title: Genetic and genomic diversity studies of Acacia symbionts in Senegal reveal new species of Mesorhizobium with a putative geographical pattern.
abstract: Acacia senegal (L) Willd. and Acacia seyal Del. are highly nitrogen-fixing and moderately salt tolerant species. In this study we focused on the genetic and genomic diversity of Acacia mesorhizobia symbionts from diverse origins in Senegal and investigated possible correlations between the genetic diversity of the strains, their soil of origin, and their tolerance to salinity. We first performed a multi-locus sequence analysis on five markers gene fragments on a collection of 47 mesorhizobia strains of A. senegal and A. seyal from 8 localities. Most of the strains (60%) clustered with the M. plurifarium type strain ORS 1032T, while the others form four new clades (MSP1 to MSP4). We sequenced and assembled seven draft genomes: four in the M. plurifarium clade (ORS3356, ORS3365, STM8773 and ORS1032T), one in MSP1 (STM8789), MSP2 (ORS3359) and MSP3 (ORS3324). The average nucleotide identities between these genomes together with the MLSA analysis reveal three new species of Mesorhizobium. A great variability of salt tolerance was found among the strains with a lack of correlation between the genetic diversity of mesorhizobia, their salt tolerance and the soils samples characteristics. A putative geographical pattern of A. senegal symbionts between the dryland north part and the center of Senegal was found, reflecting adaptations to specific local conditions such as the water regime. However, the presence of salt does not seem to be an important structuring factor of Mesorhizobium species.
authors: Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal; IRD-Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet, Montpellier, France.
authors: Fatou
authors: F
authors: Diouf
authors: Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal.
authors: Diegane
authors: D
authors: Diouf
authors: IRD-Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet, Montpellier, France.
authors: Agnieszka
authors: A
authors: Klonowska
authors: Laboratoire Mixte International Biotechnologie Microbienne et Végétale (LBMV), Rabat, Morocco.
authors: Antoine
authors: A
authors: Le Queré
authors: Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal.
authors: Niokhor
authors: N
authors: Bakhoum
authors: Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal; Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal.
authors: Dioumacor
authors: D
authors: Fall
authors: Irstea, UR MALY, centre de Lyon-Villeurbanne, Villeurbanne, France.
authors: Marc
authors: M
authors: Neyra
authors: MGX-Montpellier GenomiX, Institut de Génomique Fonctionnelle, Montpellier, France.
authors: Hugues
authors: H
authors: Parrinello
authors: Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal.
authors: Mayecor
authors: M
authors: Diouf
authors: Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Centre de Recherche de Bel Air, Dakar, Senegal; Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal.
authors: Ibrahima
authors: I
authors: Ndoye
authors: Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal; IRD-Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), Campus de Baillarguet, Montpellier, France.
authors: Lionel
authors: L
authors: Moulin
mesh_terms: D000045:Acacia / Q000145:classification / Q000382:microbiology*; D001426:Bacterial Proteins / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D005843:Geography; D006863:Hydrogen-Ion Concentration; D059128:Mesorhizobium / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing / Q000379:methods; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D055049:Salt Tolerance / Q000235:genetics; D012675:Senegal; D017422:Sequence Analysis, DNA; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology; D013045:Species Specificity; D013559:Symbiosis
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012987:Soil