Taxonomy Of Rhizobia Research Articles

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria. Minutes of the closed annual meeting: videoconference on 11 October 2022 followed by online discussion until 31 December 2022.

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria. Minutes of the closed annual meeting: videoconference on 11 October 2022 followed by online discussion until 31 December 2022.

The changing paradigm of rhizobial taxonomy and its systematic growth upto postgenomic technologies.

Rhizobia are a diazotrophic group of bacteria that are usually isolated form the nodules in roots, stem of leguminous plants and are able to form nodules in the host plant owing to the presence of symbiotic genes. The rhizobial community is highly diverse, and therefore, the taxonomy and genera-wise classification of rhizobia has been constantly changing since the last three decades. This is mainly due to technical advancements, and shifts in definitions, resulting in a changing paradigm of rhizobia taxonomy. Initially, the taxonomic definitions at the species and sub species level were based on phylogenetic analysis of 16S rRNA sequence, followed by polyphasic approach to have phenotypic, biochemical, and genetic analysis including multilocus sequence analysis. Rhizobia mainly belonging to α- and β-proteobacteria, and recently new additions from γ-proteobacteria had been classified. Nowadays rhizobial taxonomy has been replaced by genome-based taxonomy that allows gaining more insights of genomic characteristics. These omics-technologies provide genome specific information that considers nodulation and symbiotic genes, along with molecular markers as taxonomic traits. Taxonomy based on complete genome sequence (genotaxonomy), average nucleotide identity, is now being considered as primary approach, resulting in an ongoing paradigm shift in rhizobial taxonomy. Also, pairwise whole-genome comparisons, phylogenomic analyses offer correlations between DNA and DNA re-association values that have delineated biologically important species. This review elaborates the present classification and taxonomy of rhizobia, vis-a-vis development of technical advancements, parameters and controversies associated with it, and describe the updated information on evolutionary lineages of rhizobia.

International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Rhizobia and Agrobacteria, minutes of the annual meeting by videoconference, 5 July 2021, followed by online discussion until 31 December 2021.

Minutes of the closed meeting of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria held by videoconference, 5 July 2021, followed by online discussion until 31 December 2021, and list of recent species.

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 6 July 2020.

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 17 July 2019.

Minutes of the closed meeting of the ICSP Subcommittee on the Taxonomy of Rhizobia and Agrobacteria held by videoconference on 17 July 2019, and list of recent species.

Minimal standards for the description of new genera and species of rhizobia and agrobacteria

Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updated minimal standards for the description of new species (and genera) in these groups. The essential requirements (minimal standards) for description of a new species are (1) a genome sequence of at least the proposed type strain and (2) evidence for differentiation from other species based on genome sequence comparisons. It is also recommended that (3) genetic variation within the species is documented with sequence data from several clearly different strains and (4) phenotypic features are described, and their variation documented with data from a relevant set of representative strains. Furthermore, it is encouraged that information is provided on (5) nodulation or pathogenicity phenotypes, as appropriate, with relevant gene sequences. These guidelines supplement the current rules of general bacterial taxonomy, which require (6) a name that conforms to the International Code of Nomenclature of Prokaryotes, (7) validation of the name by publication either directly in the International Journal of Systematic and Evolutionary Microbiology or in a validation list when published elsewhere, and (8) deposition of the type strain in two international culture collections in separate countries.

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the meeting by video conference, 11 July 2018.

Minutes of the meeting of the Subcommittee on the Taxonomy of Rhizobia and Agrobacteria (ICSP), video conference on 11 July 2018.

Comments on minutes of the Subcommittee on the Taxonomy of Chlamydiae and the Subcommittee on the Taxonomy of Rhizobia and Agrobacteria.

Two recently published minutes of sub-committees of the International Committee on the Systematics of Prokaryotes contain statements that are potentially misleading with regards the workings of the International Code of Nomenclature of Prokaryotes. These issues need clarification.

International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of rhizobia and agrobacteria Minutes of the closed meeting, Granada, 4 September 2017.

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.

International Committee on Systematics of Prokaryotes Subcommittee for the Taxonomy of Rhizobium and Agrobacterium Minutes of the meeting, Budapest, 25 August 2016.

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.

Genetic diversity of elite rhizobial strains of subtropical and tropical legumes based on the 16S rRNA and glnII genes

Biodiversity of diazotrophic symbiotic bacteria in the tropics is a valuable but still poorly studied resource. The objective of this study was to determine if a second housekeeping gene, glnII, in addition to the 16S rRNA, can be employed to improve the knowledge about taxonomy and phylogeny of rhizobia. Twenty-three elite rhizobial strains, very effective in fixing nitrogen with twenty-one herbal and woody legumes (including species from fourteen tribes in the three subfamilies of the family Leguminosae) were selected for this study; all strains are used as commercial inoculants in Brazil. Complete sequences of the 16S rRNA and partial sequences (480bp) of the glnII gene were obtained. The same primers and amplification conditions were successful for sequencing the glnII genes of bacteria belonging to five different rhizobial genera-Bradyrhizobium, Mesorhizobium, Methylobacterium, Rhizobium, Sinorhizobium)-positioned in distantly related branches. The analysis of the concatenated genes (16S rRNA+glnII) considerably improved information about phylogeny and taxonomy of rhizobia in comparison to the single analysis of the 16S rRNA. Nine strains might belong to new species. The complementary analysis of the glnII gene was successful with all strains and improved the phylogenetic clustering and clarified the taxonomic position of several strains. The strategy of including the analysis of glnII, in addition to the 16S rRNA, is cost- and time- effective for the characterization of large rhizobial culture collections or in surveys of many isolates.

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.

The taxonomy of rhizobia: an overview

The taxonomy of rhizobia, bacteria capable of nodulating leguminous plants, has changed considerably over the last 20 years, with the original genus Rhizobium, a member of the alpha-Proteobacteria, now divided into several genera. The study of new geographically dispersed host plants, has been a source of many new species and is expected to yield many more. Here we provide an overview of the history of the rhizobia, but focus on the Rhizobium-Allorhizobium-Agrobacterium relationship. Finally, we review recent reports of nodulation and nitrogen fixation with legume hosts by bacteria that are outside the traditional rhizobial phylogenetic lineages. They include species of Methylobacterium and Devosia in the alpha-Proteobacteria and of Burkholderia and Ralstonia in the beta-Proteobacteria.

Numerical taxonomy of rhizobia isolated from the nodules of Sophora alopecuroides from Xinjiang

Numerical taxonomy of rhizobia isolated from the nodules of Sophora alopecuroides from Xinjiang

Recent developments inRhizobium taxonomy

Recent developments inRhizobium taxonomy are presented from a molecular and evolutionary point of view. Analyses of ribosomal RNA gene sequences provide a solid basis to infer phylogenies in the Rhizobiaceae family. These studies confirmed thatRhizobium andBradyrhizobium are only distantly related and showed thatRhizobium andBradyrhizobium are related to other groups of bacteria that are not plant symbionts.Rhizobium andAgrobacterium species are intermixed. Differences in plasmid content may explain to a good extent the different behavior ofRhizobium andAgrobacterium as symbionts or pathogens. Other approaches to identify and classify bacteria such as DNA-DNA hybridization, fatty acid analysis, RFLP and RPD-PCR techniques and phylogenies derived from other genes are in general agreement to the groupings derived by ribosomal sequences. Only a small proportion of nodulated legumes have been sampled for their symbionts and more knowledge is required on the systematics and taxonomy ofRhizobium andBradyrhizobium species.

Taxonomy of the rhizobia

Extensive cross testing on a relatively few legume hosts led initially to a taxonomic characterization of rhizobia based on bacteria–plant cross–inoculation groups. This has gradually become less acceptable, and has been replaced by taxonomic groupings derived from numerical taxonomy, carbohydrate metabolism, antibiotic susceptiblities, serology, and various molecular techniques. It has long been recognized that there are two distinct groups of rhizobia based on growth rate. The fast-growing genus Rhizobium includes R. leguminosarum, R. meliloti, R. loti, R. galegae, R. tropici, and R. huakuii. The slow-growing genus Bradyrhizobium contains only one recognized species, B. japonicum. Two new genera have been recognized: Azorhizobium, with one recognized species (A. caulinadans), and Sinorhizobium, with two species (S. fredii and S. xinjiangensis). Genetic studies of both the fast- and slow-growing groups show unacceptably wide intrageneric and intergeneric diversity. Although there have been some elegant studies of some of the genetic relationships among rhizobia, overall there has (have) not been the comprehensive study(ies) needed to allow a conclusive taxonomic scheme. Because proposals for revision are accelerating, minimum standards have been proposed by the International Subcommittee for the Taxonomy of Rhizobium and Agrobacterium. Key words: Rhizobium taxonomy, classification of rhizobia, interrelationships of rhizobia.

Species-specific, symbiotic plasmid-located repeated DNA sequences in Rhizobium trifolii

A repeated DNA sequence has been characterized in the clover symbiont, Rhizobium trifolii. Analysis of three copies of this repeated sequence revealed that it constitutes a reiteration of the nifHDK promoter region and, in some copies, an additional reiteration of the N-terminal end of the nifH gene. This sequence, as exemplified by the nifHDK promoter region, is highly conserved within all the geographically-distinct isolates of R. trifolii examined, and is located exclusively on the Sym (symbiotic) plasmid. The R. trifolii repeated sequences (designated RtRS) were shown by DNA hybridization analysis to be specific for R. trifolii and not to hybridize to DNA of any other fastgrowing Rhizobium species examined. Based on the observed species-specificity and Sym-plasmid location of these sequences, as well as the available genetic evidence, we propose a model in which the expression of symbiotic genes is host-specifically activated via these species-specific repeated (promoter) sequences. The results presented indicate that the RtRS sequences can be used as a molecular probe for both species and strain identification and should facilitate the molecular taxonomy of Rhizobium.

A re-examination of the taxonomy of the genusRhizobium and related genera using numerical analysis

Different methods of clustering were applied to the results of a numerical study of the taxonomy ofRhizobium, Agrobacterium, Beijerinckia, Chromobacterium, andBacillus published by Graham (1964) (J. Gen. Microbiol.35: 511).