1887

Abstract

Four strains of symbiotic bacteria from root nodules of hyacinth bean (Lablab purpureus (L.) Sweet) from Namibia were previously identified as a novel group within the genus Bradyrhizobium . To confirm their taxonomic status, these strains were further characterized by taking a polyphasic approach. The type strain possessed 16S rRNA gene sequences identical to Bradyrhizobium paxllaeri LMTR 21 and Bradyrhizobium icense LMTR 13, the full-length sequences were identical to those retrieved from SAMN05230119 and SAMN05230120, respectively. However, the intergenic spacer sequences of the novel group showed identities of less than 93.1 % to described Bradyrhizobium species and were placed in a well-supported separate lineage in the phylogenetic tree. Phylogenetic analyses of six concatenated housekeeping genes, recA, glnII, gyrB, dnaK, atpD and rpoB, corroborated that the novel strains belonged to a lineage distinct from named species of the genus Bradyrhizobium , with highest sequence identities to Bradyrhizobium jicamae and B. paxllaeri (below 93 %). The species status was validated by results of DNA–DNA hybridization and average nucleotide identity values of genome sequences. The combination of phenotypic characteristics from several tests, including carbon source utilization and antibiotic resistance, could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium . Phylogenetic analysis of nodC and nifH genes placed the novel strains in a group with B. paxllaeri and B. lablabi . Novel strain 5-10 induces effective nodules on Lablab purpureus, Vigna subterranea, Vigna unguiculata and Arachis hypogaea. Based on our results, we conclude that our strains represent a novel species for which the name Bradyrhizobium namibiense sp. nov. is proposed, with type strain 5-10[LMG 28789, DSM 100300, NTCCM0017 (Windhoek)].

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002039
2017-10-16
2019-10-14
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/12/4884.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002039&mimeType=html&fmt=ahah

References

  1. Pröpper M, Gröngröft A, Falk T, Eschenbach A, Fox T et al. Causes and perspectives of land-cover change through expanding cultivation in Kavango. In Jürgens N, Schmiedel U, Hoffman T. (editors) Biodiversity in Southern Africa 3: Implications for Landuse and Management Göttingen, Windhoek: Klaus Hess; 2010; pp. 2– 31
    [Google Scholar]
  2. Grönemeyer J, Berkelmann D, Mubyana-John T, Haiyambo D, Chimwamurombe P et al. A survey for plant-growth-promoting rhizo-bacteria and symbionts associated with crop plants in the Okavango region of Southern Africa. Biodiversity and Ecology 2013; 5: 287– 294 [CrossRef]
    [Google Scholar]
  3. Maass BL, Knox MR, Venkatesha SC, Angessa TT, Ramme S et al. Lablab purpureus—a crop lost for Africa?. Trop Plant Biol 2010; 3: 123– 135 [CrossRef] [PubMed]
    [Google Scholar]
  4. Grönemeyer JL, Kulkarni A, Berkelmann D, Hurek T, Reinhold-Hurek B. Identification and characterization of rhizobia indigenous to the Okavango region in Sub-Saharan Africa. Appl Environ Microbiol 2014; 80: 7244– 7257 [Crossref]
    [Google Scholar]
  5. van Berkum P. Evidence for a third uptake Hydrogenase phenotype among the soybean bradyrhizobia. Appl Environ Microbiol 1990; 56: 3835– 3841 [PubMed]
    [Google Scholar]
  6. Grönemeyer JL, Burbano CS, Hurek T, Reinhold-Hurek B. Isolation and characterization of root-associated Bacteria from agricultural crops in the Kavango region of Namibia. Plant Soil 2012; 356: 67– 82 [CrossRef]
    [Google Scholar]
  7. Laguerre G, Mavingui P, Allard MR, Charnay MP, Louvrier P et al. Typing of rhizobia by PCR DNA fingerprinting and PCR-restriction fragment length polymorphism analysis of chromosomal and symbiotic gene regions: application to Rhizobium leguminosarum and its different biovars. Appl Environ Microbiol 1996; 62: 2029– 2036 [PubMed]
    [Google Scholar]
  8. Willems A, Munive A, de Lajudie P, Gillis M. In most Bradyrhizobium groups sequence comparison of 16S-23S rDNA internal transcribed spacer regions corroborates DNA–DNA hybridizations. Syst Appl Microbiol 2003; 26: 203– 210 [CrossRef] [PubMed]
    [Google Scholar]
  9. Vinuesa P, Silva C, Werner D, Martínez-Romero E. Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol Phylogenet Evol 2005; 34: 29– 54 [CrossRef] [PubMed]
    [Google Scholar]
  10. Stepkowski T, Moulin L, Krzyzańska A, McInnes A, Law IJ et al. European origin of Bradyrhizobium populations infecting lupins and serradella in soils of Western Australia and South Africa. Appl Environ Microbiol 2005; 71: 7041– 7052 [CrossRef] [PubMed]
    [Google Scholar]
  11. Stepkowski T, Hughes CE, Law IJ, Markiewicz Ł, Gurda D et al. Diversification of lupine Bradyrhizobium strains: evidence from nodulation gene trees. Appl Environ Microbiol 2007; 73: 3254– 3264 [CrossRef] [PubMed]
    [Google Scholar]
  12. Vinuesa P, Rojas-Jiménez K, Contreras-Moreira B, Mahna SK, Prasad BN et al. Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent. Appl Environ Microbiol 2008; 74: 6987– 6996 [CrossRef] [PubMed]
    [Google Scholar]
  13. Rivas R, Martens M, de Lajudie P, Willems A. Multilocus sequence analysis of the genus Bradyrhizobium. Syst Appl Microbiol 2009; 32: 101– 110 [CrossRef] [PubMed]
    [Google Scholar]
  14. Martens M, Delaere M, Coopman R, de Vos P, Gillis M et al. Multilocus sequence analysis of Ensifer and related taxa. Int J Syst Evol Microbiol 2007; 57: 489– 503 [CrossRef] [PubMed]
    [Google Scholar]
  15. Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA et al. CLUSTAL W and CLUSTAL X version 2.0. Bioinformatics 2007; 23: 2947– 2948 [CrossRef] [PubMed]
    [Google Scholar]
  16. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32: 1792– 1797 [CrossRef] [PubMed]
    [Google Scholar]
  17. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28: 2731– 2739 [CrossRef] [PubMed]
    [Google Scholar]
  18. Posada D, Crandall KA. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998; 14: 817– 818 [CrossRef] [PubMed]
    [Google Scholar]
  19. Schwarz G. Estimating the dimension of a model. The Annals of Statistics 1978; 6: 461– 464 [CrossRef]
    [Google Scholar]
  20. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  21. van Berkum P, Fuhrmann JJ. Evolutionary relationships among the soybean bradyrhizobia reconstructed from 16S rRNA gene and internally transcribed spacer region sequence divergence. Int J Syst Evol Microbiol 2000; 50: 2165– 2172 [CrossRef] [PubMed]
    [Google Scholar]
  22. Durán D, Rey L, Mayo J, Zúñiga-Dávila D, Imperial J et al. Bradyrhizobium paxllaeri sp. nov. and Bradyrhizobium icense sp. nov., nitrogen-fixing rhizobial symbionts of Lima bean (Phaseolus lunatus L.) in Peru. Int J Syst Evol Microbiol 2014; 64: 2072– 2078 [CrossRef] [PubMed]
    [Google Scholar]
  23. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33: 152– 155
    [Google Scholar]
  24. Willems A, Doignon-Bourcier F, Goris J, Coopman R, de Lajudie P et al. DNA–DNA hybridization study of Bradyrhizobium strains. Int J Syst Evol Microbiol 2001; 51: 1315– 1322 [CrossRef] [PubMed]
    [Google Scholar]
  25. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64: 346– 351 [CrossRef] [PubMed]
    [Google Scholar]
  26. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015; 31: 587– 589 [CrossRef] [PubMed]
    [Google Scholar]
  27. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32: 929– 931 [CrossRef] [PubMed]
    [Google Scholar]
  28. Tighe SW, de Lajudie P, Dipietro K, Lindström K, Nick G et al. Analysis of cellular fatty acids and phenotypic relationships of Agrobacterium, Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium species using the sherlock microbial identification system. Int J Syst Evol Microbiol 2000; 50: 787– 801 [CrossRef] [PubMed]
    [Google Scholar]
  29. Delamuta JR, Ribeiro RA, Ormeño-Orrillo E, Parma MM, Melo IS et al. Bradyrhizobium tropiciagri sp. nov. and Bradyrhizobium embrapense sp. nov., nitrogen-fixing symbionts of tropical forage legumes. Int J Syst Evol Microbiol 2015; 65: 4424– 4433 [CrossRef] [PubMed]
    [Google Scholar]
  30. Sarita S, Sharma PK, Priefer UB, Prell J. Direct amplification of rhizobial nodC sequences from soil total DNA and comparison to nodC diversity of root nodule isolates. FEMS Microbiol Ecol 2005; 54: 1– 11 [CrossRef] [PubMed]
    [Google Scholar]
  31. Poly F, Monrozier LJ, Bally R. Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Res Microbiol 2001; 152: 95– 103 [CrossRef] [PubMed]
    [Google Scholar]
  32. Grönemeyer JL, Chimwamurombe P, Reinhold-Hurek B. Bradyrhizobium subterraneum sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of groundnuts. Int J Syst Evol Microbiol 2015; 65: 3241– 3247 [CrossRef] [PubMed]
    [Google Scholar]
  33. Grönemeyer JL, Hurek T, Bünger W, Reinhold-Hurek B. Bradyrhizobium vignae sp. nov., a nitrogen-fixing symbiont isolated from effective nodules of Vigna and Arachis. Int J Syst Evol Microbiol 2016; 66: 62– 69 [CrossRef] [PubMed]
    [Google Scholar]
  34. Lasse Grönemeyer J, Hurek T, Reinhold-Hurek B. Bradyrhizobium kavangense sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of traditional Namibian pulses. Int J Syst Evol Microbiol 2015; 65: 4886– 4894 [CrossRef] [PubMed]
    [Google Scholar]
  35. Vincent JM. A Manual for the Practical Study of the Root Nodule Bacteria Oxford, UK: Blackwell Scientific Publications, Ltd; 1970
    [Google Scholar]
  36. Gao JL, Sun JG, Li Y, Wang ET, Chen WX. Numerical taxonomy and DNA relatedness of tropical rhizobia isolated from Hainan province, China. Int J Syst Bacteriol 1994; 44: 151– 158 [CrossRef]
    [Google Scholar]
  37. Gordon SA, Weber RP. Colorimetric estimation of indoleacetic acid. Plant Physiol 1951; 26: 192– 195 [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002039
Loading
/content/journal/ijsem/10.1099/ijsem.0.002039
Loading

Data & Media loading...

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error