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

The Root Microbiome of Camelina: From Structure to Function

Authors:

Timothy Paulitz3*, Cahya Prihatna1, Qing Yan1, Peter Andeer,2 Elle Barnes,2 Trent Northen,2 Susannah Tringe,2 Cody Willmore3, Hao Peng4, Chuntao Yin5, Wilson Craine6, Jed Eberly7, Chaofu Lu7

Institutions:

1Plant Sciences and Plant Pathology Department, Montana State University; 2Lawrence Berkeley National Laboratory; 3USDA-ARS, Pullman, WA; 4USDA-ARS, Parlier, CA; 5 USDA-ARS, Brookings, SD; 6 Washington State University; 7Montana State University

Abstract

Camelina (Camelina sativa L.) is an oilseed crop being developed as a biofuel crop for dryland agriculture. This team is investigating the role of the root microbiome in plant health, especially in relation to nutrient uptake, disease, and drought. Researchers sampled soil from 33 locations in four precipitation/cropping zones in Eastern Washington and grew cultivar Suneson in each soil in the greenhouse. Amplicon sequencing was used to describe the bulk soil, rhizosphere and endosphere bacterial and fungal communities. Plant compartment, cropping system zone, and location had significant effects on microbial composition. The group identified the core rhizosphere bacterial (several Actinobacteria including Aeromicrobium and Marmoricola, as well as the genera Rhizobium, Clostridium, and Sphingomonas) and fungal community (Pseudogymnoascus, Fusarium and Mortierella). Researchers are currently sequencing metagenomes from rhizosphere communities of 10 camelina lines grown under high and low nitrogen (N) conditions, to identify how soil N shifts the communities on the root.

More than 400 camelina-associated bacterial isolates were screened for growth promotion on camelina under normal and low nitrogen conditions. Eleven bacterial isolates were shown to promote elongation of primary roots under low nitrogen levels. Two bacterial strains Paraburkholderia tropica (isolates FMD144 and FMD568), showed consistent root growth promotion. One bacterial strain, Pseudomonas mediterranea isolate FMD348, inhibited the growth of camelina under all nitrogen levels. Co-inoculation of camelina with FMD348 and FMD144 revealed that strain 348 dominated the interaction and caused root inhibition, suppressing the growth promotion effect of strain FMD144. Interestingly, in a more complex bacteria-bacteria interaction in which FMD348 was co-inoculated with a bacterial community of either 21 isolates or the 11 beneficial isolates, root growth promotion was observed and growth inhibition by FMD348 was suppressed. The bacterial effect on camelina growth can be positively or negatively influenced by other bacteria in the community.

A diverse set of 33 bacteria selected from a larger collection of over 3,000 camelina-associated isolates were profiled by exometabolomics to determine what these bacteria consume and produce. They were cultured on Northen Lab Defined Medium, a diverse, defined media with over 60 compounds including sugars, organic acids, amino acids, and diverse nitrogenous cofactors and vitamins. Spent media was collected in late exponential phase and analyzed using liquid chromatography-tandem mass spectrometry. Almost every compound in the media was significantly reduced by at least one isolate; however, growth rates and consumption profiles varied greatly across the collection. Production of potential secondary metabolites produced by the cultures also varied greatly across the collection. This data is being analyzed to understand how these microbes are recruited by camelina and interact with one another and will aid in the targeted isolation of future isolates.