News J-WAFS project aims to replace harmful agrochemicals with microbes for sustainable agriculture

Professor Christopher Voigt will lead a team of scientists, engineers, and economists who have been awarded the 2025 J-WAFS Grand Challenge grant for this work.

Carolyn Blais, J-WAFS January 15, 2025

Microbes are the oldest forms of life on Earth and perhaps the most wondrous. Despite being too small to see with the naked eye, microbes are all around us—in water, soil, air, and even our bodies. All living things rely on microbes to conduct chemical reactions that convert key building blocks of life, like carbon, nitrogen, and oxygen, into biologically accessible forms. Common types of microbes include bacteria, viruses, and fungi, some of which are important to human health, the environment, and to growing the food we eat. In fact, since the dawn of agriculture bacteria have played a role fixing nitrogen into ammonia so that crops can grow. A key challenge in harnessing microbes to benefit agriculture, however, lies in their inconsistent performance across different plant species. Evolution did not optimize microbial functions for farming practices, so bacteria with a desirable functionality do not necessarily associate with the target crop. To address this issue, Professor Christopher Voigt of MIT’s Department of Biological Engineering is working to harness bacteria that can more reliably enhance crop growth across a range of crop species and environmental variations.

“We would like to compare bacteria from around the world for their ability to produce the most nitrogen possible for the plant,” says Voigt. He is currently leading a multidisciplinary team at MIT and Kenyatta University on a project to genetically engineer more robust strains of bacteria for sustainable, high-yield agriculture. The group has been awarded the 2025 J-WAFS Grand Challenge grant following a highly competitive multi-stage proposal process that shepherded initial ideas through to the full proposal stage, with thorough review and feedback from external experts. The team was awarded $1.5 million to conduct this groundbreaking research over the next three years.

“This project stood out for its alignment with the J-WAFS Grand Challenge objective of tackling significant challenges in the areas of water and food for human need, specifically in the context of climate change,” says J-WAFS executive director Renee J. Robins ’83. “As the world population grows, farming practices that are both more productive and more sustainable are needed to ensure we can feed the planet without harming the environment. This promising research aims to accomplish that goal,” she adds.

The root of microbial agriculture

Much of modern-day agriculture relies on synthetic chemistry to produce fertilizers, pesticides, and herbicides. These agrochemicals have adverse effects on the environment, wildlife, and human health. Synthetic nitrogen fertilizer, for example, is manufactured by fixing nitrogen through the Haber-Bosch process, which is highly energy intensive and produces extensive greenhouse gas emissions. In addition, excess nitrogen in the environment pollutes air and waterways, leading to so-called “dead zones” in bodies of water that harm aquatic life. Despite their negative impacts, agrochemicals are widely used because they boost agricultural production by decreasing pests, diseases, and weeds and increasing crop growth and yields. Yet manufactured fertilizer use in Africa remains very low due to affordability and supply chain constraints. Finding sustainable alternatives to help African farmers increase yield is a central objective of the Grand Challenge project.

Theoretically, microbes have the ability to replace the functions of many agrochemicals. Natural chemicals produced by microbes can improve nutrient uptake, act as living pesticides, and suppress plant diseases.

Most nitrogen-fixing bacteria live on the roots of legumes, such as beans and clover. Attracted to hairs on the roots of the plants, bacteria are incorporated into root nodules. There, they work to anaerobically fix nitrogen into ammonia, which plants can then use to build proteins and other essential compounds for growth. In return, the plant captures carbon from the air, converts it into sugars and other organic molecules, and provides energy to the bacteria. But the precise economics of this exchange between plant roots and soil microbes is poorly understood.

“Little is known regarding how species compete on the root spatially and for carbon resources,” says David Des Marais, an associate professor in MIT’s Department of Civil and Environmental Engineering and member of the Grand Challenge project team.

What’s more, only some plants have evolved this kind of symbiotic relationship with bacteria. The natural bacterial function provides benefits to legumes, but the same is not necessarily true for cereals or other crops. Plants like legumes have a clear ecological advantage in many ecosystems, particularly when soil nitrogen is scarce, says Des Marais.

“We also need a better understanding of how differences in soil, water, climate, weather, and farming practices might affect microbe performance,” Voigt adds. “Furthermore, microbes are sensitive to transport and storage, compounding the factors that have been prohibitive to widespread microbe use in farming,” he says.

In prior work supported by two J-WAFS seed grants, Voigt and his lab engineered strains of bacteria in the hopes of providing nitrogen to maize. They genetically engineered root-associated species to improve the secretion of fixed nitrogen and made progress towards expressing nitrogenase in crops. This past work helped to initiate collaborations with Kenyatta University—one of the largest agricultural universities in Africa. Other related research on microbial consortia was the basis for a company called Pivot Bio, which was cofounded by Voigt. Its ProveN40 bacterial product is commercially available in the U.S. and has been demonstrated to reduce synthetic nitrogen use by 20 percent; produce 97 percent less greenhouse gas; use 99.9 percent less water; and prevent excess nitrogen runoff into waterways.

For the 2025 J-WAFS project, Voigt and the team will build off of these prior research efforts to develop foundational principles for the design of enhanced, stable microbial consortia. They will also generate products ready for field trials in the corn-growing regions of Africa, where they will design a consortium to deliver nitrogen fertilizer.

Optimizing natural bacteria for farming

The first step in the group’s research strategy is to collect and analyze microbial communities present in soil across diverse farms in the U.S. and Kenya. The researchers will sample strains from farms in Kenya’s Kisumu region that are representative of diverse soil types, micro-climates, farming practices, and water access/quality. The Kenyan soil and roots will be sampled to determine the microbial populations and compared to data collected from U.S. farm soils. Based on metagenomic sequencing of the microbes’ DNA, species with nitrogen fixation capability will be identified, prioritizing species that are abundant across samples. The goal is to create a large library of promising strains.

The next step will be to test the strains for enhanced plant growth in greenhouse conditions at MIT and Kenyatta University. The microbes will be added to seeds in search for bacteria that will colonize the root surface with no additional applications.

Once stable combinations of microbe and plant are identified, testing of improved strains for enhanced maize yield will be carried out in collaboration with the Department of Biochemistry, Microbiology and Biotechnology at Kenyatta University.  Kenyatta brings access to field and greenhouse facilities, as well as adding highly relevant expertise in local agriculture to the team.

Subsequently, the researchers plan to build consortia that coat the roots of plants and are maximally metabolically active. These microbial communities will be evaluated based on two metrics. The first is increased concentrations of bacteria on the root and decreased plant-to-plant variability. The second is the stability of the consortium in the context of environmental conditions and stressors. The goal is to create combinations of specific species that can stably inoculate maize roots to provide reliable functionality in the field. While the function being studied in this project is nitrogen fixation, this approach could also be applicable to other benefits that microbes can provide such as disease resistance.

Working towards implementation

A central objective of the J-WAFS Grand Challenge grant is to promote work that encompasses actionable, solutions-oriented research. A core component of the funded project is to develop a plan for commercialization in Kenya, and subsequently throughout Africa. Through a collaboration with the economics faculty at Sloan, who are part of the Abdul Latif Jameel Poverty Action Lab (J-PAL), the group will work with farmers in the developing world to test the microbial products and understand their benefits and challenges in the field. They will develop best practices and networks to educate and train farmers and assess distribution requirements to transport active bacteria for testing and use.

Assembling the dream team

Voigt has brought together an interdisciplinary team with a wide breadth of relevant knowledge for this grand challenge. His own lab has made strides in the engineering of soil strains to enhance nitrogen fixation, and they continue to develop bacteria for this purpose.

Tami Lieberman, an associate professor in the Department of Civil and Environmental Engineering, is an expert in microbiome biology, computational biology, and high dimensional data analysis. She will develop methods to optimize the identification and selection of species and strains with high abundance across roots and soil types.  

Darcy McRose is an assistant professor in the Department of Civil and Environmental Engineering who studies soil science. Specifically, she researchers the ways microbially-mediated chemical and biological transformations in soils and sediments affect nutrient cycling and plant growth. Phosphorus is another macronutrient vital to agriculture, but it is often hard to make bioavailable due to reactions with minerals in soils. McRose’s role will be to aid in the development of microbes that can solubilize phosphorus from natural soils.

A professor in MIT’s Sloan School of Management and co-chair of the Agricultural Technology Adoption Initiative at J-PAL, Tavneet Suri has extensive knowledge of Kenya’s agronomy. She is currently running a field trial of PROVEN40 with 500 smallholder farmers, half of which are using the engineered nitrogen-fixing bacteria. She will be instrumental in working with small-scale maize farmers in Kenya to test new products and provide the necessary training and logistical support for these tests.

Assistant Professor Sixian You of MIT’s Department of Electrical Engineering & Computer Science   has developed powerful microscopy techniques which she has applied to plant roots. You will focus on applying the imaging techniques to observe how beneficial bacteria interact with plant roots. Traditional methods to study these bacteria often require invasive procedures or genetic modifications, making it hard to see how they naturally behave. Here, the team will use innovative, label-free microscopy that combines special laser light with advanced computer algorithms. This approach lets the researchers capture detailed, real-time images of bacteria on plant roots and measure their activity without altering them. By understanding exactly where these bacteria are on the roots and how active they are, the team can design better combinations of bacterial species that work together effectively.

As previously mentioned, David Des Marais is an associate professor in the Department of Civil and Environmental Engineering. He studies plant genetics and physiology. His lab will identify what specific molecules are exuded by maize roots, in what quantities, and at which points during plant development. These data will then be used to better optimize plant-soil-microbe interactions in collaboration with the microbiologists on the team.

Kenyatta University collaborators include professors Richard Oduor, Jayne Mugwe, John Maingi, Njeri Mugwe, and Ezekiel Mugendi. This group possesses complementary expertise in soil analysis, characterization of microbial content, and the isolation of nitrogen fixing strains from Kenyan farms.

Potential impacts

Replacing agricultural inputs derived from synthetic chemistry with those that can be delivered by a living microbial inoculant that is applied at planting, will not be a simple task. But the proposed plan offers exciting promise.

“If successful, this research could contribute to the development of sustainable farming practices in Africa that have the potential to improve agricultural productivity without sacrificing the environment,” says Robins. “Microbial products may serve to increase farmers’ access to fertilizer in Africa—where manufactured fertilizer use if very low—with great benefits to food security as climate change brings its own threats,” she adds.

In year three of this project, the team plans to extend the evaluation to additional crops such as sorghum, rice, and cassava that are prevalent in Kenya. If the bacteria are able to reliably meet the needs of crop plants, yields could increase while reducing water use, energy requirements, and environmental impact.