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Open Access Publications from the University of California

Scholarly Works (2 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2013)
Abstract Background The sinorhizobia are amongst the most well studied members of nitrogen-fixing root nodule bacteria and contribute substantial amounts of fixed nitrogen to the biosphere. While the alfalfa symbiont Sinorhizobium meliloti RM 1021 was one of the first rhizobial strains to be completely sequenced, little information is available about the genomes of this large and diverse species group. Results Here we report the draft assembly and annotation of 48 strains of Sinorhizobium comprising five genospecies. While S. meliloti and S. medicae are taxonomically related, they displayed different nodulation patterns on diverse Medicago host plants, and have differences in gene content, including those involved in conjugation and organic sulfur utilization. Genes involved in Nod factor and polysaccharide biosynthesis, denitrification and type III, IV, and VI secretion systems also vary within and between species. Symbiotic phenotyping and mutational analyses indicated that some type IV secretion genes are symbiosis-related and involved in nitrogen fixation efficiency. Moreover, there is a correlation between the presence of type IV secretion systems, heme biosynthesis and microaerobic denitrification genes, and symbiotic efficiency. Conclusions Our results suggest that each Sinorhizobium strain uses a slightly different strategy to obtain maximum compatibility with a host plant. This large genome data set provides useful information to better understand the functional features of five Sinorhizobium species, especially compatibility in legume-Sinorhizobium interactions. The diversity of genes present in the accessory genomes of members of this genus indicates that each bacterium has adopted slightly different strategies to interact with diverse plant genera and soil environments.
    Cover page: Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies
    • Article
    • Peer Reviewed
    LBL Publications (2006)

    Filamentous actinobacteria from the genus Frankia and diverse woody trees and shrubs together form N2-fixing actinorhizal root nodule symbioses that are a major source of new soil nitrogen in widely diverse biomes 1. Three major clades of Frankia sp. strains are defined; each clade is associated with a defined subset of plants from among the eight actinorhizal plant families 2,3. The evolution arytrajectories followed by the ancestors of both symbionts leading to current patterns of symbiont compatibility are unknown. Here we show that the competing processes of genome expansion and contraction have operated in different groups of Frankia strains in a manner that can be related to the speciation of the plant hosts and their geographic distribution. We sequenced and compared the genomes from three Frankia sp. strains having different host plant specificities. The sizes of their genomes varied from 5.38 Mbp for a narrow host range strain (HFPCcI3) to 7.50Mbp for a medium host range strain (ACN14a) to 9.08 Mbp for a broad host range strain (EAN1pec.) This size divergence is the largest yet reported for such closely related bacteria. Since the order of divergence of the strains is known, the extent of gene deletion, duplication and acquisition could be estimated and was found to be inconcert with the biogeographic history of the symbioses. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome reductions as well as expansions can occur in facultatively symbiotic soil bacteria as they respond to new environments in the context of their symbioses.

      Cover page: Genomes of three facultatively symbiotic Frankia sp. strains reflect host plant biogeography
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