Saturday, January 23, 2021

Scientists present novel approach for monitoring freshwater health

Study describes how the world's smallest portable DNA sequencing device helps simplify the monitoring of bacteria in freshwater ecosystems

ELIFE

Research News

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IMAGE: THE MINION IS A PORTABLE DEVICE THAT CAN SEQUENCE GENETIC MATERIAL SAMPLED FROM THE ENVIRONMENT - HERE, FROM THE RIVER CAM IN CAMBRIDGE, UK. view more 

CREDIT: TEAM PUNTSEQ (CC BY 4.0)

Researchers have used the world's smallest, smartphone-sized DNA sequencing device to monitor hundreds of different bacteria in a river ecosystem.

Writing in the journal eLife, the interdisciplinary team from the University of Cambridge, UK, provide practical and analytical guidelines for using the device, called the MinION (from Oxford Nanopore Technologies), to monitor freshwater health. Their guidelines promise a significantly more cost-effective and simple approach to this work outside the lab, compared to existing methods.

Rowers and swimmers in Cambridge are regularly affected by waterborne infections such as Weil's disease, sometimes leading to public closures of the city's iconic waterways. Monitoring the microbial species in freshwater can help indicate the presence of disease-causing microorganisms and even water pollution. But traditional tests for freshwater bacteria often require well-equipped laboratories and complex methods for growing colonies of individual bacterial species.

"The direct measurement of all bacterial DNA traces in freshwater, an approach known as metagenomics, is a valuable alternative, but still requires large, expensive equipment that can be hard to operate," says Andre Holzer, co-first author and PhD student at the Department of Plant Sciences, University of Cambridge. "We aimed to describe the bacterial species present in the River Cam using the new portable DNA sequencing technology."

The team used the MinION device to sequence the DNA of entire groups of microorganisms found in water samples from the River Cam. But before they could use the sequence data, they needed to optimise their experimental methods and analysis software. "It was essential to account for the quality of this new type of bacterial DNA sequence information," Holzer explains. "We tested many different algorithms for processing the data to find the most accurate methods."

The researchers then used their optimised guidelines to analyse the data and successfully measure the proportions of hundreds of different bacterial species present in the water. They took samples from nine different sites along the river, often sampling the sites at three different time points so they could compare the proportions of species in different locations and seasons.

The team was also able to distinguish closely related, harmful microbial species from non-harmful ones. By comparing the samples from different locations, they found that there were more potentially harmful bacteria and those associated with wastewater downstream of the most built-up, urban areas of the river. Chemical follow-up analyses of the water samples collected from the same urban areas revealed a matching trend of increasing wastewater pollution in those areas.

"Our work shows how MinION and the associated DNA sequencing technology can be used in the effective monitoring of freshwater health," says Lara Urban, co-lead investigator of the work and now an Alexander von Humboldt Research Fellow at the University of Otago, New Zealand. "This expands on the technology's existing applications which include the accurate tracing of viral transmissions between patients during the recent Ebola, Zika and SARS-CoV-19 virus outbreaks."

"We hope our results will encourage other independent scientists and collectives to engage in simplified freshwater management and biodiversity tests around the globe,"concludes senior author Maximilian Stammnitz, a PhD student at the Department of Veterinary Medicine, University of Cambridge.

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References

The paper 'Freshwater monitoring by nanopore sequencing' can be freely accessed online at https://doi.org/10.7554/eLife.61504. Contents, including text, figures and data, are free to reuse under a CC BY 4.0 license.

This study was supported by grants from the OpenPlant Fund (BBSRC), University of Cambridge RCUK Catalyst Seed Fund (Public Engagement Starter Grant), Natural Environment Research Council and Gates Cambridge Trust.

To find out more about the Punting & Sequencing (PuntSeq) project and the team behind it, visit http://www.puntseq.co.uk.

Media contact

Emily Packer, Media Relations Manager
eLife
e.packer@elifesciences.org
01223 855373

About eLife

eLife is a non-profit organisation created by funders and led by researchers. Our mission is to accelerate discovery by operating a platform for research communication that encourages and recognises the most responsible behaviours. We work across three major areas: publishing, technology and research culture. We aim to publish work of the highest standards and importance in all areas of biology and medicine, including Ecology and Microbiology and Infectious Disease, while exploring creative new ways to improve how research is assessed and published. We also invest in open-source technology innovation to modernise the infrastructure for science publishing and improve online tools for sharing, using and interacting with new results. eLife receives financial support and strategic guidance from the Howard Hughes Medical Institute, the Knut and Alice Wallenberg Foundation, the Max Planck Society and Wellcome. Learn more at https://elifesciences.org/about.

To read the latest Ecology research published in eLife, visit https://elifesciences.org/subjects/ecology.

And for the latest in Microbiology and Infectious Disease, see https://elifesciences.org/subjects/microbiology-infectious-disease.

A sea of rubbish: ocean floor landfills

The long journey of litter to seafloor










The Messina Strait, a submarine bridge separating the island of Sicily from the Italian Peninsula, is the area with the largest marine litter density worldwide -more than a million objects per square kilometre in some parts-, as reported in a new review paper published in the journal Environmental Research Letters.

Also, over the next thirty years, the volume of rubbish in the sea could surpass three billion metric tons (Mt), as cited in the study, whose corresponding authors are the experts Miquel Canals, from the Faculty of Earth Sciences of the University of Barcelona, and Georg Hanke from the European Commission's Joint Research Centre (JRC), where scientists carry out research in order to provide independent scientific advice and support to EU policies.

Led by the University of Barcelona, this paper gathers the results of the scientific meeting on macrolitter that took place in May 2018, promoted by the European Commission's Joint Research Centre (JRC) and the German Alfred Wegener Institute (AWI). A team of twenty-five scientists from across the world treated issues such as data needs, methodologies, harmonisation and needs for further development.

The study provides a synthesis of current knowledge on human-sourced materials lying on the seafloor and goes through the methodologies to improve future studies, "highlighting the need to understand litter occurrence, distribution and quantities in order to provide insight for appropriate (policy) measures", notes Georg Hanke, who adds that "the paper also shows the need to employ new methodologies -i.e. imaging approaches- to cover areas that had not been considered previously, and provides tools to enable quantitative assessments such as those under the EU Marine Strategy Framework Directive (MSFD)".

Among other signatories of the article are experts from the University of Açores (Portugal), Alfred Wegener Institute (Germany), Utrecht University (Netherlands), the Norwegian Institute of Marine Research (Norway), the Secretariat of the Barcelona Convention on the protection of the Mediterranean Sea, Monterey Bay Aquarium Research Institute (MBARI, California, United States), the Institute for Global Change of the Japan Agency for Marine Earth Science and Technology Research (JAMSTEC, Japan), IFREMER (France) and Oxford University (United Kingdom), among other institutions.

When litter arrives before humans do

The ocean floor is increasingly accumulating marine litter. Whereas the largest seafloor litter hotspots -likely in the deep sea- are still to be found, plastics have already been found in the deepest point on Earth, the Mariana Trench -at a depth of 10,900 meters- in the Pacific Ocean. In some cases, litter concentrations reach densities comparable to large landfills, experts warn.

Despite the scientific community efforts, "the extent of marine litter on our seas and oceans is not yet fully known. The marine regions most affected by this problem are in landlocked and semi-enclosed seas, coastal bottoms, marine areas under the influence of large river mouths, and places with high fishing activity, even far from land", says Professor Miquel Canals, head of the Consolidated Research Group on Marine Geosciences at UB.

Canals highlights that "the level of waste treatment in coastal countries is decisive: the less treatment -or the more deficient-, the more waste reaching the ocean, and therefore, the ocean floor, which is a problem that affects specially third world countries".

The long journey of litter to seafloor

Plastics, fishing gears, metal, glass, ceramics, textiles and paper are the most abundant materials in seafloor litter hotspots. Geomorphological features, the submarine relief and the nature of the seafloor determine the distribution of litter items on the seabed. Ocean dynamics, --that is, processes such as dense water cascades, ocean currents and storms-- ease the transport and dispersal of litter across the ocean, from coasts to abyssal plains, thousands of meters deep. However, these factors do not occur in all ocean ecosystems and also vary over time and in intensity where they take place.

Due to a gravitational effect, light waste is usually transported along and into marine regions where dense currents flow --i.e. submarine canyons and other submarine valleys-- and where flow lines concentrate, such as nearby large submarine reliefs. Finally, materials transported by ocean dynamics accumulate in depressions and quiet marine areas.

The properties of materials dumped in the marine environment also affect their dispersion and accumulation on the ocean floor. It is estimated that 62% of the dirt accumulated on seabeds is made of plastics, "which is relatively light and easy to transport over long distances. On the other hand, heavy objects such as barrels, cables or nets are usually left at the point where they are initially fell or got entangled", says Canals.

Litter drowns marine life

Litter is a new threat to marine biodiversity. It is already known that nearly 700 marine species, 17% of which are on the IUCN red list, have been affected by this problem in several ways. Seabed entangled fishing gears can cause serious ecological impacts for decades because of ghost fishing. The slow decomposition of fishing nets -usually made of high-strength polymers- aggravates the detrimental effects of this type of waste on the marine ecosystem.

Other human activities -dredging, trawling, etc.- trigger secondary dispersal by remobilization and fragmentation of seafloor litter. In addition, seabed waste concentrations can easily trap other objects, thus generating larger and larger litter accumulations. It is paradoxical that waste may increase the heterogeneity of the substrate, which can benefit some organisms. Some xenobiotic compounds -pesticides, herbicides, pharmaceuticals, heavy metals, radioactive substances, etc.- associated to litter are highly resistant to degradation and endanger marine life. However, the extent of the effects of litter on the habitats of the vast expanses of the deep ocean still is a chapter to be written by the scientific community.

"In the Mediterranean Sea -says Miquel Canals- seafloor marine litter already is a serious ecological problem. In some places of the Catalan coast, there are large accumulations of waste. When there are strong storms, such as Gloria, in January 2020, waves throw this waste on the beach. Some beaches in the country were literally paved with rubbish, thus showing to which extent the coastal seabed is littered. There are also noticeable concentrations of waste in some submarine canyons outside Catalonia".

Robotic technology for large depths

Beach litter and floating garbage can be identified and monitored by simple, low-cost methods. In contrast, the study of seafloor litter is a technological challenge, the complexity of which increases with water depth and remoteness of the marine area to be investigated. The study reviews both methodologies allowing physical sampling of seafloor waste and in situ observations.

New technologies have enabled major advances in the study of the environmental status of the seabed worldwide. The use of unmanned remotely operated vehicles (ROVs) is critical for in situ observation, despite the limitations for physical sampling. Classic technologies such as bottom trawling also have limitations, as they do not allow determining the precise location of the bottom-sampled objects. "Future methodologies should aim at easing the comparison of scientific data from different places. It should also be easier for observation and sampling efforts to generate consistent data sets, something that we are still far from achieving", says Canals.

Avoiding excess waste generation to take care of the planet

Knowledge and data about seafloor litter are necessary for the implementation of the Marine Strategy Framework Directive (MSFD) and other international policy frameworks, including global agreements. The publication shows how research on seafloor macrolitter can inform these international protection and conservation frameworks to prioritize efforts and measures against marine litter and its deleterious impacts.

The authors warn about the need to promote specific policies to minimize such a serious environmental problem. The study also addresses the debate on the removal of litter from the seabed, a management option that should be safe and efficient. In relation to this, the Joint Research Centre (JRC) is co-chairing the MSFD Technical Group on Marine Litter, which provides an information exchange and discussion platform to provide agreed guidance for MSFD implementation.

"Marine litter has reached the most remote places in the ocean, even the least (or never) frequented by our species and not yet mapped by science," says Miquel Canals. "In order to correct something bad, we must attack its cause. And the cause of the accumulation of waste on the coasts, seas and oceans, and all over the planet, is the excess waste generation and spillage in the environment, and poor or insufficient management practices. As humans, we have little or no care at all to prevent litter from accumulating everywhere".

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JAMSTEC's Deep-sea Debris Database [video] |

 EurekAlert! Science News

Improving long-term climate calculations

A new method reduces uncertainties in computer model estimations of climate change over thousands of years.

UNIVERSITY OF COPENHAGEN - FACULTY OF SCIENCE

Research News

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IMAGE: THE APPROACH OF BASTIANSEN ET AL. RESULTS IN MORE ACCURATE ESTIMATIONS OF LONG-TERM WARMING. view more 

CREDIT: TIPES/HP

Climate researchers have found a simple but efficient way to improve estimations of ultimate global warming from complex climate models. The finding is relevant for the evaluation and comparison of climate models and thus for accurate projections of future climate change - especially beyond the year 2100. The study is published in Geophysical Research Letters by Dr. Robbin Bastiaansen and colleagues at the Institute for Marine and Atmospheric Research Utrecht, Utrecht University, The Netherlands. The work is part of the European TiPES project coordinated by the University of Copenhagen, Denmark.

Complex climate models are rarely used to simulate the effect of global warming for a given amount of CO2 beyond a couple of centuries into the future. The reason for this is twofold. First, even on a supercomputer, such a model must already run for months to obtain a 150-year projection; reaching the end of a long simulation is therefore not practical. Second, policymakers are mainly concerned about how much climate change a given amount of CO2 will cause within the coming decades.

Earth warms for more than 1000 years

In the real world, however, temperatures continue to go up for more than a thousand years after CO2 is added to the Earth system. A typical climate model simulation therefore estimates less than half of the summed global warming. That is a challenge because, in order to improve models, it is necessary to compare and evaluate models. The final global mean temperature from a given amount of CO2 is an important parameter in the evaluation of a model.

The traditional way of solving this problem is to take the two most predominant results (called observables) from the simulation of the first 150 years and use these to estimate at which global mean surface temperature a full simulation would have ended. The two observables most often used are the global mean surface temperature and the radiation imbalance at the top of the atmosphere. This leads to a rather good estimation but the approach introduces considerable uncertainty - mainly underestimating total global warming.

More accurate estimates

However, an advanced climate model produces a multitude of other data on, for example future ocean currents, weather patterns, sea ice extend, ground color, climate belts, precipitation, and many more.

"And what we did, was add another observable on top of the two traditional ones. That is the idea. If you use additional observables, you will improve estimates over longer time scales. And our work is proof that this is possible," explains Dr. Robbin Bastiaansen.

In the best-case scenario, the new method halved the uncertainty compared to traditional methods.

The work is expected to be useful in assessing tipping points in the Earth system, as studied in the TiPES project, funded by the EU Horizon 2020.


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Earth takes thousands of years to reach the final global mean temperature.

CREDIT

TiPES/HP


With a little help from their friends, older birds breed successfully

UNIVERSITY OF GRONINGEN

Research News

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IMAGE: THIS IS A SEYCHELLES WITH A COLOUR-CODED RING. THESE RINGS MAKE IT POSSIBLE TO STUDY INDIVIDUAL ANIMALS ON THE ISLAND OF COUSIN. view more 

CREDIT: MARTIJN HAMMERS, UNIVERSITY OF GRONINGEN

The offspring of older animals often have a lower chance of survival because the parents are unable to take care of their young as well as they should. The Seychelles warbler is a cooperatively breeding bird species, meaning that parents often receive help from other birds when raising their offspring. A study led by biologists from the University of Groningen shows that the offspring of older females have better prospects when they are surrounded by helpers. This impact of social behaviour on reproductive success is described in a paper that was published on 19 January in the journal Evolution Letters.

The Seychelles warbler lives on a tiny island called Cousin Island, which is part of the Republic of Seychelles, an island country in the Indian Ocean. On Cousin Island, there are just over 300 birds, nearly all of them ringed with colour rings so that each individual bird can be recognized. The population has been studied for several decades. Martijn Hammers, a biologist at the University of Groningen, has frequently visited the island and is studying the interaction between social behaviour and ageing among these birds.

Natural laboratory

Cousin Island resembles a natural laboratory, Hammers explains. 'It is isolated, so there is no influx of new birds and birds rarely migrate to other islands. Furthermore, from 1985 onwards, we have ringed almost all warblers on the island, which allows us to observe their behaviour, reproduction and survival.' The Seychelles warbler is a cooperative breeder: each territory is held by a dominant couple and they sometimes allow helpers to stay there. 'These helpers are usually their own young from earlier breeding attempts and they can assist in breeding and in feeding the chicks. In return, these helpers can use the resources that are available in the territory and female helpers are occasionally allowed to lay an egg in the dominant birds' nest.'

As the parent birds age, their ability to feed their young diminishes. In this new study, Hammers and his colleagues from the University of Groningen (The Netherlands) and the University of East Anglia (UK) wanted to find out whether social behaviour, in particular the care for offspring provided by helpers, affects the breeding success of older birds. To this end, Hammers analysed over 20 years of data on these birds. He specifically looked at the frequency of chick feeding and the survival of young birds.


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This picture shows two Seychelles warblers on the island of Cousin, feeding a young bird that has left the nest.

CREDIT

Charlie Davies


Humans

Our prediction was that having helpers would be beneficial for the survival of chicks from older birds. And this turned out to be true, but only for older females,' says Hammers. The males of this species contribute less to feeding the chicks than females and their behaviour may therefore be less important for offspring survival than the behaviour of the females. 'That may be because the males are not always sure that they are feeding their own offspring since 40 per cent of the young are not their own,' explains Hammers.

The data show that while helpers compensate for age-related declines in female reproductive performance, individual helpers do not work harder when the dominant female is older. 'It appears to be a more passive process, in that older birds recruit more helpers who collectively help more.' The implications of his findings are that it is beneficial for older female birds to display social behaviour - allowing helpers to live in their territory - since it increases their reproductive success. 'It would be interesting to see if this is a general principle that also applies to other animal species, or even to humans.'

In a previous study, Hammers showed that getting help with the kids also slows down the ageing of the parents. 'This effect was also most pronounced in older females. This new study provides additional evidence for an interplay between age and cooperative breeding.'


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This picture shows University of Groningen biologist Martijn Hammers during fieldwork on Cousin. He holds a Seychelles warbler.

CREDIT

Charlie Davies


Reference: Martijn Hammers, Sjouke A. Kingma, Lotte A. van Boheemen, Alexandra M. Sparks, Terry Burke, Hannah L. Dugdale, David S. Richardson and Jan Komdeur: Helpers compensate for age-related declines in parental care and offspring survival in a cooperatively breeding bird. Evolution Letters 19 January 2021



Tiny particles that seed clouds can form from trace gases over open sea

Understanding previously undocumented source of new particle formation will improve models of aerosols, clouds, and their impact on Earth's climate

DOE/BROOKHAVEN NATIONAL LABORATORY

Research News

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IMAGE: BROOKHAVEN LAB ATMOSPHERIC SCIENTIST CHONGAI KUANG (CENTER) WITH ART SEDLACEK (LEFT) AND STEPHEN SPRINGSTON (RIGHT) ABOARD ARM'S GULFSTREAM-159 (G-1) AIRCRAFT DURING A 2010 ATMOSPHERIC SAMPLING MISSION THAT WAS NOT PART... view more 

CREDIT: IMAGE COURTESY OF THE U.S. DEPARTMENT OF ENERGY ATMOSPHERIC RADIATION MEASUREMENT (ARM) USER FACILITY.

UPTON, NY - New results from an atmospheric study over the Eastern North Atlantic reveal that tiny aerosol particles that seed the formation of clouds can form out of next to nothingness over the open ocean. This "new particle formation" occurs when sunlight reacts with molecules of trace gases in the marine boundary layer, the atmosphere within about the first kilometer above Earth's surface. The findings, published in the journal Nature Communications, will improve how aerosols and clouds are represented in models that describe Earth's climate so scientists can understand how the particles--and the processes that control them--might have affected the planet's past and present, and make better predictions about the future.

"When we say 'new particle formation,' we're talking about individual gas molecules, sometimes just a few atoms in size, reacting with sunlight," said study co-author Chongai Kuang, a member of the Environmental and Climate Sciences Department at the U.S. Department of Energy's Brookhaven National Laboratory. "It's interesting to think about how something of that scale can have such an impact on our climate--on how much energy gets reflected or trapped in our atmosphere," he said.

But modeling the details of how aerosol particles form and grow, and how water molecules condense on them to become cloud droplets and clouds, while taking into consideration how different aerosol properties (e.g., their size, number, and spatial distribution) affect those processes is extremely complex--especially if you don't know where all the aerosols are coming from. So a team of scientists from Brookhaven and collaborators in atmospheric research around the world set out to collect data in a relatively pristine ocean environment. In that setting, they expected the concentration of trace gases to be low and the formation of clouds to be particularly sensitive to aerosol properties--an ideal "laboratory" for disentangling the complex interactions.

"This was an experiment that really leveraged broad and collaborative expertise at Brookhaven in aerosol observations and cloud observations," Kuang said. Three of the lead researchers--lead authors Guangjie Zheng and Yang Wang, and Jian Wang, principal investigator of the Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) campaign--began their involvement with the project while working at Brookhaven and have remained close collaborators with the Lab since moving to Washington University in St. Louis in 2018.

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Using an aircraft outfitted with 55 atmospheric instrument systems, scientists traversed horizontal tracks above and through clouds and spiraled down through atmospheric layers to provide detailed measurements of aerosols and cloud properties. The aircraft data were supplemented by measurements made by ground-based radars and other instruments.

CREDIT

Image courtesy of the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility.

Land and sea

The study made use of a long-term ground-based sampling station on Graciosa Island in the Azores (an archipelago 850 miles west of continental Portugal) and a Gulfstream-1 aircraft outfitted with 55 atmospheric instrument systems to take measurements at different altitudes over the island and out at sea. Both the ground station and aircraft belong to the DOE Office of Science's Atmospheric Radiation Measurement (ARM) user facility, managed and operated by a consortium of nine DOE national laboratories.

The team flew the aircraft on "porpoise flights," ascending and descending through the boundary layer to get vertical profiles of the particles and precursor gas molecules present at different altitudes. And they coordinated these flights with measurements taken from the ground station.

The scientists hadn't expected new particle formation to be happening in the boundary layer in this environment because they expected the concentration of the critical precursor trace gases would be too low.

"But there were particles that we measured at the surface that were larger than newly formed particles, and we just didn't know where they came from," Kuang said.

The aircraft measurements gave them their answer.

"This aircraft had very specific flight patterns during the measurement campaign," Kuang said. "They saw evidence that new particle formation was happening aloft--not at the surface but in the upper boundary layer." The evidence included a combination of elevated concentrations of small particles, low concentrations of pre-existing aerosol surface area, and clear signs that reactive trace gases such as dimethyl sulfide were being transported vertically--along with atmospheric conditions favorable for those gases to react with sunlight.

"Then, once these aerosol particles form, they attract additional gas molecules, which condense and cause the particles to grow to around 80-90 nanometers in diameter. These larger particles then get transported downward--and that's what we're measuring at the surface," Kuang said.

"The surface measurements plus the aircraft measurements give us a really good spatial sense of the aerosol processes that are happening," he noted.

At a certain size, the particles grow large enough to attract water vapor, which condenses to form cloud droplets, and eventually clouds.

Both the individual aerosol particles suspended in the atmosphere and the clouds they ultimately form can reflect and/or absorb sunlight and affect Earth's temperature, Kuang explained.


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Results from a study of clouds and aerosols conducted in the Azores revealed that new particles can seed the formation of clouds in the marine boundary layer--the atmosphere up to about a kilometer above Earth's surface--even over the open ocean, where the concentration of precursor gases was expected to be low.

CREDIT

Image courtesy of the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility.

Study implications

So now that the scientists know new aerosol particles are forming over the open ocean, what can they do with that information?

"We'll take this knowledge of what is happening and make sure this process is captured in simulations of Earth's climate system," Kuang said.

Another important question: "If this is such a clean environment, then where are all these precursor gases coming from?" Kuang asked. "There are some important precursor gases generated by biological activity in the ocean (e.g., dimethyl sulfide) that may also lead to new particle formation. That can be a nice follow-on study to this one--exploring those sources."

Understanding the fate of biogenic gases such as dimethyl sulfide, which is a very important source of sulfur in the atmosphere, is key to improving scientists' ability to predict how changes in ocean productivity will affect aerosol formation and, by extension, climate.

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The research was funded by the DOE Office of Science, DOE's Atmospheric System Research, and by NASA. In addition to the researchers from Brookhaven Lab and Washington University, the collaboration included scientists from Pacific Northwest National Laboratory; Missouri University of Science and Technology; the University of Washington, Seattle; NASA Langley Research Center; Science Systems and Applications Inc. in Hampton, Virginia; the Max Planck Institute for Chemistry in Mainz, Germany; and the Scripps Institution of Oceanography, University of California, San Diego.

Brookhaven National Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Follow @BrookhavenLab on Twitter or find us on Facebook.

Related Links

Online version of this news release with photos and graphics

Scientific paper: "New particle formation in the remote marine boundary layer"

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Rediscovery of the 'extinct' Pinatubo volcano mouse

A small mouse rediscovered on a volcano that erupted 30 years ago provides hope for wildlife conservation in the Philippines



IMAGE: THE REDISCOVERED VOLCANO MOUSE, THOUGHT TO BE EXTINCT. view more
CREDIT: (C) DANNY BALETE, FIELD MUSEUM

In June 1991, Mount Pinatubo, a volcanic peak on the Philippine Island of Luzon, literally blew its top. It was the second-most powerful volcanic eruption of the 20th century, ten times stronger than Mount Saint Helens, and its effects were devastating. Lava and ash spewed into the surrounding environment in the Zambales Mountains, pooling in layers up to 600 feet thick in the valleys. Following the eruption, powerful typhoons and monsoon rains triggered landslides and ash flows that continued for many months. Eight hundred people lost their lives, and the lush forests that covered the mountain prior to the eruption were destroyed or severely damaged. In recent years, scientists returned to the region to survey the surviving mammal populations, and in a new paper in the Philippine Journal of Science, the team announced the rediscovery of a species of mouse that had long been feared to be extinct.

"When Pinatubo blew up, probably the last thing on anyone's mind was that a little species of mouse was thought to live only on that one mountain, and might well have become extinct as a result. What we've learned subsequently really blew us away", says Larry Heaney, the Negaunee Curator of Mammals at Chicago's Field Museum and one of the paper's authors.

In early 2011 and again in 2012, twenty years after the eruption, Field Museum researcher Danilo (Danny) Balete went to Mt. Pinatubo to study its mammal fauna. Over the course of several months, Balete and his team of field assistants (including local men from the Aeta tribe) surveyed the mammals on the mountain, from the bottom to near the top where the forest had been devastated by the eruption.

"Most of our field work on Luzon and elsewhere in the Philippines has been in natural forested habitats where mammals are most common" says Eric Rickart, Curator of Vertebrates at the Natural History Museum of Utah and lead author on the paper, "but Danny couldn't pass up an opportunity to see how mammals were faring on Mt. Pinatubo."

There were no surveys of the mammals on Mt. Pinatubo prior to the eruption. However, specimens housed in the US National Museum of Natural History provided some records from lower elevations around the mountain. "Most of these early records were for common species of bats collected in the 1950s," says Heaney, "but one specimen was particularly intriguing-a small rodent that became the type specimen, and only example, of a new species described in 1962 as Apomys sacobianus, the Pinatubo volcano mouse."

Conditions on Mt. Pinatubo were very harsh, and the survey work by Balete's team was both grueling and dangerous. Even after 20 years, evidence of the eruption was everywhere. The landscape was very unstable due to the constantly eroding ash and lahar deposits that made working in the steep terrain hazardous. It also greatly slowed the process of plant succession. Vegetation was a sparse mix of native and non-native plants, dense stands of grass (including bamboo), shrubs, low-growing vines, and few trees-all the characteristic of early stage second-growth habitat. It was a far cry from the old-growth tropical forest that covered the mountain before the eruption.

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Ecosystem surrounding Mount Pinatubo, recovering after the eruption in 1990.

CREDIT

(c) Danny Balete, Field Museum


Field surveys of small non-flying mammals elsewhere on Luzon have revealed that old-growth forests contain a great variety of native species and few, if any, non-native "pest" species of rats. But in heavily disturbed second-growth habitats, particularly areas near croplands, the reverse is the case-non-native rats are most abundant, and there are only a few hardy native species. "We thought the work on Pinatubo would confirm this general pattern, so we expected to see few if any of the native species," says Rickart.


A specific motivation for the Pinatubo survey was to discover the fate of Apomys sacobianus, the Pinatubo volcano mouse. "After the eruption of Pinatubo, we looked for this mouse on other peaks in the Zambales Mountains but failed to find it," notes Heaney, "suggesting a very limited geographic distribution for the species. We thought the volcano might be the only place this mouse lived." And based on expectations from islands elsewhere, at the time it seemed possible that the species might have been lost because of the eruption.

However, the survey of Pinatubo produced some very surprising results-a total of 17 species were documented, including eight bats, seven rodents (five native and two non-native species), and even two large mammals (wild pig and deer). Contrary to expectations, non-native rats were not at all common and were restricted to areas near Aeta croplands where such agricultural pests are often most abundant. Despite the fact that all areas surveyed supported sparse, scrubby second-growth vegetation rather than forest, native rodents were abundant everywhere.

Most surprising of all, the most abundant species, overwhelmingly, was the volcano mouse Apomys sacobianus. Far from being wiped out by the eruption, this species was thriving in this greatly disturbed landscape along with other native species that also have a high tolerance for disturbance. "For some time, we've known that many of the small mammals of the Philippines can tolerate habitat disturbance, both natural and human-caused," Rickart says, "but most of them are geographically widespread, not locally endemic species which usually are viewed by conservation biologists as highly vulnerable."

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Danny Balete, the researcher who led the fieldwork for this study, now deceased.

CREDIT

(c) Field Museum


As Mt. Pinatubo recovers from the damage done by the eruption, the forests will return and other species of mammals will move in. "Mt. Pinatubo could be a wonderful place to establish a long-term project to monitor habitat recovery and community re-assembly following the eruption," says Rickart, "such information would be helpful in efforts to regenerate the many areas that have been deforested by people."

After completing the Mt. Pinatubo mammal survey, Danny Balete returned to the Field Museum where he organized specimens and data from the survey, made some early notes for an eventual publication, and then set them aside to finish later. After he suddenly died in 2017 at age 56, Rickart and Heaney say that they picked up and completed the study as a tribute to Balete, who is now recognized as one of the most important figures in Philippine biodiversity science for his extensive research contributions, mentoring of younger colleagues, and promoting enjoyment of nature throughout the Philippines.

"Knowing that a species once thought to be vulnerable, even feared to be extinct, is actually thriving is the finest tribute to Danny that we can imagine," adds Heaney.

Wet and wild: There's lots of water in the world's most explosive volcano

WASHINGTON UNIVERSITY IN ST. LOUIS

 NEWS RELEASE 

Research News

IMAGE

IMAGE: SHIVELUCH VOLCANO HAS HAD MORE THAN 40 VIOLENT ERUPTIONS OVER THE LAST 10,000 YEARS. THE LAST GIGANTIC BLAST OCCURRED IN 1964, CREATING A NEW CRATER AND COVERING AN AREA OF... view more 

CREDIT: MICHAEL KRAWCZYNSKI, WASHINGTON UNIVERSITY IN ST. LOUIS

There isn't much in Kamchatka, a remote peninsula in northeastern Russia just across the Bering Sea from Alaska, besides an impressive population of brown bears and the most explosive volcano in the world.

Kamchatka's Shiveluch volcano has had more than 40 violent eruptions over the last 10,000 years. The last gigantic blast occurred in 1964, creating a new crater and covering an area of nearly 100 square kilometers with pyroclastic flows. But Shiveluch is actually currently erupting, as it has been for over 20 years. So why would anyone risk venturing too close?

Researchers from Washington University in St. Louis, including Michael Krawczynski, assistant professor of earth and planetary sciences in Arts & Sciences and graduate student Andrea Goltz, brave the harsh conditions on Kamchatka because understanding what makes Shiveluch tick could help scientists understand the global water cycle and gain insights into the plumbing systems of other volcanoes.

In a recent study published in the journal Contributions to Mineralogy and Petrology, researchers from the Krawczynski lab looked at small nodules of primitive magma that were erupted and preserved amid other materials.

"The minerals in these nodules retain the signatures of what was happening early in the magma's evolution, deep in Earth's crust," said Goltz, the lead author of the paper.

The researchers found that the conditions inside Shiveluch include roughly 10%-14% water by weight (wt%). Most volcanoes have less than 1% water. For subduction zone volcanoes, the average is usually 4%, rarely exceeding 8 wt%, which is considered superhydrous.

Of particular interest is a mineral called amphibole, which acts as a proxy or fingerprint for high water content at known temperature and pressure. The unique chemistry of the mineral tells researchers how much water is present deep underneath Shiveluch.

"When you convert the chemistry of these two minerals, amphibole and olivine, into temperatures and water contents as we do in this paper, the results are remarkable both in terms of how much water and how low a temperature we're recording," Krawczynski said.

"The only way to get primitive, pristine materials at low temperatures is to add lots and lots of water," he said. "Adding water to rock has the same effect as adding salt to ice; you're lowering the melting point. In this case, there is so much water that the temperature is reduced to a point where amphiboles can crystallize."

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