Sulfur bacteria team up to break down organic substances in the seabed

Microbes live at the thermodynamic limit / Metabolic strategies decoded for the first time

University of Oldenburg

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To find out which molecular tools the sulfate-reducing bacteria use, the researchers analysed the entire set of proteins present, known as the proteome. In total, they looked at the results of 80 different test conditions. Each time, they seperated the protein mixture in several steps, until each individual compound could be identified. Here, a separating gel containing blue bands with proteins of similar size and charge is placed on a light table. A robot arm cuts pinhead-sized pieces from the gel, which can contain from just a few to more than hundred different proteins. These pre-sorted proteins are then further analysed using a chromatograph and mass spectrometer.    

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Credit: University of Oldenburg / Mohssen Assanimoghaddam

Sulfate-reducing bacteria break down a large proportion of the organic carbon in oxygen-free zones of the Earth, and in the seabed in particular. Among these important microbes, the Desulfobacteraceae family of bacteria stands out because its members are able to break down a wide variety of compounds – including some that are poorly degradable – to their end product, carbon dioxide (CO2).

A team of researchers led by Dr Lars Wöhlbrand and Prof. Dr Ralf Rabus from the University of Oldenburg, Germany, has investigated the role of these microbes in detail and published the findings of their comprehensive study in the prestigious journal Science Advances.

The team reports that the bacteria are distributed across the globe and possess a complex metabolism that displays modular features: all the studied strains possess the same central metabolic architecture for harvesting energy, for example. However, some strains possess additional strain-specific molecular modules that enable them to utilise diverse organic substances. The researchers attribute this group of bacteria's environmental success to this versatile modular system. They also explain that their study provides new analytical tools to further advance our understanding of the role of sulfate-reducing microbes in the global carbon cycle and their relevance for the climate.

Life at the thermodynamic limit

"These sulfate reducers live their lives at the thermodynamic limit," explains Rabus, who heads the General and Molecular Microbiology working group at the University of Oldenburg's Institute for Chemistry and Biology of the Marine Environment (ICBM). These bacteria use sulfate rather than oxygen for respiration, and they harvest only a fraction of the energy that aerobic bacteria can extract from the degradation of organic substances. Yet they are extremely active and play a key role in the breakdown of organic matter in the seabed. "It is estimated that in coastal waters and shelf areas, where particularly large amounts of organic matter are deposited, sulfate-reducing bacteria account for more than half of the degradation in the seabed," Rabus notes.

He explains that the dominant members of the bacterial community often belong to the Desulfobacteraceae family, and the activity of these microbes is clearly visible in environments such as mudflats, where the sediment only a few millimetres below the surface is oxygen-free. "This results in the formation of foul-smelling hydrogen sulfide and the distinctive black iron sulfide precipitates," he explains.

However, so far little was known about the role members of the Desulfobacteraceae family play in the degradation of organic material at the global level, or about the underlying molecular mechanisms. To obtain a more detailed overview, the team first analysed the global prevalence of these sulfate-reducing bacteria. A study of the relevant literature revealed that they are distributed worldwide and occur in all marine areas between the Arctic and Antarctic – particularly in low-oxygen or oxygen-free environments, as expected.

Similar molecular strategies to break down organic compounds

In the next step, the researchers cultivated six very different strains of Desulfobacteraceae. "Some are specialists that only break down certain compounds while others can utilise a broad spectrum of substances. Some are small and spherical, others are elongated or even filamentous," the study's lead author Lars Wöhlbrand explains. In order to decode their metabolism, the researchers fed the microbes a total of 35 different substances (substrates) ranging from simple fermentation products to long-chain fatty acids and poorly degradable aromatic compounds. A total of 80 test conditions were used for the six strains studied. The team then analysed which genes are activated during the degradation of these substances and which proteins the microbes use for this process. It emerged that the different strains employ very similar molecular strategies to break down the substances and all six strains also use the same highly energy-efficient pathway for central metabolism.

The researchers conclude that the Desulfobacteraceae work together like a team, and are consequently able to break down a large pool of different substrates under a variety of geochemical conditions and at a wide range of different geographical locations. "There is no single, dominant key species," Rabus stresses. Instead, the bacteria function as a collaborative community, similar to a football team: "Every team has a goalkeeper and a striker, but each team also does things in its own way," Wöhlbrand adds. This versatility may also explain why the Desulfobacteraceae are among the most widespread sulfate reducers worldwide.

Together with Prof. Dr Michael Schloter from the Technical University of Munich, Germany, the researchers then investigated whether the genetic blueprints for certain key modules in the metabolic network could be detected in sediment samples. And in effect, they discovered the selected genes in almost all the analysed samples taken from marine areas that ranged from shallow waters to the deep sea, including nutrient-rich estuaries, hot and cold deep-sea springs and sediments from the oxygen-poor Black Sea.

The team concludes that its analysis first of all underscores the key role played by Desulfobacteriaceae in carbon breakdown on a global level, and secondly, it demonstrates that the investigated genes can be used as analytical tools to study microbial activity directly in the seabed. "The importance of sulfate reducers in the carbon cycle has probably been underestimated so far," says Prof. Dr Michael Winklhofer from the University of Oldenburg's Institute of Biology and Environmental Sciences, who was involved in the analysis. The geophysicist adds that the role of these anaerobic microbes in carbon degradation processes in coastal areas may increase in the future, because the oxygen content of the oceans has been decreasing since around 1960 as a result of over-fertilisation and global warming.

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Journal

Science Advances

DOI

10.1126/sciadv.ads5631 

Method of Research

Experimental study

Subject of Research

Cells

Article Title

Key role of Desulfobacteraceae in C-/S-cycles of marine sediments is based on congeneric catabolic-regulatory networks

Article Publication Date

7-Mar-2025

ARACHNOLOGY

Stretching spider silk makes it stronger

New study finds the amount of stretching determines the fibers’ properties

Peer-Reviewed Publication

Northwestern University

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Scanning electron microscopy images of fibers from engineered spider silk. To validate their computational findings, the Northwestern team used spectroscopy techniques to examine how the protein chains stretched and aligned in real fibers from engineered spider silk.

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Credit: Washington University at St. Louis

When spiders spin their webs, they use their hind legs to pull silk threads from their spinnerets. This pulling action doesn’t just help the spider release the silk, it’s also a crucial step in strengthening the silk fibers for a more durable web.

In a new study, Northwestern University researchers have discovered why the role of stretching is so important. By simulating spider silk in a computational model, the team discovered the stretching process aligns the protein chains within the fibers and increases the number of bonds between those chains. Both factors lead to stronger, tougher fibers.

The team then validated these computational predictions through laboratory experiments using engineered spider silk. These insights could help researchers design engineered silk-inspired proteins and spinning processes for various applications, including strong, biodegradable sutures and tough, high-performance, blast-proof body armor.

The study will be published on Friday (March 7) in the journal Science Advances.

“Researchers already knew this stretching, or drawing, is necessary for making really strong fibers,” said Northwestern’s Sinan Keten, the study’s senior author. “But no one necessarily knew why. With our computational method, we were able to probe what’s happening at the nanoscale to gain insights that cannot be seen experimentally. We could examine how drawing relates to the silk’s mechanical properties.”

“Spiders perform the drawing process naturally,” said Northwestern Jacob Graham, the study’s first author. “When they spin silk out of their silk gland, spiders use their hind legs to grab the fiber and pull it out. That stretches the fiber as it’s being formed. It makes the fiber very strong and very elastic. We found that you can modify the fiber’s mechanical properties simply through modifying the amount of stretching.”

An expert in bioinspired materials, Keten is the Jerome B. Cohen Professor of Engineering, professor and associate chair of mechanical engineering and professor of civil and environmental engineering at Northwestern’s McCormick School of Engineering. Graham is a Ph.D. student in Keten’s research group.

Stronger than steel, tougher than Kevlar

Researchers long have been interested in spider silk because of its remarkable properties. It’s stronger than steel, tougher than Kevlar and stretchy like rubber. But farming spiders for their natural silk is expensive, energy-intensive and difficult. So, scientists instead want to recreate silk-like materials in the lab.

“Spider silk is the strongest organic fiber,” Graham said. “It also has the advantage of being biodegradable. So, it’s an ideal material for medical applications. It could be used for surgical sutures and adhesive gels for wound-closure because it would naturally, harmlessly degrade in the body.”

Study coauthor Fuzhong Zhang, the Francis F. Ahmann Professor at Washington University (WashU) in St. Louis, has been engineering microbes to produce spider-silk materials for several years. By extruding engineered spider silk proteins and then stretching them by hand, the team has developed artificial fibers similar to threads from the golden silk orb weaver, a large spider with a spectacularly strong web.

Simulating stretchiness

Despite developing this “recipe” for spider silk, researchers still don’t fully understand how the spinning process changes fiber structure and strength. To tackle this open-ended question, Keten and Graham developed a computational model to simulate the molecular dynamics within Zhang’s artificial silk.

Through these simulations, the Northwestern team explored how stretching effects the proteins’ arrangement within the fibers. Specifically, they looked at how stretching changes the order of proteins, the connection of proteins to one another and the movement of molecules within the fibers.

Keten and Graham found that stretching caused the proteins to “line up,” which increased the fiber’s overall strength. They also found that stretching increased the number of hydrogen bonds, which act like bridges between the protein chains to make up the fiber. The increase in hydrogen bonds contributes to the fiber’s overall strength, toughness and elasticity, the researchers found.

“Once a fiber is extruded, its mechanical properties are actually quite weak,” Graham said. “But when it’s stretch up to six times its initial length, it becomes very strong.”

Experimental validation

To validate their computational findings, the team used spectroscopy techniques to examine how the protein chains stretched and aligned in real fibers from the WashU team. They also used tensile testing to see how much stretching the fibers could tolerate before breaking. The experimental results agreed with the simulation’s predictions.

“If you don’t stretch the material, you have these spherical globs of proteins,” Graham said. “But stretching turns these globs into more of an interconnected network. The protein chains stack on top of one another, and the network becomes more and more interconnected. Bundled proteins have more potential to unravel and extend further before the fiber breaks, but initially extended proteins make for less extensible fibers that require more force to break.”

Although Graham used to think spiders were just creepy-crawlies, he now sees their potential to help solve real problems. He notes that engineered spider silk provides a stronger, biodegradable alternative to other synthetic materials, which are mostly petroleum-derived plastics.

“I definitely look at spiders in a new light,” Graham said. “I used to think they were nuisances. Now, I see them as a source of fascination.”

The study, “Charting the envelope of mechanical properties of synthetic silk fibers through predictive modeling of the drawing process,” was supported by the National Science Foundation (grant numbers OIA-2219142 and DMR-2207879).

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Journal

Science Advances

DOI

10.1126/sciadv.adr3833 

Article Title

Charting the envelope of mechanical properties of synthetic silk fibers through predictive modeling of the drawing process

Article Publication Date

7-Mar-2025

Silk-inspired in situ web spinning for situated robots

Estonian Research Council

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Natural spider kiting silk, released fibre by fibre after being used up by spiders, spontaneously forms uniform surfaces between tree branches, inspiring our technological discovery.
Additional video or photographic material is kindly provided by the Authors on request.

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Credit: Those included in the manuscript are covered by by-nc-nd/4.0/ licence. Credit: All Authors' work.

Can robots be predesigned for unpredictability?

While today’s large language models adapt situationally on the fly, their bodies remain fixed. They are either optimized for a specific task or built into a one-size-fits-all principle that rarely excels. But what if a machine could develop any structure demanded by its situatedness, right when and where it’s needed?

Researchers at Tartu University’s Institute of Technology have unveiled a robotics concept that redefines adaptability by literally weaving its body on demand, much like spiders spin their webs. By extruding a heated polymer solution that cools into fine fibers, the robot creates custom components in situ. The result is a dynamic melding of machine and environment! A seamless transition that bypasses the rigid separation of traditional robotic design.

In a series of experiments, the team showcased the robot’s remarkable ability to operate in complex environments. In one demonstration, the machine spun a continuous, flexible fiber network across a simulated debris field, building its own bridge over obstacles indifferently whether the path was lined with razor-sharp glass shards or soft bird feathers. In another test, the robot spun itself a fibrous “limb” to gently retrieve a fragile flower, illustrating a level of dexterity that predesigned embodiments cannot match.

The team demonstrated indiscriminate adhesion and anchoring of in-situ spun webs on virtually any substrate, regardless of shape, material, or state of aggregation. Much like spiderwebs, the synthetic web leveraged both physical adhesion and mechanical entanglement to secure itself to a broad range of supports.

In experiments, the web successfully anchored on challenging surfaces such as Teflon, a sponge saturated with mineral oil, and a waxy plant leaf.

“Our approach takes a cue from spiders as nature’s ingenious engineers, yet we found a loophole that lets us sidestep the limitations and excessive complexity of directly imitating spiders,” said Marie Vihmar, lead author of the study published in npj Robotics.

With a background in design studies, Vihmar brings a fresh perspective on non-anthropocentric design and how the form and shape of materials create functionality, while the senior author Indrek Must, who is trained in material science, ensures the technological robustness of the innovation.

This interdisciplinary collaboration converges design thinking, material science, and robotics, yielding insights and solutions that remain elusive to conventional approaches within any single discipline.

By exploiting the self-assembling properties of polymer fibers, also observed in cast-off kiting silk of spiders in nature, the team has created a system that dynamically assembles itself to meet the immediate challenges of unpredictable environments. This not only broadens the scope of robotics in disaster relief but also rethinks how machines interact with the world.

This contribution paves the way for robots that don’t simply adapt to their surroundings, but actively transform them! From search-and-rescue operations in disaster zones to adaptive construction methods that seamlessly merge machines with landscapes, the technology challenges conventional industrial thinking. Instead of forcing the environment to accommodate rigid, predesigned systems, this innovative “forest thinking” approach empowers machines to grow and evolve on the spot.

Supported by the Estonian Research Council, this research marks a significant step forward in the convergence of biological inspiration and robotics. Introducing an era where machines are not static tools, but dynamic entities capable of reinventing themselves not only mentally, but also physically.

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Journal

npj Robotics

DOI

10.1038/s44182-025-00019-2 

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Silk-inspired in situ web spinning for situated robots

In situ spinning bridges voids between walls. The video shows the gradual development of a funnel-shaped pathway. 

An obstacle course simulating a disaster zone and lined with sharp glass shards is made passable by in situ spinning a movement pathway. (VIDEO)

Pathway through glass shard obstacle course.

Additional video or photographic material is kindly provided by the Authors on request.

Credit

Those included in the manuscript are covered by by-nc-nd/4.0/ licence. Credit: All Authors' work.

A gripper was spun as an example of ad hoc embodiment. Several task-specific gripper preforms are shown. (IMAGE)

Estonian Research Council

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A gripper was spun as an example of ad hoc embodiment. Several task-specific gripper preforms are shown.

 AS ABOVE,SO BELOW

Earth's orbital rhythms link timing of giant eruptions and climate change

MARUM - Center for Marine Environmental Sciences, University of Bremen

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Thick basaltic rock sequences of the West Indian Deccan Trap volcanic rocks. Photo: Blair Schoene, Princeton University

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Credit: Blair Schoene, Princeton University

On ten thousand to million years time scales, climate dynamics on the Earth’s surface are driven by both external and internal processes. Earth`s interior provides heat from radioactive decay and chemical compounds by volcanic degassing, such as sulfur dioxide (SO2) and carbon dioxide (CO2). Quasiperiodic changes in Earth’s orbit around the sun regulate the amount of incoming solar radiation on the planet’s surface as well as its distribution across latitudes, affecting the length and intensity of the seasons. The interplay of both processes through complex geochemical interactions on the surface of our planet shape and regulate the climate we live in.

“Just like a metronome, we used the rhythmic changes in solar insolation imprinted in geological data to synchronize geological climate archives from the South Atlantic and the Northwest Pacific. These key records span the last million years of the Cretaceous and are synchronized down to 5,000 years or less, geologically a blink of an eye 66 million years ago,” says lead author Thomas Westerhold from MARUM – Center for Marine Environmental Sciences at the University of Bremen. To unravel causality arguments in Earth climate history across regions, this kind of synchronization is essential. “So, we had the geological records perfectly lined up in time, and observed that two major changes in climate and biota occurred at the same time in both oceans. But we had to find a way to test if these changes are caused by large scale volcanic eruptions related to the Deccan Traps in India,” says Westerhold.

The up to two kilometers thick basaltic rocks of the Deccan Traps cover a large part of western India. This large-scale volcanism flooding entire landscapes is referred to as Large Igneous Province by geoscientists. Several times in Earth’s history these caused mass extinction events of life on the surface of the planet. Particularly the release of volcanic gases like carbon and sulfur dioxide during the formation of the flood basalts may have played a key role.

“The formation of the flood basalts and its subsequent weathering will leave a geochemical fingerprint in the ocean. Therefore, we measured the Osmium isotope composition of the South Atlantic and the Northwest Pacific deposits. They should show the same fingerprint at the same time,” says co-author Junichiro Kuroda (University Tokyo, Japan), who conducted the geochemical analyses.

“To our surprise we found two steps in the Osmium isotope composition in both oceans contemporaneous with major eruption phases of the Deccan Traps in the latest Cretaceous. And even more surprising those steps had different impacts on the environment as recorded by fossil remains in the drill cores,” says Thomas Westerhold.

The new data were difficult to understand, but geochemical modeling helped to unravel their secrets. “The volume of the erupted flood basalt must have been much larger than previously though during this early phase of Deccan Trap volcanism. And the related distinct emissions of carbon and sulfur dioxide had diverse effects on the global climate system,” says Don Penman (Utah State University, USA) who did the geochemical modeling. According to the new finding, it seems plausible that at the onset of major Deccan Trap volcanism, independently dated 66.288 Million years by radioisotopic methods, an initial pulse with sulfur rich eruptions occurred stressing the ecosystem locally and possibly also globally.

 

Original publication:

Thomas Westerhold, Edoardo Dallanave, Donald Penman, Blair Schoene, Ursula Röhl, Nikolaus Gussone, Junichiro Kuroda: Earth Orbital Rhythms links Timing of Deccan Trap Volcanism Phases and Global Climate Change. Science Advances 2025. DOI:10.1126/sciadv.adr8584

 

Contact:

Dr. Thomas Westerhold

MARUM – Center for Marine Environmental Sciences, University of Bremen, Germany

Email: twesterhold@marum.de

Phone: +49 421 218 65672

 

Junichiro Kuroda

Atmosphere & Ocean Research Institute (AORI), University of Tokyo, Japan

Email: kuroda@aori.u-tokyo.ac.jp

Phone: +81 4 7136 6120

 

Don Penman

Department of Geosciences, Utah State University, USA

Email: donald.penman@usu.edu

Phone: +1 4357971273

 

 

MARUM produces fundamental scientific knowledge about the role of the ocean and the seafloor in the total Earth system. The dynamics of the oceans and the seabed significantly impact the entire Earth system through the interaction of geological, physical, biological and chemical processes. These influence both the climate and the global carbon cycle, resulting in the creation of unique biological systems. MARUM is committed to fundamental and unbiased research in the interests of society, the marine environment, and in accordance with the sustainability goals of the United Nations. It publishes its quality-assured scientific data to make it publicly available. MARUM informs the public about new discoveries in the marine environment and provides practical knowledge through its dialogue with society. MARUM cooperation with companies and industrial partners is carried out in accordance with its goal of protecting the marine environment.

 

 

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Journal

Science Advances

DOI

10.1126/sciadv.adr8584 

Article Title

Earth Orbital Rhythms links Timing of Deccan Trap Volcanism Phases and Global Climate Change

Article Publication Date

7-Mar-2025