Agrobacterium is a definable genus of the family Rhizobiaceae

Traversing the Cell: Agrobacterium T-DNA's Journey to the Host Genome

The genus Agrobacterium is unique in its ability to conduct interkingdom genetic exchange. Virulent Agrobacterium strains transfer single-strand forms of T-DNA (T-strands) and several Virulence effector proteins through a bacterial type IV secretion system into plant host cells. T-strands must traverse the plant wall and plasma membrane, traffic through the cytoplasm, enter the nucleus, and ultimately target host chromatin for stable integration. Because any DNA sequence placed between T-DNA "borders" can be transferred to plants and integrated into the plant genome, the transfer and intracellular trafficking processes must be mediated by bacterial and host proteins that form complexes with T-strands. This review summarizes current knowledge of proteins that interact with T-strands in the plant cell, and discusses several models of T-complex (T-strand and associated proteins) trafficking. A detailed understanding of how these macromolecular complexes enter the host cell and traverse the plant cytoplasm will require development of novel technologies to follow molecules from their bacterial site of synthesis into the plant cell, and how these transferred molecules interact with host proteins and sub-cellular structures within the host cytoplasm and nucleus.

Rhizobium taibaishanense sp. nov., isolated from a root nodule of Kummerowia striata

During a study of the diversity and phylogeny of rhizobia in the root nodules of Kummerowia striata grown in north-western China, four strains were classified in the genus Rhizobium on the basis of their 16S rRNA gene sequences. The 16S rRNA gene sequences of three of these strains were identical and that of the other strain, which was the only one isolated in Yangling, differed from the others by just 1 bp. The16S rRNA gene sequences of the four strains showed a mean similarity of 99.3 % with the most closely related, recognized species, Rhizobium vitis. The corresponding recA and glnA gene sequences showed similarities with established species of Rhizobium of less than 86.5 % and less than 89.6 %, respectively. These low similarities indicated that the four strains represented a novel species of the genus Rhizobium. The strains were also found to be distinguishable from the closest related, established species (R. vitis) by rep-PCR DNA fingerprinting, analysis of cellular fatty acid profiles and from the results of a series of phenotypic tests. The level of DNA–DNA relatedness between the representative strain CCNWSX 0483T and Rhizobium vitis IAM 14140T was only 40.13 %. Therefore, a novel species, Rhizobium taibaishanense sp. nov., is proposed, with strain CCNWSX 0483T ( = ACCC 14971T = HAMBI 3214T) as the type strain. In nodulation and pathogenicity tests, none of the four strains of Rhizobium taibaishanense sp. nov. was able to induce any nodule or tumour formation on plants. As no amplicons were detected when DNA from the strains was run in PCR with primers for the detection of nodA, nifH and virC gene sequences, the strains probably do not carry sym or vir genes.

Multilocus sequence-based analysis delineates a clonal population of Agrobacterium (Rhizobium) radiobacter (Agrobacterium tumefaciens) of human origin

The genus Agrobacterium includes plant-associated bacteria and opportunistic human pathogens. Taxonomy and nomenclature within the genus remain controversial. In particular, isolates of human origin were all affiliated with the species Agrobacterium (Rhizobium) radiobacter, while phytopathogenic strains were designated under the synonym denomination Agrobacterium tumefaciens. In order to study the relative distribution of Agrobacterium strains according to their origins, we performed a multilocus sequence-based analysis (MLSA) on a large collection of 89 clinical and environmental strains from various origins. We proposed an MLSA scheme based on the partial sequence of 7 housekeeping genes (atpD, zwf, trpE, groEL, dnaK, glnA, and rpoB) present on the circular chromosome of A. tumefaciens C58. Multilocus phylogeny revealed that 88% of the clinical strains belong to genovar A7, which formed a homogeneous population with linkage disequilibrium, suggesting a low rate of recombination. Comparison of genomic fingerprints obtained by pulsed-field gel electrophoresis (PFGE) showed that the strains of genovar A7 were epidemiologically unrelated. We present genetic evidence that genovar A7 may constitute a human-associated population distinct from the environmental population. Also, phenotypic characteristics, such as culture at 42°C, agree with this statement. This human-associated population might represent a potential novel species in the genus Agrobacterium.

Rapid and efficient identification of Agrobacterium species by recA allele analysis: Agrobacterium recA diversity

The analysis of housekeeping recA gene sequences from 138 strains from 13 species or genomic species of Agrobacterium, nine being biovar 1 genomospecies, and the others Agrobacterium larrymoorei, Agrobacterium rubi, Agrobacterium sp. NCPPB 1650, and Agrobacterium vitis and one "former" Agrobacterium species, Rhizobium rhizogenes, led to the identification of 50 different recA alleles and to a clear delineation of the 14 species or genomospecies entirely consistent with that obtained by amplified fragment length polymorphism (AFLP) analysis. The relevance of a recA sequencing approach for epidemiological analyses was next assessed on agrobacterial Tunisian isolates. All Tunisian isolates were found to belong to the Agrobacterium tumefaciens/biovar 1 species complex by both biochemical tests and rrs sequencing. recA sequence analysis further permitted their unambiguous assignment to A. tumefaciens genomospecies G4, G6, G7, and G8 in total agreement with the results of an AFLP-based analysis. At subspecific level, several Tunisian recA alleles were novel, indicating the power and accuracy of recA-based typing for studies of Agrobacterium spp.

Rhizobium herbae sp. nov. and Rhizobium giardinii-related bacteria, minor microsymbionts of various wild legumes in China

Seven Rhizobium strains associated with various legume species grown in different geographical regions of China were defined into four genomic groups related to Rhizobium giardinii, based upon ribosomal intergenic spacer RFLP, phylogenies of 16S rRNA and housekeeping (atpD, recA and glnII) genes, and DNA relatedness. Three strains in group I were classified as R. giardinii, as they showed high gene sequence similarities (>97 %) and DNA relatedness (64.3-67.5 %) to R. giardinii H152(T). Groups II, III and IV differed from all defined Rhizobium species based upon the consensus of all analyses. As group II contained two strains that originated from two distinct populations, we propose this group as a novel species, Rhizobium herbae sp. nov., with strain CCBAU 83011(T) ( = LMG 25718(T) = HAMBI 3117(T)) as the type strain.

Analysis of core genes supports the reclassification of strains Agrobacterium radiobacter K84 and Agrobacterium tumefaciens AKE10 into the species Rhizobium rhizogenes

Some strains of the former genus Agrobacterium have high biotechnological interest and are currently misclassified. Consequently, in this study, the taxonomic status of the non-pathogenic strain Agrobacterium radiobacter K84, used in biological control, and the tumourigenic strain Agrobacterium tumefaciens AKE10, able to regenerate tobacco transgenic plants, was revised. The phylogenetic analysis of the chromosomal genes rrs, atpD and recA showed that they should be reclassified into Rhizobium rhizogenes. The analysis of virulence genes located in the Ti plasmid (pTi) outside T-DNA showed a common phylogenetic origin among strains AKE10, R. rhizogenes 163C and A. tumefaciens (currently R. radiobacter) C58. However, the genes located inside the T-DNA, mainly the 6b gene, of strain AKE10 were phylogenetically close to those of strain 163C but divergent from those of strain C58. Furthermore, the T-DNA of tumourigenic strains from R. rhizogenes conferred on them the ability to regenerate tumour tissue resembling fasciation in tobacco plants. These results showed the existence of a highly mosaic genetic organization in tumourigenic strains of the genus Rhizobium and provided evidence of the involvement of T-DNA from tumourigenic strains of R. rhizogenes in fasciation of Nicotiana leaves. The data further suggested that pathogenic strains of Rhizobium could be good models to analyse bacterial evolution.

Health considerations regarding horizontal transfer of microbial transgenes present in genetically modified crops

The potential effects of horizontal gene transfer on human health are an important item in the safety assessment of genetically modified organisms. Horizontal gene transfer from genetically modified crops to gut microflora most likely occurs with transgenes of microbial origin. The characteristics of microbial transgenes other than antibiotic-resistance genes in market-approved genetically modified crops are reviewed. These characteristics include the microbial source, natural function, function in genetically modified crops, natural prevalence, geographical distribution, similarity to other microbial genes, known horizontal transfer activity, selective conditions and environments for horizontally transferred genes, and potential contribution to pathogenicity and virulence in humans and animals. The assessment of this set of data for each of the microbial genes reviewed does not give rise to health concerns. We recommend including the above-mentioned items into the premarket safety assessment of genetically modified crops carrying transgenes other than those reviewed in the present study.

Genetic characterization of root-nodule bacteria associated with Acacia salicina and A. stenophylla (Mimosaceae) across south-eastern Australia

Symbiotic relationships between legumes and nitrogen-fixing soil micro-organisms are of ecological importance in plant communities worldwide. For example, nutrient-poor Australian soils are often dominated by shrubby legumes (e.g. species of Acacia). However, relatively few studies have quantified patterns of diversity, host-specificity and effectiveness of these ecologically important plant-microbe interactions. In this study, 16S rRNA gene sequence and PCR-RFLP analyses were used to examine bacterial strains isolated from the root nodules of two widespread south-eastern Australian legumes, Acacia salicina and Acacia stenophylla, across nearly 60 sites. The results showed that there was extensive genetic diversity in microbial populations, including a broad range of novel genomic species. While previous studies have suggested that most native Australian legumes nodulate primarily with species of the genus Bradyrhizobium, our results indicate significant associations with members of other root-nodule-forming bacterial genera, including Rhizobium, Ensifer, Mesorhizobium, Burkholderia, Phyllobacterium and Devosia. Genetic analyses also revealed a diverse suite of non-nodulating bacterial endophytes, only a subset of which have been previously recorded. Although the ecological roles of these endosymbionts are not well understood, they may play both direct and indirect roles in promoting plant growth, nodulation and disease suppression.

Microbial phylogeny and diversity: small subunit ribosomal RNA sequence analysis and beyond

Small subunit ribosomal RNA (16S rRNA) gene sequence analysis is used for the identification and classification of prokaryotes. In addition, sequencing of 16S rRNA genes amplified directly from the environment is used to estimate microbial diversity. The presence of mosaicism, intra-genomic heterogeneity and the lack of a universal threshold sequence identity value limit 16S rRNA-based phylogenetic analysis. PCR-amplification bias and cloning bias can also result in an inaccurate representation of the microbial diversity. In this review, recently reported complexities of 16S rRNA gene sequence analyses and the requirement of additional tools for microbial phylogeny and diversity analyses are discussed.

Taxonomy of Bacteria Nodulating Legumes

Over the years, the term “rhizobia” has come to be used for all the bacteria that are capable of nodulation and nitrogen fixation in association with legumes but the taxonomy of rhizobia has changed considerably over the last 30 year. Recently, several non-rhizobial species belonging to alpha and beta subgroup of Proteobacteria have been identified as nitrogen-fixing legume symbionts. Here we provide an overview of the history of the rhizobia and the widespread phylogenetic diversity of nitrogen-fixing legume symbionts.

Biodegradation of nicotine by a newly isolated Agrobacterium sp. strain S33

AIMS

To isolate and characterize bacteria capable of degrading nicotine from the rhizospheric soil of a tobacco plant and to use them to degrade the nicotine in tobacco solid waste.

METHODS AND RESULTS

A bacterium, strain S33, was newly isolated from the rhizospheric soil of a tobacco plant, and identified as Agrobacterium sp. based on morphology, physiological tests, Biolog MicroLog3 4.20 system and 16S rRNA gene sequence. Using nicotine as the sole source of carbon and nitrogen in the medium, it grew optimally with 1.0 g l(-1) of nicotine at 30 degrees C and pH 7.0, and nicotine was completely degraded within 6 h. The resting cells prepared from the glucose-ammonium medium or LB medium could not degrade nicotine within 10 h, while those prepared from the nicotine medium could completely degrade 3 g l(-1) of nicotine in 1.5 h at a maximal rate of 1.23 g nicotine h(-1) g(-1) dry cell. Using the medium containing nicotine, glucose and ammonium simultaneously to cultivate strain S33, the resting cells could degrade 98.87% of nicotine in tobacco solid waste with the concentration as 30 mg nicotine g(-1) dry weight tobacco solid waste within 7 h at a maximal rate of 0.46 g nicotine h(-1) g(-1) dry cell.

CONCLUSIONS

This is the first report that Agrobacterium sp. has the ability to degrade nicotine. Agrobacterium sp. S33 could use nicotine as the sole source of carbon and nitrogen. The use of resting cells of the strain S33 prepared from the nicotine-glucose-ammonium medium was an effective method to degrade nicotine and detoxify tobacco solid waste.

SIGNIFICANCE AND IMPACT OF THE STUDY

Nicotine in tobacco wastes is both toxic and harmful to human health and the environment. This study showed that Agrobacterium sp. S33 may be suitable for the disposal of tobacco wastes and reducing the nicotine content in tobacco leaves.

Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia

Concatenated sequence analysis with 16S rRNA, rpoB and fusA genes identified a bacterial strain (IRBG74) isolated from root nodules of the aquatic legume Sesbania cannabina as a close relative of the plant pathogen Rhizobium radiobacter (syn. Agrobacterium tumefaciens). However, DNA:DNA hybridization with R. radiobacter, R. rubi, R. vitis and R. huautlense gave only 44%, 5%, 8% and 8% similarity respectively, suggesting that IRBG74 is potentially a new species. Additionally, it contained no vir genes and lacked tumour‐forming ability, but harboured a sym‐plasmid containing nifH and nodA genes similar to those in other Sesbania symbionts. Indeed, IRBG74 effectively nodulated S. cannabina and seven other Sesbania spp. that nodulate with Ensifer (Sinorhizobium)/Rhizobium strains with similar nodA genes to IRBG74, but not species that nodulate with Azorhizobium or Mesorhizobium. Light and electron microscopy revealed that IRBG74 infected Sesbania spp. via lateral root junctions under flooded conditions, but via root hairs under non‐flooded conditions. Thus, IRBG74 is the first confirmed legume‐nodulating symbiont from the Rhizobium (Agrobacterium) clade. Cross‐inoculation studies with various Sesbania symbionts showed that S. cannabina could form fully effective symbioses with strains in the genera Rhizobium and Ensifer, only ineffective ones with Azorhizobium strains, and either partially effective (Mesorhizobium huakii) or ineffective (Mesorhizobium plurifarium) symbioses with Mesorhizobium. These data are discussed in terms of the molecular phylogeny of Sesbania and its symbionts.

The chaperone GroESL enhances the accumulation of soluble, active TraR protein, a quorum-sensing transcription factor from Agrobacterium tumefaciens

TraR of Agrobacterium tumefaciens is a LuxR-type quorum-sensing transcription factor that regulates genes required for replication and conjugation of the tumor-inducing (Ti) plasmid. TraR requires its cognate autoinducer N-3-oxooctanoyl-homoserine lactone (OOHL) for resistance of proteolysis in wild-type bacteria and for correct protein folding and solubility when overexpressed in E. coli. In this study, we ask whether GroESL might also play a role in TraR folding, as this molecular chaperone assists many proteins in attaining their native tertiary structure. Expression of E. coli GroESL in a strain expressing TraR increases the solubility of TraR and increases transcriptional activity of a TraR-dependent promoter. Both solubility and activity still require OOHL. We also studied the folding of TraR in the closely related bacterium Sinorhizobium meliloti. A mutation in one groEL gene slightly decreased the expression of a TraR-dependent promoter, strongly decreased the accumulation of TraR in Western immunoblot assays, and also strongly influenced the fate of pulse-labeled TraR.

Biological control of crown gall of grapevine, rose, and tomato by nonpathogenic Agrobacterium vitis strain VAR03-1

A nonpathogenic strain of Agrobacterium vitis VAR03-1 was tested as a biological control agent for crown gall of grapevine (Vitis vinifera). When roots of grapevine, rose (Rose multiflora), and tomato (Lycopersicon esculentum) were soaked in a cell suspension of antagonists before planting in soil infested with tumorigenic A. vitis, A. rhizogenes, and A. tumefaciens, respectively, treatment with VAR03-1 significantly reduced the number of plants with tumors and disease severity in the three plant species. The inhibitory effects of treatment with VAR03-1 and the nonpathogenic A. rhizogenes strain K84 on crown gall of rose and tomato were almost identical, and the inhibitory effect of VAR03-1 on grapevine was superior to that of K84. Moreover, VAR03-1 greatly controlled crown gall of grapevine due to tumorigenic A. vitis in the field. VAR03-1 established populations averaging 10(6) colony forming units (CFU)/g of root in the rhizosphere of grapevine and persisted on roots for 2 years. VAR03-1 was bacteriocinogenic, producing a halo of inhibition against those three species of Agrobacterium. This is the first report that a nonpathogenic strain, VAR03-1, can effectively control crown gall caused by tumorigenic A. vitis, A. rhizogenes, and A. tumefaciens.

Cell-cell signaling and the Agrobacterium tumefaciens Ti plasmid copy number fluctuations

The Agrobacterium tumefaciens oncogenic Ti plasmids replicate and segregate to daughter cells via repABC cassettes, in which repA and repB are plasmid partitioning genes and repC encodes the replication initiator protein. repABC cassettes are encountered in a growing number of plasmids and chromosomes of the alpha-proteobacteria, and findings from particular representatives of agrobacteria, rhizobia and Paracoccus have began to shed light on their structure and functions. Amongst repABC replicons, Ti plasmids and particularly the octopine-type Ti have recently stood as model in regulation of repABC basal expression, which acts in plasmid copy number control, but also appear to undergo pronounced up-regulation of repABC, upon interbacterial and host-bacterial signaling. The last results in considerable Ti copy number increase and collective elevation of Ti gene expression. Inhibition of the Ti repABC is in turn conferred by a plant defense compound, which primarily affects Agrobacterium virulence and interferes with cell-density perception. Altogether, the above suggest that the entire Ti gene pool is subjected to the bacterium-eukaryote signaling network, a phenomenon quite unprecedented for replicons thought of as stringently controlled. It remains to be seen whether similar copy number variations characterize related replicons or if they are of even broader significance in plasmid biology.

The effect of chromosome geometry on genetic diversity

Although organisms with linear chromosomes must solve the problem of fully replicating their chromosome ends, this chromosome configuration has emerged repeatedly during bacterial evolution and is evident in three divergent bacterial phyla. The benefit usually ascribed to this topology is the ability to boost genetic variation through increased recombination. But because numerous processes can impact linkage disequilibrium, such an effect is difficult to assess by comparing across bacterial taxa that possess different chromosome topologies. To test directly the contribution of chromosome architecture to genetic diversity and recombination, we examined sequence variation in strains of Agrobacterium Biovar 1, which are unique among sequenced bacteria in having both a circular and a linear chromosome. Whereas the allelic diversity among strains is generated principally by mutations, intragenic recombination is higher within genes situated on the circular chromosome. In contrast, recombination between genes is, on average, higher on the linear chromosome, but it occurs at the same rate as that observed between genes mapping to the distal portion of the circular chromosome. Collectively, our findings indicate that chromosome topology does not contribute significantly to either allelic or genotypic diversity and that the evolution of linear chromosomes is not based on a facility to recombine.

Rhizobium radiobacter as an opportunistic pathogen in central venous catheter-associated bloodstream infection: case report and review

Rhizobium radiobacter is an uncommon opportunistic pathogen present in soil. It has been particularly associated with indwelling intravascular devices in immunocompromised patients. In this report, we summarise the case of a patient with multiple myeloma who developed R. radiobacter bacteraemia during autologous stem cell leucopheresis. Retrospective investigation revealed exposure to soil after central venous catheter placement for chemotherapy and leucopheresis access. This is the first reported case of R. radiobacter bacteraemia following probable colonisation of the catheter from soil exposure. We further review the existing literature to delineate prevention and treatment recommendations for line-associated R. radiobacter infections.

Rhizobium selenireducens sp. nov.: a selenite-reducing alpha-Proteobacteria isolated from a bioreactor

A Gram-negative, nonpigmented bacterium designated strain B1 was isolated from a laboratory bioreactor that reduced selenate to elemental red selenium (Se(0)). 16S rRNA gene-sequence alignment identified the isolate as a Rhizobium sp. belonging to the Rhizobium clade, which includes R. daejeonense, R. giardinii, R. undicola, R. larrymoorei, R. radiobacter, R. rubi, and R. vitis. R. radiobacter and R. rubi are its closest relatives as indicated by 16S rRNA gene-sequence alignments, which differ from strain B1 by 2.6% and 2.8%, respectively. Within this group, strains that show variances > 0.8% to 2.2% have been classified as different species. The major cellular fatty acids present in the B1 strain were C16:0 (1.8%), C18:0 (3.38%), 18:0 3-OH (1.6%), 18:1 omega7c (86.8%), 19:0 cycloomega8c (1.5%), and summed features 2 (3.8%) and 3 (1.2%). The large amount of 18:1 omega7c present is constant with members of this group of bacteria, but the small amounts of 16:0, 19:0 cycloomega8c, and summed feature 3 shows variance from R. radiobacter and R. rubi. The strain's phenotypic and biochemical characteristics are consistent with its placement in this genus.

Phylogenetic assignment and mechanism of action of a crop growth promoting Rhizobium radiobacter strain used as a biofertiliser on graminaceous crops in Russia

The taxonomic position of "Agrobacterium radiobacter strain 204," used in Russia as a cereal crop growth promoting inoculant, was derived by a polyphasic approach. The phenotypic analyses gave very similar biochemical profiles for strain 204, Rhizobium radiobacter NCIMB 9042 (formerly the A. radiobacter type strain) and R. radiobacter NCIMB 13307 (formerly the Agrobacterium tumefaciens type strain). High percentage similarities, above the species separation level, were observed between the 16S rRNA, fusA and rpoB housekeeping gene sequences of these three strains, and the genomic DNA-DNA hybridisation of strain 204 against the type strain of R. radiobacter NCIMB 9042 was over 70%. Strain 204 is not phytopathogenic and it does not fix atmospheric N2 or form a physical association with the roots of barley. Strain 204 culture and culture supernatant stimulated the rate of mobilisation of seed reserves of barley in darkness and promoted its shoot growth in the light. Gibberellic acid (GA) concentration was 1.3 microM but indole acetic acid was undetectable (< 50 nM) in cultures of strain 204. It is concluded that strain 204 is phenotypically and genotypically very similar to the current R. radiobacter type strain and that the mechanism of its effect on growth of cereals is via the production of plant growth promoting substances. GA is likely to play an important role in the strain 204 stimulation of early growth of barley.

Diverse rhizobia that nodulate two species of Kummerowia in China

A total of 63 bacterial strains were isolated from root nodules of Kummerowia striata and K. stipulacea grown in different geographic regions of China. These bacteria could be divided into fast-growing (FG) rhizobia and slow-growing (SG) rhizobia according to their growth rate. Genetic diversity and taxonomic relationships among these rhizobia were revealed by PCR-based 16 S rDNA RFLP and sequencing, 16 S-IGS RFLP, SDS-PAGE of whole cell soluble proteins, BOX-PCR and symbiotic gene (nifH/nodC) analyses. The symbiotic FG strains were mainly isolated from temperate regions and they were identified as four genomic species in Rhizobium and Sinorhizobium meliloti based on the consensus of grouping results. The SG strains were classified as five genomic species within Bradyrhizobium and they were mainly isolated fron the subtropic and tropical regions. The phylogenetic analyses of nifH and nodC genes showed relationships similar to that of 16 S rDNA but the symbiotic genes of Bradyrhizobium strains isolated from Kummerowia were distinct from those isolated from Arachis and soybean. These results offered evidence for rhizobial biogeography and demonstrated that the Kummerowia-nodulating ability might have evolved independently in different regions in association with distinctive genomic species of rhizobia.

Characterization of two novel biovar of Agrobacterium tumefaciens isolated from root nodules of Vicia faba

A total of eight strains of bacteria were isolated from the root nodule of Vicia faba on the selective media of Rhizobium. Two of these strains produced phenotypically distinct mucoid colonies (one slow growing and the other fast growing) and were examined using a polyphasic approach for taxonomic identification. The two strains (MTCC 7405 and MTCC 7406) turned out to be new strains of biovar 1 Agrobacterium rather than Rhizobium, as they showed growth on alkaline medium as well as on 2% NaCl and neither catabolized lactose as the carbon source nor oxidized Tween-80. The distinctness between the two strains was marked with respect to their growth on dextrose and the production of lysine dihydrolase, ornithine decarboxylase and DNA G + C content. 16S rDNA sequencing and their comparison with the 16S rDNA sequences of previously described agrobacteria as well as rhizobia strains confirmed the novelty of the two strains. Both of the strains clustered with strains of Agrobacterium tumefaciens in the 16S rDNA-based phylogenetic tree. The phenotypic and biochemical properties of the two strains differed from those of the recognized biovar of A. tumefaciens. It is proposed that the strains MTCC 7405 and MTCC 7406 be classified as novel biovar of the species A. tumefaciens (Type strains MTCC 7405 = DQ383275 and MTCC 7406 = DQ383276).

Multilocus sequence analysis of Ensifer and related taxa

Multilocus sequence analysis (MLSA) was performed on representatives of Ensifer (including species previously assigned to the genus Sinorhizobium) and related taxa. Neighbour-joining (NJ), maximum-parsimony (MP) and maximum-likelihood (ML) phylogenies of dnaK, gltA, glnA, recA, thrC and 16S rRNA genes were compared. The data confirm that the potential for discrimination of Ensifer species is greater using MLSA of housekeeping genes than 16S rRNA genes. In incongruence-length difference tests, the 16S rRNA gene was found to be significantly incongruent with the other genes, indicating that this gene should not be used as a single indicator of relatedness in this group. Significant congruence was detected for dnaK, glnA and thrC. Analyses of concatenated sequences of dnaK, glnA and thrC genes yielded very similar NJ, MP and ML trees, with high bootstrap support. In addition, analysis of a concatenation of all six genes essentially produced the same result, levelling out potentially conflicting phylogenetic signals. This new evidence supports the proposal to unite Ensifer and Sinorhizobium in a single genus. Support for an alternative solution preserving the two genera is less strong. In view of the opinions expressed by the Judicial Commission, the name of the genus should be Ensifer, as proposed by Young [Young, J. M. (2003). Int J Syst Evol Microbiol 53, 2107–2110]. Data obtained previously and these new data indicate that Ensifer adhaerens and ‘Sinorhizobium morelense’ are not heterotypic synonyms, but represent separate species. However, transfer to the genus Ensifer is not possible at present because the species name is the subject of a pending Request for an Opinion, which would affect whether a novel species in the genus Ensifer or a new combination based on a basonym would be created.

Primary bacteraemia caused by Rhizobium radiobacter in a patient with solid tumours

A case of Rhizobium radiobacter primary bacteraemia in a patient with solid tumours is reported. Corticosteroid therapy and diabetes mellitus were the predisposing factors. The patient was treated successfully with amikacin and piperacillin/tazobactam. The clinical isolate was identified as R. radiobacter by 16S rRNA gene sequencing. Phytopathogenicity tests and a PCR assay demonstrated that the organism was not a plant pathogen.

Identification of genomic species in Agrobacterium biovar 1 by AFLP genomic markers

Biovar 1 of the genus Agrobacterium consists of at least nine genomic species that have not yet received accepted species names. However, rapid identification of these organisms in various biotopes is needed to elucidate crown gall epidemiology, as well as Agrobacterium ecology. For this purpose, the AFLP methodology provides rapid and unambiguous determination of the genomic species status of agrobacteria, as confirmed by additional DNA-DNA hybridizations. The AFLP method has been proven to be reliable and to eliminate the need for DNA-DNA hybridization. In addition, AFLP fragments common to all members of the three major genomic species of agrobacteria, genomic species G1 (reference strain, strain TT111), G4 (reference strain, strain B6, the type strain of Agrobacterium tumefaciens), and G8 (reference strain, strain C58), have been identified, and these fragments facilitate analysis and show the applicability of the method. The maximal infraspecies current genome mispairing (CGM) value found for the biovar 1 taxon is 10.8%, while the smallest CGM value found for pairs of genomic species is 15.2%. This emphasizes the gap in the distribution of genome divergence values upon which the genomic species definition is based. The three main genomic species of agrobacteria in biovar 1 displayed high infraspecies current genome mispairing values (9 to 9.7%). The common fragments of a genomic species are thus likely "species-specific" markers tagging the core genomes of the species.

Rapid and specific identification of four Agrobacterium species and biovars using multiplex PCR

On the basis of 23S rRNA gene sequences, 1 universal forward and 4 taxon (species/biovar)-specific reverse primers were designed for multiplex PCR to aid in identification and differentiation of Agrobacterium rubi, Agrobacterium vitis and Agrobacterium biovars 1 and 2. In reactions with DNA of 119 bacterial strains belonging to: Agrobacterium, Allorhizobium, Mesorhizobium, Rhizobium, Sinorhizobium and Phyllobacterium, as well as phytopathogenic bacteria representing various genera, the primers developed for identification of A. vitis, A. rubi or Agrobacterium biovar 1 amplified only DNA of strains belonging to these taxa, producing fragments of the expected sizes: 478, 1006 and 184bp, respectively. However, in the case of the primer developed for identification of Agrobacterium biovar 2, the characteristic 1066bp PCR product was obtained not only with DNA of this biovar, but also with DNA of 3 atypical biovar 1 strains and some rhizobial strains. Differentiation between Agrobacterium biovar 2 and the other strains was possible using the restriction analysis of this product with endonuclease Alw26I. The method developed is an excellent tool for rapid classification of these 4 taxa of Agrobacterium.

The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumors or hairy roots in plants

Bacteria belonging to the family Rhizobiaceae may establish beneficial or harmful relationships with plants. The legume endosymbionts contain nod and nif genes responsible for nodule formation and nitrogen fixation, respectively, whereas the pathogenic strains carry vir genes responsible for the formation of tumors or hairy roots. The symbiotic and pathogenic strains currently belong to different species of the genus Rhizobium and, until now, no strains able to establish symbiosis with legumes and also to induce tumors or hairy roots in plants have been reported. Here, we report for the first time the occurrence of two rhizobial strains (163C and ATCC11325T) belonging to Rhizobium rhizogenes able to induce hairy roots or tumors in plants and also to nodulate Phaseolus vulgaris under natural environmental conditions. Symbiotic plasmids (pSym) containing nod and nif genes and pTi- or pRi-type plasmids containing vir genes were found in these strains. The nodD and nifH genes of the strains from this study are phylogenetically related to those of Sinorhizobium strains nodulating P. vulgaris. The virA and virB4 genes from strain 163C are phylogenetically related to those of R. tumefaciens C58, whereas the same genes from strain ATCC 11325T are related to those of hairy root-inducing strains. These findings may be of high relevance for the better understanding of plant-microbe interactions and knowledge of rhizobial phylogenetic history.

Diverse rhizobia associated with woody legumes Wisteria sinensis, Cercis racemosa and Amorpha fruticosa grown in the temperate zone of China

Fifty-nine bacterial isolates from root nodules of the woody legumes Wisteria sinensis, Cercis racemosa and Amorpha fruticosa grown in the central and eastern regions of China were characterized with phenotypic analysis, PCR-based 16S and 23S rRNA gene RFLP, Box PCR and 16S rRNA gene sequencing. Seven main phena were defined in numerical taxonomy, which corresponded to distinct groups within the genera Agrobacterium, Bradyrhizobium, Mesorhizobium and Rhizobium in 16S and 23S rRNA gene PCR-RFLP. The phylogenetic relationships of the 16S rRNA genes supported the grouping results of PCR-RFLP. Most of the isolates from Amorpha fruticosa were classified into two groups closely related to Mesorhizobium amorphae. Seventeen of the 21 isolates from Wisteria sinensis were identified as two groups related to Rhizobium and Agrobacterium. Six out of 10 isolates from Cercis racemosa were identified as a group related to Bradyrhizobium. Our results indicated that each of the investigated legumes nodulated mainly with one or two rhizobial groups, although isolates from different plants intermingled in some small bacterial groups. In addition, correlation between geographic origin and grouping results was found in the isolates from Amorpha fruticosa. These results revealed that the symbiotic bacteria might have been selected by both the legume hosts and the geographic factors.

Detection of and response to signals involved in host-microbe interactions by plant-associated bacteria

Diverse interactions between hosts and microbes are initiated by the detection of host-released chemical signals. Detection of these signals leads to altered patterns of gene expression that culminate in specific and adaptive changes in bacterial physiology that are required for these associations. This concept was first demonstrated for the members of the family Rhizobiaceae and was later found to apply to many other plant-associated bacteria as well as to microbes that colonize human and animal hosts. The family Rhizobiaceae includes various genera of rhizobia as well as species of Agrobacterium. Rhizobia are symbionts of legumes, which fix nitrogen within root nodules, while Agrobacterium tumefaciens is a pathogen that causes crown gall tumors on a wide variety of plants. The plant-released signals that are recognized by these bacteria are low-molecular-weight, diffusible molecules and are detected by the bacteria through specific receptor proteins. Similar phenomena are observed with other plant pathogens, including Pseudomonas syringae, Ralstonia solanacearum, and Erwinia spp., although here the signals and signal receptors are not as well defined. In some cases, nutritional conditions such as iron limitation or the lack of nitrogen sources seem to provide a significant cue. While much has been learned about the process of host detection over the past 20 years, our knowledge is far from being complete. The complex nature of the plant-microbe interactions makes it extremely challenging to gain a comprehensive picture of host detection in natural environments, and thus many signals and signal recognition systems remain to be described.

Rhizobial 16S rRNA and dnaK genes: mosaicism and the uncertain phylogenetic placement of Rhizobium galegae

The phylogenetic relatedness among 12 agriculturally important species in the order Rhizobiales was estimated by comparative 16S rRNA and dnaK sequence analyses. Two groups of related species were identified by neighbor-joining and maximum-parsimony analysis. One group consisted of Mesorhizobium loti and Mesorhizobium ciceri, and the other group consisted of Agrobacterium rhizogenes, Rhizobium tropici, Rhizobium etli, and Rhizobium leguminosarum. Although bootstrap support for the placement of the remaining six species varied, A. tumefaciens, Agrobacterium rubi, and Agrobacterium vitis were consistently associated in the same subcluster. The three other species included Rhizobium galegae, Sinorhizobium meliloti, and Brucella ovis. Among these, the placement of R. galegae was the least consistent, in that it was placed flanking the A. rhizogenes-Rhizobium cluster in the dnaK nucleotide sequence trees, while it was placed with the other three Agrobacterium species in the 16S rRNA and the DnaK amino acid trees. In an effort to explain the inconsistent placement of R. galegae, we examined polymorphic site distribution patterns among the various species. Localized runs of nucleotide sequence similarity were evident between R. galegae and certain other species, suggesting that the R. galegae genes are chimeric. These results provide a tenable explanation for the weak statistical support often associated with the phylogenetic placement of R. galegae, and they also illustrate a potential pitfall in the use of partial sequences for species identification.

[The genome of alpha-proteobacteria : complexity, reduction, diversity and fluidity]

The alpha-proteobacteria displayed diverse and often unconventional life-styles. In particular, they keep close relationships with the eucaryotic cell. Their genomic organization is often atypical. Indeed, complex genomes, with two or more chromosomes that could be linear and sometimes associated with plasmids larger than one megabase, have been described. Moreover, polymorphism in genome size and topology as well as in replicon number was observed among very related bacteria, even in a same species. Alpha-proteobacteria provide a good model to study the reductive evolution, the role and origin of multiple chromosomes, and the genomic fluidity. The amount of new data harvested in the last decade should lead us to better understand emergence of bacterial life-styles and to build the conceptual basis to improve the definition of the bacterial species.

Isolation of a strain of Agrobacterium tumefaciens (Rhizobium radiobacter) utilizing methylene urea (ureaformaldehyde) as nitrogen source

Methylene ureas (MU) are slow-release nitrogen fertilizers degraded in soil by microbial enzymatic activity. Improved utilization of MU in agricultural production requires more knowledge about the organisms and enzymes responsible for its degradation. A Gram-negative, MU-degrading organism was isolated from a soil in Sacramento Valley, California. The bacterium was identified as Agrobacterium tumefaciens (recently also known as Rhizobium radiobacter) using both genotypic and phenotypic characterization. The pathogenic nature of the organism was confirmed by a bioassay on carrot disks. The MU-hydrolyzing enzyme (MUase) was intracellular and was induced by using MU as a sole source of nitrogen. The bacterial growth was optimized in NH4Cl, urea, or peptone, whereas the production and specific activity of MUase were maximized with either NH4Cl or urea as a nitrogen source. The result has a practical significance, demonstrating a potential to select for this plant pathogen in soils fertilized with MU.

Classification and nomenclature of Agrobacterium and Rhizobium

Farrand et al. [Int J Syst Evol Microbiol 53 (2003), 1681-1687] have presented a critique of the proposal of Young et al. [Int J Syst Evol Microbiol 51 (2001), 89-103] to revise the nomenclature and classification of RHIZOBIUM: They argued that Young et al. (2001) are mistaken in their reclassification of all Agrobacterium species within Rhizobium, and that the resulting nomenclatural revision is 'unnecessary and unwarranted'. These objections arise because the authors appear not to understand the role of formal nomenclature, and fail to distinguish between formal and special-purpose nomenclatures (Bacteriological Code, 1990 Revision). The arguments set out by Farrand et al. (2003) can be addressed in terms of (1) the taxonomic status of the genera Agrobacterium and Rhizobium; (2) the status of species and biovars and their nomenclature; and (3) the role of transmissible genomic elements in classification and nomenclature. Finally, an attempt is made to unravel the confusion underpinning their discussion with a consideration of the relationship between formal and special-purpose nomenclatures.

Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts

As of February 2003, bacteria that form nitrogen-fixing symbiotic associations with legumes have been confirmed in 44 species of 12 genera. Phylogenies of these taxa containing legume symbionts based on the comparative analysis of 16S rDNA sequences show that they are not clustered in one lineage but are distributed in the classes Alphaproteobacteria and Betaproteobacteria, and dispersed over the following nine monophyletic groups, being intermingled with other taxa that do not contain legume symbionts (shown in parentheses below): Group 1, which comprises Rhizobium and Allorhizobium species containing legume symbionts (intermingled with Agrobacterium and Blastobacter species, which are nonsymbionts); Group 2, Sinorhizobium and Ensifer species (with unclassified nonsymbionts); Group 3, Mesorhizobium species (with nonsymbiotic Aminobacter and Pseudaminobacter species); Group 4, Bradyrhizobium species and Blastobacter denitrificans (with nonsymbiotic Agromonas, Nitrobacter, Afipia, and Rhodopseudomonas species); Group 5, 'Methylobacterium nodulans" (with nonsymbiotic Methylobacterium species); Group 6, Azorhizobium species (with nonsymbiotic Xanthobacter and Aquabacter species); Group 7, 'Devosia neptuniae" (with nonsymbiotic Devosia species and unclassified nonsymbionts); Group 8, symbiotic Burkholderia strains (with nonsymbiotic Burkholderia species); and Group 9, Ralstonia taiwanensis (with nonsymbiotic Ralstonia species). For Groups 5, 8, and 9, the present classification, in which 'each monophyletic group comprises one genus wherein legume symbionts and nonsymbionts are intermingled with each other, " is considered to be retained as is because they are clearly separated from other genera at high bootstrap values and have already been sufficiently characterized based on polyphasic taxonomy. As for the remaining six monophyletic groups, on the other hand, there are currently three options for emending their current classification (definitions and circumscriptions) at the generic level: A) the current classification shall be retained as is; B) all the genera within each monophyletic group shall be amalgamated into one single genus in conformity with the results of phylogenetic analysis; or C) each subordinate lineage in each monophyletic group shall be proposed as a genus. It is considered that research and discussions will be continuously conducted for emending the classification of these monophyletic groups based chiefly on Options B and C as preferable candidates.