1887

Abstract

To analyse determinants of biogeographic structure in members of the genus , isolates were obtained from 41 legume genera, originating from North American sites spanning 48.5 ° of latitude (Alaska to Panama). Sequencing of portions of six gene loci (3674 bp) in 203 isolates showed that there was only a weak trend towards higher nucleotide diversity in tropical regions. Phylogenetic relationships for , in the symbiosis island region of the chromosome, conflicted substantially with a tree inferred for five housekeeping gene loci. For both and housekeeping gene trees, bacteria from each region were significantly more similar, on average, than would be expected if the source location was permuted at random on the tree. Within-region permutation tests also showed that bacteria clustered significantly on particular host plant clades at all levels in the phylogeny of legumes (from genus up to subfamily). Nevertheless, some bacterial groups were dispersed across multiple regions and were associated with diverse legume host lineages. These results indicate that migration, horizontal gene transfer and host interactions have all influenced the geographical divergence of populations on a continental scale.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.059238-0
2012-08-01
2020-01-25
Loading full text...

Full text loading...

/deliver/fulltext/micro/158/8/2050.html?itemId=/content/journal/micro/10.1099/mic.0.059238-0&mimeType=html&fmt=ahah

References

  1. Ardley J. K., Parker M. A., De Meyer S. E., Trengove R. D., O'Hara G. W., Reeve W. G., Yates R. J., Dilworth M. J., Willems A., Howieson J. G.. ( 2011;). Microvirga lupini sp. nov., Microvirga lotononidis sp. nov., and Microvirga zambiensis sp. nov. are Alphaproteobacterial root nodule bacteria that specifically nodulate and fix nitrogen with geographically and taxonomically separate legume hosts. Int J Syst Evol Microbiol [CrossRef][PubMed]
    [Google Scholar]
  2. Benjamini Y., Krieger A. M., Yekutieli D.. ( 2006;). Adaptive linear step-up procedures that control the false discovery rate. Biometrika93:491–507[CrossRef]
    [Google Scholar]
  3. Giraud E., Moulin L., Vallenet D., Barbe V., Cytryn E., Avarre J.-C., Jaubert M., Simon D., Cartieaux F.. & other authors ( 2007;). Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science316:1307–1312[PubMed][CrossRef]
    [Google Scholar]
  4. Graham A.. ( 1987;). Tropical American tertiary floras and paleoenvironments: Mexico, Costa Rica, and Panama. Am J Bot74:1519–1531[CrossRef]
    [Google Scholar]
  5. Gyaneshwar P., Hirsch A. M., Moulin L., Chen W.-M., Elliott G. N., Bontemps C., Estrada-de Los Santos P., Gross E., Dos Reis F. B.. & other authors ( 2011;). Legume-nodulating betaproteobacteria: diversity, host range, and future prospects. Mol Plant Microbe Interact24:1276–1288[PubMed][CrossRef]
    [Google Scholar]
  6. Huson D. H., Bryant D.. ( 2006;). Application of phylogenetic networks in evolutionary studies. Mol Biol Evol23:254–267[PubMed][CrossRef]
    [Google Scholar]
  7. Jombart T., Balloux F., Dray S.. ( 2010;). Adephylo: new tools for investigating the phylogenetic signal in biological traits. Bioinformatics26:1907–1909[PubMed][CrossRef]
    [Google Scholar]
  8. Kajita T., Ohashi H., Tateishi Y., Bailey C. D., Doyle J. J.. ( 2001;). rbcL and legume phylogeny, with particular reference to Phaseoleae, Millettieae, and allies. Syst Bot26:515–536
    [Google Scholar]
  9. Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S., Watanabe A., Idesawa K., Iriguchi M.. & other authors ( 2002;). Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res9:189–197[PubMed][CrossRef]
    [Google Scholar]
  10. Lewis G., Schrire B., Mackinder B., Lock M.. ( 2005;). Legumes of the world Kew, UK: Royal Botanic Gardens;
    [Google Scholar]
  11. Librado P., Rozas J.. ( 2009;). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics25:1451–1452[PubMed][CrossRef]
    [Google Scholar]
  12. Moulin L. G., Béna G., Boivin-Masson C., Stepkowski T.. ( 2004;). Phylogenetic analyses of symbiotic nodulation genes support vertical and lateral gene co-transfer within the Bradyrhizobium genus. Mol Phylogenet Evol30:720–732[PubMed][CrossRef]
    [Google Scholar]
  13. Nzoué A., Miché L., Klonowska A., Laguerre G., de Lajudie P., Moulin L.. ( 2009;). Multilocus sequence analysis of bradyrhizobia isolated from Aeschynomene species in Senegal. Syst Appl Microbiol32:400–412[PubMed][CrossRef]
    [Google Scholar]
  14. Parker M. A.. ( 1999;). Relationships of bradyrhizobia from the legumes Apios americana and Desmodium glutinosum . Appl Environ Microbiol65:4914–4920[PubMed]
    [Google Scholar]
  15. Parker M. A.. ( 2002;). Bradyrhizobia from wild Phaseolus, Desmodium, and Macroptilium species in northern Mexico. Appl Environ Microbiol68:2044–2048[PubMed][CrossRef]
    [Google Scholar]
  16. Parker M. A.. ( 2003;). Genetic markers for analysing symbiotic relationships and lateral gene transfer in Neotropical bradyrhizobia. Mol Ecol12:2447–2455[PubMed][CrossRef]
    [Google Scholar]
  17. Parker M. A.. ( 2004;). rRNA and dnaK relationships of Bradyrhizobium sp. nodule bacteria from four papilionoid legume trees in Costa Rica. Syst Appl Microbiol27:334–342[PubMed][CrossRef]
    [Google Scholar]
  18. Parker M. A.. ( 2008;). Symbiotic relationships of legumes and nodule bacteria on Barro Colorado Island, Panama: a review. Microb Ecol55:662–672[PubMed][CrossRef]
    [Google Scholar]
  19. Parker M. A.. ( 2012;). Legumes select symbiosis island sequence variants in Bradyrhizobium . Mol Ecol21:1769–1778 [CrossRef][PubMed]
    [Google Scholar]
  20. Parker M. A., Lafay B., Burdon J. J., van Berkum P.. ( 2002;). Conflicting phylogeographic patterns in rRNA and nifD indicate regionally restricted gene transfer in Bradyrhizobium . Microbiology148:2557–2565[PubMed]
    [Google Scholar]
  21. Ramírez-Bahena M. H., Peix A., Rivas R., Camacho M., Rodríguez-Navarro D. N., Mateos P. F., Martínez-Molina E., Willems A., Velázquez E.. ( 2009;). Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus . Int J Syst Evol Microbiol59:1929–1934[PubMed][CrossRef]
    [Google Scholar]
  22. Rivas R., Martens M., de Lajudie P., Willems A.. ( 2009;). Multilocus sequence analysis of the genus Bradyrhizobium . Syst Appl Microbiol32:101–110[PubMed][CrossRef]
    [Google Scholar]
  23. Ronquist F., Huelsenbeck J. P.. ( 2003;). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics19:1572–1574[PubMed][CrossRef]
    [Google Scholar]
  24. Sachs J. L., Kembel S. W., Lau A. H., Simms E. L.. ( 2009;). In situ phylogenetic structure and diversity of wild Bradyrhizobium communities. Appl Environ Microbiol75:4727–4735[PubMed][CrossRef]
    [Google Scholar]
  25. Stepkowski T., Hughes C. E., Law I. J., Markiewicz L., Gurda D., Chlebicka A., Moulin L.. ( 2007;). Diversification of lupine Bradyrhizobium strains: evidence from nodulation gene trees. Appl Environ Microbiol73:3254–3264[PubMed][CrossRef]
    [Google Scholar]
  26. Stepkowski T., Watkin E., McInnes A., Gurda D., Gracz J., Steenkamp E. T.. ( 2012;). Distinct Bradyrhizbium communities nodulate legumes native to temperate and tropical monsoon Australia. Mol Phylogenet Evol63:265–277 [CrossRef][PubMed]
    [Google Scholar]
  27. 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 Evol34:29–54[PubMed][CrossRef]
    [Google Scholar]
  28. 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 Microbiol74:6987–6996[PubMed][CrossRef]
    [Google Scholar]
  29. Webb C. O., Ackerly D. D., Kembel S. W.. ( 2008;). Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics24:2098–2100[PubMed][CrossRef]
    [Google Scholar]
  30. Willems A.. ( 2006;). The taxonomy of rhizobia: an overview. Plant Soil287:3–14[CrossRef]
    [Google Scholar]
  31. Wojciechowski M. F., Lavin M., Sanderson M. J.. ( 2004;). A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family. Am J Bot91:1846–1862[PubMed][CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.059238-0
Loading
/content/journal/micro/10.1099/mic.0.059238-0
Loading

Data & Media loading...

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