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

2023 Abstracts

Examine Plant-Microbe-Soil Interactions Using Fabricated Ecosystems Across Scales


Hsiao-Han Lin1* ([email protected]), Albina Khasanova1, Shwetha M. Acharya1, Mon O. Yee1, Spencer Diamond2, Peter F. Andeer1, Nameera F. Baig1, Omolara T. Aladesanmi1, Catharine A. Adams2, Marta Torres Béjar1, Catharine A. Adams2, Trenton K. Owen1, Hans Carlson1, Nick Downs1, Jillian Banfield2, N. Louise Glass2, Romy Chakraborty1, Kateryna Zhalnina1, Jenny C. Mortimer1, 3, Adam M. Deutschbauer1, and Trent R. Northen1*([email protected])


1Lawrence Berkeley National Laboratory; 2University of California–Berkeley; and 3University of Adelaide, Australia



Understanding the interactions, localization, and dynamics of grass rhizosphere communities at the molecular level (genes, proteins, metabolites) to predict responses to perturbations and understand the persistence and fate of engineered genes and microbes for secure biosystems design. To do this, advanced fabricated ecosystems are used in combination with gene-editing technologies such as CRISPR-Cas and bacterial virus (phage)-based approaches for interrogating gene and microbial functions in situ—addressing key challenges highlighted in recent DOE reports. This work is integrated with the development of predictive computational models that are iteratively refined through simulations and experimentation to gain critical insights into the functions of engineered genes and interactions of microbes within soil microbiomes as well as the biology and ecology of uncultivated microbes. Together, these efforts lay a critical foundation for developing secure biosystems design strategies—harnessing beneficial microbiomes to support sustainable bioenergy and improving understanding of nutrient cycling in the rhizosphere.


Studying plant-microbe-soil interactions including those mediated by root glycans is challenging due to the complexity and variability found in natural ecosystems. Fabricated ecosystems offer an opportunity to recapitulate aspects of these systems in reduced complexity and controlled laboratory settings. However, it is important to benchmark their performance against established systems and identify specific protocols for these studies. Here, researchers compared the colonization and persistence of a field-derived microbiome in colonizing the model grass Brachypodium distachyon when grown in sterile devices called EcoFABs as compared to conventional containers like pots and tubes (Acharya et al. 2023). Comparable plant growth and microbial community composition was obtained between conventional containers and the EcoFAB. The team also observe a distinct microbiome profile for the rhizosphere (root tip or root base) and the bulk soil. Researchers then used a synthetic community (SynCom) to study how different growth media and inoculation methods affect microbial community assembly (Coker et al. 2022). The results showed that sample types (sand, rhizosphere, and root) but not the inoculation method significantly affects microbial community assembly. Next, the team studied how plant cell wall composition and root exudates affect microbial community assembly in the rhizosphere by using a lignin biosynthetic B. distachyon transgenic line that has an altered root cell wall composition.

Researchers observed a higher Rhizobium colonization in the transgenic line than in the wild type line Bd21-3 suggesting a possible connection between root aromatics and root colonization. To explore this in more detail, the team performed metabolomic analysis of a diverse collection of Brachypodium accessions to identify lines with elevated aromatic compounds in the exudates. Researchers then used a meter-scale fabricated ecosystem to investigate SynCom colonization between two lines with dramatically different aromatic exudate compositions and again observed altered rhizosphere community compositions. Together, these results highlight the potential for using fabricated ecosystems to study the molecular ecology of plant-microbe interactions.


Acharya, S.M., et al. 2023. “Fine Scale Sampling Reveals Spatial Heterogeneity of Rhizosphere Microbiome in Young Brachypodium Plants.” BioRxiv.

Coker, J., et al. 2022. “A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology.” mSystems, e0095122.

Funding Information

This material by m-CAFEs Microbial Community Analysis and Functional Evaluation in Soils, ([email protected]) a science focus area led by Lawrence Berkeley National Laboratory is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under contract number DE-AC02-05CH11231.