1887

Abstract

A considerable number of species of the possess multiple copies of the 16S rRNA gene that exhibit more than 5 % divergence, complicating phylogenetic interpretations. Two additional problems have been pointed out: (i) the genera and show a very close relationship, with some species being shown to overlap in phylogenetic trees reconstructed by the neighbour-joining method, and (ii) alkaliphilic and neutrophilic species of the genus form definitely separate clusters in neighbour-joining trees, suggesting that these two clusters could be separated into two genera. In an attempt to solve these problems, the RNA polymerase B′ subunit has been used as an additional target molecule for phylogenetic analysis, using partial sequences of 1305 bp. In this work, a primer set was designed that consistently amplified the full-length RNA polymerase B′ subunit gene (′) (1827–1842 bp) from 85 strains in 27 genera of the . Differences in sequence length were found within the first 15 to 31 nt, and their downstream sequences (1812 bp) were aligned unambiguously without any gaps or deletions. Phylogenetic trees reconstructed from nucleotide sequences and deduced amino acid sequences by the maximum-likelihood method demonstrated that multiple species/strains in most genera individually formed cohesive clusters. Two discrepancies were observed: (i) the two species of were placed in definitely different positions, in that was placed in the / cluster, while was closely related to , and (ii) was segregated from the three other species in the protein tree, while all four species formed a cluster in the gene tree, although supported by a bootstrap value of less than 50 %. The six species/strains and the five species of formed a large cluster in both trees, with and located in the cluster in the protein tree and in the gene tree. broke into the cluster of the genus , instead of the / cluster, in the gene tree. The six species formed a tight cluster with two subclusters, of neutrophilic species and alkaliphilic species, in both trees. Overall, our data strongly suggest that (i) is a member of /, (ii) might represent a new genus and (iii) the two genera and might constitute a single genus. As more and more novel species and genera are proposed in the family , the full sequence of the ′ gene may provide a supplementary tool for determining the phylogenetic position of new isolates.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.017160-0
2010-10-01
2019-09-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/60/10/2398.html?itemId=/content/journal/ijsem/10.1099/ijs.0.017160-0&mimeType=html&fmt=ahah

References

  1. Acinas, S. G., Marcelino, A. L., Klepac-Ceraj, V. & Polz, F. M. ( 2004; ). Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186, 2629–2635.[CrossRef]
    [Google Scholar]
  2. Adékambi, T., Colson, P. & Drancourt, M. ( 2003; ). rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J Clin Microbiol 41, 5699–5708.[CrossRef]
    [Google Scholar]
  3. Adékambi, T., Shinnick, T. M., Raoult, D. & Drancourt, M. ( 2008; ). Complete rpoB gene sequencing as a suitable supplement to DNA–DNA hybridization for bacterial species and genus delineation. Int J Syst Evol Microbiol 58, 1807–1814.[CrossRef]
    [Google Scholar]
  4. Boucher, Y., Douady, C. J., Sharma, A. K., Kamekura, M. & Doolittle, W. F. ( 2004; ). Intragenomic heterogeneity and intergenomic recombination among haloarchaeal ribosomal RNA genes. J Bacteriol 186, 3980–3990.[CrossRef]
    [Google Scholar]
  5. Case, R. J., Boucher, Y., Dahllöf, I., Holmström, C., Doolittle, W. F. & Kjelleberg, S. ( 2007; ). Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73, 278–288.[CrossRef]
    [Google Scholar]
  6. Cilia, V., Lafay, B. & Christen, R. ( 1996; ). Sequence heterogeneities among 16S ribosomal RNA sequences, and their effect on phylogenetic analyses at the species level. Mol Biol Evol 13, 451–461.[CrossRef]
    [Google Scholar]
  7. Cui, H.-L., Zhou, P.-J., Oren, A. & Liu, S.-J. ( 2009; ). Intraspecific polymorphism of 16S rRNA genes in two halophilic archaeal genera, Haloarcula and Halomicrobium. Extremophiles 13, 31–37.[CrossRef]
    [Google Scholar]
  8. Dahllöf, I., Baillie, H. & Kjelleberg, S. ( 2000; ). rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66, 3376–3380.[CrossRef]
    [Google Scholar]
  9. Enache, M., Itoh, T., Fukushima, T., Usami, R., Dumitru, L. & Kamekura, M. ( 2007; ). Phylogenetic relationships within the family Halobacteriaceae inferred from rpoB′ gene and protein sequences. Int J Syst Evol Microbiol 57, 2289–2295.[CrossRef]
    [Google Scholar]
  10. Fukushima, T., Usami, R. & Kamekura, M. ( 2007; ). A traditional Japanese-style salt field is a niche for haloarchaeal strains that can survive in 0.5 % salt solution. Saline Syst 3, 2.[CrossRef]
    [Google Scholar]
  11. Grant, W. D., Kamekura, M., McGenity, T. J. & Ventosa, A. ( 2001; ). Class III. Halobacteria class. nov. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1, pp. 294–334. Edited by Boone, D. R., Castenholz, R. W. & Garrity, G. M.. New York. : Springer.
    [Google Scholar]
  12. Itoh, T., Yamaguchi, T., Zhou, P. & Takashina, T. ( 2005; ). Natronolimnobius baerhuensis gen. nov., sp. nov. and Natronolimnobius innermongolicus sp. nov., novel haloalkaliphilic archaea isolated from soda lakes in Inner Mongolia, China. Extremophiles 9, 111–116.[CrossRef]
    [Google Scholar]
  13. Korczak, B., Christensen, H., Elmer, S., Frey, J. & Kuhnert, P. ( 2004; ). Phylogeny of the family Pasteurellaceae based on rpoB sequences. Int J Syst Evol Microbiol 54, 1393–1399.[CrossRef]
    [Google Scholar]
  14. 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 and clustal_x version 2.0. Bioinformatics 23, 2947–2948.[CrossRef]
    [Google Scholar]
  15. Leffers, H., Gropp, F., Lottspeich, F., Zillig, W. & Garret, R. A. ( 1989; ). Sequence, organization, transcription and evolution of RNA polymerase subunit genes from the archaebacterial extreme halophiles Halobacterium halobium and Halococcus morrhuae. J Mol Biol 206, 1–17.[CrossRef]
    [Google Scholar]
  16. McGenity, T. J., Gemmell, R. T. & Grant, W. D. ( 1998; ). Proposal of a new halobacterial genus Natrinema gen. nov., with two species Natrinema pellirubrum nom. nov. and Natrinema pallidum nom. nov. Int J Syst Bacteriol 48, 1187–1196.[CrossRef]
    [Google Scholar]
  17. Minegishi, H., Mizuki, T., Echigo, A., Fukushima, T., Kamekura, M. & Usami, R. ( 2008; ). Acidophilic haloarchaeal strains are isolated from various solar salts. Saline Syst 4, 16.[CrossRef]
    [Google Scholar]
  18. Mylvaganam, S. & Dennis, P. P. ( 1992; ). Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130, 399–410.
    [Google Scholar]
  19. Romano, I., Poli, A., Finore, I., Huertas, F. J., Gambacorta, A., Pelliccione, S., Nicolaus, G., Lama, L. & Nicolaus, B. ( 2007; ). Haloterrigena hispanica sp. nov., an extremely halophilic archaeon from Fuente de Piedra, southern Spain. Int J Syst Evol Microbiol 57, 1499–1503.[CrossRef]
    [Google Scholar]
  20. Ross, H. N. M. & Grant, W. D. ( 1985; ). Nucleic acid studies on halophilic archaebacteria. J Gen Microbiol 131, 165–173.
    [Google Scholar]
  21. Savage, K. N., Krumholz, L. R., Oren, A. & Elshahed, M. S. ( 2007; ). Haladaptatus paucihalophilus gen. nov., sp. nov., a halophilic archaeon isolated from a low-salt, sulfide-rich spring. Int J Syst Evol Microbiol 57, 19–24.[CrossRef]
    [Google Scholar]
  22. Savage, K. N., Krumholz, L. R., Oren, A. & Elshahed, M. S. ( 2008; ). Halosarcina pallida gen. nov., sp. nov., a halophilic archaeon from a low-salt, sulfide-rich spring. Int J Syst Evol Microbiol 58, 856–860.[CrossRef]
    [Google Scholar]
  23. Schmidt, H. A., Strimmer, K., Vingron, M. & von Haeseler, A. ( 2002; ). tree-puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502–504.[CrossRef]
    [Google Scholar]
  24. Shimodaira, H. ( 2002; ). An approximately unbiased test of phylogenetic tree selection. Syst Biol 51, 492–508.[CrossRef]
    [Google Scholar]
  25. Shimodaira, H. & Hasegawa, M. ( 2001; ). consel: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17, 1246–1247.[CrossRef]
    [Google Scholar]
  26. Stamatakis, A., Ludwig, T. & Meier, H. ( 2005; ). RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21, 456–463.[CrossRef]
    [Google Scholar]
  27. Tindall, B. J. ( 2003; ). Taxonomic problems arising in the genera Haloterrigena and Natrinema. Int J Syst Evol Microbiol 53, 1697–1698.[CrossRef]
    [Google Scholar]
  28. Ventosa, A., Gutiérrez, M. C., Kamekura, M. & Dyall-Smith, M. L. ( 1999; ). Proposal to transfer Halococcus turkmenicus, Halobacterium trapanicum JCM 9743 and strain GSL-11 to Haloterrigena turkmenica gen. nov., comb. nov. Int J Syst Bacteriol 49, 131–136.[CrossRef]
    [Google Scholar]
  29. Walsh, D. A., Bapteste, E., Kamekura, M. & Doolittle, W. F. ( 2004; ). Evolution of the RNA polymerase B′ subunit gene (rpoB′) in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol Biol Evol 21, 2340–2351.[CrossRef]
    [Google Scholar]
  30. Wright, A.-D. G. ( 2006; ). Phylogenetic relationships within the order Halobacteriales inferred from 16S rRNA gene sequences. Int J Syst Evol Microbiol 56, 1223–1227.[CrossRef]
    [Google Scholar]
  31. Xin, H., Itoh, T., Zhou, P., Suzuki, K., Kamekura, M. & Nakase, T. ( 2000; ). Natrinema versiforme sp. nov., an extremely halophilic archaeon from Aibi salt lake, Xinjiang, China. Int J Syst Evol Microbiol 50, 1297–1303.[CrossRef]
    [Google Scholar]
  32. Xu, Y., Wang, W., Xue, Y., Zhou, R., Ma, Y., Ventosa, A. & Grant, W. D. ( 2001; ). Natrialba hulunbeirensis sp. nov. and Natrialba chahannaoensis sp. nov., novel haloalkaliphilic archaea from soda lakes in Inner Mongolia Autonomous Region, China. Int J Syst Evol Microbiol 51, 1693–1698.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.017160-0
Loading
/content/journal/ijsem/10.1099/ijs.0.017160-0
Loading

Data & Media loading...

vol. , part 10, pp. 2398 - 2408

Strains used in this study and accession numbers of 16S rRNA and ′ gene sequences.

Pairwise similarities of ′ gene sequences amongst the type species of 26 genera of the .

Alternative subtrees used in the analyses of Table 1 (tree 5).

Optimal ML tree inferred from 16S rRNA gene sequences for the family .

NJ tree inferred from 16S rRNA gene sequences for the family from the same dataset used in Supplementary Fig. S2.

[PDF file of Supplementary Tables and Figures](163 KB)



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