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

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3447-y) contains supplementary material, which is available to authorized users.

Diversity and phenotypic analyses of salt- and heat-tolerant wild bean Phaseolus filiformis rhizobia native of a sand beach in Baja California and description of Ensifer aridi sp. nov.

“…The optimal growth of strains belonging to the genus Ensifer is generally obtained at temperatures around 25-33 °C (De Lajudie et al 1994), but some species are capable of growing at temperatures ranges from 12 °C (Li et al 2011) to 44 °C (De Lajudie et al 1994). All P. filiformis strains presented here were tolerant to high temperatures (40 °C), similarly to E. saheli (De Lajudie et al 1994) or to strains belonging to the proposed species E. aridi (Le Queré et al 2017), to which most of the presented isolates were belonging. This capacity to withstand high temperatures was expected when considering the biome from which they were isolated.…”

“…The phylogenetic relationships obtained using atpD, recA and glnII, genes that have been sequenced in most Ensifer species showed that there might be several species among the isolated strains. One strain (LEM456) was grouped with E. meliloti, while the remaining strains isolated from P. filiformis were sharing a separate clade with strains of "Ensifer aridi" that, based on comparative genomics, includes the strains LEM451 and LEM457 (Le Queré et al 2017). The use of six housekeeping genes (atpD, rpoB, gyrB, thrC, recA and glnII) for MLSA confirmed that the strain LEM456 is related to Ensifer meliloti, while the other strains clustered with "Ensifer aridi"; being different from already described Ensifer species nodulating Phaseolus, including E. americanum, a dominant P. vulgaris symbiont isolated from alkaline soils in Mexico (Verástegui-Valdés et al 2014).…”

“…1) showed that the P. filiformis isolates belonged to the Ensifer genus and grouped into three different clusters. The majority of the partial 16S rDNA sequences (8/10) showed high sequence similarities to those of Ensifer strains recovered from Asian or African deserts recently described, and for which the name "Ensifer aridi" was proposed based on genomic data which included the two P. filiformis rhizobial strains LEM451 and LEM457 (Le Queré et al 2017). The 16S rDNA sequences of the strains LEM451, LEM453, LEM457 and LEM462 were 100% identical over 1227 bp aligned sequences to that of African and Asian "Ensifer aridi" isolates; LEM459 and LEM466 presented a single substitution, while LEM551 and LEM465 presented 2 and 4 substitutions, respectively.…”

“…Colonies are circular, from slightly to highly mucous, white opaque, convex and 1-3 mm diameter upon 48 h of growth on YMA medium at 30 °C. They can grow at particularly high temperatures (40 °C), tolerate pH ranging from 6 to 9.5 and all Ensifer aridi strains tested including the eight Mexican, the two Moroccan (LMR001, LMR013) and the two Indian (TP6, TW10) isolates were capable of growing using glycerol, l-arabinose, d-fructose, l-rhamnose, inositol, d-mannitol, d-maltose, d-sucrose, d-trehalose, d-raffinose, d-turanose or d-arabitol as sole carbon sources (Sakrouhi et al 2016;Le Queré et al 2017). The type strain is Ensifer aridi LMR001 T (= LMG 31426 T ; = HAMBI 3707 T ) isolated from Moroccan Merzouga desert sand dune (GPS coordinates: N 31°5′42.7″/W 3°57′56.1″) using Vachellia gummifera as a host (Sakrouhi et al 2016).…”

“…The type strain is Ensifer aridi LMR001 T (= LMG 31426 T ; = HAMBI 3707 T ) isolated from Moroccan Merzouga desert sand dune (GPS coordinates: N 31°5′42.7″/W 3°57′56.1″) using Vachellia gummifera as a host (Sakrouhi et al 2016). The genome sequence of the type strain is accessible under the Genbank accession LUAV00000000.1 together with those of five other strains including the Mexican strains LEM451 and LEM457 (Accessions LUFV00000000.1 and LUFW00000000.1, respectively) (Le Queré et al 2017). Strains belonging to this new species present variable accessory genomes that explain the variable host ranges and C sources they can utilize (Le Queré et al 2017).…”