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Natural Diversity of Nodular Microsymbionts of Alnus glutinosa in the Tormes River Basin

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Abstract

The genetic diversity of Frankia strains nodulating Alnus glutinosa along the basin of the Tormes River was studied on DNA extracted directly from nodules. Frankia strains inhabiting root nodules at 12 different locations, ranging in altitude from 409 to 1181 m, were characterized. For that, we amplified the whole IGS region between 16S–23S rDNA and performed a restriction fragment length polymorphism (RFLP) analysis with four restriction enzymes. Two different RFLP patterns (termed A and B) were obtained with HaeIII, indicating the existence of two different groups of Frankia strains. Three different nodule extracts from each of the two RFLP groups were selected for further analyses. Sequencing of the 16S–23S rDNA IGS showed a 100% of intragroup homology and also confirmed the difference (98.4% level of similarity) between the Frankia strains in the two nodule extract groups. The phylogenetic analyses based on the two 16S–23S rDNA IGS sequences obtained in this study and other previously published sequences indicated that Frankia strains TFAg5 and TFAg23 (chosen as representative of HaeIII–RFLP group A and B, respectively) are quite similar to other strains nodulating plants of A. rhombifolia and A. viridis in California (pairwise levels of similarity including gaps ranged from 97.8% to 98.6%), together with which they form a single group. To put the Frankia strains representative of each HaeIII–RFLP group in the context of overall Frankia diversity we amplified and sequenced the 16S rDNA and glnII gene from nodular DNA. An also remarkable fact found in this study was that Frankia strains belonging to the HaeIII–RFLP group A were distributed all along the river course, from the lowest site sampled to the highest, while Frankia strains placed into RFLP group B were restricted to the upper Tormes River, being exclusively found at altitudes of 946 m or higher.

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References

  • M L Clawson D R Benson (1999) ArticleTitleNatural diversity of Frankia strains in actinorhizal root nodules from promiscuous hosts in the family Myricaceae Appl. Environ. Microbiol. 65 4521–4527 Occurrence Handle1:CAS:528:DyaK1MXms1Oitr4%3D Occurrence Handle10508084

    CAS  PubMed  Google Scholar 

  • M L Clawson A Bourret D R Benson (2004) ArticleTitleAssessing the phylogeny of Frankia-actinorhizal plant nitrogen-fixing root nodule symbioses with Frankia 16S rRNA and glutamine synthetase gene sequences Mol. Phylogenet. Evol. 31 131–138 Occurrence Handle1:CAS:528:DC%2BD2cXhvFSks7s%3D Occurrence Handle15019614

    CAS  PubMed  Google Scholar 

  • M L Clawson M Caru D R Benson (1998) ArticleTitleDiversity of Frankia strains in root nodules of plants from the families Elaeagnaceae and Rhamnaceae Appl. Environ. Microbiol. 64 3539–3543 Occurrence Handle1:CAS:528:DyaK1cXmtVajur8%3D Occurrence Handle9726914

    CAS  PubMed  Google Scholar 

  • M L Clawson J Gawronski D R Benson (1999) ArticleTitleDominance of Frankia strains in stands of Alnus incana subsp. rugosa and Myrica pensylvanica Can. J. Bot. 77 1203–1207 Occurrence Handle10.1139/cjb-77-9-1203

    Article  Google Scholar 

  • B Cournoyer C Lavire (1999) ArticleTitleAnalysis of Frankia evolutionary radiation using glnII sequences FEMS Microbiol. Lett. 177 29–34 Occurrence Handle1:CAS:528:DyaK1MXls1SmsLY%3D Occurrence Handle10436920

    CAS  PubMed  Google Scholar 

  • B Cournoyer P Normand (1994) ArticleTitleCharacterization of a Spontaneous Thiostrepton-Resistant Frankia alni Infective Isolate Using PCR–RFLP of Nif and GlnII Genes Soil Biol. Biochem. 26 553–559 Occurrence Handle10.1016/0038-0717(94)90242-9 Occurrence Handle1:CAS:528:DyaK2MXhsFChsA%3D%3D

    Article  CAS  Google Scholar 

  • Y M Dai X Y He C G Zhang Z Z Zhang (2004) ArticleTitleCharacterization of genetic diversity of Frankia strains in nodules of Alnus nepalensis (D. Don) from the Hengduan Mountains on the basis of PCR–RFLP analysis of the nifD–nifK IGS Plant Soil 267 207–212 Occurrence Handle10.1007/s11104-005-5028-8 Occurrence Handle1:CAS:528:DC%2BD2MXht1Wkur0%3D

    Article  CAS  Google Scholar 

  • M Gtari L Brusetti G Skander D Mora A Boudabous D Daffonchio (2004) ArticleTitleIsolation of Elaeagnus-compatible Frankia from soils collected in Tunisia FEMS Microbiol. Lett. 234 349–355 Occurrence Handle1:CAS:528:DC%2BD2cXjvVGmu7o%3D Occurrence Handle15135543

    CAS  PubMed  Google Scholar 

  • D Hahn A Nickel J O Dawson (1999) ArticleTitleAssessing Frankia populations in plants and soil using molecular methods FEMS Microbiol. Ecol. 29 215–227 Occurrence Handle1:CAS:528:DyaK1MXksFWrs7Y%3D

    CAS  Google Scholar 

  • B D V Heuvel D R Benson E Bortiri D Potter (2004) ArticleTitleLow genetic diversity among Frankia spp. strains nodulating sympatric populations of actinorhizal species of Rosaceae, Ceanothus (Rhamnaceae) and Datisca glomerata (Datiscaceae) west of the Sierra Nevada (California) Can. J. Microbiol. 50 989–1000

    Google Scholar 

  • V Huguet J M Batzli J F Zimpfer P Normand J O Dawson M P Fernandez (2001) ArticleTitleDiversity and specificity of Frankia strains in nodules of sympatric Myrica gale, Alnus incana, and Shepherdia canadensis determined by rrs gene polymorphism Appl. Environ. Microbiol. 67 2116–2122 Occurrence Handle10.1128/AEM.67.5.2116-2122.2001 Occurrence Handle1:CAS:528:DC%2BD3MXjtlGnu70%3D Occurrence Handle11319089

    Article  CAS  PubMed  Google Scholar 

  • V Huguet E O Land J G Casanova J F Zimpfer M P Fernandez (2005) ArticleTitleGenetic diversity of Frankia microsymbionts from the relict species Myrica faya (Ait.) and Myrica rivas-martinezii (S.) in Canary Islands and Hawaii Microb. Ecol. 49 617–625 Occurrence Handle10.1007/s00248-004-0107-6 Occurrence Handle1:STN:280:DC%2BD2MvnsVOisg%3D%3D Occurrence Handle16047099

    Article  CAS  PubMed  Google Scholar 

  • V Huguet J M McCray-Batzli J F Zimpfer F Gourbiere J O Dawson M P Fernandez (2004a) ArticleTitleNodular symbionts of Shepherdia, Alnus, and Myrica from a sand dune ecosystem: Trends in occurrence of soilborne Frankia genotypes Can. J. Bot. 82 691–699 Occurrence Handle10.1139/b04-043 Occurrence Handle1:CAS:528:DC%2BD2cXmtlSns70%3D

    Article  CAS  Google Scholar 

  • V Huguet M Mergeay E Cervantes M P Fernandez (2004b) ArticleTitleDiversity of Frankia strains associated to Myrica gale in Western Europe: impact of host plant (Myrica vs. Alnus) and of edaphic factors Environ. Microbiol. 6 1032–1041 Occurrence Handle10.1111/j.1462-2920.2004.00625.x Occurrence Handle1:CAS:528:DC%2BD2cXptVemsbk%3D

    Article  CAS  Google Scholar 

  • K HussDanell (1997) ArticleTitleActinorhizal symbioses and their N2 fixation New Phytol. 136 375–405 Occurrence Handle1:CAS:528:DyaK2sXls1ent7w%3D

    CAS  Google Scholar 

  • J M Igual A Valverde R Rivas P F Mateos C Rodríguez-Barrueco E Martínez-Molina E Cervantes E Velázquez (2003) ArticleTitleGenomic fingerprinting of Frankia strains by PCR-based techniques. Assessment of a primer based on the sequence of 16S rRNA gene of Escherichia coli Plant Soil 254 115–123 Occurrence Handle10.1023/A:1024978426934 Occurrence Handle1:CAS:528:DC%2BD3sXlvVKhtL8%3D

    Article  CAS  Google Scholar 

  • S Jamann M P Fernandez A Moiroud (1992) ArticleTitleGenetic diversity of Elaeagnaceae-infective Frankia strains isolated from various soils Acta Oecol. 13 395–405

    Google Scholar 

  • S Jamann M P Fernandez P Normand (1993) ArticleTitleTyping method for N2-fixing bacteria based on PCR–RFLP. Application to the characterization of Frankia strains Mol. Ecol. 2 17–26 Occurrence Handle1:CAS:528:DyaK3sXkt1Wnu7k%3D Occurrence Handle7910092

    CAS  PubMed  Google Scholar 

  • S C Jeong D D Myrold (1999) ArticleTitleGenomic fingerprinting of Frankia microsymbionts from Ceanothus copopulations using repetitive sequences and polymerase chain reactions Can. J. Bot. 77 1220–1230 Occurrence Handle10.1139/cjb-77-9-1220 Occurrence Handle1:CAS:528:DC%2BD3cXhtFShurc%3D

    Article  CAS  Google Scholar 

  • Kajba D and Gracan J 2003 EUFORGEN Technical Guidelines for Genetic Conservation and Use for Black Alder (Alnus glutinosa). International Plant Genetic Resources Institute Rome, Italy, 4 pages

  • InstitutionalAuthorNameKimura M (1980) ArticleTitleA simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences J. Mol. Evol. 16 111–120 Occurrence Handle7463489

    PubMed  Google Scholar 

  • Kumar S, Tamura K, Jakobsen I B and Nei M 2001 Molecular Evolutionary Genetics Analysis Software

  • L Maggia S Nazaret P Simonet (1992) ArticleTitleMolecular characterization of Frankia isolates from Casuarina equisetifolia root nodules harvested in West Africa (Senegal and Gambia) Acta Oecol. 13 453–461

    Google Scholar 

  • R Nalin A M Domenach P Normand (1995) ArticleTitleMolecular structure of the Frankia spp Nif D–K intergenic spacer and design of Frankia genus compatible primer Mol. Ecol. 4 483–491 Occurrence Handle1:CAS:528:DyaK2MXosFertL4%3D Occurrence Handle8574444

    CAS  PubMed  Google Scholar 

  • E Navarro T Jaffre D Gauthier F Gourbiere G Rinaudo P Simonet P Normand (1999) ArticleTitleDistribution of Gymnostoma spp. microsymbiotic Frankia strains in New Caledonia is related to soil type and to host-plant species Mol. Ecol. 8 1781–1788 Occurrence Handle10.1046/j.1365-294x.1999.00742.x Occurrence Handle10620222

    Article  PubMed  Google Scholar 

  • P Normand B Cournoyer P Simonet S Nazaret (1992) ArticleTitleAnalysis of a ribosomal RNA operon in the actinomycete Frankia Gene 111 119–124 Occurrence Handle10.1016/0378-1119(92)90612-S Occurrence Handle1:CAS:528:DyaK3sXhs1ajur0%3D Occurrence Handle1372279

    Article  CAS  PubMed  Google Scholar 

  • P Normand S Orso B Cournoyer P Jeannin C Chapelon J Dawson L Evtushenko A K Misra (1996) ArticleTitleMolecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae Int. J. Syst. Bacteriol. 46 1–9 Occurrence Handle1:CAS:528:DyaK28Xhtl2ls7s%3D Occurrence Handle8573482

    CAS  PubMed  Google Scholar 

  • B Oakley M North J F Franklin B P Hedlund J T Staley (2004) ArticleTitleDiversity and distribution of Frankia strains symbiotic with Ceanothus in California Appl. Environ. Microbiol. 70 6444–6452 Occurrence Handle10.1128/AEM.70.11.6444-6452.2004 Occurrence Handle1:CAS:528:DC%2BD2cXhtVSjurfJ Occurrence Handle15528504

    Article  CAS  PubMed  Google Scholar 

  • W R Pearson D J Lipman (1988) ArticleTitleImproved tools for biological sequence comparison Proc. Natl. Acad. Sci. USA 85 2444–2448 Occurrence Handle1:CAS:528:DyaL1cXktFyit78%3D Occurrence Handle3162770

    CAS  PubMed  Google Scholar 

  • N J Ritchie D D Myrold (1999a) ArticleTitlePhylogenetic placement of uncultured Ceanothus microsymbionts using 16S rRNA gene sequences Can. J. Bot. 77 1208–1213 Occurrence Handle10.1139/cjb-77-9-1208 Occurrence Handle1:CAS:528:DC%2BD3cXhtFShurs%3D

    Article  CAS  Google Scholar 

  • N J Ritchie D D Myrold (1999b) ArticleTitleGeographic distribution and genetic diversity of Ceanothus-infective Frankia strains Appl. Environ. Microbiol. 65 1378–1383 Occurrence Handle1:CAS:528:DyaK1MXitlarsb8%3D

    CAS  Google Scholar 

  • C Rouvier Y Prin P Reddell P Normand P Simonet (1996) ArticleTitleGenetic diversity among Frankia strains nodulating members of the family Casuarinaceae in Australia revealed by PCR and restriction fragment length polymorphism analysis with crushed root nodules Appl. Environ. Microbiol. 62 979–985 Occurrence Handle1:CAS:528:DyaK28XhsVWqsbw%3D Occurrence Handle8975625

    CAS  PubMed  Google Scholar 

  • N Saitou M Nei (1987) ArticleTitleThe neighbor-joining method: A new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 406–425 Occurrence Handle1:STN:280:BieC1cbgtVY%3D Occurrence Handle3447015

    CAS  PubMed  Google Scholar 

  • P Simonet M C Grosjean A K Misra S Nazaret B Cournoyer P Normand (1991) ArticleTitleFrankia genus-specific characterization by polymerase chain-reaction Appl. Environ. Microbiol. 57 3278–3286 Occurrence Handle1:CAS:528:DyaK3MXmslGmtLk%3D Occurrence Handle1781685

    CAS  PubMed  Google Scholar 

  • P Simonet E Navarro C Rouvier P Reddell J Zimpfer Y Dommergues R Bardin P Combarro J Hamelin A M Domenach F Gourbiere Y Prin J O Dawson P Normand (1999) ArticleTitleCo-evolution between Frankia populations and host plants in the family Casuarinaceae and consequent patterns of global dispersal Environ. Microbiol. 1 525–533 Occurrence Handle10.1046/j.1462-2920.1999.00068.x Occurrence Handle1:STN:280:DC%2BD3Mzit1Wksw%3D%3D Occurrence Handle11207774

    Article  CAS  PubMed  Google Scholar 

  • J D Thompson T J Gibson F Plewniak F Jeanmougin D G Higgins (1977) ArticleTitleThe CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res. 25 4876–4882

    Google Scholar 

  • R Varghese V S Chauhan A K Misra (2003) ArticleTitleEvolutionary implications of nucleotide sequence relatedness between Alnus nepalensis and Alnus glutinosa and also between corresponding Frankia microsymbionts Plant Soil 254 219–227 Occurrence Handle10.1023/A:1024963215959 Occurrence Handle1:CAS:528:DC%2BD3sXlvVKhtbk%3D

    Article  CAS  Google Scholar 

  • E Velázquez E Cervantes J M Igual A Peix P F Mateos S Benamar A Moiroud C T Wheeler J Dawson D Labeda C Rodríguez-Barrueco E Martínez-Molina (1998) ArticleTitleAnalysis of LMW RNA profiles of Frankia strains by staircase electrophoresis Syst. Appl. Microbiol. 21 539–545 Occurrence Handle9924822

    PubMed  Google Scholar 

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Authors and Affiliations

  1. Instituto de Recursos Naturales y Agrobiología de Salamanca (CSIC), Apartado 257, 37080, Salamanca, Spain

    José M. Igual, Angel Valverde, Ignacio Santa Regina & Claudino Rodríguez-Barrueco

  2. Departamento de Microbiología y Genética, Universidad de Salamanca, Spain

    Encarna Velázquez

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  1. José M. Igual
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  2. Angel Valverde
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  3. Encarna Velázquez
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  4. Ignacio Santa Regina
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  5. Claudino Rodríguez-Barrueco
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Correspondence to José M. Igual.

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Igual, J.M., Valverde, A., Velázquez, E. et al. Natural Diversity of Nodular Microsymbionts of Alnus glutinosa in the Tormes River Basin. Plant Soil 280, 373–383 (2006). https://doi.org/10.1007/s11104-005-3700-7

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