A genome-wide deletion library is a powerful tool for probing gene functions and one has recently become available for the fission yeast Schizosaccharomyces pombe. Here we use deep sequencing to accurately characterize the barcode sequences in the deletion library, thus enabling the quantitative measurement of the fitness of fission yeast deletion strains by barcode sequencing.

To investigate the community composition and biogeography of soybean rhizobia in Xinjiang, a total of 151 strains were investigated with RFLP and phylogenetic analyses of 16S rRNA gene, 16S-23S intergenic spacer, three housekeeping genes (atpD, glnII and recA), and two symbiotic genes (nifH and nodC), as well as cross-nodulation. Two rhizobial species, Bradyrhizobium liaoningense and Sinorhizobium fredii, were found as dominant groups in communities of soybean rhizobia in Xinjiang, whereas three Rhizobium genomic species, B. yuanmingense and B. japonicum, were minor groups. These genomic species showed clear correlations with eco-regions, and their symbiotic genes were identical or very similar to those of the reference strains for the corresponding species. Conclusively, the dominant soybean rhizobia S. fredii and B. liaoningense in Xinjiang might be introduced from other Chinese regions, but they have been selected as the rhizobia adapted to the saline-alkaline soils. The high pH, salinity, and phosphate concentration in soil might be the environmental factors determining the biogeography of these bacteria. It is worth mentioning that a novel Rhizobium species that may have acquired the symbiotic genes from a Bradyrhizobium lineage was identified.

Great genetic diversity was revealed among 75 rhizobal isolates associated with Vicia faba grown in Chinese fields with AFLP, ARDRA, 16S rDNA sequencing, DNA-DNA hybridization, BOX-PCR and RFLP of PCR-amplified nodD and nodC. Most of the isolates were Rhizobium leguminosarum, and six isolates belonged to an unnamed Rhizobium species. In the homogeneity analysis, the isolates were grouped into three clusters corresponding to (1) autumn sowing (subtropical) region where the winter ecotype of V. faba was cultivated, (2) spring sowing (temperate) region where the spring ecotype was grown, and (3) Yunnan province where the intermediate ecotype was sown either in spring or in autumn. Nonrandom associations were found among the nod genotypes, genomic types and ecological regions, indicating an epidemic symbiotic gene transfer pattern among different genomic backgrounds within an ecological region and a relatively limited transfer pattern between different regions. Conclusively, the present results suggested an endemic population structure of V. faba rhizobia in Chinese fields and demonstrated a novel rhizobium associated with faba bean.

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...

Six strains were isolated from root nodules of Vicia faba grown in Nanchang, Yifeng, Taihu, Huaibei, Bengbu and Lujiang, in the middle and lower reaches of the Yangtze River. According to phylogenetic analyses of 16S rRNA gene, atpD and recA sequences, these strains belong to the genus Rhizobium, with Rhizobium etli and Rhizobium leguminosarum as the closest related species. CCBAU 33202 T , a representative of these novel isolates, showed sequence similarity to its closest relatives R. etli CFN 42 T and R. leguminosarum USDA 2370 T of 99.5 and 99.1 % for the 16S rRNA gene, 91.9 and 91.9 % for atpD and 90.3 and 93.2 % for recA. The strains from this study could also be differentiated from R. etli CFN 42 T and R. leguminosarum USDA 2370T by 16S-IGS RFLP and SDS-PAGE of whole-cell proteins, fatty acid profiles and several phenotypic characteristics. DNA-DNA hybridization yielded relatedness of 19 and 14-43 %, respectively, with R. etli CFN 42 T and strains representing different biovars of R. leguminosarum.All data obtained in this study showed that these V. faba isolates belong to a novel species, for which the name Rhizobium fabae sp. nov. is proposed. The type strain, CCBAU 33202 T (5LMG 23997 T 5JCM 14381 T ), was isolated from Nanchang.It is well known that Vicia faba and other species of Vicia, Pisum, Lathyrus and Lens form nodules with Rhizobium leguminosarum bv. viciae, one of the three biovars of R. leguminosarum (Jordan 1984). Earlier studies revealed that rhizobia isolated from nodules of V. faba in different geographical locations were diverse in their chromosomal background and plasmid content, and rhizobial strains of V. faba were distinguishable from rhizobial strains of Pisum sativum, especially in the nodulation genotypes (van Berkum et al., 1995;Laguerre et al., 2003;Young et al., 2003;Mutch et al., 2003;Mutch & Young, 2004). However, no species other than Rhizobium leguminosarum bv. viciae has been reported to nodulate V. faba. In our previous study, wide diversity was revealed amongst rhizobia associated with V. faba in Chinese fields (Tian et al., 2007). Six strains isolated from six sites in the middle and lower reaches of the Yangtze River formed a distinct group belonging to Rhizobium based upon analysis of BOX-A1R PCR, amplified fragment length polymorphism analysis, amplified 16S rDNA restriction analysis (ARDRA), 16S rRNA gene phylogeny and DNA-DNA hybridization (Tian et al., 2007). In the present study, a polyphasic approach was used to clarify the taxonomic affiliation of this Rhizobium group.Strains CCBAU 33202 T and CCBAU 33201, isolated from Nanchang and Yifeng in Jiangxi province, and CCBAU 23123, CCBAU 23122, CCBAU 23127 and CCBAU 23132, isolated from Taihu, Huaibei, Bengbu and Lujiang in Anhui province, all isolated from V. faba, were used in this study. Standard procedures and YMA medium (Vincent, 1970) were used to isolate and cultivate the strains. DNA samples were prepared as described by Terefework et al. (2001).Previously, these six strains have been grouped in the same ARDR...