations remain possible. For example, the animals may have simply evaded New Jersey trawl nets for years.

With changes in the oceans owing to climate, chemical pollution, debris, noise, night-time illumination, and other factors, Mr. Ausubel stresses, “this study further establishes aquatic environmental DNA (eDNA) as an innovative, inexpensive, low-impact way to monitor marine life migrations, changing ranges, diversity and distribution.”

Says Dr. Stoeckle: “Promising work is also underway to confirm a relationship between the concentration of a species’ DNA in seawater and the abundance of that species in the water. If water samples can provide an index of the number or total weight of fish of a given species in a defined ocean area, that offers a potential leap forward for sustainable fisheries and ocean management, improving the rationality with which fish quotas are set and the quality and reliability of their monitoring around the world.”

Tony MacDonald, Director of Monmouth University’s Urban Coast Institute, which helped initiate the work, adds: “Censusing marine fish and other animals that move typically involves costly, time-consuming surveys with specialized equipment and personnel. eDNA science is granting humanity a very old wish: an easy way to estimate the distribution and abundance of diverse fish species and other forms of aquatic life in the dark waters of rivers, lakes, and seas.”

Dr. Stoeckle, who has worked with high school and college students to study New York Harbor and the Hudson River, adds that “the collection process is simple enough for supervised schoolchildren or citizen scientists on any coast anywhere to help monitor the changing ranges of all marine life.” Co-author Mithun Das Mishu joined the project when he was a sophomore at Hunter College.

After water is drawn, it is filtered to concentrate the DNA for extraction. The target segment of the DNA is amplified in a laboratory and then sent for “next-generation” sequencing, the result of which–a record of all the DNA sequences in the sample–is fed into computer software that counts the number of copies of each sequence and searches for matches in an online public reference library.

The New Jersey study, co-authored by Mishu and bioinformatics expert Zachary Charlop-Powers, detected bony fish species in consistent seasonal patterns. And they found a small number of species accounted for the great majority of DNA obtained.

Detection of rays and other cartilaginous marine species, meanwhile, was confined mostly to warmer months.

In addition to straining its genetic material from the water, researchers used DNA to identify the decayed remains of a Brazilian cownose ray washed ashore in the sampling area in August 2017.

The researchers also added to growing global databases the first DNA reference sequences for 31 regional species catalogued by New Jersey scientists from trawl surveys over the past 30 years.

Dr. Stoeckle’s earlier studies of New York’s East and Hudson Rivers revealed the presence or absence of several key fish species passing through those waters. The weekly data snapshots created a moving picture that largely reinforced and correlated with knowledge from years of fishnet trawls.

By conducting a series of tests over time, the work pioneered a novel way to record fish migration. eDNA has a goldilocks quality just right for research, Dr. Stoeckle notes: If it disappeared too quickly, sampling wouldn’t tell us much; if it lingered too long, too much DNA would be in the water, undermining useful, timely insights.

Next steps include fine tuning calibrations, comparing eDNA “reads” and results with data from traditional surveys conducted with nets and sonar. Do 100 DNA “reads” indicate the presence of 1 fish or 10 fish?

Also to be determined: the rate at which different fish and other marine species shed DNA.

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About The Rockefeller University

http://www.rockefeller.edu/about

About the Program for the Human Environment

phe.rockefeller.edu

Support from the Marine Science and Policy Initiative of the Program for the Human Environment (The Rockefeller University) and the Urban Coast Institute (Monmouth University) initiated the work on aquatic DNA.

About Program for the Human Environment eDNA studies

https://phe.rockefeller.edu/barcode/blog/nycnj-aquatic-vertebrate-edna-project/

Photos of sampling, key tables: https://bit.ly/3coA8rG

Credit: Mark Stoeckle, The Rockefeller University

Other images and tables used in the paper (https://bit.ly/2WD6OXE) are also available on request

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Coverage highlights

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News release in full, click here

Organizers of 1st National Conference on Marine Environmental DNA call for official US Government marine eDNA program; investments to speed sampling results, standard sampling / reporting protocols; priority exploration / baseline monitoring site

Advanced technologies capable of analyzing DNA in seawater will help answer some of humanity’s oldest, most profound questions and concerns, including “who lives in the sea?” – beginning with species of interest in specific areas, including clownfish (Nemo) and blue tang fish (Dory).

To accelerate the pace towards the potentially far-reaching benefits of these technologies-both environmental and economic-organizers of the 1st US National Conference on Marine Environmental DNA (eDNA) (Nov. 29-30, hosted by The Rockefeller University, New York), today prescribed priority steps for government, researchers, industry and investors, including:

• Initiate marine eDNA observations in key US Exclusive Economic Zone basins, including the Gulfs of Mexico and Maine, Monterey Bay, the California Current area, New York Bight, and the Bering Sea / Arctic
• Establish long-term eDNA observational platforms at multiple sites-these will afford crucial insights, e.g., about effects of human activities
• Systematically address unresolved science questions, observation rules and standard operating procedures, reference standards, and archival capabilities
• Anticipate impacts on existing statutes, regulations, permitting/licensing processes as marine eDNA is introduced as a credible ecosystem census indicator
• Explore the decision-making value of marine eDNA and seize commercial opportunities
• Create a US Government National Ocean Partnership Program (NOPP) for marine eDNA,with multi-year, multi-investor, multi-participant projects

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Says the conference summary report, available in full at

phe.rockefeller.edu/eDNAmarine2018/report: “Marine eDNA is already a surprisingly reliable, feasible, and affordable ocean observation technology ready for rapid adoption and poised for giant steps forward. In short, it works….Get going.”

Additional source materials:

• Conference website
• Marine eDNA Primer
• sponsored paper: The Ocean as a Living Sensor: Environmental DNA and Acoustics for Detecting Marine Life
• pre-conference news release
• Conference program

Newly sampled areas ranged from Holy Land waters to Coney Island and the White Shark Cafe.

The meeting of approximately 100 US ocean scientists and associated stakeholders with experience, skill and/or interest in marine eDNA was sponsored by the Monmouth University-Rockefeller University (MURU) Marine Science and Policy Initiative.

Related news releases from this source:

Marine species quickly revealed by new ‘Go Fish’ tool, highlights potential of emerging eDNA science: http://bit.ly/2KJgM3p

Naked DNA in water tells if fish have arrived: http://bit.ly/2VUC9E3

Exploring vast ‘submerged America,’ marine scientists discover 500 bubbling methane vents: http://bit.ly/2SWfOEr

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Example coverage:

Science Magazine (potential reach online: 4,604,140; print edition (“News in Brief”) readership: 400,000) The ocean is full of drifting DNA. The United States needs to start to collect it, researchers say , click here

“Science Insider” blog by Jeffrey Mervis, click here

Saving Seafood, USA, The Ocean is Full of Drifting DNA. The United States Needs to Collect it, Researchers Say, click here

Deep Carbon Observatory collaborators, exploring the ‘Galapagos of the deep,’ add to what’s known, unknown, and unknowable about Earth’s most pristine ecosystem

Barely living “zombie” bacteria and other forms of life constitute an immense amount of carbon deep within Earth’s subsurface – 245 to 385 times greater than the carbon mass of all humans on the surface, according to scientists nearing the end of a 10-year international collaboration to reveal Earth’s innermost secrets.

On the eve of the American Geophysical Union’s annual meeting, scientists with the Deep Carbon Observatory today reported several transformational discoveries, including how much and what kinds of life exist in the deep subsurface under the greatest extremes of pressure, temperature, and low nutrient availability.

Drilling 2.5 kilometers into the seafloor, and sampling microbes from continental mines and boreholes more than 5 km deep, scientists have used the results to construct models of the ecosystem deep within the planet.

With insights from now hundreds of sites under the continents and seas, they have approximated the size of the deep biosphere – 2 to 2.3 billion cubic km (almost twice the volume of all oceans) – as well as the carbon mass of deep life: 15 to 23 billion tonnes (an average of at least 7.5 tonnes of carbon per cu km subsurface).

The work also helps determine types of extraterrestrial environments that could support life.

Among many key discoveries and insights:

• The deep biosphere constitutes a world that can be viewed as a sort of “subterranean Galapagos” and includes members of all three domains of life: bacteria and archaea (microbes with no membrane-bound nucleus), and eukarya (microbes or multicellular organisms with cells that contain a nucleus as well as membrane-bound organelles)
• Two types of microbes – bacteria and archaea – dominate Deep Earth. Among them are millions of distinct types, most yet to be discovered or characterized. This so-called microbial “dark matter” dramatically expands our perspective on the tree of life. Deep Life scientists say about 70% of Earth’s bacteria and archaea live in the subsurface
• Deep microbes are often very different from their surface cousins, with life cycles on near-geologic timescales, dining in some cases on nothing more than energy from rocks
• The genetic diversity of life below the surface is comparable to or exceeds that above the surface
• While subsurface microbial communities differ greatly between environments, certain genera and higher taxonomic groups are ubiquitous – they appear planet-wide
• Microbial community richness relates to the age of marine sediments where cells are found – suggesting that in older sediments, food energy has declined over time, reducing the microbial community
• The absolute limits of life on Earth in terms of temperature, pressure, and energy availability have yet to be found. The records continually get broken. A frontrunner for Earth’s hottest organism in the natural world is Geogemma barossii, a single-celled organism thriving in hydrothermal vents on the seafloor. Its cells, tiny microscopic spheres, grow and replicate at 121 degrees Celsius (21 degrees hotter than the boiling point of water). Microbial life can survive up to 122°C, the record achieved in a lab culture (by comparison, the record-holding hottest place on Earth’s surface, in an uninhabited Iranian desert, is about 71°C – the temperature of well-done steak)
• The record depth at which life has been found in the continental subsurface is approximately 5 km; the record in marine waters is 10.5 km from the ocean surface, a depth of extreme pressure; at 4000 meters depth, for example, the pressure is approximately 400 times greater than at sea level
• Scientists have a better understanding of the impact on life in subsurface locations manipulated by humans (e.g., fracked shales, carbon capture and storage)

Ever-increasing accuracy and the declining cost of DNA sequencing, coupled with breakthroughs in deep ocean drilling technologies (pioneered on the Japanese scientific vessel Chikyu, designed to ultimately drill far beneath the seabed in some of the planet’s most seismically-active regions) made it possible for researchers to take their first detailed look at the composition of the deep biosphere.

There are comparable efforts to drill ever deeper beneath continental environments, using sampling devices that maintain pressure to preserve microbial life (none thought to pose any threat or benefit to human health).

To estimate the total mass of Earth’s subcontinental deep life, for example, scientists compiled data on cell concentration and microbial diversity from locations around the globe.

Led by Cara Magnabosco of the Flatiron Institute Center for Computational Biology, New York, and an international team of researchers, subsurface scientists factored in a suite of considerations, including global heat flow, surface temperature, depth and lithology – the physical characteristics of rocks in each location – to estimate that the continental subsurface hosts 2 to 6 × 10^29 cells.

Combined with estimates of subsurface life under the oceans, total global Deep Earth biomass is approximately 15 to 23 petagrams (15 to 23 billion tonnes) of carbon.

Says Mitch Sogin of the Marine Biological Laboratory Woods Hole, USA, co-chair of DCO’s Deep Life community of more than 300 researchers in 34 countries: “Exploring the deep subsurface is akin to exploring the Amazon rainforest. There is life everywhere, and everywhere there’s an awe-inspiring abundance of unexpected and unusual organisms.

“Molecular studies raise the likelihood that microbial dark matter is much more diverse than what we currently know it to be, and the deepest branching lineages challenge the three-domain concept introduced by Carl Woese in 1977. Perhaps we are approaching a nexus where the earliest possible branching patterns might be accessible through deep life investigation.

“Ten years ago, we knew far less about the physiologies of the bacteria and microbes that dominate the subsurface biosphere,” says Karen Lloyd, University of Tennessee at Knoxville, USA. “Today, we know that, in many places, they invest most of their energy to simply maintaining their existence and little into growth, which is a fascinating way to live.

“Today too, we know that subsurface life is common. Ten years ago, we had sampled only a few sites – the kinds of places we’d expect to find life. Now, thanks to ultra-deep sampling, we know we can find them pretty much everywhere, albeit the sampling has obviously reached only an infinitesimally tiny part of the deep biosphere.”

“Our studies of deep biosphere microbes have produced much new knowledge, but also a realization and far greater appreciation of how much we have yet to learn about subsurface life,” says Rick Colwell, Oregon State University, USA. “For example, scientists do not yet know all the ways in which deep subsurface life affects surface life and vice versa. And, for now, we can only marvel at the nature of the metabolisms that allow life to survive under the extremely impoverished and forbidding conditions for life in deep Earth.”

Among the many remaining enigmas of deep life on Earth:

Movement: How does deep life spread – laterally through cracks in rocks? Up, down? How can deep life be so similar in South Africa and Seattle, Washington? Did they have similar origins and were separated by plate tectonics, for example? Or do the communities themselves move? What roles do big geological events (such as plate tectonics, earthquakes; creation of large igneous provinces; meteoritic bombardments) play in deep life movements?

Origins: Did life start deep in Earth (either within the crust, near hydrothermal vents, or in subduction zones) then migrate up, toward the sun? Or did life start in a warm little surface pond and migrate down? How do subsurface microbial zombies reproduce, or live without dividing for millions to tens of millions of years?

Energy: Is methane, hydrogen, or natural radiation (from uranium and other elements) the most important energy source for deep life? Which sources of deep energy are most important in different settings? How do the absence of nutrients, and extreme temperatures and pressure, impact microbial distribution and diversity in the subsurface?

Comments

“Discoveries regarding the nature and extent of the deep microbial biosphere are among the crowning achievements of the Deep Carbon Observatory. Deep life researchers have opened our eyes to remarkable vistas – emerging views of life that we never knew existed.”
– Robert Hazen, Senior Staff Scientist, Geophysical Laboratory, Carnegie Institution for Science, and DCO Executive Director

“They are not Christmas ornaments, but the tiny balls and tinsel of deep life look they could decorate a tree as well as Swarovski glass. Why would nature make deep life beautiful when there is no light, no mirrors?”
– Jesse Ausubel, The Rockefeller University, a founder of the DCO

“Deep life probably has an important impact on global biogeochemical cycles, and thus on the surface world. However, we are still far from quantifying this impact.”
– Kai-Uwe Hinrichs, MARUM University of Bremen, Germany

“Even in dark and energetically challenging conditions, intraterrestrial ecosystems have uniquely evolved and persisted over millions of years. Expanding our knowledge of deep life will inspire new insights into planetary habitability, leading us to understand why life emerged on our planet and whether life persists in the Martian subsurface and other celestial bodies.”
– Fumio Inagaki, Japan Agency for Marine-Earth Science and Technology

“While we are far from being able to quantify it, we believe Deep Life has an important impact on global biogeochemical cycles and chemical equilibria in habitable rocks. Deep Life plays a role in aquifer quality, for example, or carbon capture and storage (CCS). Unfortunately, the deep biosphere is very poorly considered in engineering operations carried out in the subsurface. We recently demonstrated the high reactivity of deep biota to CO2 injections (CCS), which ultimately led to the bioclogging of the injection well, and surrounding reservoir.”
– Benedicte Menez, Institut de Physique du Globe de Paris, France

“A decade ago, we had no idea that the rocks beneath our feet could be so vastly inhabited. Experimental investigations told us that microbes could potentially survive to great depth; at that time, we had no evidence, and this has become real ten years later. This is simply fascinating and will surely foster enthusiasm to look for the biotic-abiotic fringe on Earth and elsewhere.”
– Isabelle Daniel, University of Lyon 1, France

###

This Deep Life research is part of the Deep Carbon Observatory program, which will issue its final report in October 2019 after a decade of work by a global community of more than 1000 scientists to better understand the quantities, movements, forms, and origins of carbon inside Earth.

Sponsored by the Alfred P. Sloan Foundation, the DCO sheds unprecedented light on Earth’s highly active subterranean environment, including the secrets of volcanoes and diamonds, sources of oil and gas, and the origins of life itself, contributing to new understanding of this and other planets.

DCO directly provided a major contribution to opportunities for collaboration between deep subsurface microbiologists that wouldn’t have existed otherwise.

Mysteries of deep carbon include:

Quantities:

How much carbon is stored inside Earth?
What are the reservoirs of that carbon?

Movements:

How does carbon move among reservoirs?
Where are the most significant carbon fluxes between Earth’s deep interior and the surface?

Origins:

How much rising carbon is primordial and how much is recycled from the surface?
Are there deep abiotic sources of methane and other hydrocarbons?

Forms:

What is the nature and extent of deep microbial life?
Did deep organic chemistry play a role in life’s origins?

The four scientific communities of the Deep Carbon Observatory:

Extreme Physics and Chemistry

Dedicated to improving our understanding of the physical and chemical behavior of carbon at extreme conditions, as found in the deep interiors of Earth and other planets.

Image description

Reservoirs and Fluxes

Dedicated to identifying deep carbon reservoirs, determining how carbon moves among these reservoirs, and assessing Earth’s total carbon budget.

Image description

Deep Energy

Dedicated to understanding the volume and rates of abiogenic hydrocarbons and other organic species in the crust and mantle through geological time.

Deep Life

Dedicated to assessing the nature and extent of the deep microbial and viral biosphere.

Deep Carbon Observatory Secretariat: Carnegie Institution for Science
Washington, DC

Coverage presentation, click here

Coverage hyperlinks:

New York Times, USA (333M) Deep Beneath Your Feet, They Live in the Octillions, click here

Agence France Presse

• Vast, zombie-like microbial life lurks beneath seabed, click here
• French: Les entrailles de la Terre grouillent de vie intraterrestre, click here
• Spanish: Las entrañas de la Tierra están repletas de vida “intraterrestre”, click here
• Portuguese: Entranhas da Terra estão repletas de vida ‘intraterrestre’, click here
• Japanese: 地下深部に広大な「生命体の森」 国際研究で発見, click here

Xinhua, China
Subsurface dark community hundreds of times more than humans: study, click here

The Canadian Press
Eat sulphur, breathe rust: Scientists find life deep underground, click here

Europa Press, Spain
La vida en la Tierra profunda constituye una asombora masa de carbono, click here

Agencia EFE, Spain
Biomasa de la vida subterránea es miles de millones de toneladas de carbono, click here

Deutsche Presse-Agentur, Germany
Tief im Boden leben Millionen verschiedener Mikroben, click here

搜狐新闻-搜狐, (China News Network) China (19,788,227)
地下深处微生物总重量首次测出 是人类总重量385倍_生物圈 (The total weight of microorganisms in the depth of the ground is measured for the first time, which is 385 times the total human weight), click here

RIA News, Russia (19,149,117)
Геологи подсчитали массу «зомби-бактерий» в недрах Земли (Geologists have calculated the mass of “zombie bacteria” in the depths of the Earth), click here

Fars, Iran
Deep Earth: Earth’s Most Pristine Ecosystem, click here

* * * * *

UK

BBC:

• Science in Action (7 minutes, starts just after the introduction), click here
• The scale of life beneath our feet (6 min interview with Bob Hazen, audio), click here
• Newsday (4 minute interview with Karen Lloyd, audio, starts at 43 minutes), click here
• BBC Online: Amount of deep life on Earth quantified, click here
• BBC Mundo: El increíble ecosistema oculto bajo la superficie de la Tierra, click here

Daily Telegraph (22 million)
Earth teeming with strange underground organisms which may be planet’s first inhabitants, click here

The Guardian (1,583,615)
Scientists identify vast underground ecosystem containing billions of micro-organisms, click here

Daily Mail (33,237,767)
Barely living ‘zombie’ bacteria in Deep Earth are made up of 15 to 23 billion tons of carbon – 385 times more than in every human on the planet put together, click here

Metro
Weird ‘alien’ lifeforms living underground could be the real rulers of Planet Earth, click here

Nature (7,844,115)
Daily briefing: Subterranean biosphere contains billions of tonnes of life, click here

The Independent (24,275,324)
Massive ‘deep life’ study reveals billions of tonnes of microbes living far beneath Earth’s surface, click here

The Times (15 million)
Earth’s subterranean ecosystem uncovered, click here

The Sun
BUGS BELOW Barely living ‘ZOMBIE’ bacteria lurking in Deep Earth outweigh humanity by nearly 400 to one, click here

CNET UK (60,946,380)
Scientists discover underworld ecosystem teeming with life, click here

* * * * *

USA

CNN International (14,806,025)
Scientists discover billions of tonnes of ‘zombie’ bacteria inhabits the ground beneath our feet, click here
en Español: Millones de bacterias zombis habitan el suelo bajo nuestros pies, descubren científicos, click here

Science Magazine
Scientists uncover massive, diverse ecosystem deep beneath Earth’s surface, click here

Gizmodo
Deep Earth Is Teeming with Mysterious Life, click here

Live Science (via NBC News)
Earth’s Mysterious ‘Deep Biosphere’ Is Home to Millions of Undiscovered Species, Scientists Say, click here

KQED (NPR, San Francisco)
Under Earth’s Surface, a Wild Menagerie of Strange Organisms, click here

The Epoch Times
Scientists Reveal Vast World of Creatures Living 3.5 Miles Underground, click here
Chinese: 研究：高溫高壓的地下深處有無數未知生命, click here

Forbes (36,657,058)
There Is A Colossal Cornucopia Of Exotic Life Hiding Within Earth’s Crust, click here
Russian (1,376,993): Под землей обнаружена неизвестная жизнь | Технологии, click here

* * * * *

RT, Russia (10,506,399)
«Подземный Галапагос»: геобиологи выяснили, что скрывает невидимая часть Земли, click here

Cosmos Magazine, Australia (255,985)
Deep life: exploring microbial dark matter, click here

Bild der Wissenschaft, Germany (116,852)
Reiches Leben in der Unterwelt, click here

Folha de S.Paulo, Brazil (12,615,692)
Ecossistema subterrâneo com bilhões de microorganismos é encontrado por cientistas, click here

National Geographic Polska, Poland (239,063)
Pod ziemią jest cały nowy świat. Dookoła są niesamowite i niespodziewanie niecodzienne organizmy, click here

National Geographic France​ (236,430​)

Le plus grand écosystème microbien du monde découvert sous la croûte terrestre​, click here

Sciences et Avenir, France (1,050,964)
70% des microbes terrestres se cachent dans les sous-sols, click here

Greenreport, Italy (46,005)
Scoperto un mondo sconosciuto: è la Terra. Nel sottosuolo c’è molta più vita di quanto credevamo, click here

El Mercurio, Chile (31,646)
Casi dos tercios de todos los microorganismos viven en el subsuelo profundo de la Tierra, click here

بلد نيوز Egypt (37,567)
حقائق مذهلة عن حياة الزومبي في أعماق الأرض!, click here

ABC, Spain (8,366,627)
Hay un mundo perdido a 5 kilómetros bajo la superficie de la Tierra, click here

* * * * *

News release in full, click here
Full coverage summary, click here

Coverage summary presentation, click here

Metrics (to 4 PM US ET Jan. 25): Languages: 31, Countries: 87, online news sites that published one or more stories: 950, total hits, online news sites: 1,181,aggregate circulation / potential reach (online only): 1.35 billion, Advertising value equivalency (online only): $12.5 million (per Meltwater — assumes 2.5% of visitors to a news site will view a particular article x $0.37 per viewer)

Experts convene for 1st US National Conference on Marine Environmental DNA, a far-reaching, potent complement to traditional monitoring systems; initiates coordinated US research theme, standardized sampling/reporting protocols; baseline monitoring sites

New York — An innovative tool that can confirm the recent presence of any given fish species in a sample of water is among the marvels to be highlighted at the first National Conference on Marine Environmental DNA, New York City, Nov. 29-30.

About 100 pioneering practitioners and users of eDNA science — a mighty complement to traditional marine life monitoring systems — will convene in Manhattan to detail and share discoveries, state-of-the-art technologies, and new methods.

A new tool created at The Rockefeller University, which will host the conference, offers, for example, a chemical shortcut for researchers to test for the eDNA of a specific, individual species in a water sample.

It makes use of the fact that every species leaves a trail of genetic residue — skin cells, excretions, other DNA — as it moves. Scientists can now test water and soil for these traces and identify which species left them behind.

The eDNA tester can confirm the genetic presence of a given species in a water sample within three days — a small fraction of the usual month or more involved in the current practice of lab testing for any and all species, or to mount an expedition with nets and analyze the results.

Its creator, Mark Stoeckle, Senior Research Associate at The Rockefeller University’s Program for the Human Environment (PHE), says many reasons make authorities want to know when a given marine species is present — to determine for example when to open or close a commercial fishery, or when dredging can be done without harm to marine life. New York Harbor, he notes, restricts dredging if winter flounder are present.

“Go Fish”

He likens his innovation to Go Fish, the children’s game in which a player asks another for a given rank of card, for example: do you have any jacks in your hand? Says Dr. Stoeckle. “In the case of New York, the question would be ‘Where in the harbor do we have winter flounder?'”

The current cost to produce a Go Fish eDNA tool is $15 per sample (1 species); additional species can be added for $8 per sample.

Says conference lead organizer Jesse Ausubel, Director of the PHE: “‘Go Fish’ brings us close to a ‘chatbot’ or small smart personal assistant — like Siri, Alexa, or Cortana — that can quickly identify species from eDNA.”

“Presence of a species is easier to confirm than absence,” Dr. Stoeckle underlines. “Sampling may be conducted on the wrong day or at the wrong depth. Nevertheless, the genetic trail that animals leave behind is helping us find them without having them physically in hand — a breakthrough with major environmental and economic implications.”

National Conference on Marine Environmental DNA

Combined with traditional trawls with nets, tagging, visual observations, and acoustic instruments, experts believe remote eDNA sampling and analysis can one day help create near real-time monitoring of the marine environment.

In the US, several marine eDNA research hotspots have developed, including Monterey Bay, CA, New York / New Jersey, and Seattle, WA.

Expected at the conference are about 100 leading US scientists, officials, inventors, and investors exploring the emerging field of environmental DNA and its application in marine settings.

The event will highlight insights provided by eDNA to date and the potential of this new science to further enlarge our knowledge and inform ocean management.

Major themes:

• Technology development — faster, cheaper, more portable
• Bioinformatics — genetic reference databases, analytic software, data compatibility
• eDNA biology — improving detection reliability, and relating eDNA abundance to species abundance

Organizers aim to initiate a commitment by leading scientists and stakeholders to take up eDNA as a cooperative national or regional research theme.

They also aim to encourage:

• Federal, state, and local governments to incorporate eDNA into traditional ongoing . marine life surveys. (Monmouth University and Rockefeller U scientists are exploring integration of eDNA working with New Jersey Department of Marine Fisheries’ trawl surveys)
• The private sector to collaborate in development of technologies to improve the speed and lower the cost of testing
• Non-governmental organizations to help build genetic reference databases and monitor national and regional hotspots

Priority questions to be addressed include:

• Whether and how the rate of decay of eDNA differs by taxa and context. Do some fish shed more than others? Do fish shed more than turtles? How do water temperature, sunlight, chemical variation, currents and turbulence, pressure, and other factors affect decay?
• How to better calibrate the abundance of DNA in the water column as an index of abundance of specific species of fish and other animals
• How to make eDNA reliable for very rare as well as more abundant species
• How to formally integrate eDNA in the conduct of marine surveys, augmenting nets, cameras, and acoustic fish finders
• What is needed to make eDNA data suitable for regulatory and policy purposes?

Says Paul Gaffney, Vice-Admiral (ret.), former President and Urban Coast Institute Ocean Policy Fellow at Monmouth University: “eDNA opens the door to cheap, frequent, widespread, potentially automated monitoring of the diversity, distribution, and abundance of aquatic life. Government agencies need to take notice.”

Bruce Nash, an innovator in adapting cutting-edge science for authentic student research, stressed the importance in years past of establishing protocols related to DNA barcoding, which identifies species from the DNA of tissue taken from physical specimens. Confirming a continuous chain of custody, time of testing, and other protocols made DNA barcode evidence sufficiently reliable to stand up in court.

To achieve reliable eDNA results, water or filtered material from the water needs to be stored and processed properly.

Dr. Nash will share the development of approachable and affordable methods that support eDNA work, including a new open-access tool developed at Cold Spring Harbor Laboratory’s DNA Learning Center for getting reliable identifications from the multitude of letters in the eDNA sequence data. Users upload their sequence data and then ride the Purple Line of DNA Subway in an appealing and intuitive interface to learn about the diversity contained in their sample.

Uses: eDNA’s applications to date include

Exploration

• discovering species previously unknown in certain ranges
• discovering rare species and others unknown to science (or absent from genome databases)
• sampling remote, difficult-to-reach, and intriguing places

Assessment

• health and stocks of fish in commercially harvested areas, informing decisions on when fisheries should open or close
• range of marine animals
• effect of protected area designation on fish and other marine animal populations and other forms of ecological restoration
• effect of fish farming operations on native species
• effect of offshore oil and gas operations or wind farms on marine life
• effects of artificial reefs
• effects of severe storms and other disturbances to marine ecosystems such as harmful algal blooms

Monitoring

• presence of vulnerable, threatened or endangered species
• presence of species dangerous to swimmers
• impacts of climate change and variability
• mapping marine animal diversity, distribution, migration and abundance, including invasive species, and species popular with sport fishers

Resolving mysteries (or not, in the case of Scotland’s Loch Ness monster)

Examples:

Sampling intriguing, remote, and difficult-to-reach intriguing places

• Bob Ballard, who discovered the wreck of the Titanic in 1985, and colleagues on an expedition led by Dwight Coleman of the University of Rhode Island this month collected water from sediments from ancient sea caves including, for example, those about 70-100 meters deep on Osborn Bank in the Channel Islands, about 50 kilometers off the Southern California coast. The caves were above sea level 15,000 years ago and the team searched for ancient paleoshoreline features, and will analyse the samples for DNA that might have been left behind by human or other cave dwellers

Jesse Ausubel comments: “In cool, dark, undisturbed environments eDNA could persist long enough in water in the mud to provide clues about the critters, including humans, that lived in a spot thousands of years earlier.”

• Scientist David Burg provided a set of fresh water samples from the Sea of Galilee and Jordan River to the Rockefeller U team, who found DNA of 15 fish species — more than half of known resident species. They include Galilee tilapia (Sarotherodon galilaeus) and blue tilapia (Oreochromis aureus), species that have sustained Sea of Galilee fishers for thousands of years to the present. In a 2006 book, marine biologist Eugene H. Kaplan speculated that one of those species was at the centre of St. Matthew’s New Testament story of the “miracle of the loaves and fishes” (depicted in a mosaic, dated to 420 A.D., in the Basilica of Sant’Apollinare Nuovo in Ravenna, Italy). There has been similar speculation that a Sea of Galilee tilapia was “St. Peter’s fish,” referred to in another Biblical passage.

• An eDNA test this summer off Inkwell Beach on Martha’s Vineyard, MA discovered hard-to-spot leatherback turtles. Collection of eDNA at Inkwell Beach is part of the plot of Secrets from the Deep, latest of the popular Devlin Quick teenage detective books whose author, New York’s former sex crimes prosecutor Linda Fairstein, will attend the conference.

Last year, several dead leatherback washed ashore on the island, perhaps killed by boats. A GoFish eDNA turtle ‘dipstick’ might alert boaters to take extra care.

• In June 2018, Dr. Stoeckle and colleague Jennifer Miksis-Olds sampled water from 500 meters depth to find elusive mid-water fish — species very easy to miss with nets on expensive trawls.

Tracking and mapping migrations of vulnerable, threatened, endangered and other species

• In a major expedition this year, scientists led by Stanford Prof. Barbara Block at Hopkins Marine Station documented predators and prey in the White Shark Café — an area of the Pacific Ocean about half-way between Hawaii and the west coast of North America mysteriously visited regularly by white sharks. To determine what draws these predatory sharks to these seemingly inhospitable waters, they deployed a combination of satellite tags on white sharks, underwater robots, wind-powered Saildrones, and eDNA sampling to identify how and why animal species use these waters.

• For three years, The Rockefeller University researchers have successfully monitored fish migrations in New York’s East and Hudson Rivers using only eDNA tests on weekly water samples. Over 30 months, the data snapshots created a moving picture of the presence or absence of several key fish species passing through, the results correlating closely with prior migration studies done with fishnet trawls.
• Meanwhile, for 12 years New York City has been trying to coax the Alewife species of herring back to a former breeding habitat in the Bronx River, building fish ladders and reintroducing spawning adults. eDNA sampling of an 18-mile stretch of river this summer turned up no juveniles after the adults left to return the ocean, suggesting the need for further rehabilitation efforts.

Health and safety

• Researchers have used eDNA to ‘sniff’ for sharks around beaches, and this year confirmed that a California boy’s shark bite was delivered by a Great White.
• New York high school students drew 1 litre samples of water weekly from the fishing pier at Coney Island during the spring and summer of 2017 and discovered 34 species of marine life had passed by, including sharks and rays.

Invasive species

• Foreign invader and pest species — both plant and animal — can be located and monitored quickly, easily and less expensively using eDNA instead of traditional methods. Examples of species already targeted in this way include lionfish in Bermuda, Asian black-spined toad and red-eared slider turtles in Australian waters, zebra mussels in the Great Lakes, and clams in the lakes of California and Nevada.
• In Wisconsin, researchers documented five invasive species of marine zooplankton in the ballast water of ships plying Lake Superior, including the eDNA of a “bloody red shrimp” originally from the Black Sea area.

Encouraging citizen science

• Students from Boynton Middle School are in a collaboration with Cornell University to find invasive fish species in their part of upstate New York.
• And a Westchester high school senior spent the past year tracking water-loving mammals — river otter, muskrat, racoon, and beaver — by testing eDNA in streams in upstate New York and Rhode Island.

Limitations

Finding the eDNA of some species might not indicate its living presence in the vicinity. In their study of fish migration in the rivers surrounding Manhattan, for example, The Rockefeller University researchers found the DNA of species thought to have passed through humans and the wastewater treatment system — tilapia, salmon, red snapper — species you shouldn’t find swimming in the Hudson River. eDNA could therefore help identify vulnerable or threatened species being sold as food in local stores and restaurants.

Meanwhile, experts expect newer technologies will better detect the amount of DNA in a water sample but high concentrations might not indicate an abundance of animals passing through the water. It might be caused by an animal that is spawning, wounded or decaying, for example.

Says Alison Watts of the University of New Hampshire: “Modern genetic and acoustic tools provide complementary data identifying organisms at a range of distances, to comprehensively detect aquatic species. eDNA and passive acoustic monitoring are evolving technologies which may transform our understanding of marine communities.”

At the conference, Dr. Watts and co-author Jennifer Miksis-Olds will present a new paper (available at http://bit.ly/2zuyrqo): “The Ocean as a Living Sensor: Environmental DNA and Acoustics for Detecting Marine Life.”

Among many new eDNA-related technologies

Researchers working towards the automation and simplification of eDNA sampling are pursuing several interconnected technological directions. For example:

• Using drones to collect water samples
• Extracting eDNA from a water sample in the field (as it is easier to store DNA (a bit of goo on a filter) than the much larger water sample
• Sequencing and analysing DNA in situ on board a sampling device, such as a remotely controlled glider, with digital results stored or relayed by satellite

Cold Spring Harbor “subway lines”

This is an innovation for analysing sequence data, with free and open access for all. It works for more than just eDNA sequences (microbiomes, etc.) but it works great for sequences eDNA’ers generate. (See https://dnasubway.cyverse.org/ and https://learning.cyverse.org/projects/dnasubway_guide/en/latest/step8.html)

At the University of Maryland, meanwhile, 3D printing is being deployed to create an ocean floor device that houses a water filter and pump that can collect eDNA samples at any depth.

California’s Monterey Bay Aquarium Research Institute is trying to integrate and automate collection of water, filtering of eDNA from water, and sequencing of the filtered DNA. Autonomous underwater vehicles and gliders could collect the water samples over large areas without sending humans out to sea.

Potential illustrations:
http://bit.ly/2FCqHZy
http://bit.ly/2P5R4qi

Background: eDNA

Almost 20 years ago, ecologist Pierre Taberlet of the Laboratoire d’Ecologie Alpine in France envisioned noninvasive sampling allowing genetic studies of free-ranging animals without the need to capture or even observe them.

After a decade of work, the technique emerged in papers such as: Species detection using environmental DNA from water samples, by Gentile Francesco Ficetola, Claude Miaud, Francois Pompanon, Pierre Taberlet, August 2008.

Taberlet’s fellow pioneers included Danish geneticist Eske Willerslev, who obtained ancient DNA directly from ice cores, and American marine biologist, Ann Bucklin, whose “Zoogene” project initiated in 2000 created a database of DNA type sequences for about 300 species of zooplankton.

Taberlet’s applications occurred mainly in freshwater habitats (paper here: http://bit.ly/2TNF0xM). In the US, champions of the technique have included David Lodge of Cornell University, also mainly in a freshwater context. Lodge appreciated the charisma of eDNA in titles of his papers such as Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA, and ‘Sight unseen’, detection of rare aquatic species using environmental DNA.

In April, 2018, Taberlet co-authored with Aurelie Bonin, Lucie Zinger, and Eric Coissac the first book about eDNA: Environmental DNA For Biodiversity Research and Monitoring. The book aims to demonstrate the power and potential of environmental DNA as a research and conservation tool; describe available techniques and protocols; and guide researchers in efficient production of high-quality eDNA data and facilitate proper analysis and interpretation.

Marine eDNA 101: a Primer click here: http://bit.ly/2FDOBnC

Comments

“eDNA can turn millions of people into trustworthy environmental detectives.” – Linda Fairstein, New York lawyer and author of the Alexandra Cooper detective books

“Over 1,000 miles from shore we were able in 48 hours to identify the presence of white sharks in the water column beneath the ship using nanopore eDNA sequencing at sea. Censusing our oceans — knowing what is there or what we are losing — will be easier to document in the next decade with these powerful techniques.” – Barbara Block, Prothro Professor in Marine Sciences, Stanford University

“The Mid-Atlantic region is a leader in developing and deploying eDNA science and technology, and can benefit enormously because of the importance of marine fisheries and other living marine resources, and the need to minimize conflicts with navigation and proposed offshore wind farms that contribute to our Blue Economy.” – Tony MacDonald, Director, Urban Coast Institute, Monmouth University

National Conference on Marine Environmental DNA

Nov. 29-30, The Rockefeller University, 1230 York Ave, New York, NY

Speakers, agenda, click here: http://bit.ly/2zqxOPj

To conclude the conference, Monmouth University will recognize the president of the National of Academy of Sciences, Dr. Marcia McNutt with its Champion of the Ocean award. As director of the Monterey Bay Aquarium Research Institute, Dr. McNutt invested heavily in genomics and technologies for ocean observation that now cause the revolution in eDNA.

Organizers

• Jason Adolf, Monmouth University
• Liz Alter, York College, CUNY
• Jesse Ausubel, Rockefeller University
• Chris Chambers, NOAA
• Sam Chew Chin, York College, CUNY
• Alison Cucco, Cold Spring Harbor Laboratory
• Keith Dunton, Monmouth University
• Paul Gaffney, Monmouth University
• Jeanne Garbarino, Rockefeller University
• Thomas Herrington, Monmouth University
• Yuan Liu, NOAA
• Tony MacDonald, Monmouth University
• Christine Marizzi, Cold Spring Harbor Laboratory
• Bruce Nash, Cold Spring Harbor Laboratory
• Thomas Noji, NOAA
• Beth Phelan, NOAA
• Megan Phifer-Rixey, Monmouth University
• Howard Rosenbaum, Wildlife Conservation Society
• Mark Stoeckle, Rockefeller University
• Dennis Suszkowski, Hudson River Foundation

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About the Monmouth-Rockefeller University Partnership

In 2015, Monmouth University and The Rockefeller University entered into a five-year agreement to pursue collaborative activities supporting ocean research, education and marine policy. The partnership is the fruit of Monmouth University’s successful philanthropic Marine Science and Policy Initiative Challenge Grant campaign, and an especially generous gift of Joan and Robert Rechnitz.

Collaboration between Monmouth University’s Urban Coast Institute (UCI) and The Rockefeller University’s Program for the Human Environment (PHE) offers a rare opportunity for timely, flexible support of influential marine science and policy. Speedy, reliable, affordable use of environmental DNA fragments, or eDNA, to detect the presence and abundance of marine species is one focus of the initiative.

The National Conference on Marine Environmental DNA is the third of four annual conferences in the Marine Science & Policy Series, which are alternating between the campuses of Monmouth in West Long Branch, N.J., and Rockefeller in New York City. Prior conferences addressed the nation’s priorities in Ocean Exploration and the region’s Blue Economy.

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Coverage:

National Geographic,

• English (8 million): New DNA tool ‘changes everything in marine science’, click here
• Italian (236,000): I progressi della genetica rivoluzionano la biologia marina, click here

Vineyard Gazette, Swimming With the Fishes, Naming Them Too, click here

Columbia Basin Fish and Wildlife Bulletin, Leading Practitioners Of eDNA Science Gather To Discuss New Tool’s Possibilities, click here

IndoAsian News Service, New ‘Go Fish’ tool to study marine life, click here

News release in full, click here

Full coverage summary, click here

Far from special: Humanity’s tiny DNA differences are ‘average’ in animal kingdom

Paper offers new insights into evolution; as with humans, over 90 percent of animal species today likely originated 100,000-200,000 years ago

Researchers report important new insights into evolution following a study of mitochondrial DNA from about 5 million specimens covering about 100,000 animal species.

Mining “big data” insights from the world’s fast-growing genetic databases and reviewing a large literature in evolutionary theory, researchers at The Rockefeller University in New York City and the Biozentrum at the University of Basel in Switzerland, published several conclusions today in the journal Human Evolution. Among them:

• In genetic diversity terms, Earth’s 7.6 billion humans are anything but special in the animal kingdom. The tiny average genetic difference in mitochondrial sequences between any two individual people on the planet is about the same as the average genetic difference between a pair of the world’s house sparrows, pigeons or robins. The typical difference within a species, including humans, is 0.1% or 1 in 1,000 of the “letters” that make up a DNA sequence.
• Genetic variation – the average difference in mitochondria DNA between two individuals of the same species – does not increase with population size. Because evolution is relentless, however, the lack of genetic variation offers insights into the timing of a species’ emergence and its maintenance.
• The mass of evidence supports the hypothesis that most species, be it a bird or a moth or a fish, like modern humans, arose recently and have not had time to develop a lot of genetic diversity. The 0.1% average genetic diversity within humanity today corresponds to the divergence of modern humans as a distinct species about 100,000 – 200,000 years ago – not very long in evolutionary terms. The same is likely true of over 90% of species on Earth today.
• Genetically the world “is not a blurry place.” Each species has its own specific mitochondrial sequence and other members of the same species are identical or tightly similar. The research shows that species are “islands in sequence space” with few intermediate “stepping stones” surviving the evolutionary process.

Among 1st “big data” insights from a growing collection of mitochondrial DNA

“DNA barcoding” is a quick, simple technique to identify species reliably through a short DNA sequence from a particular region of an organism. For animals, the preferred barcode regions are in mitochondria – cellular organelles that power all animal life. (See also http://bit.ly/2HGduvD)

The new study, “Why should mitochondria define species?” relies largely on the accumulation of more than 5 million mitochondrial barcodes from more than 100,000 animal species, assembled by scientists worldwide over the past 15 years in the open access GenBank database maintained by the US National Center for Biotechnology Information.

The researchers have made novel use of the collection to examine the range of genetic differences within animal species ranging from bumblebees to birds and reveal surprisingly minute genetic variation within most animal species, and very clear genetic distinction between a given species and all others.

“If a Martian landed on Earth and met a flock of pigeons and a crowd of humans, one would not seem more diverse than the other according to the basic measure of mitochondrial DNA,” says Jesse Ausubel, Director of the Program for the Human Environment at The Rockefeller University, where the research was led by Senior Research Associate Mark Stoeckle and Research Associate David Thaler of the University of Basel, Switzerland.

“At a time when humans place so much emphasis on individual and group differences, maybe we should spend more time on the ways in which we resemble one another and the rest of the animal kingdom.”

Says Dr. Stoeckle: “Culture, life experience and other things can make people very different but in terms of basic biology, we’re like the birds.”

“By determining the genetic variety within species of the animal kingdom, made possible only recently by the burgeoning number of DNA sequences, we’ve documented the absence of human exceptionalism.”

Says. Dr. Thaler: “Our approach combines DNA barcodes, which are broad but not deep, from the entire animal kingdom with more detailed sequence information available for the entire mitochondrial genome of modern humans and a few other species. We analyzed DNA barcode sequences from thousands of modern humans in the same way as those from other animal species.”

“One might have thought that, due to their high population numbers and wide geographic distribution, humans might have led to greater genetic diversity than other animal species,” he adds. “At least for mitochondrial DNA, humans turn out to be low to average in genetic diversity.”

“Experts have interpreted low genetic variation among living humans as a result of our recent expansion from a small population in which a sequence from one mother became the ancestor for all modern human mitochondrial sequences,” says Dr. Thaler.

“Our paper strengthens the argument that the low variation in the mitochondrial DNA of modern humans also explains the similar low variation found in over 90% of living animal species – we all likely originated by similar processes and most animal species are likely young.”

Genetic variation does not increase with population

The study results represent a surprise given predictions found in textbooks, and based on mathematical models of evolution, that the bigger the population of a species, the greater the genetic variation one expects to find.

“Is genetic diversity related to the size of the population?” asks Dr. Stoeckle. “The answer is no. The mitochondrial diversity within 7.6 billion humans or 500 million house sparrows or 100,000 sandpipers from around the world is about the same.”

The paper notes, however, that evolution is relentless, that species are always changing, and, therefore, the degree of variation within a given species offers a clue into how long ago it emerged distinctly — in other words, the older the species the greater the average genetic variation between its members.

Evolutionary bottlenecks: the fresh new beginning of a species

While asteroids and ice ages have played major roles in evolutionary history, scientists speculate that another great driver may have been the microbial world, notably viruses, which periodically cull populations, leaving behind only those able to survive the deadly challenge.

“Life is fragile, susceptible to reductions in population from ice ages and other forms of environmental change, infections, predation, competition from other species and for limited resources, and interactions among these forces,” says Dr. Thaler. Adds Dr. Thaler, “The similar sequence variation in many species suggests that all of animal life experiences pulses of growth and stasis or near extinction on similar time scales.”

“Scholars have previously argued that 99% of all animal species that ever lived are now extinct. Our work suggests that most species of animals alive today are like humans, descendants of ancestors who emerged from small populations possibly with near-extinction events within the last few hundred thousand years.”

‘Islands in sequence space’

Another intriguing insight from the study, says Mr. Ausubel, is that “genetically, the world is not a blurry place. It is hard to find ‘intermediates’ – the evolutionary stepping stones between species. The intermediates disappear.”

Dr. Thaler notes: “Darwin struggled to understand the absence of intermediates and his questions remain fruitful.”

“The research is a new way to show that species are ‘islands in sequence space.’ Each species has its own narrow, very specific consensus sequence, just as our phone system has short, unique numeric codes to tell cities and countries apart.”

Adds Dr. Thaler: “If individuals are stars, then species are galaxies. They are compact clusters in the vastness of empty sequence space.”

The researchers say that with the bones or teeth of an ancient hominid, like those found in southern France or northern Spain, scientists might shed further light on the rate of evolution of the human species.

“It would be very exciting if over the next few years physical anthropologists and others were able to compare mitochondrial DNA from hominid species over the last 500,000 years,” says Dr. Stoeckle.

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Today’s study,

“Why should mitochondria define species?” published as an open-access article (DOI: 10.14673/HE2018121037) in the journal

Human Evolution,

builds on earlier work by Drs. Stoeckle and Thayer, including an examination of the mitochondrial genetic diversity of humans vs. our closest living and extinct relatives. The amount of color variation within each red box of the Klee diagram illustrates the far greater mitochondrial diversity among chimpanzees and bonobos than among living humans.

About The Rockefeller University
http://www.rockefeller.edu/about

About the Program for the Human Environment
phe.rockefeller.edu

The work was carried out in part through the Marine Science and Policy Initiative of the Program for the Human Environment (The Rockefeller University) and the Urban Coast Institute (Monmouth University).

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Media coverage highlights:

Naked DNA in water tells if fish have arrived

Scientists demonstrate harmless, economical new way to log fish migration;

Environmental DNA researchers foresee a revolution in how we assess the movement, diversity, distribution and abundance of fish

For the first time, scientists have recorded a spring fish migration simply by conducting DNA tests on water samples.

“Environmental DNA” (eDNA), strained from one-liter (quart) samples drawn weekly from New York’s East and Hudson Rivers over six months last year, revealed the presence or absence of several key fish species passing through the water on each test day.

The convenient weekly data snapshots created a moving picture that largely reinforced and correlated with knowledge hard won from migration studies conducted over many years with fishnet trawls.

The Rockefeller University study, published April 12 in PLOS ONE, pioneers a way to monitor fish migrations that involves a fraction of the effort and cost of trawling, all without harming the fish.

It demonstrates as well another in the growing list of eDNA uses, which experts expect to upend soon the way fish assessments are conducted worldwide.

Indeed, eDNA science is quickly granting humanity a very old wish: an easy way to estimate the abundance and distribution of diverse fish species and other forms of marine life in the dark waters of rivers, lakes, and seas.

Led by Senior Research Associate Mark Stoeckle and co-authored by student researcher Lyubov Soboleva and Rockefeller University scientist Zachary Charlop-Powers, the project originated in the university’s Program for the Human Environment under Director Jesse Ausubel, co-founder of the Census of Marine Life, a decade-long international collaboration that ended in 2010.

As they swim, fish leave traces of their DNA in the water, sloughed off their slimy, gelatinous outer coating or in excretions, for example.

Says Dr. Stoeckle: “Researchers in Europe first demonstrated that relatively small volumes of freshwater and seawater environments have enough invisible bits of DNA floating in them to detect dozens of fish species.”

Introducing the time element: an important and innovative twist

“By conducting a series of tests over time, collecting surface water from the same point on both the Hudson and East Rivers once a week for six months, we’ve successfully demonstrated a novel way to record fish migration.”

“Our work also offers clear new insight into the durability of DNA in the water, which persists despite currents and tides with a goldilocks quality just right for research. If the DNA disappeared too quickly, we couldn’t obtain an informative sample; if it persisted for too long, there would be too much DNA in the water to yield useful, timely insights.”

In all, Dr. Stoeckle and colleagues obtained the DNA of 42 fish species, including most (81%) of the species known to be locally abundant or common, and relatively few (23%) of the uncommon ones.

“We didn’t find anything shocking about the fish migration — the seasonal movements and the species we found are known already,” says Dr. Stoeckle. “That’s actually good news, adding to evidence that eDNA is a good proxy. It amazes me that we can get the same information from a small cup of water and a large net full of fish.”

Some species, he adds, couldn’t yet be distinguished, notably some in the herring family, which have identical sequences in the region of DNA used for testing. As well, some of the DNA obtained couldn’t be identified because the DNA reference library, while steadily growing, is incomplete.

“We knew that we had DNA from a fish, but couldn’t pinpoint the species,” says Dr. Stoeckle.

Pacific red snapper DNA in the Hudson River?

Notes Mr. Ausubel, the tests turned up the DNA from fish commonly eaten by New Yorkers but not known to inhabit the city’s waters — European sea bass and Nile tilapia, for example — leading the group to conclude that the DNA of those species entered via the wastewater system.

“We found the DNA of species that we think passed through humans and the wastewater treatment system — tilapia, salmon and red snapper, for example — species you shouldn’t find swimming in the Hudson River,” he says, adding that eDNA could therefore help identify endangered species being sold as food in local stores and restaurants.

One other surprise, says Dr. Stoeckle: the extraordinarily frequent occurrence in samples of Atlantic menhaden, a member of the herring family and a cornerstone species in the food chain.

“One could test the hypothesis that larger populations of menhaden associate with the recent wave of whales in New York Harbor, or the celebrated 2013 dolphin sighting in the East River,” he says.

Also intriguingly common: the oyster toadfish, which looks like it could eat a corned beef sandwich, and a strong candidate for the emblematic fish of New York City.

Says Dr. Stoeckle: “Identifying all local species with eDNA, including all the uncommon or rare ones, might be accomplished by collecting and analyzing more water, collecting at different locations, or using a different DNA analysis approach that targets each species individually.”

A new frontier: estimating fish abundance from eDNA

The research found that the number of “reads” of eDNA — how many copies of tiny DNA segments of a particular species turn up in a sample — roughly corresponds with data from net surveys.

And that, according to Mr. Ausubel, opens an intriguing new frontier: eDNA may provide a major advance on catch data from trawls, the traditional proxy for assessing the abundance of certain types of fish in a body of water.

Next steps involve fine tuning calibrations, comparing more eDNA “reads” and results with data from traditional surveys conducted with nets and sonar. It is unclear, for example, if 100 DNA “reads” indicate the presence of 1 fish or 10 fish.

Also to be determined: the rate at which different fish and other marine species shed DNA. How much DNA is shed by a particular fish species, or by a hard shelled turtle, for example?

“If future research confirms that an index of species’ abundance can be derived from the naked DNA extracted from water, it would address a challenge that has bedevilled scientists for ages. And it could easily improve the rationality with which fish quotas are set and the quality and reliability of their monitoring around the world,” says Mr. Ausubel.

“Blood tests,” he adds, “have now become so sensitive they can provide evidence of all kinds of conditions in a human body, so it is not really surprising that that we can now learn much more from tests for biological molecules circulating in water.”

Creative eDNA uses

Beyond low cost and wide applicability, advantages of eDNA surveying include the ability to collect samples without disturbing the fish — bow waves and engine noise cause many fish to move out of the way and avoid boats conducting net or sonar surveys.

Also, nets often cannot reach bottom and are difficult to deploy in some environments. For example, it’s hard to sample fish in the East River, a notoriously difficult channel for ships of all kinds with its strong currents and rocky sides.

“eDNA sampling can be done using standard biology laboratory equipment and techniques” says Rockefeller co-author Zachary Charlop-Powers. “It uses the same methods that medical researchers employ to analyze human “microbiomes,” for instance. With current technology, the marginal cost not including labor is about $50/sample when samples are analyzed in batches of 20 or more. Future DNA sequencing developments may lower the cost.”

After water is drawn, it is filtered to concentrate the DNA for extraction. The target segment of the DNA is amplified and then sent to a lab for “next-generation” sequencing, the result of which–a record of all the DNA sequences in the sample–is fed into computer software that counts the number of copies of each sequence and searches for matches in an online public reference library.

“Concerned officials and citizen scientists could monitor, for example, the impact of a new oyster farm on local fish populations,” added Lyubov Soboleva, a student at New York City’s John Bowne High School and in Rockefeller’s Learning At The Bench After School Program (LAB-ASP) and Summer Science Research Program (SSRP).

Other examples of eDNA’s practical uses include:

• The NY Port Authority, prohibited from dredging when winter flounder are in the water, could time the task more easily, and inexpensively
• Tourism boards could identify which lakes contain pickerel, pike, perch and other species popular with anglers
• Given that certain species inhabit only waters of a certain quality, their absence could become an early sentinel of pollution problems.
• eDNA could help check for invasive or exotic species transported in a ship’s ballast, or inform the study of genetic diversity among fish stocks.

“Though this field of research is still in its early days, it’s easy to foresee many applications for eDNA sampling,” says Tony MacDonald, Director of the Urban Coast Institute at Monmouth University, and a collaborator on scientific projects at Rockefeller University’s Program for the Human Environment. “It represents a potentially important advance in our capability to detect, understand and more effectively and efficiently manage fisheries and marine biodiversity.” “If you are a fishery scientist, there is a very good chance that you are going to be using eDNA as part of your work in the next 10 years.”

Central Park

The research follows an earlier study The Rockefeller University group conducted in Central Park with the help of high school students, in which over a dozen species were identified in a half-cup of pond water drawn from “The Loch.”

The species found:

• 7 fish (black crappie, golden shiner, brown bullhead, largemouth bass, banded killifish, bluegill, and pumpkinseed)
• 6 mammals and birds (racoon, songbird, mallard, norway rat, dog, and human)

Surveys done in the same pond using electrofishing methods turned up two fish species not found using eDNA. On the other hand, the electrofishing survey missed two species found by eDNA.

Other tests of eDNA’s reliability were conducted successfully using water from the tanks of the New York City Aquarium.

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About The Rockefeller University

http://www.rockefeller.edu/about

About the Program for the Human Environment

The work on aquatic DNA was carried out as part of the Marine Science and Policy Initiative of the Program for the Human Environment (The Rockefeller University) and the Urban Coast Institute (Monmouth University).

About Program for the Human Environment eDNA studies

https://phe.rockefeller.edu/barcode/blog/nycnj-aquatic-vertebrate-edna-project/

Images (available for download at http://bit.ly/2oHSWd4)

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Example coverage:

Agence France Presse, France, US scientists track fish migration using DNA in water samples, click here

Reuters, UK, Fish tracked from DNA ‘finprints’ left in waters off New York, click here

BBC World Service Radio (Science in Action, starts at the 47 sec. mark, 5 1/2 minutes), click here

Deutsche Presse Agentur (DPA / APA), Germany / Austria, DNA-Spuren im Wasser entlarven Fische, click here

Nautisme – Météo Consult, France, Le mouvement des espèces de poissons traqué par l’ADN laissé dans l’eau, click here

NY1, USA, High School Student, University Researchers Team Up for Breakthrough on Documenting Fish in NY Waters, click here

IndoAsian News Service, India, DNA test on river waters reveals fish diversity, click here

Agencia EFE, Spain, El ADN residual puede revolucionar el conocimiento de las especies marinas, click here

Focus, Italy, Dna ambientale per lo studio della fauna acquatica, click here

The Conversation, USA, Fishing for DNA: Free-floating eDNA identifies presence and abundance of ocean life, click here

United Press International, USA, Migrating fish leave behind a trail of DNA, click here

Nature World News, USA, ‘Environmental DNA’ Helps Scientists in Monitoring Fish Migration, click here

Asbury Park Press, USA, DNA used to track fish in Hudson and East rivers, click here

RAI Vista News, Russia, Миграцию рыбы отследили через образцы ДНК Источник, click here

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Full coverage summary, click here

News release in full, click here

Global ‘barcode blitz’ accelerates; 450 experts converge on Adelaide Nov. 28-Dec. 3

The newfound scientific power to quickly “fingerprint” species via DNA is being deployed to unmask quack herbal medicines, reveal types of ancient Arctic life frozen in permafrost, expose what eats what in nature, and halt agricultural and forestry pests at borders, among other applications across a wide array of public interests.

The explosion of creative new uses of DNA “barcoding” — identifying species based on a snippet of DNA — will occupy centre stage as 450 world experts convene at Australia’s the University of Adelaide Nov. 28 to Dec. 3.

DNA barcode technology has already sparked US Congressional hearings by exposing widespread “fish fraud” — mislabelling cheap fish as more desirable and expensive species like tuna or snapper. Other studies this year revealed unlisted ingredients in herbal tea bags.

Example coverage: Associated Press, click here; Canadian Press, click here, Agencia EFE (Spanish) click here

Coverage summary: click here

Full news release: click here

23 Aug 2011

Eight million, seven hundred thousand species (give or take 1.3 million).

That is a new, estimated total number of species on Earth — the most precise calculation ever offered — with 6.5 million species found on land and 2.2 million (about 25 percent of the total) dwelling in the ocean depths.

Announced today by Census of Marine Life scientists, the figure is based on an innovative, validated analytical technique that dramatically narrows the range of previous estimates. Until now, the number of species on Earth was said to fall somewhere between 3 million and 100 million.

Furthermore, the study, published today by PLoS Biology, says a staggering 86% of all species on land and 91% of those in the seas have yet to be discovered, described and catalogued.

Full text, click here

Coverage summary, click here

Sample coverage: stories by The Associated Press, click here; the Washington Post, click here, and the New York Times, click here.  New York Times editorial, click here.