Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts

BMC Genomics

Research Article

Nisha Tak¹  Hukam Singh Gehlot¹  Sonam Rathi¹  Jose-Antonio Munive²  Guadalupe Rocha²  Ilham Sakrouhi³  Abdelkarim Filali-Maltouf³  Antoine Le Quéré⁴  Dany Severac⁵  Marine Rohmer⁵  Thibault Meyer⁶  David Chapulliot⁶  Celine Lavire⁶ 

[1] BNF & Microbial Genomics Lab, Department of Botany, Jai Narain Vyas University, 342001, Jodhpur, India;Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif. IC10, Ciudad Universitaria, Col. San Manuel, CP 72570, Puebla, Mexico;Laboratoire de Microbiologie et Biologie Moléculaire, Université Mohammed V, Av Ibn Batouta BP 1014, Rabat, Morocco;Laboratoire de Microbiologie et Biologie Moléculaire, Université Mohammed V, Av Ibn Batouta BP 1014, Rabat, Morocco;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;Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34 094, Montpellier, Cedex, France;Université de Lyon, F69622, Lyon, France;CNRS, UMR5557, Ecologie Microbienne and INRA, UMR1418, Université Lyon 1, Villeurbanne, France;

关键词: Rhizobium- legume symbiosis;    Ensifer;    Desert;    Adaptation;    Comparative genomics;   

DOI  :  10.1186/s12864-016-3447-y

 received in 2016-03-25, accepted in 2016-12-20,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundNitrogen 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.ResultsDraft 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© The Author(s). 2017