16S Ribosomal DNA Sequence Analysis Confirms the Close Relationship between the Genera Xanthobacter, Azorhizobium, and Aquabacter and Reveals a Lack of Phylogenetic Coherence among Xanthobacter Species

Abstract

A comparative 16s ribosomal DNA (rDNA) sequence analysis was used to investigate the phylogenetic position of members of the genus Xunthobacter. We determined 16s rDNA sequence data for the type strains of the three Xunthobucter species and five additional Xunthobucter strains. The close relationship between the genera Xanthobacter, Azorhizobiurn, and Aquabucter previously demonstrated by DNA-rRNA hybridization studies was confirmed. The results of our phylogenetic analysis indicate that members of the genera Xunthobucter, Azorhizobiurn, and Aquabucter are intermixed and that there is no clear generic cluster consisting of the Xunthobucter species. A comparison of the Xunthobucter sequences with the 16s rDNA sequences available from environmental clone studies indicated that members of this genus have not been detected by nonculturing approaches.Phylogenetic analysis based on comparisons of 16s ribosomal DNA (rDNA) sequence data is now routinely used in the determination of taxonomic relationships between microorganisms and in the design of taxon-specific probes for use in microbial identification and molecular ecology studies (1,10,15,21).One genus for which no full 16s rDNA sequence data are currently available is the genus Xanthobacter. The genus Xanthobacter consists of three species, Xanthobacter agilis (5), Xanthobacter autotrophicus (23), and Xanthobacter jlavus (6,12,17). These organisms are gram-negative, pleomorphic rods that are able to obtain energy by the oxidation of hydrogen and can fix dinitrogen (22). Xanthobacter species have been isolated from soils, marine and freshwater sediments, the soil of rice fields, and the rhizosphere of rice plants (22).DNA-rRNA hybridization studies have shown that the three species of the genus Xanthobacter fall within the alpha-2 subclass of the Proteobacteria and are the closest relatives of Aquabacter spiritensis and Azorhizobium caulinodans (2-4).In order to investigate the relationships of the genera Aquabacter, Azorhizobium, and Xanthobacter, we determined the complete 16s rDNA sequences of the type strains of the three Xanthobacter species and additional strains. The 16s rDNA sequence of the type strain ofhorhizobium caulinodans was redetermined in order to clarify some ambiguous nucleotide positions in the sequence currently available from the public databases.The strains were grown on nutrient agar. 16s rDNA sequences were determined by directly sequencing the 16s rRNA genes amplified by PCR (16). The PCR products were directly sequenced by using a Taq DyeDeoxy terminator cycle sequencing kit (Applied Biosystems, Inc., Foster City, Calif.), and the purified sequence reaction mixtures were electrophoresed by using a model 373A automatic DNA sequencer (Applied Biosystems). The sequences were manually aligned with

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The xylem of rice (Oryza sativa) is colonized byAzorhizobium caulinodans

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Joint Improvised Explosive Device Defeat Organization: Anomaly or Future Roadmap

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