title: Discovery of Novel Plant Interaction Determinants from the Genomes of 163 Root Nodule Bacteria.
abstract: Root nodule bacteria (RNB) or "rhizobia" are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. In this study, we sequenced the genomes of 110 RNB from diverse hosts and biogeographical regions, and undertook a global exploration of all available RNB genera with the aim of identifying novel genetic determinants of symbiotic association and plant growth promotion. Specifically, we performed a subtractive comparative analysis with non-RNB genomes, employed relevant transcriptomic data, and leveraged phylogenetic distribution patterns and sequence signatures based on known precepts of symbiotic- and host-microbe interactions. A total of 184 protein families were delineated, including known factors for nodulation and nitrogen fixation, and candidates with previously unexplored functions, for which a role in host-interaction, -regulation, biocontrol, and more, could be posited. These analyses expand our knowledge of the RNB purview and provide novel targets for strain improvement in the ultimate quest to enhance plant productivity and agricultural sustainability.
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, USA.
authors.forename: Rekha
authors.initials: R
authors.lastname: Seshadri
authors.affiliation: Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Murdoch 6150, Australia.
authors.forename: Wayne G
authors.initials: WG
authors.lastname: Reeve
authors.affiliation: Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Murdoch 6150, Australia.
authors.forename: Julie K
authors.initials: JK
authors.lastname: Ardley
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, USA.
authors.forename: Kristin
authors.initials: K
authors.lastname: Tennessen
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, USA.|Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudia Arabia.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, USA.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D007887:Fabaceae / Q000145:classification / Q000382:microbiology*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D005843:Geography; D054884:Host-Pathogen Interactions; D009586:Nitrogen Fixation / Q000235:genetics; D009876:Operon / Q000235:genetics; D010802:Phylogeny; D055170:Plant Root Nodulation / Q000235:genetics; D012231:Rhizobium / Q000145:classification / Q000235:genetics / Q000502:physiology*; D053204:Root Nodules, Plant / Q000382:microbiology*; D013045:Species Specificity; D013559:Symbiosis / Q000235:genetics
chemical_list: D001426:Bacterial Proteins