16S rDNA sequencing

Fig. 8. Phylogenetic analysis of 16S rDNA sequence of the isolate V 33 (Tanamool et al, 2011)...

Figure 17.1. Phylogenetic tree based on 16S rDNA sequence analysis showing the placement of the novel chemolithoautotrophic Fe(III) reducers. Capital and bold face letters, respiratory Fe(III) reducers , tested heterotrophic species that probably reduce Fe(III) predominantly in an assimilatory fashion.

Acknowledgments. The authors are indebted to Anna Louise Reysenbach for the 16S rDNA sequence analysis. The authors also acknowledge Alex Slobodkin who introduced Fe(III) reduction to the laboratory. The initial work was supported by Genencor International. 

Assimilable organic carbon (AOC) was determined in water using flow-cytometric enumeration and a natural microbial consortium as inoculum.134 Two bacterial species were used for the measurement of AOC in water, based on their respective 16S rDNA sequences. The AOC content in 41 water samples was determined with these two sets by quantitative real-time polymerase chain reaction (qRT-PCR).135... 

DNA-DNA hybridization is a method that provides more resolution than 16S rDNA sequencing, and has been used to describe bacterial species (Wayne et al. 1987). The 16S-23S rRNA spacer region has been suggested as a suitable region of the bacterial genome from which to derive useful taxonomic information, particularly with regard to identification at the species level (Whiley et al. 1995) and probes have been synthesized on its sequences to characterize bacterial species. 

Ward DM, Wller R, Bateson MM. (1990). 16S rDNA sequence reveal numerous uncultured microorganisms in a natural community. Nature 345,. 

Shi, T. et al. (1997). Characterization of viable bacteria from Siberian permafrost by 16S rDNA sequencing. Microbial Ecology, 33, 169. 

Luminous bacteria were isolated from seawater, sediment and marine organisms around the coastal areas of Japan. Some of the isolates having strong luminescence were identified by their 16S-rDNA sequences. Luminous bacterial isolates were usually cultured in half-strength SWC medium at 20 °C. 

Phylogenetic affiliation was determined by comparing near-full-length 16S rDNA sequences of these isolates to sequences in the GenBank database (90). Source Ref. 88. 

DNA HYBRIDIZATION AND 16S RDNA SEQUENCE ANALYSIS IN THE DETERMINATION OF RELATIONSHIPS... 

Studies of 16S rDNA sequences obtained from clone libraries generated from PCR amplified 16S rDNA have included a broad selection of different environments from different parts of the world, such as marine sites (Atlantic, Pacific, Antarctic Sea), freshwater lakes and sewage plants, groundwater, terrestrial sites (deserts, peat bogs, forrested soil, rocks), human infected tissues, plant surfaces and the rhizosphere of different plants, as well as the gut content fi om invertertebrates and vertebrates (to name the most well studied sites). Due to space limitations only a few references on 16S rDNA environmental clone libraries will be included in the summary of the most importan results ... 

Table 1. Examples of the phylogenetic distance of 16S rDNA clones to their nearest 16S rDNA sequence which are clone sequences (in percent similarity). Analysis is based on 1000 nucleotides.

Comparative 16S rDNA sequence analysis of pure cultures has shown that it is not possible to delineate ranks at any level purely on the basis of similarity or dissimilarity values. For example, the phylogenetic depth of the taxon "species" (higher than about 70% DNA reassociation) may range from 97% 16S rDNA similarity to absolute sequence identity [3]. 

In order to determine whether the as yet unknown strains are members of described species, the environmental strains need to be isolated, and their phenotype and, if necessary, their DNA similarity be determined. The low numbers of absolutely matching sequences indicate that the vast majority of clone sequences indeed represent novel species in the environment. For the assessment of a more complete picture, it is however necessary to have a complete reference bank of 16S rDNA sequences which would include the type strains of all validly described species. 

Escalante, A., Wacher, C., Farres, A. (2001). Lactic acid bacterial diversity in the traditional mexican fermented dough pozol as determined by 16S rDNA sequence analysis. International Journal of Eood Microbiology, 64, 21-31. 

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