Doctoral defence: Saleh Rahimlouye Barabi “Investigation of diazotrophic bacteria association with plants”

On 2 September at 10:15 Saleh Rahimlouye Barabi will defend his doctoral thesis “Investigation of diazotrophic bacteria association with plants” for obtaining the degree of Doctor of Philosophy (in Botany and Mycology).

Supervisors:
Professor Leho Tedersoo, University of Tartu
Associate Professor Mohammad Bahram, University of Tartu

Opponent:
Professor Euan Kevin James, The James Hutton Institute (Scotland)

Summary
Nitrogen (N) is essential to life because it is required for the biosynthesis of all N-containing organic compounds, such as proteins. Three main groups of bacteria – Nostocaceae (Cyanobacteria), rhizobia (Proteobacteria), and Frankia (Actinobacteria) fix atmospheric N both in a free-living form and in root symbiosis with plants. Here, we introduce the NodDB database of N-fixing plants based on morphological and phylogenetic evidence and discuss plant groups with conflicting reports and interpretations. We screened the Nod factor production capacity of nodule-inducing Proteobacteria genera using their genome sequences and assessed the evolutionary history of symbiosis based on phylogenomics. Based on molecular clock analysis, we estimate that rhizobial N-fixing symbiosis appeared for the first time in about 51 Mya (Eocene epoch) in Rhizobiaceae, and it was laterally transferred to multiple symbiotic taxa in the α- and β-Proteobacteria. We collected root samples of Tribulus terrestris L. (Zygophyllaceae) and R. regia Cook (Arecaceae) forming an atypical root nodule from the Middle East and the Caribbean, respectively. Genomes of five bacterial strains isolated from surface-sterilized root nodules were sequenced and metagenome data were generated for 14 nodule samples from T. terrestris and R. regia. Phylogenomic analysis indicates that the dominant bacterial species isolated from T. terrestris and R. regia are clustered with Klebsiella and Kosakonia (γ-Proteobacteria), respectively. structural nod/nif genes identified to Sinorhizobium meliloti could be amplified from T. terrestris root nodule samples. In contrast to previous reports, cyanobacterial infection in root nodules of T. terrestris was not detected based on metagenome sequence data analysis. We conclude that T. terrestris and R. regia evolved to produce natural 'empty nodules' without intracellular rhizobial infection. The demonstrated biological N fixation of T. terrestris and R. regia can be attributed to S. meliloti and K. sacchari respectively, which colonize the nodule-like structures as epi- or endophytes. Knowledge generated here adds to the body of evidence rejecting the hypothesis that nodulation was gained or predisposed on a single occasion in the common ancestor of the currently known N-fixing clade of angiosperms.