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© 2017 The Author(s). The type strain of the prospective Bradyrhizobium shewensesp. nov. ERR11T, was isolated from a nodule of the leguminous tree Erythrina bruceinative to Ethiopia. The type strain Bradyrhizobium yuanmingenseCCBAU 10071T, was isolated from the nodules of Lespedeza cuneatain Beijing, China. The genomes of ERR11Tand CCBAU 10071Twere sequenced by DOE-JGI and deposited at the DOE-JGI genome portal as well as at the European Nucleotide Archive. The genome of ERR11Tis 9,163,226 bp in length and has 102 scaffolds, containing 8548 protein-coding and 86 RNA genes. The CCBAU 10071Tgenome is arranged in 108 scaffolds and consists of 8,201,522 bp long and 7776 protein-coding and 85 RNA genes. Both genomes contain symbiotic genes, which are homologous to the genes found in the complete genome sequence of Bradyrhizobium diazoefficiensUSDA110T. The genes encoding for nodulation and nitrogen fixation in ERR11Tshowed high sequence similarity with homologous genes found in the draft genome of peanut-nodulating Bradyrhizobium arachidisLMG 26795T. The nodulation genes nolYA-nodD2D1YABCSUIJ-nolO-nodZ of ERR11Tand CCBAU 10071Tare organized in a similar way to the homologous genes identified in the genomes of USDA110T, Bradyrhizobium ottawaenseUSDA 4and Bradyrhizobium liaoningenseCCBAU 05525. The genomes harbor hupSLCFHK and hypBFDE genes that code the expression of hydrogenase, an enzyme that helps rhizobia to uptake hydrogen released by the N2-fixation process and genes encoding denitrification functions napEDABC and norCBQD for nitrate and nitric oxide reduction, respectively. The genome of ERR11Talso contains nosRZDFYLX genes encoding nitrous oxide reductase. Based on multilocus sequence analysis of housekeeping genes, the novel species, which contains eight strains formed a unique group close to the B. ottawaensebranch. Genome Average Nucleotide Identity (ANI) calculated between the genome sequences of ERR11Tand closely related sequences revealed that strains belonging to B. ottawaensebranch (USDA4and CCBAU15615 ), were the closest strains to the strain ERR11Twith 95.2% ANI. Type strain ERR11Tshowed the highest DDH predicted value with CCBAU15615(58.5%), followed by USDA 4(53.1%). Nevertheless, the ANI and DDH values obtained between ERR11Tand CCBAU 15615or USDA 4were below the cutoff values (ANI ≥ 96.5%; DDH ≥ 70%) for strains belonging to the same species, suggesting that ERR11Tis a new species. Therefore, based on the phylogenetic analysis, ANI and DDH values, we formally propose the creation of B. shewensesp. nov. with strain ERR11T(HAMBI 3532T=LMG 30162T) as the type strain.

Bioremediation potential of the nitrogen-fixing leguminous plant Galega orientalis Lam. and its microsymbiont Rhizobium galegae was evaluated in microcosm and mesocosm scale in oil and BTEX (benzene, toluene, ethylbenzene, xylene) contaminated soils, with m-toluate serving as a model for the latter group. G. orientalis and Rhizobium galegae remained viable in m-toluate fractions up to 3000 ppm. Plant growth and nodulation were inhibited in 500 ppm m-toluate, but were restored when plants were transferred to clean medium. In soil, G. orientalis nodulated and showed good growth in 2000 ppm m-toluate as well as in diesel-contaminated soil in the field, where the plant was stimulating bacterial growth in the rhizosphere. A collection of 52 indigenous m-toluate-tolerating bacteria isolated from oil-contaminated rhizosphere of G. orientalis was characterised and identified by classical and molecular biological methods. 16SrDNA PCR-RFLP and (GTG)5-PCR genomic fingerprinting combined with partial sequencing indicated the presence of five major lineages of the Bacteria domain. A TOL plasmid-specific xylE-PCR was developed in order to detect both active and potential degraders of m-toluate. The ability to degrade m-toluate in the presence of the gene xylE was detected only within the genus Pseudomonas. The isolates were tested for capacity to grow on m-toluate as their sole carbon and energy source. In laboratory experiments, the best rhizosphere isolates performed equally well to the positive control strain and are good candidates for inoculant production in the future. They have been tagged with marker genes for further studies on colonisation and persistence.

The genera Agrobacterium, Allorhizobium, and Rhizobium belong to the family Rhizobiaceae. However, theplacement of a phytopathogenic group of bacteria, the genus Agrobacterium, among the nitrogen-fixingbacteria and the unclear position of Rhizobium galegae have caused controversy in previous taxonomicstudies. To resolve uncertainties in the taxonomy and nomenclature within this family, the phylogeneticrelationships of generic members of Rhizobiaceae were studied, but with particular emphasis on the taxaincluded in Agrobacterium and the “R. galegae complex” (R. galegae and related taxa), using multilocussequence analysis (MLSA) of six protein-coding housekeeping genes among 114 rhizobial and agrobac-terial taxa. The results showed that R. galegae, R. vignae, R. huautlense, and R. alkalisoli formed a separateclade that clearly represented a new genus, for which the name Neorhizobium is proposed. Agrobacteriumwas shown to represent a separate cluster of mainly pathogenic taxa of the family Rhizobiaceae. A. vitisgrouped with Allorhizobium, distinct from Agrobacterium, and should be reclassified as Allorhizobium vitis,whereas Rhizobium rhizogenes was considered to be the proper name for former Agrobacterium rhizogenes.This phylogenetic study further indicated that the taxonomic status of several taxa could be resolved bythe creation of more novel genera.