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

Integrated Experimental Approaches to Understand Bioenergy Crop Productivity Through Rhizosphere Processes

Authors:

Trent R. Northen1,3* (trnorthen@lbl.gov), Vlastimil Novak1, Yi Zhai1, Qing Zheng2, Peter Andeer1, John P. Vogel1,3, Amélie C. M. Gaudin2, Karsten Zengler4

Institutions:

1Lawrence Berkeley National Laboratory; 2University of California–Davis; 3DOE Joint Genome Institute; 4University of California–San Diego

Goals

This project couples novel laboratory and field studies to develop the first predictive model of grass-microbiomes based on new mechanistic insights into dynamic plant-microbe interactions in the grasses Sorghum bicolor and Brachypodium distachyon that improve plant nitrogen (N)-use efficiency (NUE). The results will be used to predict plant mutants and microbial amendments that improve low-input biomass production for laboratory and field studies validation. To achieve this goal, researchers will determine the mechanistic basis of dynamic exudate exchange in the grass rhizosphere with a specific focus on the identification of plant transporters and proteins that regulate root exudate composition. Researchers will also focus on how specific exudates select for beneficial microbes that increase plant biomass and NUE. The team will further develop a predictive plant-microbe model for advancing sustainable bioenergy crops and will predictively shift plant-microbe interactions to enhance plant biomass production and N acquisition from varied N forms.

Abstract

Microbial amendments are a powerful approach for promoting plant (N) acquisition, uptake, and cycling using less inputs. Yet, the performance of microbial amendments is highly variable due to the dynamic and complex nature of soil abiotic and biotic interactions. Understanding the factors driving rhizosphere assembly and dynamics, especially when combined with plants with tailored exudates, has the potential to greatly improve the reliable performance of beneficial microbial amendments at lower N levels. The team assessed the potential of a grass rhizosphere synthetic microbiome in promoting Brachypodium distachyon growth in soils under replete and limited N levels and observed enhanced ability to extract N from soil organic N pools when subjected to limited N conditions. For a more detailed analysis of N cycling in the rhizosphere, including the potential role of root exudates in mediating beneficial microbial interactions, the team grew B. distachyon hydroponically in novel fabricated ecosystem devices (EcoFAB 2.0) under three inorganic nitrogen forms (nitrate, ammonium, or ammonium nitrate), followed by nitrogen starvation. EcoFAB 2.0 achieved low intratreatment data variability and reproducible plant phenotypes. Analyses of exudates with LC-MS/MS revealed that the three inorganic nitrogen forms caused differential exudation, generalized by an increase in amino acids/peptides and alkaloids. Comparatively, N-deficiency decreased N-containing compounds but increased carbon-rich shikimates/phenylpropanoids. Subsequent bioassays with two shikimates-phenylpropanoids (shikimic and p-coumaric acids) revealed their distinct capacity to regulate bacterial and plant growth. Given the importance of root exudates in structuring rhizosphere communities, researchers are also investigating transport mechanisms for root exudation, particularly nitrogen by using B. distachyon plant mutants. Hydroponic growth of these mutants with knockout N transporters resulted in significant phenotypic and exometabolic changes. Concurrently, researchers are analyzing the microbiome communities of these mutants in calcined clay treated with a field-soil extract to explore the role of root exudation in plant-microbe interactions. Sequencing of rhizosphere and root microbiomes has shown significant changes in bacterial species, indicating that membrane-transport engineering can alter plant-root exudates and microbiome composition. Together, these findings advance the understanding of the mechanisms that drive plant microbe interactions to inform the development of more robust microbial amendments for sustainable bioenergy.

Funding Information

Researchers gratefully acknowledge funding from the DOE Office of Science, BER program. The research described was funded under contract DE-AC02-05CH11231 to Lawrence Berkeley National Laboratory as part of a project led by University of California–San Diego (DE-SC0021234). The EcoFAB 2.0 was developed as part of the Trial Ecosystem Advancement for Microbiome Science (TEAMS) under contract DE-AC02-05CH11231 to Lawrence Berkeley National Laboratory project.