Shinella kummerowiae sp. nov., a symbiotic bacterium isolated from root nodules of the herbal legume Kummerowia stipulacea

Abstract

Bacterial strain CCBAU 25048 T was isolated from root nodules of Kummerowia stipulacea grown in Shandong province of China. Cells of the strain were Gram-negative, strictly aerobic, nonspore-forming, motile short rods. Phylogeny of 16S rRNA gene sequences revealed that the strain belonged to the genus Shinella, a member of family Rhizobiaceae. Its closest phylogenetic relatives were Shinella granuli Ch06 T and Shinella zoogloeoides IAM 12669 T , respectively showing 98.3 and 98.9 % 16S rRNA gene sequence similarity. Strain CCBAU 25048 T had DNA-DNA relatedness of 43.5 and 34.8 %, respectively, with S. zoogloeoides JCM 20728 T and S. granuli JCM 13254 T . In addition, in TP-RAPD analysis, different patterns were obtained for these three strains and some rhizobial strains. The nifH, nodC and nodD sequences of CCBAU 25048 T were identical or very similar to those of bean-nodulating Rhizobium tropici strains. Several phenotypic characteristics, including the use of citrate and D-ribose as carbon sources and growth at pH 11.0, as well as the fatty acid composition, could differentiate CCBAU 25048 T from the two defined Shinella species. Therefore, a novel species Shinella kummerowiae sp. nov. is proposed, with strain CCBAU 25048 T (5JCM 14778 T 5LMG 24136 T ) as the type strain.Rhizobia are soil bacteria capable of eliciting nodules on leguminous plant roots and/or stems in which the bacteria fix nitrogen. In addition to species in the genera Allorhizobium, Azorhizobium, Bradyrhizobium, Mesorhizobium, Rhizobium and Ensifer (former Sinorhizobium species), symbiotic strains belonging to a wide range of bacterial genera have been reported recently from root nodules of several legume species, including Devosia neptuniae In a survey of Kummerowia rhizobia , we isolated strain CCBAU 25048 T from a root nodule of Kummerowia stipulacea grown in Shandong province of China. This strain was related only distantly to Rhizobium giardinii and was quite different from the defined species of Bradyrhizobium, Rhizobium and Ensifer in the 16S rRNA gene phylogeny . Therefore, it might represent a novel lineage of symbiotic bacteria. With the aim of clarifying the taxonomic position of this strain, we made a serial of analyses, including reconstruction of the 16S rRNA gene phylogenetic tree by adding the recently defined Shinella species, detection and sequencing of symbiotic genes from CCBAU 25048 T , DNA-DNA hybridization, twoprimers randomly amplified polymorphic DNA (TP-RAPD) analysis and phenotypic characterization.The 16S rRNA gene sequence of strain CCBAU 25048 T was closely related to those of Shinella species, recently described members of the family Rhizobiaceae , in the phylogenetic tree of 16S rRNA gene sequences (Fig. 1) reconstructed with the neighbourjoining method and bootstrapped with 1000 replications using MEGA program version 3.1 (Kumar et al., 2004). In this tree, CCBAU 25048 T was most similar to Shinella Abbreviation: TP-RAPD, two-primers randomly amplified polymorphic DNA.The GenBank/EMBL/DDBJ accession number fo...

Characterization of Rhizobial Bacteria Nodulating Astragalus corrugatus and Hippocrepis areolata in Tunisian Arid Soils

“…Rhizobia currently consist of 98 species belonging to 13 different genera. The predominant symbionts for most legume species in habitats throughout the world are found in the a-class of Proteobacteria: Rhizobium, Azorhizobium, Ensifer (formerly Sinorhizobium), Mesorhizobium, Bradyrhizobium, Methylobacterium (Jaftha et al, 2002;Jourand et al, 2004), Devosia (Rivas et al, 2003), Shinella (Lin et al, 2008), Ochrobactrum (Trujillo et al, 2005;ZurdoPineiro et al, 2007), Phyllobacterium (Valverde et al, 2005;Mantelin et al, 2006) and Microvirga (Ardley et al, 2012). Moreover, about eight species within two genera of β-class of Proteobacteria -Burkholderia and Cupriavidus have been reported (Moulin et al, 2001;Chen et al, 2001;Klonowska et al, 2012).…”

Exopolysaccharides produced by the symbiotic nitrogen-fixing bacteria of leguminosae

“…However, some authors found that bacteria of the genera Burkholderia (Moulin et al, 2001) and Cupriavidus (Ralstonia) (Chen et al, 2001;Vandamme & Conye, 2004), both belonging to the class β-proteobacteria are also able to fix N 2 and form nodules on legumes. Besides, other genera and families in Rhizobiales (α-proteobacteria) were described as N 2 -fixing bacteria able to establish symbiosis with legumes: Devosia (Rivas et al, 2002(Rivas et al, , 2003, Phyllobacterium (Valverde et al, 2005), Methylobacterium (Sy et al, 2001;Jourand et al, 2004), Ochrobactrum (Trujillo et al, 2005) and Shinella (Lin et al, 2008).…”

A large diversity of non-rhizobial endophytes found in legume root nodules in Flanders (Belgium)

“…In the absence of positive nodulation tests, they can be regarded as non-rhizobial endophytes (NRE). These include i.a., Alphaproteobacteria (Aminobacter (Estrella et al, 2009), Ochrobactrum (Zurdo-Pineiro et al, 2007Imran et al, 2010), Methylobacterium (Palaniappan et al, 2010), Devosia (Bautista et al, 2010) and Phyllobacterium (Mantelin et al, 2006)), Betaproteobacteria (Herbaspirillum (Valverde et al, 2003) and Shinella (Lin et al, 2008)), Gammaproteobacteria (Pantoea, Enterobacter and Pseudomonas (Benhizia et al, 2004;Ibañez et al ., 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 R-40421, R-45534, R-45535, R-45537, R-45540, R-45543, 23,30,161,170,188,303,362,375,376,377,378,380,420,421,422,423,424,425,432,…”