Phenotype profiling of Rhizobium leguminosarum bv. trifolii clover nodule isolates reveal their both versatile and specialized metabolic capabilities

Abstract

Rhizobium leguminosarum bv. trifolii (Rlt) are soil bacteria inducing nodules on clover, where they fix nitrogen. Genome organization analyses of 22 Rlt clover nodule isolates showed that they contained 3–6 plasmids and majority of them possessed large (>1 Mb), chromid-like replicon with exception of four Rlt strains. The Biolog phenotypic profiling comprising utilization of C, N, P, and S sources and tolerance to osmolytes and pH revealed metabolic versatility of the Rlt strains. Statistical analyses of our results showed a clear bias toward specific metabolic preferences, tolerance to unfavorable osmotic conditions, and increased nodulation activity of the strains having smaller amount of extrachromosomal DNA. The K5.4 and K4.15 lacking a large megaplasmid possessed substantially diverse metabolism and belonged to effective clover inoculants. In conclusion, besides overall metabolic versatility, some metabolic specialization may enable rhizobia to persist in variable environments and to compete successfully with other bacteria.Electronic supplementary materialThe online version of this article (doi:10.1007/s00203-013-0874-x) contains supplementary material, which is available to authorized users.

Host-dependent symbiotic efficiency of Rhizobium leguminosarum bv. trifolii strains isolated from nodules of Trifolium rubens

“…The symbiotic genes of R. leguminosarum located on the pSym plasmid were also found to be highly variable and affected efficient symbioses with several host plants (Ramirez-Bahena et al 2008 , 2009 ; Marek-Kozaczuk et al 2013 ). In this study, the genomes of the T. rubens nodule isolates were found to be highly differentiated based on the plasmid content showing considerable genetic variability as described earlier for Rlt isolated from nodules of T. pratense (Mazur et al 2011 , 2013 ). The taxonomic position of the selected T. rubens isolates was unambiguously defined as R. leguminosarum .…”

“…The genome of Rhizobium leguminosarum is large and complex, consisting of a chromosome and a variable number of large plasmids (Young et al 2006 ; Mazur et al 2011 ; Kumar et al 2015 ). Symbiotic functions are encoded by genes located in symbiotic plasmids (pSym) (Perret et al 2000 ; Young et al 2006 ; Mazur et al 2011 , 2013 ). The plasmids constitute a pool of accessory genetic information and contribute to the plasticity and dynamic state of the genome commonly observed among members of the Rhizobiaceae family (Palacios and Newton 2005 ).…”

Characterization of Phosphate Solubilizing Faba Bean (<i>Vicia faba</i> L.) Nodulating Rhizobia Isolated from Acidic Soils of Wollega, Ethiopia

“…to persist in adverse environments and compete successfully with other bacteria (Mazur et al, 2013). Therefore, the ability of legume-nodulating rhizobia to solubilise different inorganic phosphates sources, the potential to tolerate wide range of stress, and versatility in metabolism should be considered when selecting strains as biofertilizer.…”

Synthesis of Rhizobial Exopolysaccharides and Their Importance for Symbiosis with Legume Plants

“…RtTA1 derivatives cured of pRleTA1b or pRleTA1d and especially deleted in pRleTA1a (in which no genes related with polysaccharide biosynthesis were previously mapped) produced slightly higher amounts of EPS in comparison to the wild type, suggesting the existence of a complex regulatory network of EPS synthesis consisting of genes located on different plasmids and especially on pSym [ 175 ]. Extrachromosomal replicons were previously shown to confer the significant metabolic versatility to bacteria, which is important for their adaptation in the soil and nodulation competitiveness [ 7 , 8 , 176 ] and may also be exerted by modulation of the rhizobial surface composition. It has been shown that the quality and quantity of surface polysaccharides, particularly exopolysaccharides (EPSs) and lipopolysaccharides (LPSs), produced by rhizobia may influence both their autoaggregation and biofilm formation [ 177 , 178 , 179 ].…”