Since the Green Revolution, the intensive use of synthetic fertilizers is the most common strategy to alleviate the limitation of nitrogen (N) availability on crop yields. With the desire to produce bioenergy crops on low-productivity lands to avoid competition with food production, the heavy use of fertilizers necessary to ensure reasonable yields not only increases the cost of production but also increases the environmental footprint of producing bioenergy crops. Besides the significant energy inputs from natural gas, a non-renewable resource, required to produce synthetic fertilizers, the use of fertilizers also comes with adverse environmental effects such as nitrate leaching and the production of greenhouse gases. Taking advantage of biological N fixation in bioenergy crops like sorghum is a promising approach to reduce the dependence on synthetic fertilizers and improve the economic and environmental sustainability of bioenergy production.
We have reported recently that some corn landraces from the Sierra Mixe region in Mexico can acquire 29–82% of their N from the air by hosting N-fixing bacteria in a mucilage produced by aerial roots after rain.
Initially considered to be a trait unique to this corn, we have also demonstrated that some sorghum accessions also support efficient N-fixation in the mucilage produced by their aerial roots and obtain a significant amount of N from the air through such symbiotic associations.
The overall goal of this proposal is to understand better the molecular and cellular networks controlling this N-fixation trait in sorghum using a combination of genetics, synthetic bacterial communities, and systems biology.
Our overall hypotheses are that plant and bacterial gene networks control the efficiency of N-fixation in sorghum and that understanding these networks will allow us to improve N-fixation in sorghum for bioenergy production. To evaluate these hypotheses, we will carry out the following aims:
1- Identify sorghum accessions that maximize N-fixation via their aerial roots and use genome-wide association studies to map biological N fixation-related traits (GWAS). We will assess the dependence of N-fixation on environmental factors such as rain and soil N, map genetic loci that associate with the trait, and start breeding improved bioenergy sorghum varieties able to fix N efficiently.
2- Characterize the bacterial communities associated with these sorghum accessions in the field. We will isolate bacteria from sorghum mucilage and evaluate phenotypes related to mucilage degradation and utilization, oxygen consumption, N-fixation, and N transfer to the plant.
3- Develop simplified and representative bacterial communities of the sorghum aerial mucilage and study their dynamics. We will explore the functional and compositional design space of synthetic communities using high-throughput techniques and computational modeling, test the stability of synthetic communities, infer significant inter-species interactions, and sequence the genomes of the most promising isolates.
4- Characterize the integrated plant and microbial gene networks controlling critical functions in the system using a synthetic bacterial community. We will profile the transcriptome of plant and bacterial genes during mucilage production and N fixation, infer cell type-specific gene regulatory networks and their dynamics, and predict plant and bacterial regulators.
5- Validate the predictions of the systems biology approach using genetics in plants and bacteria to improve the efficiency of N-fixation in sorghum aerial root mucilage. We will use reverse genetics in sorghum and in bacteria to test predictions in the lab and the field and confirm the key elements needed to support biological N fixation in sorghum.
The sorghum varieties that we are working with are publicly available and come from the University of Florida and the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)
