Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes.

Abstract

The relationship between 16S rRNA sequence similarity (S) and the extent of DNA hybridization (D) was well described by the equation ln(NlnD) l 053 [ln(NlnS)]M2201 when D was determined by either the S1 nuclease or membrane filter methods. When the presence of nonultrametric rRNA sequences and differences between genera or families were controlled, this relationship accounted for 78 % of the variability of D given S, and it was possible to estimate the distribution of D from S with a known precision. Thus, D T 070 was expected to occur 50, 95 and 99 % of the time when S was 0998, 0992 and 0986, respectively. The relationship between D and S varied between prokaryotic taxa even within the same subphylum, and more precise estimates of D could be made when the relationship for a particular taxon was known. The relationship between D and S was not significantly different between the prokaryotic domains, and S appeared to be a quasi-molecular clock of approximately constant rate when averaging effects and stochastic factors were taken into account. The relationship between logD and logS was nonlinear, and D provided a very poor measure of relatedness for distantly related organisms. For instance, within the range 10 S S S 095, D decreased from 10 to 015 ; and within the range 095 S S S 090, D decreased from 015 to 006. Lastly, at least some of the rRNA sequences from about one-third of the taxa examined had nonultrametric properties where S was much lower than expected from the value of D. For these taxa, S was a poor indicator of relatedness for closely related strains. Thus, the ultrametric properties of rRNA sequences should be tested before making taxonomic or phylogenetic conclusions based upon S.

Microlunatus panaciterrae sp. nov., a -glucosidase-producing bacterium isolated from soil in a ginseng field

“…There is general agreement that a DNA-DNA relatedness level of approximately 70 % is the threshold value for defining species (Wayne et al, 1987). On the basis of the available data, organisms that share less than 97.0 % 16S rRNA gene sequence similarity will not show more than 60 % reassociation, irrespective of the hybridization method used (Stackebrandt & Goebel, 1994;Keswani & Whitman, 2001). Thus, the phylogenetic results for strain Gsoil 954 T demonstrated that the strain was not related to any of the recognized members of the genus Microlunatus.…”

Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle

“…1). A similarity of less than 98 % in a 16S rRNA gene sequence is generally considered evidence for separate species (Keswani & Whitman, 2001). Furthermore, deduced amino acid sequences from mcrA gene analyses showed 89 % similarity between all the isolated strains and Table 1.…”

Mycobacterium canariasense sp. nov.

“…In addition, the blots were stripped and rehybridized with a PCR amplicon from the 16S rRNA gene as the new probe, as described by Domenech et al (1997). This procedure has several advantages compared to previous methods (Keswani & Whitman, 2001), mainly because the amount of DNA fixed in each dot can be determined by measuring the amount of radioactivity when using the 16S rRNA gene as the second probe. Due to the high sequence conservation within mycobacterial species inherent within this probe (Menendez et al, 2002), the radioactivity level can be considered to be proportional to the amount of target molecules on the filter.…”