Draft Genome Sequence of the Nitrogen-Fixing Rhizobium sullae Type Strain IS123T Focusing on the Key Genes for Symbiosis with its Host Hedysarum coronarium L.

Gaurav Sablok,Robin Van Velzen,Andrea Squartini,Rene Geurts,Nicola La Porta,Elisa Polone,Torsten Seeman,Alessio Giacomini,Rosella Muresu,Riccardo Rosselli

doi:10.3389/fmicb.2017.01348

Abstract

The prominent feature of rhizobia is their molecular dialogue with plant hosts. Such interaction is enabled by the presence of a series of symbiotic genes encoding for the synthesis and export of signals triggering organogenetic and physiological responses in the plant. The genome of the Rhizobium sullae type strain IS123T nodulating the legume Hedysarum coronarium, was sequenced and resulted in 317 scaffolds for a total assembled size of 7,889,576 bp. Its features were compared with those of genomes from rhizobia representing an increasing gradient of taxonomical distance, from a conspecific isolate (Rhizobium sullae WSM1592), to two congeneric cases (Rhizobium leguminosarum bv. viciae and Rhizobium etli) and up to different genera within the legume-nodulating taxa. The host plant is of agricultural importance, but, unlike the majority of other domesticated plant species, it is able to survive quite well in the wild. Data showed that that the type strain of R. sullae, isolated from a wild host specimen, is endowed with a richer array of symbiotic genes in comparison to other strains, species or genera of rhizobia that were rescued from domesticated plant ecotypes. The analysis revealed that the bacterium by itself is incapable of surviving in the extreme conditions that its host plant can tolerate. When exposed to drought or alkaline condition, the bacterium depends on its host to survive. Data are consistent with the view of the plant phenotype as the primary factor enabling symbiotic nitrogen fixing bacteria to survive in otherwise limiting environments.

Highlights

The interaction between rhizobia and legumes in root nodules is an essential element in sustainable agriculture, as this symbiotic association is able to enhance biological fixation of atmospheric nitrogen (N2), and is a paradigm in plant–microbe signaling (Young et al, 2006; Giraud et al, 2007; Wang et al, 2012)
The prominent feature of this group of bacteria is their molecular dialogue with plant hosts, an interaction that is enabled by the presence of a series of symbiotic genes encoding for the synthesis and export of signals triggering organogenetic and physiological responses in the plant (Spaink et al, 1987; Long, 2001)
In a previous study (Squartini et al, 2002), we described a novel species, R. sullae, that induces symbiotic nodulation in the legume sulla

Summary

INTRODUCTION

The interaction between rhizobia and legumes in root nodules is an essential element in sustainable agriculture, as this symbiotic association is able to enhance biological fixation of atmospheric nitrogen (N2), and is a paradigm in plant–microbe signaling (Young et al, 2006; Giraud et al, 2007; Wang et al, 2012). It is of particular importance in agriculture due to its ability to adapt to drought and coastal conditions (Douglas, 1984), and is an ideal subject for studying salt tolerance (range limit 150–700 mM NaCl), alkaline tolerance (up to pH 9– 10.5), and drought stress (ranging from 0.5 to −0.95 MPa for PEG; Fitouri et al, 2012; Issolah et al, 2012). Viciae and R. etli), and various genera within the legume-nodulating taxa; (2) determine whether or not the type strain of R. sullae, which comes from a plant that still grows in the wild, carries a richer array of genes for the symbiotic interaction with its host; (3) assess whether or not the traits allowing the host plant to endure extreme soil conditions (drought and alkalinity) are mirrored by appropriate determinants in the bacterial genome In particular, on the genes ruling the symbiotic association with the host plant, we sequenced the genome of the R. sullae type strain IS123T in order to: (1) compare this genome with other members of the order Rhizobiales, including a conspecific isolate (R. sullae WSM1592, Yates et al, 2015), two congeneric cases (R. leguminosarum bv. viciae and R. etli), and various genera within the legume-nodulating taxa; (2) determine whether or not the type strain of R. sullae, which comes from a plant that still grows in the wild, carries a richer array of genes for the symbiotic interaction with its host; (3) assess whether or not the traits allowing the host plant to endure extreme soil conditions (drought and alkalinity) are mirrored by appropriate determinants in the bacterial genome

MATERIALS AND METHODS

Findings

RESULTS