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    Creeping crystals: Scientists observe “salt creep” at the single-crystal scale

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    Salt creeping, a phenomenon that occurs in both natural and industrial processes, describes the collection and migration of salt crystals from evaporating solutions onto surfaces. Once they start collecting, the crystals climb, spreading away from the solution. This creeping behavior, according to researchers, can cause damage or be harnessed for good, depending on the context. New research published June 30 in the journal Langmuir is the first to show salt creeping at a single-crystal scale and beneath a liquid’s meniscus.“The work not only explains how salt creeping begins, but why it begins and when it does,” says Joseph Phelim Mooney, a postdoc in the MIT Device Research Laboratory and one of the authors of the new study. “We hope this level of insight helps others, whether they’re tackling water scarcity, preserving ancient murals, or designing longer-lasting infrastructure.”The work is the first to directly visualize how salt crystals grow and interact with surfaces underneath a liquid meniscus, something that’s been theorized for decades but never actually imaged or confirmed at this level, and it offers fundamental insights that could impact a wide range of fields — from mineral extraction and desalination to anti-fouling coatings, membrane design for separation science, and even art conservation, where salt damage is a major threat to heritage materials.In civil engineering applications, for example, the research can help explain why and when salt crystals start growing across surfaces like concrete, stone, or building materials. “These crystals can exert pressure and cause cracking or flaking, reducing the long-term durability of structures,” says Mooney. “By pinpointing the moment when salt begins to creep, engineers can better design protective coatings or drainage systems to prevent this form of degradation.”For a field like art conservation, where salt can be devastating to murals, frescoes, and ancient artifacts, often forming beneath the surface before visible damage appears, the work can help identify the exact conditions that cause salt to start moving and spreading, allowing conservators to act earlier and more precisely to protect heritage objects.The work began during Mooney’s Marie Curie Fellowship at MIT. “I was focused on improving desalination systems and quickly ran into [salt buildup as] a major roadblock,” he says. “[Salt] was everywhere, coating surfaces, clogging flow paths, and undermining the efficiency of our designs. I realized we didn’t fully understand how or why salt starts creeping across surfaces in the first place.”That experience led Mooney to team up with colleagues to dig into the fundamentals of salt crystallization at the air–liquid–solid interface. “We wanted to zoom in, to really see the moment salt begins to move, so we turned to in situ X-ray microscopy,” he says. “What we found gave us a whole new way to think about surface fouling, material degradation, and controlled crystallization.”The new research may, in fact, allow better control of a crystallization processes required to remove salt from water in zero-liquid discharge systems. It can also be used to explain how and when scaling happens on equipment surfaces, and may support emerging climate technologies that depend on smart control of evaporation and crystallization.The work also supports mineral and salt extraction applications, where salt creeping can be both a bottleneck and an opportunity. In these applications, Mooney says, “by understanding the precise physics of salt formation at surfaces, operators can optimize crystal growth, improving recovery rates and reducing material losses.”Mooney’s co-authors on the paper include fellow MIT Device Lab researchers Omer Refet Caylan, Bachir El Fil (now an associate professor at Georgia Tech), and Lenan Zhang (now an associate professor at Cornell University); Jeff Punch and Vanessa Egan of the University of Limerick; and Jintong Gao of Cornell.The research was conducted using in situ X-ray microscopy. Mooney says the team’s big realization moment occurred when they were able to observe a single salt crystal pinning itself to the surface, which kicked off a cascading chain reaction of growth.“People had speculated about this, but we captured it on X-ray for the first time. It felt like watching the microscopic moment where everything tips, the ignition points of a self-propagating process,” says Mooney. “Even more surprising was what followed: The salt crystal didn’t just grow passively to fill the available space. It pierced through the liquid-air interface and reshaped the meniscus itself, setting up the perfect conditions for the next crystal. That subtle, recursive mechanism had never been visually documented before — and seeing it play out in real time completely changed how we thought about salt crystallization.”The paper, “In Situ X-ray Microscopy Unraveling the Onset of Salt Creeping at a Single-Crystal Level,” is available now in the journal Langmuir. Research was conducted in MIT.nano.  More

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      Why animals are a critical part of forest carbon absorption

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      A lot of attention has been paid to how climate change can drive biodiversity loss. Now, MIT researchers have shown the reverse is also true: Reductions in biodiversity can jeopardize one of Earth’s most powerful levers for mitigating climate change.In a paper published in PNAS, the researchers showed that following deforestation, naturally-regrowing tropical forests, with healthy populations of seed-dispersing animals, can absorb up to four times more carbon than similar forests with fewer seed-dispersing animals.Because tropical forests are currently Earth’s largest land-based carbon sink, the findings improve our understanding of a potent tool to fight climate change.“The results underscore the importance of animals in maintaining healthy, carbon-rich tropical forests,” says Evan Fricke, a research scientist in the MIT Department of Civil and Environmental Engineering and the lead author of the new study. “When seed-dispersing animals decline, we risk weakening the climate-mitigating power of tropical forests.”Fricke’s co-authors on the paper include César Terrer, the Tianfu Career Development Associate Professor at MIT; Charles Harvey, an MIT professor of civil and environmental engineering; and Susan Cook-Patton of The Nature Conservancy.The study combines a wide array of data on animal biodiversity, movement, and seed dispersal across thousands of animal species, along with carbon accumulation data from thousands of tropical forest sites.The researchers say the results are the clearest evidence yet that seed-dispersing animals play an important role in forests’ ability to absorb carbon, and that the findings underscore the need to address biodiversity loss and climate change as connected parts of a delicate ecosystem rather as separate problems in isolation.“It’s been clear that climate change threatens biodiversity, and now this study shows how biodiversity losses can exacerbate climate change,” Fricke says. “Understanding that two-way street helps us understand the connections between these challenges, and how we can address them. These are challenges we need to tackle in tandem, and the contribution of animals to tropical forest carbon shows that there are win-wins possible when supporting biodiversity and fighting climate change at the same time.”Putting the pieces togetherThe next time you see a video of a monkey or bird enjoying a piece of fruit, consider that the animals are actually playing an important role in their ecosystems. Research has shown that by digesting the seeds and defecating somewhere else, animals can help with the germination, growth, and long-term survival of the plant.Fricke has been studying animals that disperse seeds for nearly 15 years. His previous research has shown that without animal seed dispersal, trees have lower survival rates and a harder time keeping up with environmental changes.“We’re now thinking more about the roles that animals might play in affecting the climate through seed dispersal,” Fricke says. “We know that in tropical forests, where more than three-quarters of trees rely on animals for seed dispersal, the decline of seed dispersal could affect not just the biodiversity of forests, but how they bounce back from deforestation. We also know that all around the world, animal populations are declining.”Regrowing forests is an often-cited way to mitigate the effects of climate change, but the influence of biodiversity on forests’ ability to absorb carbon has not been fully quantified, especially at larger scales.For their study, the researchers combined data from thousands of separate studies and used new tools for quantifying disparate but interconnected ecological processes. After analyzing data from more than 17,000 vegetation plots, the researchers decided to focus on tropical regions, looking at data on where seed-dispersing animals live, how many seeds each animal disperses, and how they affect germination.The researchers then incorporated data showing how human activity impacts different seed-dispersing animals’ presence and movement. They found, for example, that animals move less when they consume seeds in areas with a bigger human footprint.Combining all that data, the researchers created an index of seed-dispersal disruption that revealed a link between human activities and declines in animal seed dispersal. They then analyzed the relationship between that index and records of carbon accumulation in naturally regrowing tropical forests over time, controlling for factors like drought conditions, the prevalence of fires, and the presence of grazing livestock.“It was a big task to bring data from thousands of field studies together into a map of the disruption of seed dispersal,” Fricke says. “But it lets us go beyond just asking what animals are there to actually quantifying the ecological roles those animals are playing and understanding how human pressures affect them.”The researchers acknowledged that the quality of animal biodiversity data could be improved and introduces uncertainty into their findings. They also note that other processes, such as pollination, seed predation, and competition influence seed dispersal and can constrain forest regrowth. Still, the findings were in line with recent estimates.“What’s particularly new about this study is we’re actually getting the numbers around these effects,” Fricke says. “Finding that seed dispersal disruption explains a fourfold difference in carbon absorption across the thousands of tropical regrowth sites included in the study points to seed dispersers as a major lever on tropical forest carbon.”Quantifying lost carbonIn forests identified as potential regrowth sites, the researchers found seed-dispersal declines were linked to reductions in carbon absorption each year averaging 1.8 metric tons per hectare, equal to a reduction in regrowth of 57 percent.The researchers say the results show natural regrowth projects will be more impactful in landscapes where seed-dispersing animals have been less disrupted, including areas that were recently deforested, are near high-integrity forests, or have higher tree cover.“In the discussion around planting trees versus allowing trees to regrow naturally, regrowth is basically free, whereas planting trees costs money, and it also leads to less diverse forests,” Terrer says. “With these results, now we can understand where natural regrowth can happen effectively because there are animals planting the seeds for free, and we also can identify areas where, because animals are affected, natural regrowth is not going to happen, and therefore planting trees actively is necessary.”To support seed-dispersing animals, the researchers encourage interventions that protect or improve their habitats and that reduce pressures on species, ranging from wildlife corridors to restrictions on wildlife trade. Restoring the ecological roles of seed dispersers is also possible by reintroducing seed-dispersing species where they’ve been lost or planting certain trees that attract those animals.The findings could also make modeling the climate impact of naturally regrowing forests more accurate.“Overlooking the impact of seed-dispersal disruption may overestimate natural regrowth potential in many areas and underestimate it in others,” the authors write.The researchers believe the findings open up new avenues of inquiry for the field.“Forests provide a huge climate subsidy by sequestering about a third of all human carbon emissions,” Terrer says. “Tropical forests are by far the most important carbon sink globally, but in the last few decades, their ability to sequester carbon has been declining. We will next explore how much of that decline is due to an increase in extreme droughts or fires versus declines in animal seed dispersal.”Overall, the researchers hope the study helps improves our understanding of the planet’s complex ecological processes.“When we lose our animals, we’re losing the ecological infrastructure that keeps our tropical forests healthy and resilient,” Fricke says.The research was supported by the MIT Climate and Sustainability Consortium, the Government of Portugal, and the Bezos Earth Fund. More

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      in Energy

      Theory-guided strategy expands the scope of measurable quantum interactions

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      A new theory-guided framework could help scientists probe the properties of new semiconductors for next-generation microelectronic devices, or discover materials that boost the performance of quantum computers.Research to develop new or better materials typically involves investigating properties that can be reliably measured with existing lab equipment, but this represents just a fraction of the properties that scientists could potentially probe in principle. Some properties remain effectively “invisible” because they are too difficult to capture directly with existing methods.Take electron-phonon interaction — this property plays a critical role in a material’s electrical, thermal, optical, and superconducting properties, but directly capturing it using existing techniques is notoriously challenging.Now, MIT researchers have proposed a theoretically justified approach that could turn this challenge into an opportunity. Their method reinterprets neutron scattering, an often-overlooked interference effect as a potential direct probe of electron-phonon coupling strength.The procedure creates two interaction effects in the material. The researchers show that, by deliberately designing their experiment to leverage the interference between the two interactions, they can capture the strength of a material’s electron-phonon interaction.The researchers’ theory-informed methodology could be used to shape the design of future experiments, opening the door to measuring new quantities that were previously out of reach.“Rather than discovering new spectroscopy techniques by pure accident, we can use theory to justify and inform the design of our experiments and our physical equipment,” says Mingda Li, the Class of 1947 Career Development Professor and an associate professor of nuclear science and engineering, and senior author of a paper on this experimental method.Li is joined on the paper by co-lead authors Chuliang Fu, an MIT postdoc; Phum Siriviboon and Artittaya Boonkird, both MIT graduate students; as well as others at MIT, the National Institute of Standards and Technology, the University of California at Riverside, Michigan State University, and Oak Ridge National Laboratory. The research appears this week in Materials Today Physics.Investigating interferenceNeutron scattering is a powerful measurement technique that involves aiming a beam of neutrons at a material and studying how the neutrons are scattered after they strike it. The method is ideal for measuring a material’s atomic structure and magnetic properties.When neutrons collide with the material sample, they interact with it through two different mechanisms, creating a nuclear interaction and a magnetic interaction. These interactions can interfere with each other.“The scientific community has known about this interference effect for a long time, but researchers tend to view it as a complication that can obscure measurement signals. So it hasn’t received much focused attention,” Fu says.The team and their collaborators took a conceptual “leap of faith” and decided to explore this oft-overlooked interference effect more deeply.They flipped the traditional materials research approach on its head by starting with a multifaceted theoretical analysis. They explored what happens inside a material when the nuclear interaction and magnetic interaction interfere with each other.Their analysis revealed that this interference pattern is directly proportional to the strength of the material’s electron-phonon interaction.“This makes the interference effect a probe we can use to detect this interaction,” explains Siriviboon.Electron-phonon interactions play a role in a wide range of material properties. They affect how heat flows through a material, impact a material’s ability to absorb and emit light, and can even lead to superconductivity.But the complexity of these interactions makes them hard to directly measure using existing experimental techniques. Instead, researchers often rely on less precise, indirect methods to capture electron-phonon interactions.However, leveraging this interference effect enables direct measurement of the electron-phonon interaction, a major advantage over other approaches.“Being able to directly measure the electron-phonon interaction opens the door to many new possibilities,” says Boonkird.Rethinking materials researchBased on their theoretical insights, the researchers designed an experimental setup to demonstrate their approach.Since the available equipment wasn’t powerful enough for this type of neutron scattering experiment, they were only able to capture a weak electron-phonon interaction signal — but the results were clear enough to support their theory.“These results justify the need for a new facility where the equipment might be 100 to 1,000 times more powerful, enabling scientists to clearly resolve the signal and measure the interaction,” adds Landry.With improved neutron scattering facilities, like those proposed for the upcoming Second Target Station at Oak Ridge National Laboratory, this experimental method could be an effective technique for measuring many crucial material properties.For instance, by helping scientists identify and harness better semiconductors, this approach could enable more energy-efficient appliances, faster wireless communication devices, and more reliable medical equipment like pacemakers and MRI scanners.   Ultimately, the team sees this work as a broader message about the need to rethink the materials research process.“Using theoretical insights to design experimental setups in advance can help us redefine the properties we can measure,” Fu says.To that end, the team and their collaborators are currently exploring other types of interactions they could leverage to investigate additional material properties.“This is a very interesting paper,” says Jon Taylor, director of the neutron scattering division at Oak Ridge National Laboratory, who was not involved with this research. “It would be interesting to have a neutron scattering method that is directly sensitive to charge lattice interactions or more generally electronic effects that were not just magnetic moments. It seems that such an effect is expectedly rather small, so facilities like STS could really help develop that fundamental understanding of the interaction and also leverage such effects routinely for research.”This work is funded, in part, by the U.S. Department of Energy and the National Science Foundation. More

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      in Energy

      Model predicts long-term effects of nuclear waste on underground disposal systems

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      As countries across the world experience a resurgence in nuclear energy projects, the questions of where and how to dispose of nuclear waste remain as politically fraught as ever. The United States, for instance, has indefinitely stalled its only long-term underground nuclear waste repository. Scientists are using both modeling and experimental methods to study the effects of underground nuclear waste disposal and ultimately, they hope, build public trust in the decision-making process.New research from scientists at MIT, Lawrence Berkeley National Lab, and the University of Orléans makes progress in that direction. The study shows that simulations of underground nuclear waste interactions, generated by new, high-performance-computing software, aligned well with experimental results from a research facility in Switzerland.The study, which was co-authored by MIT PhD student Dauren Sarsenbayev and Assistant Professor Haruko Wainwright, along with Christophe Tournassat and Carl Steefel, appears in the journal PNAS.“These powerful new computational tools, coupled with real-world experiments like those at the Mont Terri research site in Switzerland, help us understand how radionuclides will migrate in coupled underground systems,” says Sarsenbayev, who is first author of the new study.The authors hope the research will improve confidence among policymakers and the public in the long-term safety of underground nuclear waste disposal.“This research — coupling both computation and experiments — is important to improve our confidence in waste disposal safety assessments,” says Wainwright. “With nuclear energy re-emerging as a key source for tackling climate change and ensuring energy security, it is critical to validate disposal pathways.”Comparing simulations with experimentsDisposing of nuclear waste in deep underground geological formations is currently considered the safest long-term solution for managing high-level radioactive waste. As such, much effort has been put into studying the migration behaviors of radionuclides from nuclear waste within various natural and engineered geological materials.Since its founding in 1996, the Mont Terri research site in northern Switzerland has served as an important test bed for an international consortium of researchers interested in studying materials like Opalinus clay — a thick, water-tight claystone abundant in the tunneled areas of the mountain.“It is widely regarded as one of the most valuable real-world experiment sites because it provides us with decades of datasets around the interactions of cement and clay, and those are the key materials proposed to be used by countries across the world for engineered barrier systems and geological repositories for nuclear waste,” explains Sarsenbayev.For their study, Sarsenbayev and Wainwright collaborated with co-authors Tournassat and Steefel, who have developed high-performance computing software to improve modeling of interactions between the nuclear waste and both engineered and natural materials.To date, several challenges have limited scientists’ understanding of how nuclear waste reacts with cement-clay barriers. For one thing, the barriers are made up of irregularly mixed materials deep underground. Additionally, the existing class of models commonly used to simulate radionuclide interactions with cement-clay do not take into account electrostatic effects associated with the negatively charged clay minerals in the barriers.Tournassat and Steefel’s new software accounts for electrostatic effects, making it the only one that can simulate those interactions in three-dimensional space. The software, called CrunchODiTi, was developed from established software known as CrunchFlow and was most recently updated this year. It is designed to be run on many high-performance computers at once in parallel.For the study, the researchers looked at a 13-year-old experiment, with an initial focus on cement-clay rock interactions. Within the last several years, a mix of both negatively and positively charged ions were added to the borehole located near the center of the cement emplaced in the formation. The researchers focused on a 1-centimeter-thick zone between the radionuclides and cement-clay referred to as the “skin.” They compared their experimental results to the software simulation, finding the two datasets aligned.“The results are quite significant because previously, these models wouldn’t fit field data very well,” Sarsenbayev says. “It’s interesting how fine-scale phenomena at the ‘skin’ between cement and clay, the physical and chemical properties of which changes over time, could be used to reconcile the experimental and simulation data.” The experimental results showed the model successfully accounted for electrostatic effects associated with the clay-rich formation and the interaction between materials in Mont Terri over time.“This is all driven by decades of work to understand what happens at these interfaces,” Sarsenbayev says. “It’s been hypothesized that there is mineral precipitation and porosity clogging at this interface, and our results strongly suggest that.”“This application requires millions of degrees of freedom because these multibarrier systems require high resolution and a lot of computational power,” Sarsenbayev says. “This software is really ideal for the Mont Terri experiment.”Assessing waste disposal plansThe new model could now replace older models that have been used to conduct safety and performance assessments of underground geological repositories.“If the U.S. eventually decides to dispose nuclear waste in a geological repository, then these models could dictate the most appropriate materials to use,” Sarsenbayev says. “For instance, right now clay is considered an appropriate storage material, but salt formations are another potential medium that could be used. These models allow us to see the fate of radionuclides over millennia. We can use them to understand interactions at timespans that vary from months to years to many millions of years.”Sarsenbayev says the model is reasonably accessible to other researchers and that future efforts may focus on the use of machine learning to develop less computationally expensive surrogate models.Further data from the experiment will be available later this month. The team plans to compare those data to additional simulations.“Our collaborators will basically get this block of cement and clay, and they’ll be able to run experiments to determine the exact thickness of the skin along with all of the minerals and processes present at this interface,” Sarsenbayev says. “It’s a huge project and it takes time, but we wanted to share initial data and this software as soon as we could.”For now, the researchers hope their study leads to a long-term solution for storing nuclear waste that policymakers and the public can support.“This is an interdisciplinary study that includes real world experiments showing we’re able to predict radionuclides’ fate in the subsurface,” Sarsenbayev says. “The motto of MIT’s Department of Nuclear Science and Engineering is ‘Science. Systems. Society.’ I think this merges all three domains.” More

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      in Security

      Study shows a link between obesity and what’s on local restaurant menus

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      For many years, health experts have been concerned about “food deserts,” places where residents lack good nutritional options. Now, an MIT-led study of three major global cities uses a new, granular method to examine the issue, and concludes that having fewer and less nutritional eating options nearby correlates with obesity and other health outcomes.Rather than just mapping geographic areas, the researchers examined the dietary value of millions of food items on roughly 30,000 restaurant menus and derived a more precise assessment of the connection between neighborhoods and nutrition.“We show that what is sold in a restaurant has a direct correlation to people’s health,” says MIT researcher Fabio Duarte, co-author of a newly published paper outlining the study’s results. “The food landscape matters.”The open-access paper, “Data-driven nutritional assessment of urban food landscapes: insights from Boston, London, Dubai,” was published this week in Nature: Scientific Reports.The co-authors are Michael Tufano, a PhD student at Wageningen University, in the Netherlands; Duarte, associate director of MIT’s Senseable City Lab, which uses data to study cities as dynamic systems; Martina Mazzarello, a postdoc at the Senseable City Lab; Javad Eshtiyagh, a research fellow at the Senseable City Lab; Carlo Ratti, professor of the practice and director of the Senseable City Lab; and Guido Camps, a senior researcher at Wageningen University.Scanning the menuTo conduct the study, the researchers examined menus from Boston, Dubai, and London, in the summer of 2023, compiling a database of millions of items available through popular food-delivery platforms. The team then evaluated the food items as rated by the USDA’s FoodData Central database, an information bank with 375,000 kinds of food products listed. The study deployed two main metrics, the Meal Balance Index, and the Nutrient-Rich Foods Index.The researchers examined about 222,000 menu items from over 2,000 restaurants in Boston, about 1.6 million menu items from roughly 9,000 restaurants in Dubai, and about 3.1 million menu items from about 18,000 restaurants in London. In Boston, about 71 percent of the items were in the USDA database; in Dubai and London, that figure was 42 percent and 56 percent, respectively.The team then rated the nutritional value of the items appearing on menus, and correlated the food data with health-outcome data from Boston and London. In London, they found a clear correlation between neighborhood menu offerings and obesity, or the lack thereof; with a slightly less firm correlation in Boston. Areas with food options that include a lot of dietary fibers, sometimes along with fruits and vegetables, tend to have better health data.In Dubai, the researchers did not have the same types of health data available but did observe a strong correlation between rental prices and the nutritional value of neighborhood-level food, suggesting that wealthier residents have better nourishment options.“At the item level, when we have less nutritional food, we see more cases of obsesity,” Tufano says. “It’s true that not only do we have more fast food in poor neighborhoods, but the nutritional value is not the same.”Re-mapping the food landscapeBy conducting the study in this fashion, the scholars added a layer of analysis to past studies of food deserts. While past work has broken ground by identifying neighborhoods and areas lacking good food access, this research makes a more comprehensive assessment of what people consume. The research moves toward evaluating the complex mix of food available in any given area, which can be true even of areas with more limited options.“We were not satisfied with this idea that if you only have fast food, it’s a food desert, but if you have a Whole Foods, it’s not,” Duarte says. “It’s not necessarily like that.”For the Senseable City Lab researchers, the study is a new technique further enabling them to understand city dynamics and the effects of the urban environment on health. Past lab studies have often focused on issues such as urban mobility, while extending to matters such as mobility and air pollution, among other topics.Being able to study food and health at the neighborhood level, though, is still another example of the ways that data-rich spheres of life can be studied in close detail.“When we started working on cities and data, the data resolution was so low,” Ratti says. “Today the amount of data is so immense we see this great opportunity to look at cities and see the influence of the urban environment as a big determinant of health. We see this as one of the new frontiers of our lab. It’s amazing how we can now look at this very precisely in cities.” More

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      in Security

      MIT chemists boost the efficiency of a key enzyme in photosynthesis

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      During photosynthesis, an enzyme called rubisco catalyzes a key reaction — the incorporation of carbon dioxide into organic compounds to create sugars. However, rubisco, which is believed to be the most abundant enzyme on Earth, is very inefficient compared to the other enzymes involved in photosynthesis.MIT chemists have now shown that they can greatly enhance a version of rubisco found in bacteria from a low-oxygen environment. Using a process known as directed evolution, they identified mutations that could boost rubisco’s catalytic efficiency by up to 25 percent.The researchers now plan to apply their technique to forms of rubisco that could be used in plants to help boost their rates of photosynthesis, which could potentially improve crop yields.“This is, I think, a compelling demonstration of successful improvement of a rubisco’s enzymatic properties, holding out a lot of hope for engineering other forms of rubisco,” says Matthew Shoulders, the Class of 1942 Professor of Chemistry at MIT.Shoulders and Robert Wilson, a research scientist in the Department of Chemistry, are the senior authors of the new study, which appears this week in the Proceedings of the National Academy of Sciences. MIT graduate student Julie McDonald is the paper’s lead author.Evolution of efficiencyWhen plants or photosynthetic bacteria absorb energy from the sun, they first convert it into energy-storing molecules such as ATP. In the next phase of photosynthesis, cells use that energy to transform a molecule known as ribulose bisphosphate into glucose, which requires several additional reactions. Rubisco catalyzes the first of those reactions, known as carboxylation. During that reaction, carbon from CO2 is added to ribulose bisphosphate.Compared to the other enzymes involved in photosynthesis, rubisco is very slow, catalyzing only one to 10 reactions per second. Additionally, rubisco can also interact with oxygen, leading to a competing reaction that incorporates oxygen instead of carbon — a process that wastes some of the energy absorbed from sunlight.“For protein engineers, that’s a really attractive set of problems because those traits seem like things that you could hopefully make better by making changes to the enzyme’s amino acid sequence,” McDonald says.Previous research has led to improvement in rubisco’s stability and solubility, which resulted in small gains in enzyme efficiency. Most of those studies used directed evolution — a technique in which a naturally occurring protein is randomly mutated and then screened for the emergence of new, desirable features.This process is usually done using error-prone PCR, a technique that first generates mutations in vitro (outside of the cell), typically introducing only one or two mutations in the target gene. In past studies on rubisco, this library of mutations was then introduced into bacteria that grow at a rate relative to rubisco activity. Limitations in error-prone PCR and in the efficiency of introducing new genes restrict the total number of mutations that can be generated and screened using this approach. Manual mutagenesis and selection steps also add more time to the process over multiple rounds of evolution.The MIT team instead used a newer mutagenesis technique that the Shoulders Lab previously developed, called MutaT7. This technique allows the researchers to perform both mutagenesis and screening in living cells, which dramatically speeds up the process. Their technique also enables them to mutate the target gene at a higher rate.“Our continuous directed evolution technique allows you to look at a lot more mutations in the enzyme than has been done in the past,” McDonald says.Better rubiscoFor this study, the researchers began with a version of rubisco, isolated from a family of semi-anaerobic bacteria known as Gallionellaceae, that is one of the fastest rubisco found in nature. During the directed evolution experiments, which were conducted in E. coli, the researchers kept the microbes in an environment with atmospheric levels of oxygen, creating evolutionary pressure to adapt to oxygen.After six rounds of directed evolution, the researchers identified three different mutations that improved the rubisco’s resistance to oxygen. Each of these mutations are located near the enzyme’s active site (where it performs carboxylation or oxygenation). The researchers believe that these mutations improve the enzyme’s ability to preferentially interact with carbon dioxide over oxygen, which leads to an overall increase in carboxylation efficiency.“The underlying question here is: Can you alter and improve the kinetic properties of rubisco to operate better in environments where you want it to operate better?” Shoulders says. “What changed through the directed evolution process was that rubisco began to like to react with oxygen less. That allows this rubisco to function well in an oxygen-rich environment, where normally it would constantly get distracted and react with oxygen, which you don’t want it to do.”In ongoing work, the researchers are applying this approach to other forms of rubisco, including rubisco from plants. Plants are believed to lose about 30 percent of the energy from the sunlight they absorb through a process called photorespiration, which occurs when rubisco acts on oxygen instead of carbon dioxide.“This really opens the door to a lot of exciting new research, and it’s a step beyond the types of engineering that have dominated rubisco engineering in the past,” Wilson says. “There are definite benefits to agricultural productivity that could be leveraged through a better rubisco.”The research was funded, in part, by the National Science Foundation, the National Institutes of Health, an Abdul Latif Jameel Water and Food Systems Lab Grand Challenge grant, and a Martin Family Society Fellowship for Sustainability. More

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      in Environment

      Study shows how a common fertilizer ingredient benefits plants

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      Lanthanides are a class of rare earth elements that in many countries are added to fertilizer as micronutrients to stimulate plant growth. But little is known about how they are absorbed by plants or influence photosynthesis, potentially leaving their benefits untapped.Now, researchers from MIT have shed light on how lanthanides move through and operate within plants. These insights could help farmers optimize their use to grow some of the world’s most popular crops.Published today in the Journal of the American Chemical Society, the study shows that a single nanoscale dose of lanthanides applied to seeds can make some of the world’s most common crops more resilient to UV stress. The researchers also uncovered the chemical processes by which lanthanides interact with the chlorophyll pigments that drive photosynthesis, showing that different lanthanide elements strengthen chlorophyll by replacing the magnesium at its center.“This is a first step to better understand how these elements work in plants, and to provide an example of how they could be better delivered to plants, compared to simply applying them in the soil,” says Associate Professor Benedetto Marelli, who conducted the research with postdoc Giorgio Rizzo. “This is the first example of a thorough study showing the effects of lanthanides on chlorophyll, and their beneficial effects to protect plants from UV stress.”Inside plant connectionsCertain lanthanides are used as contrast agents in MRI and for applications including light-emitting diodes, solar cells, and lasers. Over the last 50 years, lanthanides have become increasingly used in agriculture to enhance crop yields, with China alone applying lanthanide-based fertilizers to nearly 4 million hectares of land each year.“Lanthanides have been considered for a long time to be biologically irrelevant, but that’s changed in agriculture, especially in China,” says Rizzo, the paper’s first author. “But we largely don’t know how lanthanides work to benefit plants — nor do we understand their uptake mechanisms from plant tissues.”Recent studies have shown that low concentrations of lanthanides can promote plant growth, root elongation, hormone synthesis, and stress tolerance, but higher doses can cause harm to plants. Striking the right balance has been hard because of our lack of understanding around how lanthanides are absorbed by plants or how they interact with root soil.For the study, the researchers leveraged seed coating and treatment technologies they previously developed to investigate the way the plant pigment chlorophyll interacts with lanthanides, both inside and outside of plants. Up until now, researchers haven’t been sure whether chlorophyll interacts with lanthanide ions at all.Chlorophyll drives photosynthesis, but the pigments lose their ability to efficiently absorb light when the magnesium ion at their core is removed. The researchers discovered that lanthanides can fill that void, helping chlorophyll pigments partially recover some of their optical properties in a process known as re-greening.“We found that lanthanides can boost several parameters of plant health,” Marelli says. “They mostly accumulate in the roots, but a small amount also makes its way to the leaves, and some of the new chlorophyll molecules made in leaves have lanthanides incorporated in their structure.”This study also offers the first experimental evidence that lanthanides can increase plant resilience to UV stress, something the researchers say was completely unexpected.“Chlorophylls are very sensitive pigments,” Rizzo says. “They can convert light to energy in plants, but when they are isolated from the cell structure, they rapidly hydrolyze and degrade. However, in the form with lanthanides at their center, they are pretty stable, even after extracting them from plant cells.”The researchers, using different spectroscopic techniques, found the benefits held across a range of staple crops, including chickpea, barley, corn, and soybeans.The findings could be used to boost crop yield and increase the resilience of some of the world’s most popular crops to extreme weather.“As we move into an environment where extreme heat and extreme climate events are more common, and particularly where we can have prolonged periods of sun in the field, we want to provide new ways to protect our plants,” Marelli says. “There are existing agrochemicals that can be applied to leaves for protecting plants from stressors such as UV, but they can be toxic, increase microplastics, and can require multiple applications. This could be a complementary way to protect plants from UV stress.”Identifying new applicationsThe researchers also found that larger lanthanide elements like lanthanum were more effective at strengthening chlorophyll pigments than smaller ones. Lanthanum is considered a low-value byproduct of rare earths mining, and can become a burden to the rare earth element (REE) supply chain due to the need to separate it from more desirable rare earths. Increasing the demand for lanthanum could diversify the economics of REEs and improve the stability of their supply chain, the scientists suggest.“This study shows what we could do with these lower-value metals,” Marelli says. “We know lanthanides are extremely useful in electronics, magnets, and energy. In the U.S., there’s a big push to recycle them. That’s why for the plant studies, we focused on lanthanum, being the most abundant, cheapest lanthanide ion.”Moving forward, the team plans to explore how lanthanides work with other biological molecules, including proteins in the human body.In agriculture, the team hopes to scale up its research to include field and greenhouse studies to continue testing the results of UV resilience on different crop types and in experimental farm conditions.“Lanthanides are already widely used in agriculture,” Rizzo says. “We hope this study provides evidence that allows more conscious use of them and also a new way to apply them through seed treatments.”The research was supported by the MIT Climate Grand Challenge and the Office for Naval Research. More

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      Island rivers carve passageways through coral reefs

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      Volcanic islands, such as the islands of Hawaii and the Caribbean, are surrounded by coral reefs that encircle an island in a labyrinthine, living ring. A coral reef is punctured at points by reef passes — wide channels that cut through the coral and serve as conduits for ocean water and nutrients to filter in and out. These watery passageways provide circulation throughout a reef, helping to maintain the health of corals by flushing out freshwater and transporting key nutrients.Now, MIT scientists have found that reef passes are shaped by island rivers. In a study appearing today in the journal Geophysical Research Letters, the team shows that the locations of reef passes along coral reefs line up with where rivers funnel out from an island’s coast.Their findings provide the first quantitative evidence of rivers forming reef passes.  Scientists and explorers had speculated that this may be the case: Where a river on a volcanic island meets the coast, the freshwater and sediment it carries flows toward the reef, where a strong enough flow can tunnel into the surrounding coral. This idea has been proposed from time to time but never quantitatively tested, until now.“The results of this study help us to understand how the health of coral reefs depends on the islands they surround,” says study author Taylor Perron, the Cecil and Ida Green Professor of Earth, Atmospheric and Planetary Sciences at MIT.“A lot of discussion around rivers and their impact on reefs today has been negative because of human impact and the effects of agricultural practices,” adds lead author Megan Gillen, a graduate student in the MIT-WHOI Joint Program in Oceanography. “This study shows the potential long-term benefits rivers can have on reefs, which I hope reshapes the paradigm and highlights the natural state of rivers interacting with reefs.”The study’s other co-author is Andrew Ashton of the Woods Hole Oceanographic Institution.Drawing the linesThe new study is based on the team’s analysis of the Society Islands, a chain of islands in the South Pacific Ocean that includes Tahiti and Bora Bora. Gillen, who joined the MIT-WHOI program in 2020, was interested in exploring connections between coral reefs and the islands they surround. With limited options for on-site work during the Covid-19 pandemic, she and Perron looked to see what they could learn through satellite images and maps of island topography. They did a quick search using Google Earth and zeroed in on the Society Islands for their uniquely visible reef and island features.“The islands in this chain have these iconic, beautiful reefs, and we kept noticing these reef passes that seemed to align with deeply embayed portions of the coastline,” Gillen says. “We started asking ourselves, is there a correlation here?”Viewed from above, the coral reefs that circle some islands bear what look to be notches, like cracks that run straight through a ring. These breaks in the coral are reef passes — large channels that run tens of meters deep and can be wide enough for some boats to pass through. On first look, Gillen noticed that the most obvious reef passes seemed to line up with flooded river valleys — depressions in the coastline that have been eroded over time by island rivers that flow toward the ocean. She wondered whether and to what extent island rivers might shape reef passes.“People have examined the flow through reef passes to understand how ocean waves and seawater circulate in and out of lagoons, but there have been no claims of how these passes are formed,” Gillen says. “Reef pass formation has been mentioned infrequently in the literature, and people haven’t explored it in depth.”Reefs unraveledTo get a detailed view of the topography in and around the Society Islands, the team used data from the NASA Shuttle Radar Topography Mission — two radar antennae that flew aboard the space shuttle in 1999 and measured the topography across 80 percent of the Earth’s surface.The researchers used the mission’s topographic data in the Society Islands to create a map of every drainage basin along the coast of each island, to get an idea of where major rivers flow or once flowed. They also marked the locations of every reef pass in the surrounding coral reefs. They then essentially “unraveled” each island’s coastline and reef into a straight line, and compared the locations of basins versus reef passes.“Looking at the unwrapped shorelines, we find a significant correlation in the spatial relationship between these big river basins and where the passes line up,” Gillen says. “So we can say that statistically, the alignment of reef passes and large rivers does not seem random. The big rivers have a role in forming passes.”As for how rivers shape the coral conduits, the team has two ideas, which they call, respectively, reef incision and reef encroachment. In reef incision, they propose that reef passes can form in times when the sea level is relatively low, such that the reef is exposed above the sea surface and a river can flow directly over the reef. The water and sediment carried by the river can then erode the coral, progressively carving a path through the reef.When sea level is relatively higher, the team suspects a reef pass can still form, through reef encroachment. Coral reefs naturally live close to the water surface, where there is light and opportunity for photosynthesis. When sea levels rise, corals naturally grow upward and inward toward an island, to try to “catch up” to the water line.“Reefs migrate toward the islands as sea levels rise, trying to keep pace with changing average sea level,” Gillen says.However, part of the encroaching reef can end up in old river channels that were previously carved out by large rivers and that are lower than the rest of the island coastline. The corals in these river beds end up deeper than light can extend into the water column, and inevitably drown, leaving a gap in the form of a reef pass.“We don’t think it’s an either/or situation,” Gillen says. “Reef incision occurs when sea levels fall, and reef encroachment happens when sea levels rise. Both mechanisms, occurring over dozens of cycles of sea-level rise and island evolution, are likely responsible for the formation and maintenance of reef passes over time.”The team also looked to see whether there were differences in reef passes in older versus younger islands. They observed that younger islands were surrounded by more reef passes that were spaced closer together, versus older islands that had fewer reef passes that were farther apart.As islands age, they subside, or sink, into the ocean, which reduces the amount of land that funnels rainwater into rivers. Eventually, rivers are too weak to keep the reef passes open, at which point, the ocean likely takes over, and incoming waves could act to close up some passes.Gillen is exploring ideas for how rivers, or river-like flow, can be engineered to create paths through coral reefs in ways that would promote circulation and benefit reef health.“Part of me wonders: If you had a more persistent flow, in places where you don’t naturally have rivers interacting with the reef, could that potentially be a way to increase health, by incorporating that river component back into the reef system?” Gillen says. “That’s something we’re thinking about.”This research was supported, in part, by the WHOI Watson and Von Damm fellowships. More

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      in Environment

      When Earth iced over, early life may have sheltered in meltwater ponds

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      When the Earth froze over, where did life shelter? MIT scientists say one refuge may have been pools of melted ice that dotted the planet’s icy surface.In a study appearing today in Nature Communications, the researchers report that 635 million to 720 million years ago, during periods known as “Snowball Earth,” when much of the planet was covered in ice, some of our ancient cellular ancestors could have waited things out in meltwater ponds.The scientists found that eukaryotes — complex cellular lifeforms that eventually evolved into the diverse multicellular life we see today — could have survived the global freeze by living in shallow pools of water. These small, watery oases may have persisted atop relatively shallow ice sheets present in equatorial regions. There, the ice surface could accumulate dark-colored dust and debris from below, which enhanced its ability to melt into pools. At temperatures hovering around 0 degrees Celsius, the resulting meltwater ponds could have served as habitable environments for certain forms of early complex life.The team drew its conclusions based on an analysis of modern-day meltwater ponds. Today in Antarctica, small pools of melted ice can be found along the margins of ice sheets. The conditions along these polar ice sheets are similar to what likely existed along ice sheets near the equator during Snowball Earth.The researchers analyzed samples from a variety of meltwater ponds located on the McMurdo Ice Shelf in an area that was first described by members of Robert Falcon Scott’s 1903 expedition as “dirty ice.” The MIT researchers discovered clear signatures of eukaryotic life in every pond. The communities of eukaryotes varied from pond to pond, revealing a surprising diversity of life across the setting. The team also found that salinity plays a key role in the kind of life a pond can host: Ponds that were more brackish or salty had more similar eukaryotic communities, which differed from those in ponds with fresher waters.“We’ve shown that meltwater ponds are valid candidates for where early eukaryotes could have sheltered during these planet-wide glaciation events,” says lead author Fatima Husain, a graduate student in MIT’s Department of Earth, Atmospheric and Planetary Sciences (EAPS). “This shows us that diversity is present and possible in these sorts of settings. It’s really a story of life’s resilience.”The study’s MIT co-authors include Schlumberger Professor of Geobiology Roger Summons and former postdoc Thomas Evans, along with Jasmin Millar of Cardiff University, Anne Jungblut at the Natural History Museum in London, and Ian Hawes of the University of Waikato in New Zealand.Polar plunge“Snowball Earth” is the colloquial term for periods of time in Earth history during which the planet iced over. It is often used as a reference to the two consecutive, multi-million-year glaciation events which took place during the Cryogenian Period, which geologists refer to as the time between 635 and 720 million years ago. Whether the Earth was more of a hardened snowball or a softer “slushball” is still up for debate. But scientists are certain of one thing: Most of the planet was plunged into a deep freeze, with average global temperatures of minus 50 degrees Celsius. The question has been: How and where did life survive?“We’re interested in understanding the foundations of complex life on Earth. We see evidence for eukaryotes before and after the Cryogenian in the fossil record, but we largely lack direct evidence of where they may have lived during,” Husain says. “The great part of this mystery is, we know life survived. We’re just trying to understand how and where.”There are a number of ideas for where organisms could have sheltered during Snowball Earth, including in certain patches of the open ocean (if such environments existed), in and around deep-sea hydrothermal vents, and under ice sheets. In considering meltwater ponds, Husain and her colleagues pursued the hypothesis that surface ice meltwaters may also have been capable of supporting early eukaryotic life at the time.“There are many hypotheses for where life could have survived and sheltered during the Cryogenian, but we don’t have excellent analogs for all of them,” Husain notes. “Above-ice meltwater ponds occur on Earth today and are accessible, giving us the opportunity to really focus in on the eukaryotes which live in these environments.”Small pond, big lifeFor their new study, the researchers analyzed samples taken from meltwater ponds in Antarctica. In 2018, Summons and colleagues from New Zealand traveled to a region of the McMurdo Ice Shelf in East Antarctica, known to host small ponds of melted ice, each just a few feet deep and a few meters wide. There, water freezes all the way to the seafloor, in the process trapping dark-colored sediments and marine organisms. Wind-driven loss of ice from the surface creates a sort of conveyer belt that brings this trapped debris to the surface over time, where it absorbs the sun’s warmth, causing ice to melt, while surrounding debris-free ice reflects incoming sunlight, resulting in the formation of shallow meltwater ponds.The bottom of each pond is lined with mats of microbes that have built up over years to form layers of sticky cellular communities.“These mats can be a few centimeters thick, colorful, and they can be very clearly layered,” Husain says.These microbial mats are made up of cyanobacteria, prokaryotic, single-celled photosynthetic organisms that lack a cell nucleus or other organelles. While these ancient microbes are known to survive within some of the the harshest environments on Earth including meltwater ponds, the researchers wanted to know whether eukaryotes — complex organisms that evolved a cell nucleus and other membrane bound organelles — could also weather similarly challenging circumstances. Answering this question would take more than a microscope, as the defining characteristics of the microscopic eukaryotes present among the microbial mats are too subtle to distinguish by eye.To characterize the eukaryotes, the team analyzed the mats for specific lipids they make called sterols, as well as genetic components called ribosomal ribonucleic acid (rRNA), both of which can be used to identify organisms with varying degrees of specificity. These two independent sets of analyses provided complementary fingerprints for certain eukaryotic groups. As part of the team’s lipid research, they found many sterols and rRNA genes closely associated with specific types of algae, protists, and microscopic animals among the microbial mats. The researchers were able to assess the types and relative abundance of lipids and rRNA genes from pond to pond, and found the ponds hosted a surprising diversity of eukaryotic life.“No two ponds were alike,” Husain says. “There are repeating casts of characters, but they’re present in different abundances. And we found diverse assemblages of eukaryotes from all the major groups in all the ponds studied. These eukaryotes are the descendants of the eukaryotes that survived the Snowball Earth. This really highlights that meltwater ponds during Snowball Earth could have served as above-ice oases that nurtured the eukaryotic life that enabled the diversification and proliferation of complex life — including us — later on.”This research was supported, in part, by the NASA Exobiology Program, the Simons Collaboration on the Origins of Life, and a MISTI grant from MIT-New Zealand. More