Abstract
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.
Highlights
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)
To verify if these isolates belong to the same Ensifer species and to estimate their genomic and phenotypic specificity, 6 isolates originating from the 3 continents were selected (Table 1)
Based on assembly and scaffold ordering, recovery of genes involved in plasmid replication and mobilization and on Eckhardt gel analysis, our results suggest that the genomes studied are composed by a chromosome of approximately 3.6 Million base pairs (Mbp) which included a majority of housekeeping genes that are conserved among Ensifer species, a chromid of 1.6–1.8 Mbp containing a majority of genes conserved at the species and to a lesser extent at the genus levels and large plasmid(s) which contained mainly accessory genes among which symbiotic nod and nif genes that most probably correspond to symbiotic plasmids
Summary
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). Among the most urgent concerns we will have to face in the coming decades, the desertification, which combined to irregular rainfall intensity or frequency and extreme climatic events represent real threats for some local populations These effects will impact cultivable surfaces and limit areas where humans will be able to live, notably in developing countries where the demographic growth adds on pressure and emergency to react. Grain legumes contain high protein levels that can substitute the extremely high energy and water demanding animal derived protein sources that remain affordable for a great minority of humans Their growth promotion through natural symbioses can reduce fertilizer needs bringing economical interest in it while limiting pollution of soils and below ground waters in a context of global warming and clean water resources impoverishment
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