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Ribosomal sequences of Candidatus Glomeribacter gigasporarum and phylogenetic relationships

Arbuscular mycorrhizal fungi are obligate endosymbionts that colonise the roots of almost 80% of land plants. We describe morphological and molecular data of a bacterial endosymbiont living in the cytoplasm of dormant or germinating spores and symbiotic mycelia of the fungal species Gigaspora margarita, Gi. decipiens, Scutellospora persica, and S. castanea.

PCR-amplification of the near entire 16S ribosomal RNA gene, of a portion of the 23S rDNA and of 16S-23S rDNA spacer region of the Gi. margarita BEG 34 endosymbiont using universal bacterial primers, and subsequent sequence analysis (16S rDNA GenBank accession no. X89727, 23S rDNA accession no. AJ561042) demonstrated that this organism occupied a very distinct phylogenetic position within the beta subdivision of the Proteobacteria with the genera Burkholderia, Pandoraea, and Ralstonia as closest neighbours. The design of primers specific to the 16S rDNA (BLOf-BLOr) and the 23S rDNA (GlomGIGf-GlomGIGr) endosymbiotic bacteria of BEG 34 allowed amplification of spore DNA from endosymbionts of Gi. margarita, Gi. decipiens, S. persica, and S. castanea, but not from the Gi. gigantea endosymbiont (which was morphologically different) or from the cytoplasm of Gi. rosea (which did not contain endosymbiotic bacteria). These specific primers were successfully used as probe for the in situ hybridisation of endobacteria in Gi. margarita spores.

The overall rod-shaped morphology of the Gi. margarita, Gi. decipiens, S. persica, and S. castanea endosymbionts was similar, and amplification and sequence analysis of the near complete 16S rDNA genes of several Gi. margarita, S. persica, and S. castanea endosymbionts revealed over 98% sequence similarity. These morphological and genomic characteristics were used to assign the endosymbionts of these three species (five isolates) of arbuscular mycorrhizal fungi as ‘Candidatus Glomeribacter gigasporarum’.

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