RUI: Diurnal and circadian regulation of the plant microbiome

Chapman University, Orange CA

Investigators

Abstract

The specific interactions of plants with various soil microorganisms throughout their life cycle play important roles in plant growth and survival in nature. Being sessile organisms, plants are directly affected by the continuous but predictable changes in environmental conditions. This includes the 24-hour light/dark cycle according to which plants adjust their various physiological processes. To ensure successful interaction, plants influence the profile and possibly the biology of certain groups of soil microorganisms such that they stay in synchrony with the daily changes in the plant physiological processes. A better understanding of this dynamic regulation would provide valuable information towards understanding the mechanisms and processes through which some soil microbes successfully interact with plant roots. Since the summation of the daily plant interactions with the soil microbes is the basis for their long-term benefits on the plants, understanding these daily interactions at the molecular level is important. The manipulation of these daily interactions through plant breeding may allow for improved plant productivity through efficient interaction with certain natural microbes, reducing the dependency of agricultural operations on expensive synthetic fertilizers. This project also provides valuable opportunities to engage undergraduate and high-school students in scientific research and introduce them to the natural and sustainable approaches of food production. The microbiome has profound effect on a host's health and nutritional status. In animals, light and the host's circadian clock, a cell-autonomous internal biological timekeeper that generates roughly 24-hour rhythms in many metabolic and physiological processes, regulate host-microbiome interactions. The first aim of this research is to study the roles of the Arabidopsis thaliana's circadian clock on its interaction with the bacterial microbiome in the endosphere (inhabiting the root interior) using a metagenomic approach. The plant circadian clock will be disrupted environmentally and genetically. The 24-hour fluctuations in the endospheric and soil bacterial profiles will be determined by sequencing bacterial 16S-ribosomal (r) genes at both the DNA and RNA level to better understand the role of the circadian clock regulation. The second aim is to identify the root and bacterial pathways underlying this dynamic interaction using a metatranscriptomic approach. Both root and bacterial transcriptomes will be depleted of ribosomal RNAs and sequenced to identify possible mechanisms and processes through which some endospheric bacteria interact with Arabidopsis roots. The third aim is to investigate the role of daily bacterial fluctuations on plant performance using a physiological approach. Soils will be conditioned by growing Arabidopsis, tomato, and soybean plants in normal light/dark cycles or prolonged constant light for two generations. The performance of Arabidopsis, tomato, and soybean plants on these conditioned soils will be assessed by weekly measurements of total leaf diameter and petiole length, plant height, chlorophyll content, and stomatal conductance. The outcome from this research will be an integrated analysis of circadian impacts on the relationship between plant hosts and their endophytic microbiomes. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.