A coronavirus epidemic hit East Asia 20,000 years ago, new study shows
By Amy Sood and Zixu Wang, CNN 

© NIAID A microscope image of SARS-CoV-2, the coronavirus that causes Covid-19.


Over the past 20 years, people have faced a series of outbreaks caused by coronaviruses, including SARS, MERS, and Covid-19. But humans may have faced the disease millennia ago, new research suggests.


A team of researchers from Australia and the United States has found evidence of a coronavirus epidemic that broke out more than 20,000 years ago in East Asia, according to a study published in the Current Biology scientific journal on Thursday.

In the study, the researchers studied the genomes of more than 2,500 people from 26 different populations around the world. They pinpointed the earliest interaction of the human genome with coronaviruses, which left genetic imprints on the DNA of modern-day people in East Asia.

The genomes they studied contain evolutionary information about humans tracing back hundreds of thousands of years, said lead author Yassine Souilmi -- information we've only learned to decode in recent years.

Viruses work by making copies of themselves. However, they don't have their own tools to do the duplication. "So they actually depend on a host, and that's why they invade a host and then they hijack their machinery to create copies of themselves," Souilmi said.

That hijacking of human cells leaves a mark we can now observe -- offering concrete evidence our ancestors were once exposed to and adapted to coronaviruses.

In the genomes, researchers found these genetic signals related to a coronavirus in five different populations located in China, Japan and Vietnam. The epidemic could have spread further beyond these countries, Souilmi added, but data isn't available in other parts of the region, so there's no way of knowing.

From these populations, Souilmi said the researchers found an affected group developed a beneficial mutation which helped to protect them from the coronavirus. Those with the mutation had "an edge" in survival, he said -- meaning over time, the population was made up of more people with the mutation than without.

"Over a long period of time, and along the exposure, this leaves a very, very clear marking in the genomes of their descendants," Souilmi said. "And that's the signature we actually use to detect this ancient epidemic, and also the timing of this ancient epidemic."

The study said the coronavirus plague occurred separately among different regions and spread across East Asia as an epidemic.

However, scientists don't know how ancient people lived through the epidemic, partially because it wasn't clear whether it was something seasonal like a flu, or continuous -- like the Covid-19 pandemic -- that infects people and keeps spreading all the time.

Genome study reveals East Asian coronavirus epidemic 20,000 years ago

QUEENSLAND UNIVERSITY OF TECHNOLOGY

Research News

VIDEO: AN INTERNATIONAL STUDY HAS DISCOVERED A CORONAVIRUS EPIDEMIC BROKE OUT IN THE EAST ASIA REGION MORE THAN 20,000 YEARS AGO, WITH TRACES OF THE OUTBREAK EVIDENT IN THE GENETIC MAKEUP... view more 

CREDIT: QUT

Genome study reveals East Asian coronavirus epidemic 20,000 years ago

An international study has discovered a coronavirus epidemic broke out in the East Asia region more than 20,000 years ago, with traces of the outbreak evident in the genetic makeup of people from that area.

Professor Kirill Alexandrov from CSIRO-QUT Synthetic Biology Alliance and QUT's Centre for Genomics and Personalised Health, is part of a team of researchers from the University of Arizona, the University of California San Francisco, and the University of Adelaide who have published their findings in the journal Current Biology.

In the past 20 years, there have been three outbreaks of epidemic severe coronaviruses: SARS-CoV leading to Severe Acute Respiratory Syndrome, which originated in China in 2002 and killed more than 800 people; MERS-CoV leading to Middle East Respiratory Syndrome, which killed more than 850 people, and SARS-CoV-2 leading to COVID-19, which has killed 3.8 million people.

But this study of the evolution of the human genome has revealed another large coronavirus epidemic broke out thousands of years earlier.

"The modern human genome contains evolutionary information tracing back tens of thousands of years, like studying the rings of a tree gives us insight into the conditions it experienced as it grew," Professor Alexandrov said.

In the study, the researchers used data from the 1000 Genomes Project, which is the largest public catalogue of common human genetic variation, and looked at the changes in the human genes coding for SARS-CoV-2 interacting proteins.

They then synthetised both human and SARS-CoV-2 proteins, without using living cells, and showed that these interacted directly and specifically pointed to the conserved nature of the mechanism coronaviruses use for cell invasion.

"Computational scientists on the team applied evolutionary analysis to the human genomic dataset to discover evidence that the ancestors of East Asian people experienced an epidemic of a coronavirus-induced disease similar to COVID-19," Professor Alexandrov said.

East Asian people come from the area that is now China, Japan, Mongolia, North Korea, South Korea, and Taiwan.

"In the course of the epidemic, selection favoured variants of pathogenesis-related human genes with adaptive changes presumably leading to a less severe disease," Professor Alexandrov said.

"By developing greater insights into the ancient viral foes, we gain understanding of how genomes of different human populations adapted to the viruses that have been recently recognised as a significant driver of human evolution.

"Another important offshoot of this research is the ability to identify viruses that have caused epidemic in the distant past and may do so in the future.

"This, in principle, enables us to compile a list of potentially dangerous viruses and then develop diagnostics, vaccines and drugs for the event of their return."

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CAPTION

Professor Kirill Alexandrov

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QUT

 

When did the first COVID-19 case arise?

Novel analysis suggests much earlier, more rapid spread than confirmed cases imply

PLOS

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IMAGE: IMAGE PRESENTS GLOBAL COVID-19 SPREAD ACROSS COUNTRIES OVER TIME. COUNTRIES MARKED IN YELLOW--UPPER BOUND OF A 95% CONFIDENCE INTERVAL OF THE ESTIMATED ORIGIN DATE INCLUDES PARTICULAR DATE (I.E., PROBABILITY OF... view more 

CREDIT: ROBERTS DL ET AL., 2021, PLOS PATHOGENS

Using methods from conservation science, a new analysis suggests that the first case of COVID-19 arose between early October and mid-November, 2019 in China, with the most likely date of origin being November 17. David Roberts of the University of Kent, U.K., and colleagues present these findings in the open-access journal PLOS Pathogens.

The origins of the ongoing COVID-19 pandemic remain unclear. The first officially identified case occurred in early December 2019. However, mounting evidence suggests that the original case may have emerged even earlier.

To help clarify the timing of the onset of the pandemic, Roberts and colleagues repurposed a mathematical model originally developed by conservation scientists to determine the date of extinction of a species, based on recorded sightings of the species. For this analysis, they reversed the method to determine the date when COVID-19 most likely originated, according to when some of the earliest known cases occurred in 203 countries.

The analysis suggests that the first case occurred in China between early October and mid-November of 2019. The first case most likely arose on November 17, and the disease spread globally by January 2020. These findings support growing evidence that the pandemic arose sooner and grew more rapidly than officially accepted.

The analysis also identified when COVID-19 is likely to have spread to the first five countries outside of China, as well as other continents. For instance, it estimates that the first case outside of China occurred in Japan on January 3, 2020, the first case in Europe occurred in Spain on January 12, 2020, and the first case in North America occurred in the United States on January 16, 2020.

The researchers note that their novel method could be applied to better understand the spread of other infectious diseases in the future. Meanwhile, better knowledge of the origins of COVID-19 could improve understanding of its continued spread.

Roberts adds, "The method we used was originally developed by me and a colleague to date extinctions, however, here we use it to date the origination and spread of COVID-19. This novel application within the field of epidemiology offers a new opportunity to understand the emergence and spread of diseases as it only requires a small amount of data."

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Peer-reviewed; Simulation / modelling

In your coverage please use this URL to provide access to the freely available article in PLOS Pathogens: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009620

Citation: Roberts DL, Rossman JS, Jari? I (2021) Dating first cases of COVID-19. PLoS Pathog 17(6): e1009620. https://doi.org/10.1371/journal.ppat.1009620

Funding: I.J. was funded by The J.E. Purkyn? Fellowship of the Czech Academy of Sciences. DLR and JSR received no specific funding for this work. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

 

COVID-19 origins still a mystery

Study finds virus was 'highly human adapted'

FLINDERS UNIVERSITY

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IMAGE: PROFESSOR NIKOLAI PETROVSKY, FLINDERS UNIVERSITY. view more 

CREDIT: FLINDERS UNIVERSITY

Scientists using computer modelling to study SARS-CoV-2, the virus that caused the COVID-19 pandemic, have discovered the virus is most ideally adapted to infect human cells - rather than bat or pangolin cells, again raising questions of its origin.

In a paper published in the Nature journal Scientific Reports, Australian scientists describe how they used high-performance computer modelling of the form of the SARS-CoV-2 virus at the beginning of the pandemic to predict its ability to infect humans and a range of 12 domestic and exotic animals.

Their work aimed to help identify any intermediate animal vector that may have played a role in transmitting a bat virus to humans, and to understand any risk posed by the susceptibilities of companion animals such as cats and dogs, and commercial animals like cows, sheep, pigs and horses.

The scientists, from Flinders University and La Trobe University, used genomic data from the 12 animal species to painstakingly build computer models of the key ACE2 protein receptors for each species. These models were then used to calculate the strength of binding of the SARS-CoV-2 spike protein to each species' ACE2 receptor.

Surprisingly, the results showed that SARS-CoV-2 bound to ACE2 on human cells more tightly than any of the tested animal species, including bats and pangolins. If one of the animal species tested was the origin, it would normally be expected to show the highest binding to the virus.

"Humans showed the strongest spike binding, consistent with the high susceptibility to the virus, but very surprising if an animal was the initial source of the infection in humans," says La Trobe University Professor David Winkler.

The findings, originally released on the ArXiv preprint server, have now been peer reviewed and published in Scientific Reports (Springer Nature).

"The computer modelling found the virus's ability to bind to the bat ACE2 protein was poor relative to its ability to bind human cells. This argues against the virus being transmitted directly from bats to humans. Hence, if the virus has a natural source, it could only have come to humans via an intermediary species which has yet to be found," says Flinders affiliated Professor Nikolai Petrovsky.

The team's computer modelling shows the SARS-CoV-2 virus also bound relatively strongly to ACE2 from pangolins, a rare exotic ant-eater found in some parts of South-East Asia with occasional instances of use as food or traditional medicines. Professor Winkler says pangolins showed the highest spike binding energy of all the animals the study looked at - significantly higher than bats, monkeys and snakes.

"While it was incorrectly suggested early in the pandemic by some scientists that they had found SARS-CoV-2 in pangolins, this was due to a misunderstanding and this claim was rapidly retracted as the pangolin coronavirus they described had less than 90% genetic similarity to SARS-CoV-2 and hence could not be its ancestor," Professor Petrovsky says.

This study and others have shown, however, that the specific part of the pangolin coronavirus spike protein that binds ACE2 was almost identical to that of the SARS-CoV-2 spike protein.

"This sharing of the almost identical spike protein almost certainly explains why SARS-CoV-2 binds so well to pangolin ACE2. Pangolin and SARS-CoV-2 spike proteins may have evolved similarities through a process of convergent evolution, genetic recombination between viruses, or through genetic engineering, with no current way to distinguish between these possibilities," Professor Petrovsky says.

"Overall, putting aside the intriguing pangolin ACE2 results, our study showed that the COVID-19 virus was very well adapted to infect humans."

"We also deduced that some domesticated animals like cats, dogs and cows are likely to be susceptible to SARS-CoV-2 infection too," Professor Winkler adds.

The extremely important and open question of how the virus came to infect humans has two main explanations currently. The virus may have passed to humans from bats through an intermediary animal yet to be found (zoonotic origin), but it cannot yet be excluded that it was released accidently from a virology lab. A thorough scientific, evidence-based investigation is needed to determine which of these explanations is correct.

How and where the SARS-CoV-2 virus adapted to become such an effective human pathogen remains a mystery, the researchers conclude, adding that finding the origins of the disease will help efforts to protect humanity against future coronavirus pandemics.

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The article, In silico comparison of SARS-CoV-2 spike protein-ACE2 binding affinities across species and implications for virus origin (2021) by Sakshi Piplani (Flinders University), Puneet Kumar Singh (Vaxine Pty Ltd), David A. Winkler (La Trobe, Monash, University of Nottingham, CSIRO Data61) and Nikolai Petrovsky (Flinders University, Vaxine) has been published in Scientific Reports (link) DOI: 10.1038/s41598-021-92388-5

Cold weather cost New England electric customers nearly $1.8 billion in one month; A new study suggests ways to mitigate fuel shortages

CARNEGIE MELLON UNIVERSITY

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In New England, constraints in the supply of natural gas have led to nearly a quarter of all unscheduled power plant outages. In a new study, researchers used data from power plant failures in the 2010s to develop a supply curve of the costs required for generators to mitigate fuel shortages in the region. The study found that storing both oil and gas on-site could reduce dependence by power plants on gas grids in geographic areas with few pipelines.

The study was conducted by researchers at Carnegie Mellon University (CMU), The Pennsylvania State University, and the North American Electric Reliability Corporation. It is published in The Electricity Journal.

"Gas supply issues have affected the ability to generate electricity during times of high demand," says Jay Apt, Professor at CMU's Tepper School of Business and Department of Engineering and Public Policy, who co-authored the study. "For example, it's estimated that the extended cold weather event in January 2014 cost New England electricity ratepayers roughly $1.8 billion."

New England has no native gas production, so fuel assurance for natural gas power plants is an area of concern; half of all installed power plant capacity in the region is fueled primarily by gas and nearly half of all electricity comes from natural gas power plants. When heating demand spikes on key gas supply pipelines to the region, those pipelines cannot always meet all the region's heating demand and demand for power-plant fuel at the same time.

The effect of gas supply constraints on Northeastern power generators can be seen by comparing the average fraction of total unscheduled generator outages due to gas fuel unavailability to those during days of high demand for heating. In recent periods of high electricity and gas demand, unscheduled gas shortages accounted for 5 to 25 percent of all unscheduled generator outages during every hour of those periods.

Dual fuel capability--that is, the ability to burn either oil or gas--is one way to mitigate gas supply shortages, and about a third of ISO New England's natural gas power plant capacity has dual fuel capability (ISO New England is an independent, not-for-profit corporation that manages the high-voltage power system over six New England states). But building dual fuel storage tanks for the remainder has been considered prohibitively expensive.

In 2019, one of the study's coauthors--Seth Blumsack, Professor of Energy Policy and Economics at The Pennsylvania State University--developed a model to identify where to build distributed gas storage capability in New England. To increase reliability of the interdependent gas and electricity grids, Blumsack and his students identified economically optimal sites for distributed gas storage in the region. They concluded that power plant sites might be the optimal locations for gas storage.

In this study, researchers analyzed a database of historical power plant failures, using data from the North American Electric Reliability Corporation--NERC--a not-for-profit international reliability organization. They determined what the cost of on-site fuel storage at natural gas power plants would have to be to mitigate the worst gas shortages in New England during the seven years studied.

The study assessed 54 gas-fired units operating within ISO New England that had NERC reports of full or partial outages due to unscheduled fuel shortages between 2012 and 2018. For each unit, researchers calculated the overnight capital, fuel carrying, and land costs (when applicable) required for gas generators in the region to assure that fuel supplies using fuel storage systems were sized according to their most extreme fuel shortage failure during the study period. They also examined distributed compressed natural gas storage at generator sites and dual fuel capabilities with oil storage. The researchers compared these costs to those of installing batteries with enough capacity to cover historically observed fuel outages.

The researchers found that approximately 2.4 gigawatts (GW) of ISO New England's gas-fired capacity failed one or more times per year due to fuel shortages; up to 0.5 GW of these units failed simultaneously on three separate occasions. Of these, approximately 2 GW of gas-fired capacity could be mitigated by on-site fuel storage. Furthermore, gas plants would recoup their investment in oil backup fuel if they were compensated with an additional $3 to $7 per megawatt-hour (MWh) during their normal operations.

Using on-site compressed natural gas storage is more expensive ($7 to $16/MWh). The capital expenses associated with either on-site fuel storage option would be less than installing battery backup for resource adequacy at current battery prices, the study concluded.

"Our estimates differ from previous studies because they are based on actual failure events rather than arbitrary fuel supply durations," explains Gerad Freeman, an Energy Systems Research Engineer at Pacific Northwest National Laboratory, the study's lead author. "As such, they have implications for moving forward on increasing dual fuel capacity to increase the resilience of power systems in New England and other regions with similar gas supply constraints."

The authors note that limitations to this research include that they may oversize the dual fuel storage by basing fuel storage tank sizes on the longest observed gas outage at each unit, that batteries can receive some revenue by providing grid services during non-emergencies, and that compressed natural gas storage might help balance gas supply and demand.

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The study was funded in part by the Carnegie Mellon Climate and Energy Decision Making Center, formed through a cooperative agreement between the National Science Foundation and CMU, and in part by the Electric Power Research Institute.

 

NASA helps map impact of COVID-19 lockdowns on harmful air pollution

NASA/GODDARD SPACE FLIGHT CENTER

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IMAGE: CHANGES IN PM 2.5 CONCENTRATIONS OVER CHINA FOR FEBRUARY 2019 AND 2020 DERIVED FROM SATELLITE OBSERVATIONS. view more 

CREDIT: NASA'S EARTH OBSERVATORY

Early in the pandemic, it was expected that satellite imagery around the world would show cleaner air as a result of COVID-19 lockdowns. But not all pollutants were taken out of circulation. For tiny airborne-particle pollution, known as PM 2.5, researchers using NASA data found that variability from meteorology obscured the lockdown signals when observed from space.

"Intuitively you would think if there is a major lockdown situation, that we would see dramatic changes, but we didn't," said Melanie Hammer, a visiting research associate at Washington University in St. Louis who led the study. "It was kind of a surprise that the effects on PM 2.5 were modest."

PM 2.5 describes the mass of nose-level particles, often produced anthropogenically, that are smaller than 2.5 micrometers, or roughly 30 times smaller than the width of a human hair. PM 2.5 is small enough to linger in the atmosphere, and, when inhaled, is associated with increased risk of heart attack, cancer and a host of other implications for human health.

By combining NASA spacecraft data with ground-based monitoring and an innovative computer modeling system, the scientists mapped PM 2.5 levels across China, Europe and North America during the early months of the pandemic. The researchers found seasonal differences in PM 2.5 between recent years were driven primarily by the natural variability of the meteorology, not by pandemic lockdowns.

Published June 23 in the journal Science Advances, the new research integrates data from NASA's Terra and Aqua satellites, as well as meteorological modeling input from the NASA Global Modeling and Assimilation Office.

The meteorological effects analyzed in the study include changes in the sources of mineral dust, the way pollutants react to sunlight in the atmosphere, mixing and heat transfer, as well as the removal of pollutants from the atmosphere by precipitation.

PM 2.5 is among the most complicated pollutants to study because its particle size, composition and toxicity vary greatly depending on its source and environmental conditions.

A gas pollutant known as nitrogen dioxide, or NO2, did see dramatic declines during the lockdowns. A major byproduct of fuel burning by trucks, cars and other vehicles, the decline of nitrogen dioxide was visible from space and from the ground. Images of clear, blue skies where heavy smog had been the norm flooded popular news and social media, suggesting COVID-19 has drastically decreased all pollution in general.

When nitrogen dioxide is emitted, it can also interact with other chemicals in the atmosphere and form PM 2.5. However, the two pollutants do not have a linear relationship. Half as much nitrogen dioxide in the atmosphere does not necessarily lead to half as much PM 2.5 produced by nitrogen dioxide.

Because PM 2.5 often comes from the same sources as NO2, the researchers also began to question whether the lockdowns resulted in a decline of PM 2.5.

Early pandemic studies of PM 2.5 changes analyzed data from ground monitoring sites, which test the surrounding air. But because those ground sites are few and far between, their data alone are unable to piece together the bigger picture of PM 2.5 concentrations in the air, Hammer said.

"We were most interested in looking at changes in PM 2.5 because PM 2.5 is the leading environmental risk factor for premature mortality globally," Hammer said. "We decided to look again, using a more complete picture from satellite images."

The study was co-led by Randall Martin at Washington University in St. Louis, who pioneered research integrating modeling and remote sensing to study atmospheric pollutants such as PM 2.5.

"Many countries in the world have no operational PM 2.5 monitoring at all," Martin said. "These tools enable insight into ground level PM 2.5 at the global or regional scale."

To ensure a comprehensive analysis, the team focused on regions with extensive ground monitoring systems in place and compared monthly estimates of PM 2.5 from January to April in 2018, 2019 and 2020.

When the researchers compared PM 2.5 levels over the three years during the months that coincided with each region's lockdown phases, there weren't many clear signals over North America or Europe. The most significant lockdown-related differences were detected in China.

"We found the most clearly detectable signal was a significant reduction over the North China Plain, where the strictest lockdowns were concentrated," Hammer said.

To figure out whether the lockdown was responsible for that signal, and several smaller ones dotted around the areas surveyed, the team ran different "sensitivity simulations" using GEOS-Chem, a chemical transport model to which Martin's team helps lead.

CAPTION

Changes in simulated PM 2.5 in China during the lockdown periods due to meteorology and emissions. The image on the left shows 2020-2019 concentrations due to meteorology with emissions from transportation held constant. The image on the right combines the effects of meteorology with a 50% transportation emission reduction.

CREDIT

NASA's Earth Observatory

They simulated a scenario where anthropogenic emissions of nitrogen dioxide were held constant and meteorological variability was solely responsible for year over year differences in PM 2.5 during the key lockdown months. They also ran simulations in which they reduced transportation-related emissions and other anthropogenic sources of nitrogen dioxide, mirroring lockdown, when fewer people were driving and fewer industrial sites were operational.

They found the simulation where both meteorology and transportation effects were included most closely mirrored the real-world situation.

"Tackling PM 2.5 is a very complex issue, and you have to take into account its multiple sources, not just the fact that fewer people are on the road," Hammer said. "Just decreasing transportation emissions would not be enough to account for the complexity of the problem."

Most satellites sample the atmosphere through vertical columns spanning the ground to the edge of space. Identifying the concentrations of airborne particles near the surface, where they affect air quality, cannot be determined from these satellites alone.

The satellite data used in this study, referred to as aerosol optical depth, were related to surface PM 2.5 concentrations using GEOS-Chem, which simulates the composition of the atmosphere, the reactions and relationships among its different components, and the way they move horizontally as well as vertically through the air.

The model is a sophisticated tool that helps paint a more complete picture of air quality, said Ralph A. Kahn, senior research scientist at NASA's Goddard Space Flight Center in Greenbelt, Maryland and adjunct professor at University of Maryland in College Park.

"The bigger story is actually the global characterization of air quality, especially in places where there aren't surface monitors," said Kahn, who was part of the study. "The satellites provide an important piece of it, the models provide an important piece of it, and the ground-based measurements make an important contribution as well."

Hammer suspects the change in PM 2.5 levels over the North China Plain was more apparent because of the region's higher pollution levels during "normal" times.

The new insights also highlight a relevant point that may not at first be intuitive: Average PM 2.5 levels have been dropping steadily in North America and Europe. Pollution concentrations that are already low are more difficult to change, Hammer said.

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By Brandie Jefferson
Washington University in St. Louis

Media Contact: Roberto Molar Candanosa, NASA's Earth Science News Team

Coral offspring physiology impacted by parental exposure to intense environmental stresses

Environmental disturbances, such as bleaching events, can have lasting consequences across generations of corals

BERMUDA INSTITUTE OF OCEAN SCIENCES

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IMAGE: A RECENT PUBLICATION IN THE JOURNAL GLOBAL CHANGE BIOLOGY DOCUMENTS THE RESULTS OF TWO YEARS OF EXPERIMENTS CONDUCTED AT BIOS BY A TEAM OF RESEARCHERS INCLUDING KEVIN WONG (SHOWN HERE),... view more 

CREDIT: KEVIN WONG

Adult corals that survive high-intensity environmental stresses, such as bleaching events, can produce offspring that are better suited to survive in new environments. These results from a series of experiments conducted at the Bermuda Institute of Ocean Sciences (BIOS) in 2017 and 2018 are deepening scientists' understanding of how the gradual increase of sea surface temperatures and other environmental disturbances may influence future coral generations.

Researchers on the project included BIOS marine ecologists Samantha de Putron and Gretchen Goodbody-Gringley (now with the Central Caribbean Marine Institute), ecophysiologist Hollie Putnam at the University of Rhode Island (URI), and Kevin Wong, then a first-year doctoral student at URI. Primary funding came from the Heising-Simons Foundation International, Ltd. with additional funding from the National Geographic Society and the Canadian Associates of BIOS (CABIOS).

The team spent last year working the data into a manuscript, which was published this month in the journal Global Change Biology and listed Wong as the first author. Wong, now nearing the end of his fourth year of studies at URI under the mentorship of Putnam, plans to graduate in May 2022.

"We know parental history influences the characteristics of offspring in corals, however the experimental design used in this study provides us with a unique perspective on how multiple types of thermal events can accumulate over time and have lasting consequences across generations," Wong said.

Coral Collection and Study The multi-year field and lab-based study began in the summer of 2017. Departing from BIOS on a small boat with diving gear, the team collected 40 adult Porites astreoides (mustard hill) corals from two different reef sites northwest of Bermuda: a patch reef (Crescent Reef), which is located in a shallower lagoon environment, and a rim reef (Hog Reef) which is a barrier reef more exposed to open ocean conditions.

They next placed the live corals in the then newly-constructed BIOS mesocosm facility, where large outdoor aquaria "flow-through" seawater systems allowed researchers to control and adjust water temperature in the tanks for completing the study.

A variety of baseline data were collected on the corals in each colony, such as metabolic rates and the density of Symbiodinaceae, the symbiotic algae that live within the coral tissues. To simulate a thermal stress event, the adult corals were exposed to two different temperature treatments--ambient (84°F or 29°C) or heated (88°F or 31°C)--for a period of 21 days over their reproductive period. Afterward, the team assessed the physiology of the adult corals, looking at key functions such as respiration and photosynthetic rates. They also monitored the release of coral larvae and assessed its physiology, measuring the larval size and density of Symbiodinaceae within each larva, among other factors.

Upon completion of the experiment, the adult corals were divided in half and reciprocally transplanted, with half of the fragments positioned in the new environments and half returned to their originating environments. All of the fragments remained in place until the summer of 2018, when they were re-collected, and the physiologies of both adult corals and coral larvae were assessed in the same manner as in 2017.

A Stronger Coral Generation The results of this two-year investigation showed that adult corals that experienced the thermal stress event produced offspring more capable of thriving in their current environment. This means that parent corals that experience stressors may be able to "pre-condition" their offspring to survive in new environments in the following year. The results also indicate that high-intensity environmental stress events, such as bleaching, can have lasting impacts on adult colonies and how they produce their offspring.

"The coral used in this study is a notoriously resilient coral and these findings potentially demonstrate how this species is so persistent across the Caribbean," Putnam said. "Not all coral species are this robust to environmental stressors. However, this system allows us to unravel the mechanisms leading to resilience and identify which corals are most sensitive to climate change."

CAPTION

The team of researchers, which included BIOS marine ecologists Samantha de Putron and Gretchen Goodbody-Gringley (now with the Central Caribbean Marine Institute) and ecophysiologist Hollie Putnam (URI), utilized the outdoor mesocosm facility at BIOS to study the impacts of a simulated thermal stress event on adult corals collected from two different reef sites northwest of Bermuda. The results of the study showed that parent corals that experience stressors may be able to "pre-condition" their offspring to survive in new environments in the following year.

CREDIT

Rebecca Ju

Long-time Member of BIOS Community Wong, 27, is a familiar face at BIOS, having first arrived on campus in the summer of 2014 as a CABIOS intern when he spent 12 weeks working with de Putron on a research project investigating the role of temperature and light on the growth and survivorship of juvenile mustard hill corals from two different reef zones. The following year, he received CABIOS funding to work with then-faculty member Gretchen Goodbody-Gringley on a project focused on the reproductive ecology of corals from mesophotic reef ecosystems, deeper-water reefs which typically extend from 100 to almost 500 feet (30 to 150 meters) in depth.

While presenting the results of his research at the 2016 International Coral Reef Symposium meeting in Hawaii, he had the opportunity to interview with Putnam for URI's Biological and Environmental Sciences doctoral program. Wong then returned to BIOS to spend six months in 2016 as a teaching assistant for several summer and fall courses. He also received BIOS Grants-in-Aid funding for a research project with Goodbody-Gringley and de Putron focused on the reproductive ecology of mustard hill coral from various reef sites around Bermuda, resulting in a publication in the journal Coral Reefs.

"It is wonderful to see an undergraduate intern progress to a successful graduate student who is publishing manuscripts," de Putron said. "Many years of hard work and plenty of exhausting, yet fun, days in the field and laboratory all culminated in interesting and critically relevant discoveries that further our understanding of coral resilience."

Now, a year from graduation, Wong is diving deeper into the mechanisms that drive environmental memory within and across coral generations at a molecular level. By using approaches such as metabolomics (the identification and quantification of metabolic by-products), transcriptomics (quantification of gene expression), and epigenetics (features that regulate gene expression), Wong aims to determine the key linkages between metabolism and coral bleaching phenotypes at a cellular level.

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PSU study finds chemicals from human activities in transplanted oysters far from population centers

PORTLAND STATE UNIVERSITY

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IMAGE: AMY EHRHART CHECKING TRANSPLANTED OYSTERS ALONG THE PACIFIC COAST. view more 

CREDIT: ELISE GRANEK

Wastewater treatment facilities clean the water that goes down our sinks and flushes our toilets, but they do not remove everything. A recent study by Portland State researchers detected low levels of pharmaceuticals and personal care product chemicals in oysters the team deployed at various distances from wastewater effluent pipes along the Oregon and Washington coast. Elise Granek, professor of environmental science and management at Portland State University, and Amy Ehrhart, a recent graduate of PSU's Earth, Environment, and Society doctoral program, conducted the study.

To explore how aquatic pollution varies based on proximity to wastewater facilities, Ehrhart and Granek placed one-week-old Pacific oysters at wastewater sites (not approved by state agencies as oyster growing sites) and near oyster aquaculture sites (approved for growing oysters) along the Oregon and Washington coastline. Nine and twelve months later, they collected the oysters, measured their health and size, and tested their tissues for pharmaceuticals and chemicals called alkylphenols, which are used in a variety of personal care and industrial products. Alkylphenols are endocrine disruptors that can alter the growth and reproduction of aquatic organisms.

Out of the 63 compounds tested, Granek and Ehrhart found only six in the oysters. The two pharmaceuticals detected in the oysters were miconazole, an over-the-counter drug for fungal infections like Athlete's foot, and virginiamycin, a veterinary antibiotic used in livestock. As expected, the concentrations of pharmaceuticals were higher near the wastewater sites. The condition of the oysters was also poorer at wastewater sites compared to the sites near oyster farms.

Four types of alkylphenols were found in oysters from all the sites.

"This makes sense because they are really ubiquitous," said Ehrhart. "They're found in all sorts of common household and industrial products."

Everyday products like detergents, cosmetics, soaps, and cleaners often contain alkylphenols as do forestry pesticide application mixtures. While detectable, the chemical levels were much lower than reported in other estuarine studies near more populated areas.

"The levels that we found were very low," Ehrhart said. She noted that the levels detected are significantly lower than the Environmental Protection Agency's no effect level for nonylphenol exposure in humans and the Food and Drug Administration's allowable limits for antibiotics in meat. "It's unlikely to pose a risk to human consumers of shellfish," she said. Additionally, the Oregon Department of Agriculture and Washington Department of Health continually monitor and approve areas for shellfish growing to ensure they meet strict water quality standards for food safety.

That said, the very presence of these chemicals in oysters relatively far from wastewater sites and in sparsely populated coastal areas suggests that current wastewater treatment technology, stormwater mitigation strategies, and industrial use guidelines for alkylphenol use may not be sufficient. This could be bad news for aquatic animals, including shellfish.

"It's not an aquaculture-driven problem. It's coming from upstream, but it's making its way to aquaculture and it may be negatively affecting oysters, given other studies on how alkylphenols can affect animals," says Granek. "So it really points to a need to address the sources of these alkylphenols."

Granek suggested that possible solutions for this kind of aquatic pollution include upgrading wastewater treatment plants and creating regulations that target the use of industrial products containing alkylphenols.

Individuals can also do their part by not flushing medications down sinks or toilets and instead using drop boxes available at many pharmacies.

"For the pharmaceuticals it's better disposal, for the alkylphenols it's buying products that don't have them," said Ehrhart.

It can be difficult to determine which products contain alkylphenols just from reading ingredient lists, so Ehrhart suggests looking for the EPA's Safer Choice label. "If you see that on cleaning products and detergents, that means that those products don't have alkylphenols, so they are better for the environment."

The study was published in Marine Pollution Bulletin on June 20.

CAPTION

Amy Ehrhart conducting research with transplanted oysters along the Pacific coast.

CREDIT

Elise Granek