Our Research Food security in Africa through microbiome engineering

Researchers Malik George (left) and Miles George (right) hold up the roots of a plant

Researchers Malik George (left) and Miles George (right) hold an uprooted maize plant from field sampling in Embu, Kenya. The plant features its root and rhizosphere region, where soil was sampled for potential nitrogen fixing bacteria.

Researchers Miles George (Left) and Malik George (right) lean over a maize plant and its roots that is outside on the ground

Researchers Miles George (left) and Malik George (right) conduct phenotypic analysis of harvested maize plant from maize field in Embu, Kenya. Measurements included plant and root characteristics such as age, root depth, root density, and root architecture.
 

Miles George (left), Malik George (middle) and Mourine Mutati (right), work in the lab

Researchers Miles George (left), Malik George (middle), and Mourine Mutai (right) work in the lab on bacterial isolation and plating of rhizosphere and root samples collected from Kenyan maize fields, conducted at Kenyatta University in Kenya in collaboration with the Voigt lab.

Close up of the roots of a maize plant with someone's hands holding tweezers, inspecting the roots

Acquiring field samples of roots from uprooted maize plants from a local farm in Kenya. Bacteria was isolated from these samples to search for nitrogen fixing bacteria colonizing the rhizoplane of Kenyan maize crops.

Corn roots pulled out of the soil covered in dirt with green corn crops growing in the background

Maize roots.

Petri dish with a small plant sprouting out

Growth chamber to image an intact, growing, plant root system.

Plant roots shown under a microscope, dyed with different colors to indicate different environmental stresses

Metabolic imaging (You Lab) of Arabidopsis roots under different environmental stress in situ (McRose Lab). This preliminary image shows the metabolic contrast within the root without destructive slicing or staining.

Soil samples in petri dishes photographed from above

Soil bacteria like the ones shown here growing on plates often produce metabolites that can help release phosphorus from iron minerals. In this image, the different colors are very likely bacterial metabolites. Photo Credit: Darcy McRose.

Researchers Malik George (left) and Miles George (right) hold up the roots of a plant

Researchers Malik George (left) and Miles George (right) hold an uprooted maize plant from field sampling in Embu, Kenya. The plant features its root and rhizosphere region, where soil was sampled for potential nitrogen fixing bacteria.

Researchers Miles George (Left) and Malik George (right) lean over a maize plant and its roots that is outside on the ground

Researchers Miles George (left) and Malik George (right) conduct phenotypic analysis of harvested maize plant from maize field in Embu, Kenya. Measurements included plant and root characteristics such as age, root depth, root density, and root architecture.
 

Miles George (left), Malik George (middle) and Mourine Mutati (right), work in the lab

Researchers Miles George (left), Malik George (middle), and Mourine Mutai (right) work in the lab on bacterial isolation and plating of rhizosphere and root samples collected from Kenyan maize fields, conducted at Kenyatta University in Kenya in collaboration with the Voigt lab.

Close up of the roots of a maize plant with someone's hands holding tweezers, inspecting the roots

Acquiring field samples of roots from uprooted maize plants from a local farm in Kenya. Bacteria was isolated from these samples to search for nitrogen fixing bacteria colonizing the rhizoplane of Kenyan maize crops.

Corn roots pulled out of the soil covered in dirt with green corn crops growing in the background

Maize roots.

Petri dish with a small plant sprouting out

Growth chamber to image an intact, growing, plant root system.

Plant roots shown under a microscope, dyed with different colors to indicate different environmental stresses

Metabolic imaging (You Lab) of Arabidopsis roots under different environmental stress in situ (McRose Lab). This preliminary image shows the metabolic contrast within the root without destructive slicing or staining.

Soil samples in petri dishes photographed from above

Soil bacteria like the ones shown here growing on plates often produce metabolites that can help release phosphorus from iron minerals. In this image, the different colors are very likely bacterial metabolites. Photo Credit: Darcy McRose.

Principal Investigators

Challenge:

Can we replace agricultural inputs derived from synthetic chemistry with those that can be delivered by microbes, applied at planting?

Research Strategy

  • Catalog microbial species from crop roots from farms in the U.S. and Kenya, in collaboration with Kenyatta University, and isolate and engineer nitrogen-fixing bacteria to do so continuously with cereal crops
  • Build consortia that coat the roots of plants and are maximally metabolically active. Success will be measured by lower plant-to-plant variability, higher total activity, and stability of the consortium against stresses and environmental conditions
  • Work with the Jameel Poverty Action Lab (J-PAL) and small stakeholder farmers to establish protocols for using microbial products. Best practices and networks to educate and train farmers will be developed, along with the distribution requirements to transport active bacteria for testing and use

Project description

Agrichemicals, including herbicides and fertilizer, are essential to obtain the crop yields required to feed the world. However, in their chemical form, they are responsible for most of the air and water pollution from agriculture. Microbes have the theoretical ability to replace the functions of agrochemicals, but the challenge has been poorly understood variability between plants and farms. In this project, the team will address this problem by analyzing microbial communities present in soil across diverse farms in the U.S. and Kenya. Data will be obtained to rationally combine species into stable consortia that reliably coat the root and maximize their agricultural function(s). Each species within the consortium offers the capability to enhance activity through redundancy or introduce multiple functions. Consortium design will be applied to the goal of increasing microbial nitrogen delivery to a cereal crop, while reducing variability. Beyond these specific applications, a successful platform to have bacteria reliably deliver traits to crops could increase yields while reducing water use, energy requirements, and environmental impact. 

The MIT team will work with Kenyatta University collaborators. They 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. 

News

Additional Details

Impact Areas

  • Food
  • Climate & Sustainability

Research Themes

  • Technology & Commercialization
  • Sustainability & Adaptation
  • Soil Fertility & Crop Productivity
  • Economics, Policy, & Practices
  • Transforming Food Systems
  • Equity & Access

Year Funded

  • 2025

Grant Type

  • Grand Challenge Grant

Status

  • Ongoing