Skip to main content
SpringerLink
Log in

Recent developments in Rhizobium taxonomy

  • Chapter
Book cover Symbiotic Nitrogen Fixation

Part of the book series: Developments in Plant and Soil Sciences ((DPSS,volume 57))

Abstract

Recent developments in Rhizobium 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 that Rhizobium and Bradyrhizobium are only distantly related and showed that Rhizobium and Bradyrhizobium are related to other groups of bacteria that are not plant symbionts. Rhizobium and Agrobacterium species are intermixed. Differences in plasmid content may explain to a good extent the different behavior of Rhizobium and Agrobacterium 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 of Rhizobium and Bradyrhizobium species.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Allen O N and Allen E K 1981 The Leguminosae. A Source Book of Characteristics Uses and Nodulation. The University of Wisconsin Press, USA.

    Google Scholar 

  • Bjourson A J, Stone C E and Cooper J E 1992 Combined subtraction hybridization and polymerase chain reaction amplification procedure for isolation of strain-specific Rhizobium DNA sequences. Appl. Environ. Microbiol. 58,2296–2301.

    PubMed  CAS  Google Scholar 

  • Brom S, Garcia de los Santos A, Stepkowsky T, Flores M, Dávila G, Romero D and Palacios R 1992 Different plasmids of Rhizobium leguminosarum bv. phaseoli are required for optimal symbiotic performance. J. Bacteriol. 174,5183–5189.

    PubMed  CAS  Google Scholar 

  • Bull A T, Goodfellow M and Slater J H 1992 Biodiversity as a source of innovation in biotechnology. Annu. Rev. Microbiol. 46, 219–252.

    Article  PubMed  CAS  Google Scholar 

  • De Bruijn F J 1992 Use of repetitive (repetitive extragenic palindromic and enterobacterial repetitive intergeneric consensus) sequences and the polymerase chain reaction to fingerprint the genomes of Rhizobium meliloti isolates and other soil bacteria. Appl. Environ. Microbiol. 58, 2180–2187.

    PubMed  Google Scholar 

  • Eardly B D, Materon L A, Smith N H, Johnson D A, Rumbaugh M D and Selander R K 1990 Genetic structure of natural populations of the nitrogen-fixing bacterium Rhi zobium meliloti. Appl. Environ. Microbiol. 56, 187–194.

    PubMed  CAS  Google Scholar 

  • Eardly B D, Young J P W and Selander R K 1992 Phylogenetic position of Rhizobium sp. strain Or 191, a symbiont of both Medicago sativa and Phaseolus vulgaris ,based on partial sequences of the 16S rRNA and nifH genes. Appl. Environ. Microbiol. 58, 1809–1815.

    PubMed  CAS  Google Scholar 

  • Flores M, González V, Pardo M A, Leija A, Martínez E, Romero D, Piñero D, Dávila G and Palacios R 1988 Genomic instability in Rhizobium phaseoli. J. Bacteriol. 170,1191–1196.

    PubMed  CAS  Google Scholar 

  • Gepts P 1990 Biochemical evidence bearing on the domestication of Phaseolus (Fabaceae) beans. Econ. Bot. 44, 28–38.

    Article  Google Scholar 

  • Goethals K, Gao M, Tomekpe K, Van Montagu M and Holsters M 1989 Common nodABC genes in nod locus 1 of Azorhizobium caulinodans: nucleotide sequence and plant inducible expression. Mol. Gen. Genet. 219, 289–298.

    Article  PubMed  CAS  Google Scholar 

  • Graham P H, Sadowsky M J, Keyser H H, Barnet Y M, Bradley R S, Cooper J E, de Ley D J, Jarvis B D W, Roslycky E B, Strijdom B W and Young J P W 1991 Proposed minimal standards for the description of new genera and species of root-and stem-nodulating bacteria. Int. J. Syst. Bacteriol. 41, 582–587.

    Article  Google Scholar 

  • Graham P H, Viteri S E, Mackie F, Vargas A A T and Palacios A 1982 Variation in acid soil tolerance among strains of Rhizobium phaseoli. Field Crops Res. 5, 121–128.

    Article  Google Scholar 

  • Hahn M and Hennecke H 1988 Cloning and mapping of a novel nodulation region from Bradyrhizobiumjaponicum by genetic complementation of a deletion mutant. Appl. Environ. Microbiol. 54, 55–61.

    PubMed  CAS  Google Scholar 

  • Haugland R and Verma D P S 1981 Interspecific plasmid and genomic DNA sequence homologies and localization of nit genes in effective and ineffective strains of Rhizobium japonicum. J. Mol. Appl. Genet. 1, 205–217.

    PubMed  CAS  Google Scholar 

  • Hennecke H, Kaluza K, Thöny B, Fuhrmann M, Ludwig W and Stackebrandt E 1985 Concurrent evolution of nitrogenase genes and 16S rRNA in Rhizobium species and other nitrogen fixing bacteria. Arch. Microbiol. 142, 342–348.

    Article  CAS  Google Scholar 

  • Hooykaas P J J, den Dulk-Ras H, Regensburg-Twink A J G, van Brussel A A and Schilperoort R A 1985 Expression of a Rhizobium phaseoli sym plasmid in R. trifolii and Agrobacterium tumefaciens: incompatibility with a R. trifolii sym plasmids. Plasmid 14, 47–52.

    Article  PubMed  CAS  Google Scholar 

  • Hooykaas P J J, Klapwijk P M, Nuti M P, Schilperoort R A and Rorsch A 1977 Transfer of the Agrobacterium tumefaciens Ti plasmid to avirulent agrobacteria and to Rhizobium explanta. J. Gen. Microbiol. 98, 477–484.

    Article  Google Scholar 

  • Hooykaas P J J, Snijdewint F G M and Schilperoort R A 1982 Identification of the Sym plasmid of Rhizobium leguminosarum strain 1001 and its transfer to and expression in other rhizobia and Agrobacterium tumefaciens. Plasmid 8, 73–82.

    Article  PubMed  CAS  Google Scholar 

  • Hynes M F and McGregor N F 1990 Two plasmids other than the nodulation plasmid are necessary for formation of nitrogen-fixing nodules by Rhizobium leguminosarum. Mol. Microbiol. 4, 567–574.

    Article  PubMed  CAS  Google Scholar 

  • Judd A K, Schneider M, Sadowsky M J and de Bruijn F J 1993 Use of repetitive sequences and the polymerase chain reaction technique to classify genetically related Bradyrhizobiumjaponicum serocluster 123 strains. Appl. Environ. Microbiol. 59, 1702–1708.

    PubMed  CAS  Google Scholar 

  • Kaijalainen S and Lindström K 1989 Restriction fragment length polymorphism analysis of Rhizobium galegae strains. J. Bacteriol. 171, 5561–5566.

    PubMed  CAS  Google Scholar 

  • Kersters K and de Ley J 1984 Agrobacterium. In Bergey’s Manual of Systematic Bacteriology. Eds. N R Kreig and J Holt. pp 244–254. Williams and Wilkins, Baltimore.

    Google Scholar 

  • Kinkle B K, Sadowsky M J, Schmidt E L and Koskinen W C 1993 Plasmids pJP4 and r68.45 can be transferred between populations of Bradyrhizobia in nonsterile soil. Appl. Environ. Microbiol. 59, 1762–1766.

    PubMed  CAS  Google Scholar 

  • Kondorosi A, Kondorosi E, Pankhurst C E, Broughton W J and Banfalvi Z 1982 Mobilization of a Rhizobium meliloti megaplasmid carrying nodulation and nitrogen fixation genes into other rhizobia and Agrobacterium. Mol. Gen. Genet. 188,433–439.

    Article  CAS  Google Scholar 

  • Laguerre G, Fernández M P, Edel V, Normand P and Amarger N 1993 Genomic heterogeneity among French Rhizobium strains isolated from Phaseolus vulgaris L. Int. J. Syst. Bacteriol. 43, 761–767.

    Article  CAS  Google Scholar 

  • Ludwig W, Kirchhof G, Klugbauer N, Weizenegger M, Betzl D, Ehrmann M, Hertel C, Jilg S, Tatzel R, Zitzelsberger H, Liebl S, Hockberger M, Shah J, Lane D, Wallnöfer P R and Scheifer K H 1992 Complete 23S ribosomal RNA sequences of gram-positive bacteria with a low DNA G+C content. System. Appl. Microbiol. 15, 487–501.

    Article  CAS  Google Scholar 

  • Martinez E, Palacios R and Sánchez F 1987 Nitrogen-fixing nodules induced by Agrobacterium tumefaciens harboring Rhizobium phaseoli plasmids. J. Bacteriol. 169, 2828–2834.

    PubMed  CAS  Google Scholar 

  • Martinez E, Pardo M A, Palacios R and Cevallos M A 1985 Reiteration of nitrogen fixation gene sequences and specificity of Rhizobium in nodulation and nitrogen fixation in Phaseolus vulgaris. J. Gen. Microbiol. 131, 1779–1786.

    CAS  Google Scholar 

  • Martinez E, Poupot R, Promé J C, Pardo M A, Segovia L, Truchet G and Dénarié J 1993 Chemical signaling of Rhizobium nodulating bean. In New Horizons in Nitrogen Fixation. Eds. R Palacios, J Mora and W E Newton. pp 171–175, Kluwer Academic Publishers. Dordrecht.

    Google Scholar 

  • Martinez E, Romero D and Palacios R 1990 The Rhizobium genome. Crit. Rev. Plant Sci. 9, 59–93.

    Article  CAS  Google Scholar 

  • Martinez-Romero E and Rosenblueth M 1990 Increased bean (Phaseolus vulgaris L.) nodulation competitiveness of genetically modified Rhizobium strains. Appl. Environ. Microbiol. 56, 2384–2388.

    PubMed  CAS  Google Scholar 

  • Martinez-Romero, E, Segovia L, Martins Mercante F, Franco A A, Graham P and Pardo M A 1991 Rhizobium tropici ,a novel species nodulating Phaseolus vulgaris L. beans and Leucaena sp. trees. Int. J. Syst. Bacteriol. 41, 417–426.

    Article  PubMed  CAS  Google Scholar 

  • Nelson K, Whittam T S and Selander R K 1991 Nucleotide polymorphism and evolution in the glyceraldehyde-3phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli. Proc. Natl. Acad. Sci. USA. 88, 6667–6671.

    Article  PubMed  CAS  Google Scholar 

  • Norris D O 1956 Legumes and the Rhizobium symbiosis. Empire J. Experimental Agric. 24, 246–270.

    Google Scholar 

  • Ochman H and Wilson A C 1987 Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Mol. Evol. 26, 74–86.

    Article  PubMed  CAS  Google Scholar 

  • Pardo M A, Lagúnez J, Miranda J and Martínez E 1994 Nodulating ability of Rhizobium tropici is conditioned by a plasmid-encoded citrate synthase. Mol. Microbiol. 11, 315–321.

    Article  PubMed  CAS  Google Scholar 

  • Piñero D, Martínez E and Selander R K 1988 Genetic diversity and relationships among isolates of Rhizobium legumi nosarum biovar phaseoli. Appl. Environ. Microbiol. 54, 2825–2832.

    PubMed  Google Scholar 

  • Saitou N and Nei M 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.

    PubMed  CAS  Google Scholar 

  • Sawada H and Ieki H 1992 Phenotypic characteristics of the genus Agrobacterium. Ann. Phytopath. Soc. Japan 58, 37–45.

    Article  Google Scholar 

  • Sawada H, Ieki H, Oyaizu H and Matsumoto S 1993 Proposal for rejection of Agrobacterium tumefaciens and revised descriptions for the genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhi zogenes. Int. J. Syst. Bacteriol. 43, 694–702.

    Article  PubMed  CAS  Google Scholar 

  • Schleifer K H and Stackebrandt E 1983 Molecular systematics of prokaryotes. Annu. Rev. Microbiol. 37, 143–187.

    Article  PubMed  CAS  Google Scholar 

  • Segovia L, Piñero D, Palacios R and Martínez-Romero 1991 Genetic structure of a soil population of nonsymbiotic Rhizobium leguminosarum. Appl. Environ. Microbiol. 57, 426–433.

    PubMed  CAS  Google Scholar 

  • Segovia L, Young J P W and Martínez-Romero E 1993 Reclassification of American Rhizobium leguminosarum biovar phaseoli type I strains as Rhizobium etli sp. nov. Int. J. Syst. Bacteriol. 43, 374–377.

    Article  CAS  Google Scholar 

  • Selander R K, Caugant D A, Ochman H, Musser J M, Gilmour M N and Whittam T S 1986 Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol. 51, 873–884.

    PubMed  CAS  Google Scholar 

  • Souza V, Nguyen T T, Hudson R R, Piñero D and Lenski R E 1992 Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence of sex? Proc. Natl. Acad. Sci. USA 89, 8389–8393.

    Article  CAS  Google Scholar 

  • Taboada H, Encarnación S, Vargas M C, Narváez V, Mora Y, Martínez E and Mora J 1993 Glutamine synthetase II as a biological marker of the Rhizobiaceae family. In New Horizons in Nitrogen Fixation. Eds. R. Palacios, J Mora and W E Newton. p. 657. Kluwer Academic Publishers. Dordrecht.

    Google Scholar 

  • Torsvik V, Goksoyr J and Daae F L 1990 High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56, 782–787.

    PubMed  CAS  Google Scholar 

  • Truchet G, Rosenberg C, Vasse J, Julliot J S, Camut S and Dénarié J 1984 Transfer of Rhizobium meliloti pSym genes into Agrobacterium tumefaciens: host-specific nodulation by atypical infection. J. Bacteriol. 157, 134–142.

    PubMed  CAS  Google Scholar 

  • Van Brussel A A N, Tak T, Wetselaar A, Pees E and Wijffelman C A 1982 Small leguminosae as test plants for nodulation of Rhizobium leguminosarum and other rhizobia and agrobacteria harbouring a leguminosarum sym plasmid. Plant. Sci. Lett. 27, 317–325.

    Article  Google Scholar 

  • Wheatcroft R and Watson R J 1988 A positive strain identification method for Rhizobium meliloti. Appl. Environ. Microbiol. 54, 574–576.

    PubMed  CAS  Google Scholar 

  • Willems A and Collins M D 1992 Evidence for a close genealogical relationship between Afipia ,the casual organism of cat scratch disease, Bradyrhizobium japon icum and Blastobacter denitrificans. FEMS Microbiol. Lett. 96, 241–246.

    Article  CAS  Google Scholar 

  • Willems A and Collins M D 1993 Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 43, 305–313.

    Article  PubMed  CAS  Google Scholar 

  • Woese C R 1987 Bacterial evolution. Microbiol. Rev. 51, 221–271.

    PubMed  CAS  Google Scholar 

  • Yanagi M and Yamasato K 1993 Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer. FEMS Microbiol. Lett. 107,115–120.

    Article  PubMed  CAS  Google Scholar 

  • Young J P W 1992 Phylogenetic classification of nitrogenfixing organisms In Biological Nitrogen Fixation. Eds. G. Stacey, R H Burris and J H Evans. pp 43–86. Chapman and Hall, New York.

    Google Scholar 

  • Young J P W 1993 Molecular phylogeny of rhizobia and their relatives. In New Horizons in Nitrogen Fixation. Eds. R Palacios. J Mora and W E Newton. pp 587–592, Kluwer Academic Publishers. Dordrecht.

    Google Scholar 

  • Young J P W, Downer H L and Eardly B D 1991 Phylogeny of the phototrophic Rhizobium strain BTail by polymerase chain reaction-based sequencing of a 16S rRNA gene segment. J. Bacteriol. 173, 2271–2277.

    PubMed  CAS  Google Scholar 

  • Young P, Martínez E, Barnet Y, Cooper J and Lindström K 1993 Report from the taxonomy meeting, subcommittee on Agrobacterium and Rhizobium. In New Horizons in Nitrogen Fixation. Eds. R Palacios, J Mora and W E Newton. pp 777–778. Kluwer Academic Publishers. Dordrecht.

    Google Scholar 

  • Zhang X, Harper R, Karsisto M and Lindström K 1991 Diversity of Rhizobium bacteria isolated from the root nodules of leguminous trees. Int. J. Syst. Bacteriol. 41, 104–113.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Centro de Investigación sobre Fijación de Nitrógeno, UNAM, Apdo. postal 565-A, Cuernavaca, Mor, México

    Esperanza Martínez-Romero

Authors
  1. Esperanza Martínez-Romero
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

P. H. Graham M. J. Sadowsky C. P. Vance

Rights and permissions

Reprints and permissions

Copyright information

© 1994 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Martínez-Romero, E. (1994). Recent developments in Rhizobium taxonomy. In: Graham, P.H., Sadowsky, M.J., Vance, C.P. (eds) Symbiotic Nitrogen Fixation. Developments in Plant and Soil Sciences, vol 57. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-1088-4_2

Download citation

  • DOI: https://doi.org/10.1007/978-94-011-1088-4_2

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-010-4475-2

  • Online ISBN: 978-94-011-1088-4

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation