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Species Delineation and Biogeography of Symbiotic Bacteria Associated with Cultivated and Wild Legumes

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Biological Resources and Migration

Abstract

Here, we review key issues in bacterial population genetics and evolutionary biology pertinent to the controversial topics of bacterial species concepts and bacterial biogeography. We present a summary of our results and working hypotheses on the latter topics, based on our population genetic and molecular phylogenetic analyses of diverse populations of rhizobial microsymbionts associated with cultivated and wild legumes. This contribution describes our current understanding and thoughts on the biogeography and nature of rhizobial species associated with (1) common beans (Phaseolus vulgaris, L.), one of the major grain legume crops worldwide, and (2) with wild genistoid legumes from the Canary Islands, Morocco, and continental Spain.

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References

  • Achtman M, Azuma T, Berg DE, Ito Y, Morelli G, Pan ZJ, Suerbaum S, Thompson SA, van der Ende A, van Doom LJ (1999) Recombination and clonal groupings within Helicobacter pylori from different geographical regions. Mol Microbiol 32: 459–470

    Article  PubMed  CAS  Google Scholar 

  • Amarger N, Macheret V, Laguerre G (1997) Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris nodules. Int J Syst Bacteriol 47: 996–1006

    Google Scholar 

  • Bala A, Murphy P, Giller KE (2003) Distribution and diversity of rhizobia nodulating agro- forestry legumes in soils from three continents in the tropics. Mol Ecol 12: 917–929

    Article  PubMed  CAS  Google Scholar 

  • Baldwin BG, Crawford DJ, Francisco-Ortega J, Kim S-C, Sang T, Stuessy TF (1998) Molecular phylogenetic insights on the origin and evolution of oceanic island plants. In: Soltis DE, Soltis PS, Doyle JJ (eds) Molecular systematics of plants II: DNA sequencing. Kluwer, Dordrecht, pp 410–441

    Chapter  Google Scholar 

  • Bent SJ, Gucker CL, Oda Y, Forney LJ (2003) Spatial distribution of Rhodopseudomonas palustris ecotypes on a local scale. Appl Environ Microbial 69: 5192–5197

    Article  CAS  Google Scholar 

  • Carlquist S (1974) Island Biology. Columbia Univ Press, New York

    Google Scholar 

  • Chen WM, Laevens S, Lee TM, Coenye T, de Vos P, Mergeay M, Vandamme P (2001) Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol 51: 1729–1735

    Google Scholar 

  • Cho JC, Tiedje JM (2000) Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil. Appl Environ Microbiol 66: 5448–5456

    Article  PubMed  CAS  Google Scholar 

  • Cohan FM (2002) What are bacterial species? Annu Rev Microbiol 56: 457–487

    Article  PubMed  CAS  Google Scholar 

  • Darling KF, Wade CM, Stewart IA, Kroon D, Dingle R, Brown AJ (2000) Molecular evidence for genetic mixing of Arctic and Antarctic subpolar populations of planktonic foraminifers. Nature 405: 43–47

    Article  PubMed  CAS  Google Scholar 

  • Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284: 2124–2129

    Article  PubMed  CAS  Google Scholar 

  • Dykhuizen DE, Green L (1991) Recombination in Escherichia coli and the definition of biological species. J Bacteriol 173: 7257–7268

    PubMed  CAS  Google Scholar 

  • Falush D, Wirth T, Linz B, Pritchard JK, Stephens M, Kidd M, Blaser MJ, Graham DY, Vacher S, Perez-Perez GI, Yamaoka Y, Megraud F, Otto K, Reichard U, Katzowitsch E, Wang X, Achtman M, Suerbaum S (2003) Traces of human migrations in Helicobacter pylori populations. Science 299: 1582–1585

    Article  PubMed  CAS  Google Scholar 

  • Feil EJ, Spratt BG (2001) Recombination and the population structures of bacterial pathogens. Annu Rev Microbiol 55: 561–590

    Article  PubMed  CAS  Google Scholar 

  • Feil EJ, Holmes EC, Bessen DE, Chan MS, Day NP, Enright MC, Goldstein R, Hood DW, Kalia A, Moore CE, Zhou J, Spratt BG (2001) Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc Natl Acad Sci USA 98: 182–187

    Article  PubMed  CAS  Google Scholar 

  • Fenchel T (2003) Biogeography for bacteria. Science 301: 925–926

    Article  PubMed  CAS  Google Scholar 

  • Finlay BJ (1998) The global diversity of protozoa and other small species. Int J Parasitol 28: 29–48

    Article  PubMed  CAS  Google Scholar 

  • Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science 296: 1061–1063

    Article  PubMed  CAS  Google Scholar 

  • Freiberg C, Fellay R, Bairoch A, Broughton WJ, Rosenthal A, Perret X (1997) Molecular basis of symbiosis between Rhizobium and legumes. Nature 387: 394–401

    Article  PubMed  CAS  Google Scholar 

  • Fulthorpe RR, Rhodes AN, Tiedje JM (1998) High levels of endemicity of 3-chlorobenzoate-degrading soil bacteria. Appl Environ Microbiol 64: 1620–1627

    PubMed  CAS  Google Scholar 

  • Futuyma DJ (1998) Evolutionary biology. Sinauer Associates, Sunderland, Mass

    Google Scholar 

  • Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dream S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J (2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293: 668–672

    Article  PubMed  CAS  Google Scholar 

  • Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19: 2226–2238

    Article  PubMed  CAS  Google Scholar 

  • Göttfert M, Rothlisberger S, Kundig C, Beck C, Marty R, Hennecke H (2001) Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome. J Bacteriol 183: 1405–1412

    Article  PubMed  Google Scholar 

  • Graham PH, Vance CP (2003) Legumes: importance and constraints to greater use. Plant Physiol 131: 872–877

    Article  PubMed  CAS  Google Scholar 

  • Griffin DW, Kellogg CA, Garrison VH, Shinn EA (2002) The global transport of dust–an intercontinental river of dust, microorganisms and toxic chemicals flows through the Earth’s atmosphere. Am Sci 90: 228–235

    Google Scholar 

  • Istock CA, Duncan KE, Ferguson N, Zhou X (1992) Sexuality in a natural population of bacteria–Bacillus subtilis challenges the clonal paradigm. Mol Ecol 1: 95–103

    Article  PubMed  CAS  Google Scholar 

  • Jain R, Rivera MC, Moore JE, Lake JA (2002) Horizontal gene transfer in microbial genome evolution. Theor Popul Biol 61: 489–495

    Article  PubMed  Google Scholar 

  • Jarabo-Lorenzo A, Velazquez E, Perez-Galdona R, Vega-Hernandez MC, Martinez-Molina E, Mateos PE, Vinuesa P, Martinez-Romero E, Leon-Barrios M (2000) Restriction fragment length polymorphism analysis of 16S rDNA and low molecular weight RNA profiling of rhizobial isolates from shrubby legumes endemic to the Canary islands. Syst Appl Microbiol 23: 418–425

    Article  PubMed  CAS  Google Scholar 

  • Jarabo-Lorenzo A, Pérez-Galdona R, Donate-Correa J, Rivas R, Velazquez E, Hernandez M, Temprano F, Martinez-Molina E, Ruiz-Argüeso T, Ledn-Barrios M (2003) Genetic diversity of bradyrhizobial populations from diverse geographic origins that nodulate Lupinus spp. and Ornithopus spp. Syst Appl Microbiol 26: 611–623

    Article  PubMed  CAS  Google Scholar 

  • Kaneko T, Nakamura Y, Sato S, Asamizu E, Kato T, Sasamoto S, Watanabe A, Idesawa K, Ishikawa A, Kawashima K, Kimura T, Kishida Y, Kiyokawa C, Kohara M, Matsumoto M, Matsuno A, Mochizuki Y, Nakayama S, Nakazaki N, Shimpo S, Sugimoto M, Takeuchi C, Yamada M, Tabata S (2000) Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res 7: 331–338

    Article  PubMed  CAS  Google Scholar 

  • Kaplan L, Lynch TF (1999) Phaseolus (Fabaceae) in archeology: AMS radiocarbon dates and their significance for pre-Columbian agriculture. Econ Bot 53: 261–272

    Google Scholar 

  • Lan R, Reeves P (2001) When does a clone deserve a nave? A perspective on bacterial species based on population genetics. Trends Microbiol 9: 419–424

    Article  PubMed  CAS  Google Scholar 

  • Lawrence JG (2002) Gene transfer in bacteria: speciation without species? Theor Popul Biol 61: 449–460

    Article  PubMed  Google Scholar 

  • Levin BR, Bergstrom CT (2000) Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes. Proc Natl Acad Sci USA 97: 6981–6985

    Article  PubMed  CAS  Google Scholar 

  • Martinez E, Palacios R, Sanchez F (1987) Nitrogen-fixing nodules induced by Agrobacte- rium tumefaciens harboring Rhizobium phaseoli plasmids. J Bacteriol 169: 2828–2834

    PubMed  CAS  Google Scholar 

  • Martinez-Romero E (2003) Diversity of Rhizobium-Phaseolus vulgaris symbiosis: overview and perspectives. Plant Soil 252: 11–23

    Article  CAS  Google Scholar 

  • Massana R, DeLong EF, Pedrôs-Alib C (2000) A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl Environ Microbiol 66: 1777–1787

    Article  PubMed  CAS  Google Scholar 

  • Maynard Smith J, Smith NH, O’Rourke M, Spratt BG (1993) How clonal are bacteria? Proc Natl Acad Sci USA 90: 4384–4388

    Article  Google Scholar 

  • Moulin L, Munive A, Dreyfus B, Boivin-Masson C (2001) Nodulation of legumes by members of the beta-subclass of Proteobacteria. Nature 411: 948–950

    Article  PubMed  CAS  Google Scholar 

  • Nichols R (2001) Gene trees and species trees are not the same. Trends Ecol Evol 16: 358–364

    Article  PubMed  Google Scholar 

  • Ochman H, Lawrence JG, Groisman EA (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299–304

    Article  PubMed  CAS  Google Scholar 

  • Oda Y, Star B, Huisman LA, Gottschal JC, Forney LJ (2003) Biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris. Appl Environ Microbiol 69: 5186–5191

    Article  PubMed  CAS  Google Scholar 

  • Papke RT, Ramsing NB, Bateson MM, Ward DM (2003) Geographical isolation in hot spring cyanobacteria. Environ. Microbiol. 5: 650–659

    Article  PubMed  CAS  Google Scholar 

  • Pérez-Ramirez NO, Rogel MA, Wang E, Castellanos JZ, Martiinez-Romero E (1998) Seeds of Phaseolus vulgaris bean carry Rhizobium etli. FEMS Microbiol Ecol 26: 289–296

    Article  Google Scholar 

  • Rivas R, Velazquez E, Willems A, Vizcaino N, Subba-Rao NS, Mateos PF, Gillis M, Dazzo FB, Martinez-Molina E (2002) A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.î) dru-ce. Appl Environ Microbiol 68: 5217–5222

    Article  PubMed  CAS  Google Scholar 

  • Rogel MA, Hemandez-Lucas I, Kuykendall LD, Balkwill DL, Martinez-Romero E (2001) Nitrogen-fixing nodules with Ensifer adhaerens harboring Rhizobium tropici symbiotic plasmids. Appl Environ Microbiol 67: 3264–3268

    Article  PubMed  CAS  Google Scholar 

  • Rosse-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25: 39–67

    Google Scholar 

  • Sawada H, Kuykendall LD, Young JM (2003) Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. J Gen Appl Microbiol 49: 155–179

    Article  PubMed  CAS  Google Scholar 

  • Segovia L, Young JP, Martinez-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  PubMed  CAS  Google Scholar 

  • Silva C, Eguiarte LE, Souza V (1999) Reticulated and epidemic population genetic structure of Rhizobium etli biovar phaseoli in a traditionally managed locality in Mexico. Mol Ecol 8: 277–287

    Article  Google Scholar 

  • Silva C, Vinuesa P, Eguiarte LE, Martinez-Romero E, Souza V (2003) Rhizobium etli and Rhizobium gallicum nodulate common bean (Phaseolus vulgaris) in a traditionally managed milpa plot in Mexico: population genetics and biogeographic implications. Appl Environ Microbiol 69: 884–893

    Google Scholar 

  • Singh SP, Gepts P, Debouck DG (1991) Races of common bean (Phaseolus vulgaris, Fabaceae). Econ Bot 45: 379–396

    Article  Google Scholar 

  • Souza V, Nguyen TT, Hudson RR, Pifiero D, Lenski RE (1992) Hierarchical analysis of linkage disequilibrium in Rhizobium populations: evidence for sex? Proc Natl Acad Sci USA 89: 8389–8393

    Article  PubMed  CAS  Google Scholar 

  • Souza V, Bain J, Silva C, Bouchet V, Valera A, Marquez E, Eguiarte LE (1997) Etlmomicrobiology: do agricultural practices modify the population structure of the nitrogen fixing bacteria Rhizobium etli biovarphaseoli? J Ethnobiol 17: 249–266

    Google Scholar 

  • Spaink HP, Kondorosi A, Hooykaas PJJ (1998) The Rhizobiaceae. Kluwer, Dordrecht

    Book  Google Scholar 

  • Sprent JI ( 2001 ) Nodulation in legumes. Royal Botanic Gardens, Kew

    Google Scholar 

  • Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44: 846–849

    Article  CAS  Google Scholar 

  • Stackebrandt E, Frederiksen W, Garrity GM, Grimont PA, Kampfer P, Maiden MC, Nesme X, Rossello-Mora R, Swings J, Truper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52: 1043–1047

    Article  PubMed  CAS  Google Scholar 

  • Sullivan JT, Ronson CW (1998) Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc Natl Acad Sci USA 95: 5145–5149

    Article  PubMed  CAS  Google Scholar 

  • Sy A, Giraud E, Jourand P, Garcia N, Willems A, de Lajudie P, Prin Y, Neyra M, Gillis M, Boivin-Masson C, Dreyfus B (2001) Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol 183: 214–220

    Article  PubMed  CAS  Google Scholar 

  • Ueda K, Seki T, Kudo T, Yoshida T, Kataoka M (1999) Two distinct mechanisms cause heterogeneity of 16S rRNA. J Bacteriol 181: 78–82

    PubMed  CAS  Google Scholar 

  • Van Berkum P, Beyene D, Bao G, Campbell TA, Eardly BD (1998) Rhizobium mongolense sp. nov. is one of three rhizobial genotypes identified which nodulate and form nitrogen-fixing symbioses with Medicago ruthenica [(L.) Ledebour]. Int J Syst Bacteriol 48: 13–22

    Google Scholar 

  • Van Berkum P, Terefework Z, Paulin L, Suomalainen S, Lindstrom K, Eardly BD (2003) Discordant phylogenies within the rrn loci of rhizobia. J Bacteriol 185: 2988–2998

    Article  PubMed  Google Scholar 

  • Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60: 407–438

    PubMed  CAS  Google Scholar 

  • Vinuesa P, Rademaker JLW, de Bruijn FJ, Werner D (1998) Genotypic characterization of Bradyrhizobium strains nodulating endemic woody legumes of the Canary Islands by PCR-restriction fragment length polymorphism analysis of genes encoding 16S rRNA (16S rDNA) and 16S–23S rDNA intergenic spacers, repetitive extragenic palindromic PCR genomic fmgerprinting and partial 16S rDNA sequencing. Appl Environ Microbiol 64: 2096–2104

    PubMed  CAS  Google Scholar 

  • Vinuesa P, Rademaker JLW, de Bruijn FJ, Werner D (1999) Characterization of Bradyrhizobium spp. strains by RFLP analysis of amplified 16S rDNA and rDNA intergenic spacer regions. In: Martinez E, Hernandez G (eds) Highlights on nitrogen fixation. Plenum, New York, pp 275–279

    Chapter  Google Scholar 

  • Vinuesa P, Silva C, Werner D, Martinez-Romero E (2004a) Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol Phylogenet Evol (in press)

    Google Scholar 

  • Vinuesa P, Leon-Barrios M, Silva C, Willems A, Jarabo-Lorenzo A, Pérez-Galdona R, Werner D, Martinez Romero E (2004b) Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont isolated from the nodules of endemic genistoid legumes ( Papilionoideae: Genisteae) growing in the Canary Islands. Int. J. Syst. Evol. Microbiol. (submitted)

    Google Scholar 

  • Wang Y, Zhang Z (2000) Comparative sequence analyses reveal frequent occurrence of short segments containing an abnormally high number of non-random base variations in bacterial rRNA genes. Microbiology 146 (11): 2845–2854

    PubMed  CAS  Google Scholar 

  • Welch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J, Stroud D, Mayhew GF, Rose DJ, Zhou S, Schwartz DC, Perna NT, Mobley HL, Donnenberg MS, Blattner FR (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 99: 17020–17024

    Article  PubMed  CAS  Google Scholar 

  • Whitaker RJ, Grogan DW, Taylor JW (2003) Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 301: 976–978

    Article  PubMed  CAS  Google Scholar 

  • Woese CR (1987) Bacterial evolution. Microbiol Rev 51: 221–271

    PubMed  CAS  Google Scholar 

  • Woese CR (2000) Interpreting the universal phylogenetic tree. Proc Natl Acad Sci USA 97: 8392–8396

    Article  PubMed  CAS  Google Scholar 

  • Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87: 4576–4579

    Article  PubMed  CAS  Google Scholar 

  • Yap WH, Zhang Z, Wang Y (1999) Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon. J Bacteriol 181: 5201–5209

    PubMed  CAS  Google Scholar 

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  1. Centro de Investigación sobre Fijación de Nitrógen, Universidad Nacional Autónoma de México, Av. Universidad S/N, Col. Chamilpa, AP 565-A, Cuernavaca, Morelos, CP62210, México

    Pablo Vinuesa & Claudia Silva

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  1. Pablo Vinuesa
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  2. Claudia Silva
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  1. Department of Biology, Institute of Cellbiology and Applied Botany, Philipps-University Marburg, Karl-von-Frisch-Straße, 35032, Marburg, Germany

    Dietrich Werner

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Vinuesa, P., Silva, C. (2004). Species Delineation and Biogeography of Symbiotic Bacteria Associated with Cultivated and Wild Legumes. In: Werner, D. (eds) Biological Resources and Migration. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-06083-4_13

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  • DOI: https://doi.org/10.1007/978-3-662-06083-4_13

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