Friday, October 27, 2023

Mystery of volcanic tsunami solved after 373 years

GEOMAR researchers reconstruct historic volcanic eruption using 3D seismics

HELMHOLTZ CENTRE FOR OCEAN RESEARCH KIEL (GEOMAR)

From the Greek island of Santorini, the eruption had been visible for several weeks. In the late summer of 1650, people reported that the colour of the water had changed and the water was boiling. About seven kilometres north-east of Santorini, an underwater volcano had risen from the sea and began ejecting glowing rocks. Fire and lightning could be seen, and plumes of smoke darkened the sky. Then the water suddenly receded, only to surge towards the coastline moments later, battering it with waves up to 20 metres high. A huge bang was heard more than 100 kilometres away, pumice and ash fell on the surrounding islands, and a deadly cloud of poisonous gas claimed several lives.

"We know these details of the historic eruption of Kolumbo because there are contemporary reports that were compiled and published by a French volcanologist in the 19th century," says Dr Jens Karstens, marine geophysicist at GEOMAR Helmholtz Centre for Ocean Research Kiel. But how did these devastating events come about? To find out, he and his German and Greek colleagues went to the Greek Aegean Sea in 2019 to study the volcanic crater with special technology. Karstens: "We wanted to understand how the tsunami came about at that time and why the volcano exploded so violently."

On board the now decommissioned research vessel POSEIDON, the team used 3D seismic methods to create a three-dimensional image of the crater, which is now 18 metres below the water's surface. Dr Gareth Crutchley, co-author of the study: "This allows us to look inside the volcano." Not only did the 3D imaging show that the crater was 2.5 kilometres in diameter and 500 metres deep, suggesting a truly massive explosion, the seismic profiles also revealed that one flank of the cone had been severely deformed. Crutchley: "This part of the volcano has certainly slipped." The researchers then took a detective’s approach, comparing the various mechanisms that could have caused the tsunami with the historical eyewitness accounts. They concluded that only a combination of a landslide followed by a volcanic explosion could explain the tsunami. Their findings are published today in the journal Nature Communications.

By combining 3D seismics with computer simulations, the researchers were able to reconstruct how high the waves would have been if they had been generated by the explosion alone. Karstens: "According to this, waves of six metres would have been expected at one particular location, but we know from the reports of eyewitnesses that they were 20 metres high there". Furthermore, the sea is said to have first receded at another point, but in the computer simulation a wave crest reaches the coast first. Thus, the explosion alone cannot explain the tsunami event. However, when the landslide was included in the simulations, the data agreed with historical observations.

Jens Karstens explains: "Kolumbo consists partly of pumice with very steep slopes. It is not very stable. During the eruption, which had been going on for several weeks, lava was continuously ejected. Underneath, in the magma chamber, which contained a lot of gas, there was enormous pressure. When one of the volcano's flanks slipped, the effect was like uncorking a bottle of champagne: the sudden release of pressure allowed the gas in the magma system to expand, resulting in a huge explosion". Something similar could have happened during the 2022 eruption of the Hunga Tonga undersea volcano, whose volcanic crater has a similar shape to Kolumbo's.

The study thus provides valuable information for the development of monitoring programmes for active submarine volcanic activity, such as SANTORY, which is led by co-author Prof. Dr Paraskevi Nomikou of the National and Kapodistrian University of Athens (NKUA). "We hope to be able to use our results to develop new approaches to monitor volcanic unrest," says Jens Karstens, "maybe even an early warning system, collecting data in real time. That would be my dream”.

About 3D Marine Reflection Seismics

3D seismics is a geophysical technique that exploits the fact that sound waves are partially reflected at the boundaries of layers. This makes it possible to create cross-sectional profiles of geological structures beneath the seabed. Unlike 2D reflection seismics, marine 3D reflection seismics uses multiple measuring cables (housing receivers) towed in parallel behind the research vessel. The result is a three-dimensional image, known as a seismic volume, which allows us to look beneath the seafloor and analyse the geology in detail.

JOURNAL

Nature Communications

DOI

10.1038/s41467-023-42261-y

METHOD OF RESEARCH

Case study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Cascading events during the 1650 tsunamigenic eruption of Kolumbo volcano

ARTICLE PUBLICATION DATE

26-Oct-2023

Action plan for better data on migration and health

Peer-Reviewed Publication

BIELEFELD UNIVERSITY

Professor Dr Kayvan Bozorgmehr — IMAGE:
PROFESSOR DR KAYVAN BOZORGMEHR FROM BIELEFELD UNIVERSITY IS ONE OF THE TWO RESEARCHERS LEADING THE STUDY, WHICH PROPOSES HOW THE DATA SITUATION ON MIGRATION AND HEALTH IN HEALTH SYSTEMS CAN BE IMPROVED.
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CREDIT: BIELEFELD UNIVERSITY/MIKE-DENNIS MÜLLER

Despite rising global mobility, the state of migrant and refugee health data in European health systems is a concern, a new study shows. The analysis by an international coalition of universities, UN organizations, government representatives, and European institutions published in the journal The Lancet Regional Health Europe reveals that coverage of migrant and refugee data remains inconsistent and of suboptimal quality. According to the study this issue is not due to a lack of knowledge or technological resources but rather arises from multiple political and structural factors at local, national, and European levels that hinder the effective implementation of existing guidelines. The coalition, led by Bielefeld University in Germany and Uppsala University in Sweden, proposes a roadmap for policy makers and European health systems to improve the situation.

‘Migrant and refugee health data is more than just statistics. It's about human lives and well-being, but also of unnoticed inequalities if health needs go unmeasured,’ says Professor Dr Kayvan Bozorgmehr. In his view health systems committed to inclusive and equitable healthcare need to ensure that migrants and refugees are not systematically excluded from data collection systems.
Bozorgmehr and his colleague Dr Soorej Puthoopparambil from Uppsala University led the international coalition of authors including ten European universities, three national public health agencies, three Collaborating Centres of the World Health Organization, as well as several institutions and United Nations (UN) agencies such as the World Health Organization Regional Office Europe, the International Organization for Migration, and the United Nations Children's Fund (UNICEF).

The article was produced in the scope of the Lancet Migration European Hub’s activities and published in the medical journal The Lancet Regional Health. The study reveals glaring gaps in including migrants and refugees in national data collection systems, which, according to the authors, hinder these groups from exercising their basic human rights and prevents the governments in creating inclusive and healthy societies. One of the study’s main conclusions is that the existing disparity in data collection reflects the low political priority given to this topic and the intricate governance challenges tied to migration and displacement.

In response to the identified shortcomings in current health information systems, the authors propose a roadmap to bridge the divide between knowledge and action. They propose four critical approaches for European health systems:

Systematic data collection: Implement strategies that ensure migrant and refugee health data is collected, analyzed, and disseminated in a systematic manner, filling the existing gaps and informing evidence-based policy decisions.
Privacy safeguards and data integration: Capitalise on methods that protect privacy while facilitating the linkage of data from various sources to generate comprehensive data at relatively low cost. This requires ensuring that the highest standards of data protection are upheld.
Inclusive survey methods: Adopt methods that consider the diverse needs and backgrounds of migrant and refugee populations when conducting surveys.
Empowerment through engagement: Engage migrants and refugees in decision-making about their health and health data. Their voices should shape the policies and practices that directly impact their lives.

The WHO European Region hosts approximately, 36 per cent of the global international migrant population. The study stresses that health of migrants and refugees is a question that cannot be ignored.

‘Countries need to move from ad-hoc to systematic approaches to pro-actively include migrants and refugees in health information systems, thereby promoting equity in health,’ says Soorej Puthoopparambil. This includes capitalizing on existing data sources while tapping new ones. The report proposes a change management approach to narrow the gap between knowledge and action, building a bridge towards healthcare policies and practices that are genuinely inclusive of migrants and refugees. ‘In doing so, societies will not only promote the well-being of migrants and refugees, but will also better serve public health needs of their societies and promote equity in European health systems,’ says Kayvan Bozorgmehr.

Original publication:
Kayvan Bozorgmehr, Martin McKee, Natasha Azzopardi-Muscat, Jozef Bartovic, Ines Campos-Matos, Tsvetelina-Ivanova Gerganova, Ailish Hannigan, Jelena Janković, Daniela Kállayová, Josiah Kaplan, Ilker Kayi, Elias Kondilis, Lene Lundberg, Isabel de la Mata, Aleksandar Medarević, Jozef Suvada, Kolitha Wickramage, Soorej Jose Puthoopparambil: Integration of migrant and refugee data in health information systems in Europe: advancing evidence, policy and practice. The Lancet Regional Health – Europe, https://doi.org/10.1016/j.lanepe.2023.100744, published on 27th October 2023.

JOURNAL

The Lancet Regional Health - Europe

DOI

10.1016/j.lanepe.2023.100744

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Integration of migrant and refugee data in health information systems in Europe: advancing evidence, policy and practice

ARTICLE PUBLICATION DATE

27-Oct-2023

A relational framework for microbiome research that includes Indigenous communities

Research and collection of microbiome samples from Indigenous communities has a history of exploiting and harming Indigenous peoples

Peer-Reviewed Publication

MCGILL UNIVERSITY

Research on the trillions of microorganisms that make up a person’s microbiome can lead to medical breakthroughs to treat diseases like inflammatory bowel syndrome and diabetes. According to Alyssa Bader, a Tsimshian Assistant Professor in the Department of Anthropology at McGill University, microbiome samples from Indigenous communities have the potential to further Western medicine, but those same communities often have been excluded from the research process and may miss out on the benefits that result from their contributions to science. There is also a history of this research exploiting and harming Indigenous peoples.

“Microbes associated with Indigenous peoples have been framed as valuable resources to restore lost microbial diversity and treat chronic disease in industrialized populations, but these research directions often do not center the research needs or interests of the Indigenous communities that researchers rely on for microbiome data,” said Bader.

Two perspectives pieces published recently in Nature Microbiology by an international team, including Bader, of Indigenous and non-Indigenous researchers from institutions, including University of Adelaide, University of Wisconsin-Madison, Pennsylvania State University and others, look to rectify the issue.

The articles lay out a framework for ethical microbiome research practices that include Indigenous communities and ensure that these communities reap the benefits from their contributions. The researchers discuss the Indigenous principle of relationality, in which people are interconnected to each other and the world around them, as a framework to guide human microbiome researchers to work in partnership with Indigenous people.

Research with Indigenous communities should be deeply collaborative and uphold Indigenous sovereignty throughout the research process, added Bader. “This includes ensuring Indigenous community partners have a central role in developing research questions, establishing protocols for research consent and data management, and interpreting and communicating results,” she said.

Two perspectives pieces published recently in Nature Microbiology by an international team, including Bader, of Indigenous and non-Indigenous researchers from institutions, including University of Adelaide, University of Wisconsin-Madison, Pennsylvania State University and others, look to rectify the issue.

A relational framework for microbiome research with Indigenous communities by Alyssa C. Bader et al., and Microbiome ownership for Indigenous peoples by Matilda Handsley-Davis et al., were published in Nature Microbiology.

JOURNAL

Nature Microbiology

DOI

10.1038/s41564-023-01471-2

ARTICLE TITLE

A relational framework for microbiome research with Indigenous communities.

The sunscreen paradox: McGill University researchers warn of ‘false sense of security’

Sunscreen is important, says Dr. Ivan Litvinov, but it is also the least effective way to protect your skin when compared to sun protective clothing and sun avoidance

Peer-Reviewed Publication

MCGILL UNIVERSITY

Sunscreen usage is climbing, but so are melanoma and skin cancer rates: this, researchers say, is the sunscreen paradox.

“The problem is that people use sunscreen as a ‘permission slip’ to tan,” said Dr. Ivan Litvinov, an Associate Professor in the Department of Medicine and Chair of the Dermatology Division at McGill University and co-author with Dr. Sandra Peláez, Dr. Richie Jeremian and Dr. Pingxing Xie of two recent studies that explore the sunscreen paradox.

“People think they are protected from skin cancer because they are using a product marketed to prevent a condition.”

Most people don’t apply enough sunscreen or stay in the sun for hours after applying sunscreen in the morning. “This gives them a false sense of security,” said Litvinov.

To understand the factors between varying incidence rates of melanoma in the Atlantic provinces of Canada, a group of researchers including Litvinov and Peláez conducted 23 focus groups.

In the study, they found that Canadians living in Nova Scotia and Prince Edward Island – provinces with high melanoma incidence rates – were more likely to report using sun protection, more aware of the health risks of sun exposure, and more apt to follow the UV index. Despite this, they also received more sun exposure due to warmer temperatures and a tendency to engage in outdoor activities.

Similarly, in a second study of the United Kingdom Biobank by Jeremian, Xie and Litvinov, the researchers documented that sunscreen use was surprisingly associated with a more than twofold risk of developing skin cancer.

The sunscreen paradox

“These combined findings suggest a sunscreen paradox, whereby individuals with higher levels of sun exposure also tend to use more but not an adequate quantity of sunscreen or other sun-protection measures, providing a false sense of security,” said Litvinov.

Interventions to address knowledge and practice gaps in sun protection and skin cancer prevention must consider this sunscreen paradox and the unique norms of communities around the world, he added.

“Sunscreen is important, but it is also the least effective way to protect your skin when compared to sun protective clothing, rash guards, and sun avoidance. People can and should enjoy the outdoors, but without getting a sun burn or a suntan,” said Litvinov.

JOURNAL

Cancers

DOI

10.3390/cancers15194726

ARTICLE TITLE

Understanding the Perceived Relationship between Sun Exposure and Melanoma in Atlantic Canada: A Consensual Qualitative Study Highlighting a “Sunscreen Paradox”

USDA grant will help MU researchers address opioid epidemic in rural Missouri

Five rural Missouri counties with highest drug overdose mortality rates will be supported with interventions related to childhood trauma.

Grant and Award Announcement

UNIVERSITY OF MISSOURI-COLUMBIA

holding hands — IMAGE:
HOLDING HANDS
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CREDIT: UNIVERSITY OF MISSOURI

COLUMBIA, Mo. -- Childhood trauma is a key risk factor for future substance use disorder, overdose, and suicide. This is particularly problematic in rural areas where children experience higher rates of adverse childhood experiences (ACEs). ACEs are commonly defined as physical and emotional abuse and neglect, sexual abuse, parental separation or divorce, intimate partner violence, and having household members with serious mental illness, substance use disorder, or a history of incarceration.

Now, a three-year, U.S. Department of Agriculture (USDA) grant awarded to the University of Missouri will help virtually train various members of the workforce — such as healthcare providers, mental health and behavioral health providers, social workers, and even childcare providers, and dentists — who serve individuals and families affected by ACEs in five high-risk rural Missouri counties with the ultimate goal of reducing opioid overdoses and suicides.

The five Missouri counties involved are Dent, Washington, Crawford, St. Francois and Phelps, all of which ranked among the highest in Missouri for drug overdose mortality rates in 2021. Julie Kapp, an associate professor in the MU College of Health Sciences and primary investigator for the grant, developed the online training module.

The grant involves collaborators from MU Extension, Show-Me ECHO; Office of Health Outreach, Policy and Education (HOPE); Missouri Telehealth Network; Missouri Center for Health Policy; and MO HealthNet (Missouri’s Medicaid program).

“More than 60% of adults nationally are exposed to ACEs in childhood, and these exposures are linked with increased risk for substance abuse and suicide,” Kapp said. “If we can target upstream factors such as ACEs, we are hopeful that we can reduce the pipeline that leads to substance abuse occurring in the first place.”

Kapp added that many health care providers and other members of the workforce are unaware of ACEs, which leaves a significant gap and the need for training opportunities.

“Our goal is to provide additional tools beyond just prescriptions,” Kapp said. “Someone struggling with substance abuse may have the desire to stop, but if they have never dealt with their childhood trauma, it will be an uphill battle. One of our former ACEs trainees who works with incarcerated individuals said, ‘Many of [these individuals] do not identify their life experiences as traumatic. They view their traumas as typical.’”

The training module, which can be taken asynchronously and completed in approximately three hours, covers such topics as: what ACEs are; the prevalence of ACEs in rural areas; strategies to support families, emphasizing positive childhood experiences, resources available and developing a trauma informed care model.

“This evidence-based training module has already been well-received by members of various organizations in the Missouri workforce, and they have reported the content is informative, helpful and relevant,” Kapp said.

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Online games use dark designs to collect player data

The privacy policies and practices of online games contain dark design patterns which could be deceptive, misleading, or coercive to users

Peer-Reviewed Publication

AALTO UNIVERSITY

Manipulated gamer — IMAGE:
GAMES SOMETIMES MANIPULATE PLAYERS INTO GIVING AWAY MORE DATA THAN THEY WANT TO
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CREDIT: MATTI AHLGREN/AALTO UNIVERSITY

Gaming is a $193 billion industry – nearly double the size of the film and music industries combined – and there are around three billion gamers worldwide. While online gaming can improve wellbeing and foster social relations, privacy and awareness issues could potentially offset these benefits and cause real harm to gamers.

The new study, by scientists at Aalto University’s Department of Computer Science, reveals potentially questionable data collection practices in online games, along with misconceptions and concerns about privacy among players. The study also offers risk mitigation strategies for players and design recommendations for game developers to improve privacy in online games.

‘We had two supporting lines of inquiry in this study: what players think about games, and what games are really up to with respect to privacy,’ says Janne Lindqvist, associate professor of computer science at Aalto. ‘It was really surprising to us how nuanced the considerations of gamers were. For example, participants said that, to protect their privacy, they would avoid using voice chat in games unless it was absolutely necessary. Our game analysis revealed that some games try to nudge people to reveal their online identities by offering things like virtual rewards.’

The authors identified instances of games using dark design – interface decisions that manipulate users into doing something they otherwise wouldn’t. These could facilitate the collection of player data and encourage players to integrate their social media accounts or allow data sharing with third parties.

‘When social media accounts are linked to games, players generally can’t know what access the games have to these accounts or what information they receive,’ says Amel Bourdoucen, doctoral researcher in usable security at Aalto. ‘For example, in some popular games, users can log in with (or link to) their social media accounts, but these games may not specify what data is collected through such integration.’

The global gaming community has been subject to increased scrutiny over the past decade because of online harassment and the industry’s burnout culture. While these issues still linger, the push for more tech regulation in the EU and US has also brought privacy issues to the forefront.

‘Data handling practices of games are often hidden behind legal jargon in privacy policies,’ says Bourdoucen. ‘When users' data are collected, games should make sure the players understand and consent to what is being collected. This can increase the player’s awareness and sense of control in games. Gaming companies should also protect players’ privacy and keep them safe while playing online.’

According to the study, participants were often unaware that their chat-based conversations might be disclosed to third parties. Games also didn’t notify players of data sharing during the game.

The study showed that players are aware of the risks, and it highlights several mitigation tactics used by players. ‘We found that players try to maintain their privacy when playing online games by choosing text chats for discussion instead of voice chats, since they believe they may be more closely watched,’ says Bourdoucen. ‘According to our findings, female players are the most impacted and feel the need to conceal their gender when playing by creating various avatars or refraining from having voice conversations with other players.’

Finally, the study proposes solutions to counter these problems, such as more transparent approaches to data collection. Overall, the authors recommend that games and gaming platforms strive to protect all their players.

‘Games really should be fun and safe for everybody, and they should support the player’s autonomy. One way of supporting autonomy would be able to let players opt out from invasive data collection,’ says Lindqvist.

JOURNAL

Proceedings of the ACM on Human-Computer Interaction

DOI

10.1145/3611064

ARTICLE TITLE

Privacy Is the Price: Player Views and Technical Evaluation of Data Practices in Online Games

Genetic methods enable the use of fossil lipids as biomarkers for oxygen-producing primordial bacteria

New study in Nature Ecology & Evolution provides important basis for deciphering the evolutionary history of life on Earth

Peer-Reviewed Publication

GFZ GEOFORSCHUNGSZENTRUM POTSDAM, HELMHOLTZ CENTRE

Landscape in the Australian Northern Territories — IMAGE:
LANDSCAPE IN THE AUSTRALIAN NORTHERN TERRITORIES ON A FIELD TRIP TO THE 1.6-BILLION-YEAR-OLD BARNEY CREEK FORMATION IN THE MCARTHUR BASIN TO COLLECT OLDEST 2-METHYLHOPANE SAMPLES FOR THIS STUDY.

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CREDIT: PHOTO: CHRISTIAN HALLMANN, GFZ

Summary

Cyanobacteria are a key species in Earth's history, as they introduced atmospheric oxygen for the first time. The analysis of their evolution therefore provides important insights into the formation of modern aerobic ecosystems. For a long time, a certain type of fossil lipid, so-called 2-methylhopanes, was considered to be an important biomarker for Cyanobacteria in sediments, some of which are hundreds of millions of years old. However, this came into doubt when it turned out that not only Cyanobacteria but also Alphaproteobacteria are genetically capable of producing these lipids.

An international research team led by Yosuke Hoshino from the GFZ German Research Centre for Geosciences and Benjamin Nettersheim from MARUM – Center for Marine Environmental Sciences at the University of Bremen has now studied the phylogenetic diversification and distribution of the genes – including HpnP – that are responsible for the synthesis of the parent lipids for 2-methylhopanes: The researchers have deciphered when these genes were acquired by certain groups of organisms. They were able to show that HpnP was probably already present in the last common ancestor of Cyanobacteria more than two billion years ago, while the gene only appeared in Alphaproteobacteria about 750 million years ago. For the times before that, 2-methylhopanes can therefore serve as a clear biomarker for oxygen-producing Cyanobacteria.

The study, which has now been published in the journal Nature Ecology & Evolution, shows how genetics, in interaction with sedimentology, paleobiology and geochemistry, can improve the diagnostic value of biomarkers and refine the reconstruction of early ecosystems.

Background: The importance of cyanobacteria in Earth's history

Cyanobacteria played a crucial role in transforming the Earth from its initial oxygen-free state to a modern, oxygen-rich system in which increasingly complex life is possible. Cyanobacteria were probably the only relevant group of organisms that converted inorganic substances into organic ones (so-called primary producers) and produced oxygen for long stretches of the Precambrian (the first four billion or so years of Earth's history, from its beginnings to about 540 million years ago). Therefore, the analysis of their evolution is of great importance for understanding the common history of life and Earth.

The importance of fossil lipids as biomarkers

In principle, the fossil remains of whole Cyanobacteria can serve as an indicator of the presence of oxygenic photosynthesis in the geological past. However, due to preservational biases and ambiguities in recognizing fossil cyanobacterial cells, geochemists rather use fossilised diagnostic lipids, such as 2-methylhopanes. 2-Methylhopanoids (non-fossilised parent molecules) are produced by the bacteria and – in contrast to the bacteria themselves– can be fossilised and detected in sedimentary rocks even after hundreds of millions of years in good quality and in quantities corresponding to their original occurrence.

However, there have recently been doubts about the suitability of 2-methylhopane as a biomarker for Cyanobacteria: the discovery of the lipid biosynthesis gene revealed that Alphaproteobacteria are also capable of producing these lipids. This means that temporally tracing oxygen-producing processes on Earth by 2-methylhopanes is no longer possible.

New approach: Comprehensive genetic analysis combined with new, high-purity sediment analyses

An international research team led by Yosuke Hoshino and Christian Hallmann, scientists in GFZ Section 3.2 “Organic Geochemistry”, and Benjamin Nettersheim from MARUM at the University of Bremen has now systematically investigated which organisms other than Cyanobacteria possess the genes (abbreviated as the SC and HpnP genes) necessary for the production of 2-methylhopanoids, and when they acquired those genes during the course of evolution. In this way, the team was able to show that the fossil lipid 2-methylhopane can still be used as a clear biomarker for the existence of Cyanobacteria for times dating back more than 750 million years.

In addition, the researchers have created an integrated record of 2-methylhopane production over the course of Earth's history. For this, they combined their molecular data with new sediment analyses carried out under high-purity conditions.

“The method we proposed is in principle applicable to any organic matter in geological archives and has great potential to trace the evolution of different ecosystems with much higher temporal and spatial resolution than before,” Hoshino sums up.

Methodology I: Computational study for genetic analysis

For the analysis of the genetic relationships, Hoshino searched publicly available databases, containing millions of gene and protein sequences, for organisms with the SC and HpnP genes. Based on this genetic data set, he created so-called phylogenetic trees, which provide information on how the SC and HpnP genes were transferred between different organisms and whether the gene transfer took place vertically via inheritance or horizontally between evolutionarily unrelated organisms. Furthermore, the researchers were also able to determine when individual gene transfers took place in the evolutionary history of the genes by comparing previous studies that utilized the so-called molecular clock technique that takes into account the DNA mutation rate and estimates the timeline for the gene evolution.

Methodology II: New type of ultra-clean sample preparation

In addition, because Precambrian biomarker records are extremely sensitive to contamination, the researchers used an ultra-clean method to extract organic matter from sediment cores. The geological samples in the form of cores were collected by several co-authors from 16 countries. They represent different geological periods from the Paleoproterozoic (2.5 billion years ago) to the present. The relative abundance of 2-methylhopanes was then measured in the organic matter.

The results in detail

There are many bacteria that possess both SC and HpnP genes, but they are mainly Cyanobacteria and Alphaproteobacteria. Each group is found to have acquired the two genes independently. This is in contrast to earlier studies that concluded that Cyanobacteria acquired these genes from Alphaproteobacteria at a late stage in their evolution. The new study further revealed that the common ancestor of Cyanobacteria already possessed both genes more than 2.4 billion years ago, when oxygen began to accumulate in the atmosphere during the so-called Great Oxidation Event.

In contrast, Alphaproteobacteria acquired the SC and HpnP genes at the earliest only 750 million years ago. Before that, 2-methylhopanoids were thus only produced by Cyanobacteria. The researchers interpret a slightly delayed increase of sedimentary 2-methylhopanes around 600 million years ago as a sign of the global spread of Alphaproteobacteria, which may have favored the concurrent evolutionary rise of eukaryotic algae.

Summary and outlook

“The individual analytical methods mentioned above are not new, but few researchers have attempted to perform comprehensive analyses for SC and HpnP and to integrate genetic data with sedimentary biomarker data before, as this requires combining two completely different scientific disciplines – molecular biology and organic geochemistry,” says Hoshino.

“The source of sedimentary 2-methylhopanes has been a topic of long debate,” adds Christian Hallmann. — “This new study not only provides clarity about the diagnosticity of 2-methylhopanes and the role of Cyanobacteria in deep time; its methodology offers a new avenue forward to refine the diagnosticity of, in theory, any biomarker lipid once the biosynthesis genes are known”.

Close-up picture of a core sample: The oldest samples are drill core samples from the 1.6-billion-year-old McArthur Basin in Northern Australia. This is among the oldest biomarker samples known to date and contains the information about primary production by photosynthetic organisms at that time.

CREDIT

Photo: Benjamin Nettersheim, MARUM University of Bremen

JOURNAL

Nature Ecology & Evolution

DOI

10.1038/s41559-023-02223-5

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Genetics re-establish the utility of 2-methylhopanes as cyanobacterial biomarkers before 750 million years ago

ARTICLE PUBLICATION DATE

26-Oct-2023

Unlocking sugar to generate biofuels and bioproducts

Engineered enzymes could generate biomass optimized for conversion into fuel and other useful products.

Peer-Reviewed Publication

DOE/BROOKHAVEN NATIONAL LABORATORY

scientists with rice plants — IMAGE:
CHANG-JUN LIU (LEFT) AND NIDHI DWIVEDI (RIGHT) IN THE BROOKHAVEN LAB GREENHOUSE WITH RICE PLANTS LIKE THOSE USED IN THIS STUDY.
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CREDIT: BROOKHAVEN NATIONAL LABORATORY

UPTON, NY—Plant biologists at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory have engineered enzymes to modify grass plants so their biomass can be more efficiently converted into biofuels and other bioproducts. As described in a paper just published in Plant Biotechnology Journal, these enzymes modify molecules that make up plant cell walls to provide access to fuel-generating sugars normally locked within complex structures.

“The concept of biomass to biofuel seems simple, but it is technically very difficult to release the sugars,” noted Chang-Jun Liu, a senior plant biologist at Brookhaven Lab who led the study.

Plant biomass is full of energy-rich complex sugar molecules generated from photosynthesis. Each plant cell is surrounded by a rigid cell wall made of sugars and a material called lignin that provides structural support. Reducing lignin to gain access to the sugars has been the focus of research aimed at using plants to generate fuels and other products commonly made from petroleum.

For nearly 15 years, Liu has been tackling this problem using engineered enzymes called monolignol 4-O-methyltransferases (MOMTs). These enzymes, which do not exist in nature, are designed to alter the chemical structure of monolignols—the main building blocks of lignin. Changing the structure of the building blocks prevents them from linking together, which reduces the lignin content of plants and makes the sugars more accessible.

In prior work, Liu and his colleagues successfully expressed MOMTs in poplar trees. These enzymes reduced the trees’ lignin content and enabled more abundant sugar release from the plants. In the new research, they tested the potential applications of the MOMT enzymes in grass plants, which have an abundant biomass yield. Grasses can also grow in harsh environments, such as on soils deficient in water or nutrients. Cultivating engineered plants in such environments could potentially produce large amounts of biomass optimized for conversion to fuel and bioproducts—without competing for land needed to produce food crops.

“However, grass plant cell walls, like those from the rice plants that we studied, are even more complicated in terms of structure and composition,” explained Nidhi Dwivedi, Brookhaven Lab research associate and lead author on the new paper. In addition to sugar and lignin, grass plant cell walls also contain additional phenolic compounds that “cross-link” the cell wall components, making them even stronger and harder to break down.

“The complexity of grass plant cell walls made us curious as to whether our enzymes would improve sugar recovery,” noted Liu. “We wanted to know if MOMTs could modify the grass cell walls in a way that would provide access to the biomass.”

Less Lignin, More Sugars

Liu and Dwivedi chose to focus on two versions of the enzyme for this study—MOMT4 and MOMT9—each of which were designed to modify a different lignin subunit.

Working with collaborators from Kyoto University in Japan, Liu’s team conducted chemical analyses on rice plants engineered to express either MOMT4 or MOMT9. These studies showed there was less lignin in the modified grass plants compared to unaltered plants. Collaborators from Appalachian State University in North Carolina examined sections of the modified plant stems using scanning electron microscopy and observed changes that were consistent with the chemical analyses.

“Throughout the stem, the cell walls appeared thinner,” said Dwivedi. “And in some cells the walls even looked deformed or buckled.”

With less lignin in the cell walls, the scientists were able to collect up to 30% more sugar from plants expressing MOMT4 and up to 15% more sugar in plants expressing MOMT9, compared to unaltered plants. Through a process called fermentation, this sugar can be converted into biofuels like ethanol, which is a common additive used to lower the fossil fuel content of gasoline.

Surprisingly Promiscuous Enzymes

Enzymes—molecules that generally facilitate chemical reactions—commonly target just one type of molecule. MOMT4 and MOMT9 were designed to act upon monolignols. But when Liu and his colleagues ran tests on these enzymes, the results revealed that these engineered enzymes exhibited “promiscuity.” In addition to acting on the monolignols, both MOMTs acted on other cell wall components—the cross-linking phenolics and also a phenolic called tricin, which is a lignin precursor unique to grass plants.

When these enzymes were expressed in rice plants, they made the expected structural changes to the traditional lignin building blocks, and thus reduced the plants’ overall lignin content. But by changing the structures of the cross-linking phenolics and tricin, the MOMTs also reduced the incorporation of those compounds into the cell walls further weakening them. The scientists also found an accumulation of modified phenolics in the rest of the plant tissue that was not present in unaltered plants.

“This was quite a difference from what we saw when we expressed the same enzymes in poplar trees,” noted Liu. “The broader effects of expressing the enzymes really surprised us. Overall, the changes were positive in terms of optimizing sugar yield from grass cell walls. But there were also some unintended effects.”

For example, plants expressing MOMT9 did not grow as tall as the unaltered plants, reducing the quantity of biomass from which sugar could be accessed. The plants also failed to produce seeds, which would be a problem if the scientists want the modified plants to reproduce as a sustainable source of biofuel sugars.

To address these challenges, the scientists plan to explore methods for controlling how lignin gets modified in different parts of the plant. For example, if the scientists can reduce lignin levels everywhere in the plant other than the reproductive organs, they could maximize the ability to extract sugars without affecting the fertility of the plants.

The scientists also want to see if their MOMT enzymes can optimize sugar yields from other grass plant species.

“After seeing the effectiveness of this enzyme technology in rice, we are confident that it can be used to modify other grass energy crops like sorghum and bamboo,” Liu said.

“Biofuels are a promising alternative to non-renewable energy sources,” Dwivedi added, “This study provides insights into how scientists can optimize the release of sugar that is present in cell walls, thus overcoming some of the waste that occurs with unmodified biomass crops.”

This work was primarily funded by the DOE Office of Science.

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, visit science.energy.gov.

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JOURNAL

Plant Biotechnology Journal

DOI

10.1111/pbi.14186

ARTICLE TITLE

Simultaneous suppression of lignin, tricin and wall-bound phenolic biosynthesis via the expression of monolignol 4-O-methyltransferases in rice