Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2023 Abstracts

Development of Synthetic Microbial Communities to Study Consortium Engraftment Dynamics and to Improve the Yield Performance of Sorghum


Citlali Fonseca1, Ryan McClure2, Dean Pettinga1, Andrew Wilson2, Henri Baldino2, Ritu Shresthra2, Jesus Sanchez1, Claudia Castro1, Joshua Elmore2, Andrew Frank2, Pubudu Handakumbura3, Devin Coleman-Derr1, and Robert Egbert2* ([email protected])


1University of California–Berkeley; 2Pacific Northwest National Laboratory (PNNL); and 3Environmental Molecular Sciences Laboratory



The PNNL Persistence Control Science Focus Area (SFA) aims to gain a fundamental understanding of factors governing the persistence of engineered microbial functions in rhizosphere environments. With this understanding, the SFA is investigating design principles to control the environmental niche of native rhizosphere microbes. Researchers are examining the efficacy of genome reduction and metabolic addiction to plant root exudates in environmental isolates as persistence control strategies using the bioenergy crop sorghum and defined microbial communities as a model ecosystem. The engraftment dynamics of non-native microbes into a reduced-complexity microbial community and the establishment of defined-isolate synthetic communities in field environments are two major areas of current investigation. Effective persistence control will lead to secure plant-microbe biosystems that promote stress-tolerant and highly productive biomass crops.


In the past 2 decades, research of the plant microbiome has shown the importance of plant-associated microbes (PAM) in modulating crop performance (Compant et al. 2019). These studies have paved the way for use of PAM to provide economic and sustainable solutions to current bioenergy cropping and, more generally, agricultural challenges. However, applying PAM within the context of field agriculture has met with mixed success, in part because the introduced microbes must persist within the context of a resilient existing microbiome to be successful. PAM engineering may help overcome these limitations, including via the use of strategies like genome reduction to control the environmental niche of target microbes in agricultural soils (Ke, Wang, and Yoshikuni 2021). A key step to implementing this approach is understanding how engineered microbes may co-colonize or be suppressed by the native microbiome.

In the Persistence Control SFA, researchers have developed two representative, reduced-complexity microbial communities to aid understanding of the colonization dynamics of engineered microbes in field-like conditions. First, a naturally evolved consortia of ~50 species was developed through repeated dilutions and plate passaging on synthetic growth media emulating the rhizosphere nutrient environment of sorghum. Here, with this reduced-complexity community, the team describes new assays examining the engraftment efficiency of an engineered host that is not part of the enrichment community, as well as taxonomic differences in communities that allowed or rejected colonization of the engineered host. These analyses showed that engraftment was possible but appeared to be the exception rather than the rule. In addition, successfully engrafted species showed strong co-abundances with other members of the community, pointing to possible points of microbial interaction that may drive engraftment. These studies begin to reveal the mechanisms behind how addition of a microbe to an existing community as a method of PAM engineering might take place.

To investigate the environmental persistence and plant-growth promotion in field environments, researchers developed a defined synthetic community from sorghum rhizosphere microbiome isolates and tested this community with sorghum in growth chambers and the field. In contrast to the reduced-complexity enrichment community, this community was established using network co-abundance analysis from Sorghum field 16S taxonomic surveys by co-culturing Sorghum isolates of 56 member strains representing 18 bacterial genera. The project demonstrates that this synthetic community can stably colonize the rhizosphere and roots of sorghum during lab-based in planta experiments, and that it enhances overall shoot biomass compared to mock treated controls. Remarkably, field experiments replicate the findings observed in the lab-based in planta data. These results reveal that the synthetic community is a stable and reproducible community that colonizes Sorghum plants and unexpectedly improves their performance in agricultural soils. The team anticipates the enrichment and defined communities will reveal the drivers of isolate colonization into rhizosphere microbiomes and enable the scaling of rhizosphere synthetic biology from laboratory to field settings. This knowledge will promote the responsible deployment of engineered microbial functions in cropping settings to reduce nutrient inputs, promote drought resilience, and suppress plant pathogens.


Compant, S., et al. 2019. “A Review on the Plant Microbiome: Ecology, Functions, and Emerging Trends in Microbial Application,” Journal of Advanced Research 19, 29–37.

Ke, J., B. Wang, and Y. Yoshikuni. 2021. “Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture,” Trends in Biotechnology 39, 244–61.

Funding Information

This research was supported by the U.S. Department of Energy’s (DOE) Biological and Environmental Research (BER) Program as part of BER’s Genomic Science program (GSP) and is a contribution of the Pacific Northwest National Laboratory (PNNL) Secure Biosystems Design SFA “Persistence Control of Engineered Functions in Complex Soil Microbiomes.” A portion of this work was performed in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by BER and located at PNNL. PNNL is a multiprogram national laboratory operated by Battelle for the DOE under Contract DE-AC05-76RL01830.