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Engineering superpowered organisms for a more sustainable world

MIT students explore algal water purifiers, programmable soil bacteria, and other biological engineering approaches to food and water security.
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Students in the biological engineering capstone design class showcase their proposed solutions to food and water security challenges over Zoom.
Students in the biological engineering capstone design class showcase their proposed solutions to food and water security challenges over Zoom.
Image: Sean Clarke

Making corn salt-tolerant by engineering its microbiome. Increasing nut productivity with fungal symbiosis. Cleaning up toxic metals in the water supply with algae. Capturing soil nutrient runoff with bacterial biofilms. These were the bio-sustainability innovations designed and presented by students in the Department of Biological Engineering (BE) last May. With the sun shining brightly on an empty Killian Court, the students gathered for the final class presentations over Zoom, physically distanced due to the Covid-19-related closing of MIT’s campus this spring.

For decades, the sustainable technologies dominating public discourse have tended toward the mechanical: wind power, solar power, saltwater distillation, etc. But in recent years, biological solutions have increasingly taken the forefront. For recent BE graduate Adrianna Amaro '20, being able to make use of “existing organisms in the natural world and improve their capabilities, instead of building whole new machines, is the most exciting aspect of biological engineering approaches to sustainability problems.”

Each semester, the BE capstone class (20.380: Biological Engineering Design) challenges students to design, in teams, biological engineering solutions to problems focused on a theme selected by the instructors. Teams are tasked with presenting their solutions in two distinct ways: as a written academic grant proposal and as a startup pitch. For Professor Christopher Voigt, one of the lead instructors, the goal of the class is to “create the climate where a half-baked concept emerges and gets transformed into a project that is both achievable and could have a real-world impact.”

A glance at the research portfolio on the MIT biological engineering homepage reveals a particular focus on human biology. But over the years, students and faculty alike have started pushing for a greater diversity in challenges to which the cutting-edge technology they were developing could be applied. Indeed, “sustainability has been one of the top areas that students raise when asked what they want to address with biological engineering,” says Sean Clarke PhD ’13, another instructor for the class.

In response to student input, the instructors chose food and water security as the theme for the spring 2020 semester. (Sustainability, broadly, was the theme the previous semester.) The topic was well-received by the 20.380 students. Recent BE graduate Cecilia Padilla '20 appreciated how wide-reaching and impactful the issues were, while teammate Abby McGee '20 was thrilled because she had always been interested in environmental issues — and is “not into pharma.”

Since this is the biological engineering capstone, students had to incorporate engineering principles in their biology-based solutions. This meant developing computational models of their proposed biological systems to predict the output of a system from a defined set of inputs. Team SuperSoil, for example, designed a genetic circuit that, when inserted into B. subtilis, a common soil bacteria, would allow it to change behavior based on water and nutrient levels. During heavy rain, for example, the bacteria would respond by producing a phosphate-binding protein biofilm. This would theoretically reduce phosphate runoff, thus preserving soil nutrients and reducing the pollution of waterways. By modeling natural processes such as protein production, bacterial activation, and phosphate diffusion in the soil using differential equations, they were able to predict the degree of phosphate capture and show that significant impact could be achieved with a realistic amount of engineered bacterial input.

Biological engineering Professor Forest White co-leads the class every spring with Voigt. White also teaches the prerequisite, where students learn how to construct computational models of biological systems. He points out how the models helped students develop their capstone projects: “In a couple of cases the model revealed true design challenges, where the feasibility of the project requires optimal engineering of particular aspects of the design.”

Models aside, simply thinking about the mathematical reality of proposed solutions helped teams early on in the idea selection process. Team Nutlettes initially considered using methane-consuming bacteria to capture methane gas from landfills, but back-of-the-envelope calculations revealed unfavorable kinetics. Additionally, further reading brought to light a possible toxic byproduct of bacterial methane metabolism: formaldehyde. Instead, they chose to develop an intervention for water-intensive nut producers: engineer the tree’s fungal symbionts to provide a boost of hormones that would promote flower production, which in turn increases nut yields.

Team Halo saw water filtration as the starting point for ideation, deeming it the most impactful issue to tackle. For inspiration, they looked to mangrove trees, which naturally take up salt from the water that they grow in. They applied this concept to their design of corn-associated, salt-tolerant bacteria that could enhance their plant host’s ability to grow in high salinity conditions — an increasingly common consequence of drought and industrial agricultural irrigation. Additional inspiration came from research in the Department of Civil and Environmental Engineering: In their design, the team incorporated a silk-based seed coating developed by Professor Benedetto Marelli’s group.

Many of the capstone students found themselves exploring unfamiliar fields of research. During their foray into plant-fungal symbiosis, Team Nutlettes was often frustrated by the prevalence of outdated and contradictory findings, and by the lack of quantitative results that they could use in their models. Still, Vaibhavi Shah, one of the few juniors in the class, says she found a lot of value in “diving into something you’ve no experience in.”

In addition to biological design, teams were encouraged to think about the financial feasibility of their proposed solutions. This posed a challenge for Team H2Woah and their algal-based solution for sequestering heavy metals from wastewater. Unlike traditional remediation methods, which produce toxic sludge, their system allows for the recycling of metals from the wastewater for manufacturing, and the opportunity to harvest the algae for biofuels. However, as they developed their concept, they realized that breaking into the existing market would be difficult due to the cost of all the new infrastructure that would be required.

Students read broadly over the course of the semester, which helped them enhance their understanding of food and water insecurity beyond their specific projects. Before the class, Kayla Vodehnal '20 of Team Nutlettes had only been exposed to policy-driven solutions. Amaro, meanwhile, came to realize how close to home the issues they were researching are: all Americans may soon have to confront inadequate access to clean water due to, among other factors, pollution, climate change, and overuse.

In any other semester, the capstone students would have done their final presentations in a seminar room before peers, instructors, a panel of judges, and the indispensable pastry-laden brunch table. This semester, however, the presentations took place, like everything else this spring, on Zoom. Instructors beamed in front of digital congratulatory messages, while some students coordinated background images to present as a single cohesive team. Despite the loss of in-person engagement, the Zoom presentations did come with benefits. This year’s class had a larger group of audience members compared to past years, including at least two dozen faculty, younger students, and alumni who joined virtually to show their support.

Coordinating a group project remotely was challenging for all the teams, but Team Nutlettes found a silver lining: Because having spontaneous conversations over Zoom is harder than in person, they found that their meetings became a lot more productive.

One attendee was Renee Robins ’83, executive director of the Abdul Latif Jameel Water and Food Systems Lab, who had previously interacted with the class as a guest speaker. “Many of the students’ innovative concepts for research and commercialization,” she says, “were of the caliber we see from MIT faculty submitting proposals to J-WAFS’ various grant programs.”

Now that they have graduated, the seniors in the class are all going their separate ways, and some have sustainability careers in mind. Joseph S. Faraguna '20 of Team Halo will be joining Ginkgo Bioworks in the fall, where he hopes to work on a bioremediation or agricultural project. His teammate, McGee, will be doing therapeutic CRISPR research at the Broad Institute of MIT and Harvard, but says that environment-focused research is definitely her end goal.

Between Covid-19 and post-graduation plans, the capstone projects will likely end with the class. Still, this experience will continue to have an influence on the student participants. Team H2Woah is open to continuing their project in the future in some way, Amaro says, since it was their “first real bioengineering experience, and will always have a special place in our hearts.”

Their instructors certainly hope that the class will prove a lasting inspiration. “Even in the face of the Covid-19 pandemic,” White says, “the problems with global warming and food and water security are still the most pressing problems we face as a species. These problems need lots of smart, motivated people thinking of different solutions. If our class ends up motivating even a couple of these students to engage on these problems in the future, then we will have been very successful.”

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