title: Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts.
abstract: Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined.
  
  
  
  Draft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced. Genome based species delineation tools demonstrated that they belong to a new species of Ensifer. Comparison of its core genome with those of E. meliloti, E. medicae and E. fredii enabled the identification of a species conserved gene set. Predicted functions of associated proteins and pathway reconstruction revealed notably the presence of transport systems for octopine/nopaline and inositol phosphates. Phenotypic characterization of this new desert rhizobium species showed that it was capable to utilize malonate, to grow at 48 °C or under high pH while NaCl tolerance levels were comparable to other Ensifer species. Analysis of accessory genomes and plasmid profiling demonstrated the presence of large plasmids that varied in size from strain to strain. As symbiotic functions were found in the accessory genomes, the differences in symbiotic interactions between strains may be well related to the difference in plasmid content that could explain the different legumes with which they can develop the symbiosis.
  
  
  
  The genomic analysis performed here confirms that the selected rhizobial strains isolated from desert regions in three continents belong to a new species. As until now only recovered from such harsh environment, we propose to name it Ensifer aridi. The presented genomic data offers a good basis to explore adaptations and functionalities that enable them to adapt to alkalinity, low water potential, salt and high temperature stresses. Finally, given the original phylogeographic distribution and the different hosts with which it can develop a beneficial symbiotic interaction, Ensifer aridi may provide new biotechnological opportunities for degraded land restoration initiatives in the future.
authors.affiliation: Laboratoire de Microbiologie et Biologie Moléculaire, Université Mohammed V, Av Ibn Batouta BP 1014, Rabat, Morocco. antoine.le-quere@ird.fr.|IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes UMR113, IRD/INRA/CIRAD/Montpellier SupAgro/Université de Montpellier, TA A82/J, Campus International de Baillarguet, 34398, Montpellier, Cedex 5, France. antoine.le-quere@ird.fr.
authors.forename: Antoine
authors.identifier: 0000-0001-7470-5730
authors.initials: A
authors.lastname: Le Quéré
authors.affiliation: BNF & Microbial Genomics Lab, Department of Botany, Jai Narain Vyas University, Jodhpur, 342001, India.
authors.forename: Nisha
authors.initials: N
authors.lastname: Tak
authors.affiliation: BNF & Microbial Genomics Lab, Department of Botany, Jai Narain Vyas University, Jodhpur, 342001, India.
authors.forename: Hukam Singh
authors.initials: HS
authors.lastname: Gehlot
authors.affiliation: Université de Lyon, F69622, Lyon, France.|CNRS, UMR5557, Ecologie Microbienne and INRA, UMR1418, Université Lyon 1, Villeurbanne, France.
authors.forename: Celine
authors.initials: C
authors.lastname: Lavire
authors.affiliation: Université de Lyon, F69622, Lyon, France.|CNRS, UMR5557, Ecologie Microbienne and INRA, UMR1418, Université Lyon 1, Villeurbanne, France.
authors.forename: Thibault
authors.initials: T
authors.lastname: Meyer
authors.affiliation: Université de Lyon, F69622, Lyon, France.|CNRS, UMR5557, Ecologie Microbienne and INRA, UMR1418, Université Lyon 1, Villeurbanne, France.
authors.forename: David
authors.initials: D
authors.lastname: Chapulliot
authors.affiliation: BNF & Microbial Genomics Lab, Department of Botany, Jai Narain Vyas University, Jodhpur, 342001, India.
authors.forename: Sonam
authors.initials: S
authors.lastname: Rathi
authors.affiliation: Laboratoire de Microbiologie et Biologie Moléculaire, Université Mohammed V, Av Ibn Batouta BP 1014, Rabat, Morocco.
authors.forename: Ilham
authors.initials: I
authors.lastname: Sakrouhi
authors.affiliation: Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. IC10, Ciudad Universitaria, Col. San Manuel, CP 72570, Puebla, Mexico.
authors.forename: Guadalupe
authors.initials: G
authors.lastname: Rocha
authors.affiliation: Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, Montpellier, Cedex, 34 094, France.
authors.forename: Marine
authors.initials: M
authors.lastname: Rohmer
authors.affiliation: Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, Montpellier, Cedex, 34 094, France.
authors.forename: Dany
authors.initials: D
authors.lastname: Severac
authors.affiliation: Laboratoire de Microbiologie et Biologie Moléculaire, Université Mohammed V, Av Ibn Batouta BP 1014, Rabat, Morocco.
authors.forename: Abdelkarim
authors.initials: A
authors.lastname: Filali-Maltouf
authors.affiliation: Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. IC10, Ciudad Universitaria, Col. San Manuel, CP 72570, Puebla, Mexico.
authors.forename: Jose-Antonio
authors.initials: JA
authors.lastname: Munive
mesh_terms: D000349:Africa; D000569:Americas; D001208:Asia; D019295:Computational Biology / Q000379:methods; D003889:Desert Climate; D019143:Evolution, Molecular; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D009586:Nitrogen Fixation / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D012231:Rhizobium / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D013559:Symbiosis / Q000235:genetics; D026801:Synteny
keywords: Adaptation; Comparative genomics; Desert; Ensifer; Rhizobium- legume symbiosis