Genome-engineered synthetic microbial consortia for soil carbon sequestration

Overview

This program develops custom-designed rhizosphere microbiomes that act as obligate synthetic symbionts of host plants, increasing soil carbon sink strength while improving crop growth. By applying genome engineering and editing to soil microbial diversity, the team builds defined microbial communities whose functional roles in carbon cycling are pre-assigned. The biocontainment strategy relies on obligate symbiosis, meaning the engineered microbes depend on the plant host for survival and are unlikely to persist or spread outside the target rhizosphere. The approach addresses two linked goals: improving the soil carbon budget and increasing agricultural productivity.

Technical specifications

• Microbiome design: Genome engineering and editing of rhizosphere isolates to create synthetic communities with assigned carbon-cycling functions.
• Obligate symbiosis biocontainment: Engineered strains are tailored to depend on the host plant, reducing environmental persistence outside the intended system.
• Field-validated foundation: Prior work showed that organic fertilization increased carbon-cycling gene abundance in the maize rhizosphere, and that Rhizobium spp. and mycorrhizal fungi improved soybean yield and seed size under semi-arid conditions.
• Planned validation methods:
  • Co-inoculation of two exogenous arbuscular mycorrhizal fungi (AMF) and Chitinophaga on maize seedling roots in unsterilized nursery soil.
  • Shotgun metagenomics and molecular network analysis to assess community impacts on carbon sequestration.
  • PCR-based ITS and 16S rRNA profiling to characterize fungal and bacterial community diversity.
  • Measurement of glomalin-related soil protein (GRSP) and soil organic carbon (SOC) using standard methods.
  • Identification of chitinase genes and biosynthetic gene clusters linked to carbon metabolism.
• Study duration: Approximately two years for the planned validation phase.

Technology readiness level

The program is at an early-to-mid stage of development. Foundational field and genomic studies have already established baseline evidence on carbon-cycling gene distributions and plant-beneficial functions of candidate isolates. The next phase will generate new metagenomic and network data from controlled co-inoculation trials in maize, with a specific need for bioinformatics expertise in molecular networking analysis to support interpretation of community-level carbon-cycling dynamics.