The Rice Microbiome and its effect on the Transcriptome

Fig: Rhizosphere of rice plant


Co-PI: Venkatesan Sundaresan
University of California, Davis.

PI: Harsh Bais
College of Agriculture & Natural Resources,
University of Delaware

Co-PI: Jonathan Eisen
Genome Center,
University of California, Davis

Fig: Rhizosphere of rice plant

Plants, much like humans and other animals, harbor rich communities of commensal and mutualistic bacteria. The collective genomes of this complex microbial network, termed the metagenome, encode diverse metabolic capabilities unfounded within plants, essentially offering a functional extension to the host plant’s genome. Soil bacteria in close proximity to plant roots (termed the rhizosphere) have been shown to have a profound effect on plant disease suppression and nutrient acquisition.


Fig: Rice rhizosphere

Using rice (Oryza sativa) as a model, we are answering questions based around how plants recruit and moderate their associated root microbiomes. Unraveling the composition and maintenance of the rice microbiome is not only important for bolstering our basic understanding of host-microbe interactions: it is of great agronomic and ecological importance as well. Rice, due to its world-wide cultivation and consumption, is recognized as one of the most important agriculturally grown cereals. Understanding how broad communities of soil bacteria impact rice plant performance and yield will provide new directions for agricultural technologies.

Rice cultivation also has ecological impacts. Rice paddies account for 15 – 20% of global methane emissions. Methane (a greenhouse gas) is produced by methanogenic archaea that feed on organic material in the paddy soil, including root exudates and decaying root material. The produced methane is taken up by the rice plant and emitted through a specialized gas vascular system known as aerenchyma. Interestingly, the rice plant inherently provides an environment conducive for methane-utilizing bacteria in the rhizosphere by partially oxygenating the soil adjacent to the roots, providing a substrate for methane oxidation. Understanding mechanisms for how a rice plant moderates levels of these methane-utilizing bacteria is of critical environmental importance.



Recent advances in metagenomic methodologies and sequencing technologies have allowed us to start answering questions involving how a plant transcriptionally responds to or recruits a microbiome. Using a sterile hydroponic system, we can monitor 1) the establishment and colonization of a root-microbiome after inoculation with field soil and 2) the transcriptional changes within the plant during the microbiome colonization. Rice serves as a unique model for our hydroponic approach due to its semi-aquatic growth habit.


We are using controlled greenhouse experiments to characterize the predominant microbes present in the rice root microbiome. Using soil taken from a local rice field, we are elucidating how microbial communities vary spatially away from the root. For instance, how do the bacteria inside the roots (the endophytes) vary from the rhizosphere and from bulk soil? By using various rice cultivars and nutrient treatments, we are exploring how specific rice genotypes modulate their root-microbes in response to different abiotic factors.


Rice plants selectively associate with sub-populations of soil microbes. Microbes associated with the roots of rice showed the greatest diversity of bacterial species. Bacterial species were present in the root sample that were not detected in the whole soil.

Fig: Taxonomic groupings from specific samples

An hydroponic system is being established to grow rice plants in the presence and absence of a standardized stable microbe population. The response of the rice plants to these microbes will be assessed by transcriptomics using next generation sequencing techniques.


Hydroponically grown rice will be analyzed for changes in gene expression.

The specific genes determined to be up or down regulated in the presence of the microbes will be used to infer plant microbe crosstalk and help establish an understanding of the underlying symbiotic networks.