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.

Thermal inactivation of Mycobacterium paratuberculosis, a suspected human pathogen, was determined in ultrahigh-temperature whole milk. Three strains of M. paratuberculosis were examined for survival at temperatures from 55 to 75 degrees C using a submerged glass capillary tube method. Clumped and declumped suspensions of the cultures were used to determine the rate of heat inactivation and survival at pasteurization temperatures. Methods for declumping M. paratuberculosis included the use of glass beads, vortexing, and passing the cells through a 26-gauge needle. The latter procedure was found to be superior over other methods and did not affect the viability of cells. Capillary tubes filled with milk containing 4 x 10(6) to 3 x 10(7) CFU/ml were heated at temperatures ranging from 55 to 75 degrees C. At 55 degrees C, minimal thermal inactivation was observed for clumped and declumped cells. At 58 degrees C, thermal inactivation ranging from 0.3 to 0.7 log reduction was observed for both clumped and declumped suspensions. D values at 60 degrees C ranged from 8.6 to 11 min and 8.2 to 14.1 min for clumped and declumped cells, respectively. At 63 degrees C, the D values ranged from 2.7 to 2.9 and 1.6 to 2.5 min for clumped and declumped cells, respectively. Survival of M. paratuberculosis at initial levels ranging from 44 to 10(5) CFU/ml at pasteurization treatment (63 degrees C for 30 min and 72 degrees C for 15 s) was also determined. No survivors were observed after incubating plates for up to 4 months on Middlebrook 7H11 agar and up to 2 months on Herrold's egg yolk medium. The sensitivity of the plating method was 1 CFU/250 microliters. These results demonstrate that low levels of M. paratuberculosis, as might be found in raw milk, will not survive pasteurization treatments.

The phylogeny and taxonomy of the mesophilic methane-producing archaea of the order Methanococcales were examined by DNA relatedness, 16s rRNA sequence analysis, cellular protein pattern, and phenotypic methods. The mesophilic species Methanococcus maripaludis, Methanococcus vannielii, Methanococcus voltaei, and 44Methanococcus aeolicus" formed a deep group with 5 to 30% DNA relatedness and 92 to 96% 16s rRNA sequence similarity. Twenty-two additional isolates and Methanococcus deltae were similar to the type strain of either M. voltaei or M. maripaludis. Two isolates, strains A2 and A3, exhibited 37% DNA relatedness and 99.2% 16s rRNA sequence similarity to M. voltaei PST (T = type strain). In the absence of phenotypic differences, these organisms were assigned to M. voltaei. Similarly, four autotrophic isolates, strains C5, C6, C7, and C8, exhibited 54 to 69% DNA relatedness and 99.2% 16s rRNA sequence similarity to M. maripaludis JJT and were assigned to M. maripaludis. While these isolates were sufficiently genetically diverse to justify classification in novel species, few differences were apparent in the phenotypic properties available for measurement. Thus, the phenotypic properties of these lithotrophic archaea were highly conserved and poor indicators of genetic diversity. Partial sequencing of about 200 bases of both the 16s and 23s rRNAs of the isolates demonstrated allelic diversity within methanococcal species. This allelic diversity did not correlate with diversity measured by DNA relatedness, cellular protein pattern, and other methods. Similarly, antisera to whole cells of the type strains did not cross-react strongly to whole cells of strains that were genetically similar, and serological cross-reactivity was not a useful taxonomic method for methanococci. Lastly, on the basis of the results of 16s rRNA sequence analyses and biochemical data, the ancestor of the mesophilic methanococci may have been an autotrophic thermophile.The genus Methanococcus belongs to the family Methanococcaceae and the order Methanococcales, which is one of five orders within the Archaea that include methanogenic bacteria (3). The order Methanococcales is composed of coccoid methane-producing bacteria of marine origin. Distinctive features of this group include rapid growth at either mesophilic or thermophilic temperatures, cell envelopes composed of protein S-layers, and a nutritional requirement for selenium (6,18,23,44,45). To date, eight Methanococcales species belonging to two families and four genera have been described. Five species, Methanococcus vannielii, Methanococcus voltaei, Methanococcus maripaludis, Methanococcus deltae, and "Methanococcus aeolicus," are mesophilic, and three species, Methanococcus ("Methanothermococcus") thermolithotrophicus, Methanococcus ("Methanoignis") igneus, and Methanococcus ("Methanocaldococcus~7) jannaschii (4) (proposed genus names in parentheses), are thermophilic. The relationships of all of the mesophilic species except "M. aeolicus" have been determined by 16s rRNA catalog...

Advances in polymerase chain reaction (PCR) have permitted accurate, rapid and quantitative identification of microorganisms in pure cultures regardless of viability or culturability. In this study, a simple sample processing method was investigated for rapid identification and quantification of fungal spores from dust samples using both conventional and real-time PCR. The proposed method was evaluated for susceptibility to interference from environmental dust samples. Stachybotrys chartarum and Aspergillus fumigatus were used as test organisms. The sensitivity of detection in pure culture was 0.1 spore DNA equivalents per PCR reaction corresponding to 20 spores ml(-1) in the sample. However, 1 spore DNA equivalent per PCR reaction corresponding to 200 spores ml(-1) in the sample was the lowest amount of spores tested without interference in dust samples spiked with spores of either fungal species. The extent of inhibition was calculated using conventional and real-time PCR reactions containing fungal spores, specific primers, specific probes (for real-time PCR) and various amounts of dust. The results indicate that the extent of inhibition by dust on PCR varies with the type and amount of dust, and number of spores. No interference in the analysis of spiked samples was detected from 0.2 mg ml(-1) of four real-life dust samples at p-value >0.05 using 2 x 10(4) spores for conventional PCR and 2 x 10(5) spores for real-time PCR. However, samples containing >0.2 mg ml(-1) real-life dust compromised the PCR assay. These results suggest the potential usefulness of a simple sample processing method in conjunction with PCR for monitoring the fungal content of aerosols collected from indoor environments.

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