1887
  1. Home
  2. Publications
  3. International Journal of Systematic and Evolutionary Microbiology
  4. Volume 66, Issue 1
  5. Article

f sp. nov., a nitrogen-fixing symbiont isolated from effective nodules of and

PDF
523.79 Kb
HTML
59.33 Kb
  • Cover date:
Preview this:
Free Preview thumbnail Magnify
Zoom in
Zoomout

sp. nov., a nitrogen-fixing symbiont isolated from effective nodules of and , Page 1 of 1

| /docserver/preview/fulltext/ijsem/66/1/62_ijsem000674-1.gif

  • Twenty one strains of symbiotic bacteria from root nodules of local races of cowpea (), Bambara groundnut () and peanuts () grown on subsistence farmers' fields in the Kavango region of Namibia, were previously characterized as a novel group within the genus . To verify their taxonomic position, the strains were further analysed using a polyphasic approach. 16S rRNA gene sequences were most similar to BR 3351, with RITF806 being the most closely related type strain in the phylogenetic analysis, and CCBAU 10071 in the ITS sequence analysis. Phylogenetic analysis of concatenated placed the strains in a highly supported lineage distinct from species of the genus with validly published names; they were most closely related to 58 2-1. The status of the species was validated by results of DNA–DNA hybridization. The combination of phenotypic characteristics from several tests, including carbon source utilization and antibiotic resistance, could be used to differentiate representative strains of species of the genus with validly published names. Novel strain 7-2 induced effective nodules on and on The DNA G+C content of strain 7-2 was 65.4 mol% (Tm). Based on the data presented, we conclude that these strains represent a novel species for which the name sp. nov. is proposed, with strain 7-2 [LMG 28791, DSMZ 100297, NTCCM0018 (Windhoek)] as the type strain.

  • The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain 7-2 is KP899563. The GenBank/EMBL/DDBJ accession numbers for the ITS, I, , , , and sequences of strain 7-2 are KM378504, KM378443, KM378374, KM378308, KR259951, KM378251 and KT362339, respectively.

  • Three supplementary figures and three supplementary tables are available with the online Supplementary Material.

  • Abbreviations:
    ITS intergenic spacer
    MLSA multilocus sequence analysis.

© 2015 IUMS | Published by the Microbiology Society

  • Burbano C. S., Liu Y., Rösner K. L., Reis V. M., Caballero-Mellado J., Reinhold-Hurek B., Hurek T.. ( 2011;). Predominant nifH transcript phylotypes related to Rhizobium rosettiformans in field-grown sugarcane plants and in Norway spruce. Environ Microbiol Rep 3: 383––389 [CrossRef] [PubMed].
     [Google Scholar]
  • Edgar R. C.. ( 2004;). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792––1797 [CrossRef] [PubMed].
     [Google Scholar]
  • Felsenstein F.. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783––791 [CrossRef].
     [Google Scholar]
  • Gao J. L., Sun J. G., Li Y., Wang E. T., Chen W. X.. ( 1994;). Numerical taxonomy and DNA relatedness of tropical rhizobia isolated from Hainan province, China. Int J Syst Evol Microbiol 44: 151––158.
     [Google Scholar]
  • Grönemeyer J. L., Burbano C. S., Hurek T., Reinhold-Hurek B.. ( 2012;). Isolation and characterization of root-associated bacteria from agricultural crops in the Kavango region of Namibia. Plant Soil 356: 67––82 [CrossRef].
     [Google Scholar]
  • Grönemeyer J., Berkelmann D., Mubyana-John T., Haiyambo D., Chimwamurombe P., Kasaona B., Hurek T., Reinhold-Hurek B.. ( 2013;). A survey for plant-growth-promoting rhizobacteria and symbionts associated with crop plants in the Okavango region or Southern Africa. Biodiv Ecol 5: 287––294 [CrossRef].
     [Google Scholar]
  • Grönemeyer J. L., Kulkarni A., Berkelmann D., Hurek T., Reinhold-Hurek B.. ( 2014;). Rhizobia indigenous to the Okavango region in Sub-Saharan Africa: diversity, adaptations, and host specificity. Appl Environ Microbiol 80: 7244––7257 [CrossRef] [PubMed].
     [Google Scholar]
  • Grönemeyer J. L., Chimwamurombe P., Reinhold-Hurek B.. ( 2015;). Bradyrhyzobium subterraneum sp. nov., a symbiotic nitrogen-fixing bacterium from root nodules of groundnuts. Int J Syst Evol Microbiol 65: 3241––3247 [CrossRef].
     [Google Scholar]
  • Kuykendall L. D., Roy M. A., O'Neill J. J., Devine T. E.. ( 1988;). Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 38: 358––361 [CrossRef].
     [Google Scholar]
  • Laguerre G., Mavingui P., Allard M. R., Charnay M. P., Louvrier P., Mazurier S. I., Rigottier-Gois L., Amarger N.. ( 1996;). 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 62: 2029––2036 [PubMed].
     [Google Scholar]
  • Larkin M. A., Blackshields G., Brown N. P., Chenna R., McGettigan P. A., McWilliam H., Valentin F., Wallace I. M., Wilm A., other authors. ( 2007;). clustal w clustal x version 2.0. Bioinformatics 23: 2947––2948 [CrossRef] [PubMed].
     [Google Scholar]
  • Lu J. K., Dou Y. J., Zhu Y. J., Wang S. K., Sui X. H., Kang L. H.. ( 2014;). Bradyrhizobium ganzhouense sp. nov., an effective symbiotic bacterium isolated from Acacia melanoxylon R. Br. nodules. Int J Syst Evol Microbiol 64: 1900––1905 [CrossRef] [PubMed].
     [Google Scholar]
  • Miller L. T.. ( 1982;). Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16: 584––586 [PubMed].
     [Google Scholar]
  • Posada D., Crandall K. A.. ( 1998;). MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817––818 [CrossRef] [PubMed].
     [Google Scholar]
  • Pröpper M., Gröngröft A., Falk T., Eschenbach A., Fox T., Gessner U., Hecht J., Hinz M. O., Hoettich C., other authors. ( 2010;). Causes and perspectives of land-cover change through expanding cultivation in Kavango. . In Biodiversity in Southern Africa 3: Implications for Landuse and Management, pp. 2––31. Edited by Jürgens N., Schmiedel U., Hoffman T.. Göttingen, Windhoek: Klaus Hess;.
     [Google Scholar]
  • Rivas R., Martens M., de Lajudie P., Willems A.. ( 2009;). Multilocus sequence analysis of the genus Bradyrhizobium. Syst Appl Microbiol 32: 101––110 [CrossRef] [PubMed].
     [Google Scholar]
  • Sarita S., Sharma P. K., Priefer U. B., Prell J.. ( 2005;). Direct amplification of rhizobial nodC sequences from soil total DNA and comparison to nodC diversity of root nodule isolates. FEMS Microbiol Ecol 54: 1––11 [CrossRef] [PubMed].
     [Google Scholar]
  • Schwarz G.. ( 1978;). Estimating the dimension of a model. Ann Stat 6: 461––464 [CrossRef].
     [Google Scholar]
  • Sene G., Thiao M., Samba-Mbaye R., Khasa D., Kane A., Mbaye M. S., Beaulieu M.-E., Manga A., Sylla S. N.. ( 2013;). The abundance and diversity of legume-nodulating rhizobia in 28-year-old plantations of tropical, subtropical, and exotic tree species: a case study from the Forest Reserve of Bandia, Senegal. Microb Ecol 65: 128––144 [CrossRef] [PubMed].
     [Google Scholar]
  • Stackebrandt E., Ebers J.. ( 2006;). Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33: 152––155.
     [Google Scholar]
  • Stepkowski T., Moulin L., Krzyzańska A., McInnes A., Law I. J., Howieson J.. ( 2005;). European origin of Bradyrhizobium populations infecting lupins and serradella in soils of Western Australia and South Africa. Appl Environ Microbiol 71: 7041––7052 [CrossRef] [PubMed].
     [Google Scholar]
  • Stepkowski T., Hughes C. E., Law I. J., Markiewicz Ł., Gurda D., Chlebicka A., Moulin L.. ( 2007;). Diversification of lupine Bradyrhizobium strains: evidence from nodulation gene trees. Appl Environ Microbiol 73: 3254––3264 [CrossRef] [PubMed].
     [Google Scholar]
  • Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731––2739 [CrossRef] [PubMed].
     [Google Scholar]
  • van Berkum P.. ( 1990;). Evidence for a third uptake hydrogenase phenotype among the soybean Bradyrhizobia. Appl Environ Microbiol 56: 3835––3841 [PubMed].
     [Google Scholar]
  • Vincent J. M.. ( 1970;). A Manual for the Practical Study of the Root Nodule Bacteria Oxford, UK: Blackwell Scientific Publications, Ltd;.
     [Google Scholar]
  • Vinuesa P., Silva C., Werner D., Martínez-Romero E.. ( 2005;). Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation. Mol Phylogenet Evol 34: 29––54 [CrossRef] [PubMed].
     [Google Scholar]
  • Vinuesa P., Rojas-Jiménez K., Contreras-Moreira B., Mahna S. K., Prasad B. N., Moe H., Selvaraju S. B., Thierfelder H., Werner D.. ( 2008;). 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 74: 6987––6996 [CrossRef] [PubMed].
     [Google Scholar]
  • Wade T. K., Le Quéré A., Laguerre G., N'zoué A., Ndione J.-A., Dorego F., Sadio O., Ndoye I., Neyra M.. ( 2014;). Eco-geographical diversity of cowpea bradyrhizobia in Senegal is marked by dominance of two genetic types. Syst Appl Microbiol 37: 129––139 [CrossRef] [PubMed].
     [Google Scholar]
  • Willems A., Doignon-Bourcier F., Goris J., Coopman R., de Lajudie P., De Vos P., Gillis M.. ( 2001;). DNA-DNA hybridization study of Bradyrhizobium strains. Int J Syst Evol Microbiol 51: 1315––1322 [CrossRef] [PubMed].
     [Google Scholar]
  • Willems A., Munive A., de Lajudie P., Gillis M.. ( 2003;). In most Bradyrhizobium groups sequence comparison of 16S-23S rDNA internal transcribed spacer regions corroborates DNA-DNA hybridizations. Syst Appl Microbiol 26: 203––210 [CrossRef] [PubMed].
     [Google Scholar]
http://sgm.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.000674
Loading

Supplementary Data

 Data loading....

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.000674
2016-01-01
2019-02-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/1/62.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.000674&mimeType=html&fmt=ahah

Author and Article Information

 Figure data loading....

Footnotes:

Validated antibodies in this article

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error