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    How marsh grass protects shorelines

    Marsh plants, which are ubiquitous along the world’s shorelines, can play a major role in mitigating the damage to coastlines as sea levels rise and storm surges increase. Now, a new MIT study provides greater detail about how these protective benefits work under real-world conditions shaped by waves and currents.

    The study combined laboratory experiments using simulated plants in a large wave tank along with mathematical modeling. It appears in the journal Physical Review — Fluids, in a paper by former MIT visiting doctoral student Xiaoxia Zhang, now a postdoc at Dalian University of Technology, and professor of civil and environmental engineering Heidi Nepf.

    It’s already clear that coastal marsh plants provide significant protection from surges and devastating  storms. For example, it has been estimated that the damage caused by Hurricane Sandy was reduced by $625 million thanks to the damping of wave energy provided by extensive areas of marsh along the affected coasts. But the new MIT analysis incorporates details of plant morphology, such as the number and spacing of flexible leaves versus stiffer stems, and the complex interactions of currents and waves that may be coming from different directions.

    This level of detail could enable coastal restoration planners to determine the area of marsh needed to mitigate expected amounts of storm surge or sea-level rise, and to decide which types of plants to introduce to maximize protection.

    “When you go to a marsh, you often will see that the plants are arranged in zones,” says Nepf, who is the Donald and Martha Harleman Professor of Civil and Environmental Engineering. “Along the edge, you tend to have plants that are more flexible, because they are using their flexibility to reduce the wave forces they feel. In the next zone, the plants are a little more rigid and have a bit more leaves.”

    As the zones progress, the plants become stiffer, leafier, and more effective at absorbing wave energy thanks to their greater leaf area. The new modeling done in this research, which incorporated work with simulated plants in the 24-meter-long wave tank at MIT’s Parsons Lab, can enable coastal planners to take these kinds of details into account when planning protection, mitigation, or restoration projects.

    “If you put the stiffest plants at the edge, they might not survive, because they’re feeling very high wave forces. By describing why Mother Nature organizes plants in this way, we can hopefully design a more sustainable restoration,” Nepf says.

    Once established, the marsh plants provide a positive feedback cycle that helps to not only stabilize but also build up these delicate coastal lands, Zhang says. “After a few years, the marsh grasses start to trap and hold the sediment, and the elevation gets higher and higher, which might keep up with sea level rise,” she says.

    The new MIT analysis incorporates details of plant morphology, such as the number and spacing of flexible leaves versus stiffer stems, and the complex interactions of currents and waves that may be coming from different directions.

    Awareness of the protective effects of marshland has been growing, Nepf says. For example, the Netherlands has been restoring lost marshland outside the dikes that surround much of the nation’s agricultural land, finding that the marsh can protect the dikes from erosion; the marsh and dikes work together much more effectively than the dikes alone at preventing flooding.

    But most such efforts so far have been largely empirical, trial-and-error plans, Nepf says. Now, they could take advantage of this modeling to know just how much marshland with what types of plants would be needed to provide the desired level of protection.

    It also provides a more quantitative way to estimate the value provided by marshes, she says. “It could allow you to more accurately say, ‘40 meters of marsh will reduce waves this much and therefore will reduce overtopping of your levee by this much.’ Someone could use that to say, ‘I’m going to save this much money over the next 10 years if I reduce flooding by maintaining this marsh.’ It might help generate some political motivation for restoration efforts.”

    Nepf herself is already trying to get some of these findings included in coastal planning processes. She serves on a practitioner panel led by Chris Esposito of the Water Institute of the Gulf, which serves the storm-battered Louisiana coastline. “We’d like to get this work into the coatal simulations that are used for large-scale restoration and coastal planning,” she says.

    “Understanding the wave damping process in real vegetation wetlands is of critical value, as it is needed in the assessment of the coastal defense value of these wetlands,” says Zhan Hu, an associate professor of marine sciences at Sun Yat-Sen University, who was not associated with this work. “The challenge, however, lies in the quantitative representation of the wave damping process, in which many factors are at play, such as plant flexibility, morphology, and coexisting currents.”

    The new study, Hu says, “neatly combines experimental findings and analytical modeling to reveal the impact of each factor in the wave damping process. … Overall, this work is a solid step forward toward a more accurate assessment of wave damping capacity of real coastal wetlands, which is needed for science-based design and management of nature-based coastal protection.”

    The work was partly supported by the National Science Foundation and the China Scholarship Council.  More

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    Research collaboration puts climate-resilient crops in sight

    Any houseplant owner knows that changes in the amount of water or sunlight a plant receives can put it under immense stress. A dying plant brings certain disappointment to anyone with a green thumb. 

    But for farmers who make their living by successfully growing plants, and whose crops may nourish hundreds or thousands of people, the devastation of failing flora is that much greater. As climate change is poised to cause increasingly unpredictable weather patterns globally, crops may be subject to more extreme environmental conditions like droughts, fluctuating temperatures, floods, and wildfire. 

    Climate scientists and food systems researchers worry about the stress climate change may put on crops, and on global food security. In an ambitious interdisciplinary project funded by the Abdul Latif Jameel Water and Food Systems Lab (J-WAFS), David Des Marais, the Gale Assistant Professor in the Department of Civil and Environmental Engineering at MIT, and Caroline Uhler, an associate professor in the MIT Department of Electrical Engineering and Computer Science and the Institute for Data, Systems, and Society, are investigating how plant genes communicate with one another under stress. Their research results can be used to breed plants more resilient to climate change.

    Crops in trouble

    Governing plants’ responses to environmental stress are gene regulatory networks, or GRNs, which guide the development and behaviors of living things. A GRN may be comprised of thousands of genes and proteins that all communicate with one another. GRNs help a particular cell, tissue, or organism respond to environmental changes by signaling certain genes to turn their expression on or off.

    Even seemingly minor or short-term changes in weather patterns can have large effects on crop yield and food security. An environmental trigger, like a lack of water during a crucial phase of plant development, can turn a gene on or off, and is likely to affect many others in the GRN. For example, without water, a gene enabling photosynthesis may switch off. This can create a domino effect, where the genes that rely on those regulating photosynthesis are silenced, and the cycle continues. As a result, when photosynthesis is halted, the plant may experience other detrimental side effects, like no longer being able to reproduce or defend against pathogens. The chain reaction could even kill a plant before it has the chance to be revived by a big rain.

    Des Marais says he wishes there was a way to stop those genes from completely shutting off in such a situation. To do that, scientists would need to better understand how exactly gene networks respond to different environmental triggers. Bringing light to this molecular process is exactly what he aims to do in this collaborative research effort.

    Solving complex problems across disciplines

    Despite their crucial importance, GRNs are difficult to study because of how complex and interconnected they are. Usually, to understand how a particular gene is affecting others, biologists must silence one gene and see how the others in the network respond. 

    For years, scientists have aspired to an algorithm that could synthesize the massive amount of information contained in GRNs to “identify correct regulatory relationships among genes,” according to a 2019 article in the Encyclopedia of Bioinformatics and Computational Biology. 

    “A GRN can be seen as a large causal network, and understanding the effects that silencing one gene has on all other genes requires understanding the causal relationships among the genes,” says Uhler. “These are exactly the kinds of algorithms my group develops.”

    Des Marais and Uhler’s project aims to unravel these complex communication networks and discover how to breed crops that are more resilient to the increased droughts, flooding, and erratic weather patterns that climate change is already causing globally.

    In addition to climate change, by 2050, the world will demand 70 percent more food to feed a booming population. “Food systems challenges cannot be addressed individually in disciplinary or topic area silos,” says Greg Sixt, J-WAFS’ research manager for climate and food systems. “They must be addressed in a systems context that reflects the interconnected nature of the food system.”

    Des Marais’ background is in biology, and Uhler’s in statistics. “Dave’s project with Caroline was essentially experimental,” says Renee J. Robins, J-WAFS’ executive director. “This kind of exploratory research is exactly what the J-WAFS seed grant program is for.”

    Getting inside gene regulatory networks

    Des Marais and Uhler’s work begins in a windowless basement on MIT’s campus, where 300 genetically identical Brachypodium distachyon plants grow in large, temperature-controlled chambers. The plant, which contains more than 30,000 genes, is a good model for studying important cereal crops like wheat, barley, maize, and millet. For three weeks, all plants receive the same temperature, humidity, light, and water. Then, half are slowly tapered off water, simulating drought-like conditions.

    Six days into the forced drought, the plants are clearly suffering. Des Marais’ PhD student Jie Yun takes tissues from 50 hydrated and 50 dry plants, freezes them in liquid nitrogen to immediately halt metabolic activity, grinds them up into a fine powder, and chemically separates the genetic material. The genes from all 100 samples are then sequenced at a lab across the street.

    The team is left with a spreadsheet listing the 30,000 genes found in each of the 100 plants at the moment they were frozen, and how many copies there were. Uhler’s PhD student Anastasiya Belyaeva inputs the massive spreadsheet into the computer program she developed and runs her novel algorithm. Within a few hours, the group can see which genes were most active in one condition over another, how the genes were communicating, and which were causing changes in others. 

    The methodology captures important subtleties that could allow researchers to eventually alter gene pathways and breed more resilient crops. “When you expose a plant to drought stress, it’s not like there’s some canonical response,” Des Marais says. “There’s lots of things going on. It’s turning this physiologic process up, this one down, this one didn’t exist before, and now suddenly is turned on.” 

    In addition to Des Marais and Uhler’s research, J-WAFS has funded projects in food and water from researchers in 29 departments across all five MIT schools as well as the MIT Schwarzman College of Computing. J-WAFS seed grants typically fund seven to eight new projects every year.

    “The grants are really aimed at catalyzing new ideas, providing the sort of support [for MIT researchers] to be pushing boundaries, and also bringing in faculty who may have some interesting ideas that they haven’t yet applied to water or food concerns,” Robins says. “It’s an avenue for researchers all over the Institute to apply their ideas to water and food.”

    Alison Gold is a student in MIT’s Graduate Program in Science Writing. More

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    Researchers design sensors to rapidly detect plant hormones

    Researchers from the Disruptive and Sustainable Technologies for Agricultural Precision (DiSTAP) interdisciplinary research group of the Singapore-MIT Alliance for Research and Technology (SMART), MIT’s research enterprise in Singapore, and their local collaborators from Temasek Life Sciences Laboratory (TLL) and Nanyang Technological University (NTU), have developed the first-ever nanosensor to enable rapid testing of synthetic auxin plant hormones. The novel nanosensors are safer and less tedious than existing techniques for testing plants’ response to compounds such as herbicide, and can be transformative in improving agricultural production and our understanding of plant growth.

    The scientists designed sensors for two plant hormones — 1-naphthalene acetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D) — which are used extensively in the farming industry for regulating plant growth and as herbicides, respectively. Current methods to detect NAA and 2,4-D cause damage to plants, and are unable to provide real-time in vivo monitoring and information.

    Based on the concept of corona phase molecular recognition (​​CoPhMoRe) pioneered by the Strano Lab at SMART DiSTAP and MIT, the new sensors are able to detect the presence of NAA and 2,4-D in living plants at a swift pace, providing plant information in real-time, without causing any harm. The team has successfully tested both sensors on a number of everyday crops including pak choi, spinach, and rice across various planting mediums such as soil, hydroponic, and plant tissue culture.

    Explained in a paper titled “Nanosensor Detection of Synthetic Auxins In Planta using Corona Phase Molecular Recognition” published in the journal ACS Sensors, the research can facilitate more efficient use of synthetic auxins in agriculture and hold tremendous potential to advance plant biology study.

    “Our CoPhMoRe technique has previously been used to detect compounds such as hydrogen peroxide and heavy-metal pollutants like arsenic — but this is the first successful case of CoPhMoRe sensors developed for detecting plant phytohormones that regulate plant growth and physiology, such as sprays to prevent premature flowering and dropping of fruits,” says DiSTAP co-lead principal investigator Michael Strano, the Carbon P. Dubbs Professor of Chemical Engineering at MIT. “This technology can replace current state-of-the-art sensing methods which are laborious, destructive, and unsafe.”

    Of the two sensors developed by the research team, the 2,4-D nanosensor also showed the ability to detect herbicide susceptibility, enabling farmers and agricultural scientists to quickly find out how vulnerable or resistant different plants are to herbicides without the need to monitor crop or weed growth over days. “This could be incredibly beneficial in revealing the mechanism behind how 2,4-D works within plants and why crops develop herbicide resistance,” says DiSTAP and TLL Principal Investigator Rajani Sarojam.

    “Our research can help the industry gain a better understanding of plant growth dynamics and has the potential to completely change how the industry screens for herbicide resistance, eliminating the need to monitor crop or weed growth over days,” says Mervin Chun-Yi Ang, a research scientist at DiSTAP. “It can be applied across a variety of plant species and planting mediums, and could easily be used in commercial setups for rapid herbicide susceptibility testing, such as urban farms.”

    NTU Professor Mary Chan-Park Bee Eng says, “Using nanosensors for in planta detection eliminates the need for extensive extraction and purification processes, which saves time and money. They also use very low-cost electronics, which makes them easily adaptable for commercial setups.”

    The team says their research can lead to future development of real-time nanosensors for other dynamic plant hormones and metabolites in living plants as well.

    The development of the nanosensor, optical detection system, and image processing algorithms for this study was done by SMART, NTU, and MIT, while TLL validated the nanosensors and provided knowledge of plant biology and plant signaling mechanisms. The research is carried out by SMART and supported by NRF under its Campus for Research Excellence And Technological Enterprise (CREATE) program.

    DiSTAP is one of the five interdisciplinary research roups in SMART. The DiSTAP program addresses deep problems in food production in Singapore and the world by developing a suite of impactful and novel analytical, genetic, and biosynthetic technologies. The goal is to fundamentally change how plant biosynthetic pathways are discovered, monitored, engineered, and ultimately translated to meet the global demand for food and nutrients.

    Scientists from MIT, TTL, NTU, and National University of Singapore (NUS) are collaboratively developing new tools for the continuous measurement of important plant metabolites and hormones for novel discovery, deeper understanding and control of plant biosynthetic pathways in ways not yet possible, especially in the context of green leafy vegetables; leveraging these new techniques to engineer plants with highly desirable properties for global food security, including high yield density production, drought, and pathogen resistance and biosynthesis of high-value commercial products; developing tools for producing hydrophobic food components in industry-relevant microbes; developing novel microbial and enzymatic technologies to produce volatile organic compounds that can protect and/or promote growth of leafy vegetables; and applying these technologies to improve urban farming.

    DiSTAP is led by Michael Strano and Singapore co-lead principal investigator Professor Chua Nam Hai.

    SMART was established by MIT, in partnership with the NRF, in 2007. SMART, the first entity in CREATE, serves as an intellectual and innovation hub for research interactions between MIT and Singapore, undertaking cutting-edge research projects in areas of interest to both. SMART currently comprises an Innovation Center and five interdisciplinary research groups: Antimicrobial Resistance (AMR), Critical Analytics for Manufacturing Personalized-Medicine (CAMP), DiSTAP, Future Urban Mobility (FM), and Low Energy Electronic Systems (LEES). SMART is funded by the NRF. More