Open Access Research article

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

Marco Galardini1, Alessio Mengoni1*, Matteo Brilli2, Francesco Pini1, Antonella Fioravanti1, Susan Lucas3, Alla Lapidus4, Jan-Fang Cheng3, Lynne Goodwin5, Samuel Pitluck3, Miriam Land6, Loren Hauser6, Tanja Woyke3, Natalia Mikhailova3, Natalia Ivanova3, Hajnalka Daligault3, David Bruce3, Chris Detter3, Roxanne Tapia3, Cliff Han3, Hazuki Teshima3, Stefano Mocali7, Marco Bazzicalupo1 and Emanuele G Biondi18

Author Affiliations

1 Department of Evolutionary Biology, University of Firenze, via Romana 17, I-50125 Firenze, Italy

2 Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, 43, bvd du 11 novembre, Lyon, France

3 DOE Joint Genome Institute, Walnut Creek, California, USA

4 Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, USA

5 Los Alamos National Laboratory, 1619 Central Avenue, Los Alamos, USA

6 Oak Ridge National Laboratory, Oak Ridge, USA

7 Agricultural Research Council- Agrobiology and Pedology Centre (ABP) P.za D'Azeglio, 30, 50121 - Firenze, Italy

8 Interdisciplinary Research Institute - CNRS, Villenenuve d'Ascq, France

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BMC Genomics 2011, 12:235  doi:10.1186/1471-2164-12-235

Published: 12 May 2011

Abstract

Background

Sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the Medicago sativa plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of S. meliloti strains AK83 and BL225C, we sequenced the complete genomes for these two strains.

Results

With sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB), AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed. Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains.

Conclusions

In conclusions, the extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity.

Keywords:
Sinorhizobium meliloti; nodulation; symbiosis; comparative genomics; pangenome; panregulon