Evolution of temperature optimum in Thermotogaceae and the prediction of trait values of uncultured organisms.

Quantitative characterization of the mode and rate of phenotypic evolution is rarely applied to prokaryotes. Here, we present an analysis of temperature optimum (T (opt)) evolution in the thermophilic family Thermotogaceae, which has a large number of cultured representatives. We use log-rate-interval analysis to show that T (opt) evolution in Thermotogaceae is consistent with a Brownian motion (BM) evolutionary model. The properties of the BM model are used to a establish confidence intervals on the unknown phenotypic trait value of an uncultured organism, given its distance to a close relative with known trait value. Cross-validation by bootstrapping indicates that the predictions are robust.

Enumeration of Archaea and Bacteria in seafloor basalt using real-time quantitative PCR and fluorescence microscopy.

A SYBR Green real-time quantitative PCR (Q-PCR) assay for the detection and quantification of Bacteria and Archaea present in the glassy rind of seafloor basalts of different ages and water depths is presented. Two sets of domain-specific primers were designed and validated for specific detection and quantification of bacterial and archaeal 16S rRNA genes in DNA extracted from basaltic glass. Total cell numbers were also estimated by fluorescence microscopy analysis of SYBR Gold-stained samples. The results from the two different approaches were concurrent, and Q-PCR results showed that the total number of cells present in basalts was in the range from 6 x 10(5) to 4 x 10(6) cells g(-1) basaltic glass. Further, it was demonstrated that these cells were almost exclusively from the domain Bacteria. When applying the same methods on samples of different ages (22 years-0.1 Ma) and water depths (139-3390 mbsl), no significant differences in cell concentrations or in the relative abundance of Archaea and Bacteria were detected.

Flaviramulus basaltis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from seafloor basalt.

Four yellow-pigmented, Gram-negative, motile strains were isolated from the glassy rind of submarine basaltic lava from the Jan Mayen area of the Norwegian/Greenland Sea at a depth of 1300 m below sea level. The four strains had identical 16S rRNA gene sequences and were indistinguishable in all phenotypic and chemotypic tests performed, indicating that they belonged to the same species. The strains had an obligately aerobic chemo-organotrophic metabolism. The strains were capable of growth at temperatures between -2 and 34 degrees C, at pH between 6.5 and 8.6, and at sea salt concentrations between 3 and 60 g l(-1). The strains were able to utilize organic acids, amino acids and sugars but not alcohols; they were also capable of hydrolysing a wide range of macromolecules. The predominant fatty acids were 15 : 0 iso, 15 : 1 iso, 15 : 0 iso 3-OH and 17 : 0 iso 3-OH. The mean DNA G+C content of the strains was 31.4 mol%. 16S rRNA gene sequence analysis indicated that the strains were affiliated to the genera Gaetbulibacter and Algibacter. However, phenotypic characteristics, especially aerobic metabolism, suggested that the strains should be placed within a new genus. On the basis of the polyphasic characterization of the four strains, it is suggested that the strains be included in the family Flavobacteriaceae as representatives of a novel species in a new genus, for which the name Flaviramulus basaltis gen. nov., sp. nov. is proposed. The type strain is H35(T) (=CIP 109091(T)=DSM 18180(T)).