Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach.

BACKGROUND: Many microorganisms have a wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments, however not many have been fully explored over their entire growth temperature range through a holistic view of its physiology, genome, and transcriptome. We used Exiguobacterium sibiricum strain 255-15, a psychrotrophic bacterium from 3 million year old Siberian permafrost that grows from -5 degrees C to 39 degrees C to study its thermal adaptation. RESULTS: The E. sibiricum genome has one chromosome and two small plasmids with a total of 3,015 protein-encoding genes (CDS), and a GC content of 47.7%. The genome and transcriptome analysis along with the organism's known physiology was used to better understand its thermal adaptation. A total of 27%, 3.2%, and 5.2% of E. sibiricum CDS spotted on the DNA microarray detected differentially expressed genes in cells grown at -2.5 degrees C, 10 degrees C, and 39 degrees C, respectively, when compared to cells grown at 28 degrees C. The hypothetical and unknown genes represented 10.6%, 0.89%, and 2.3% of the CDS differentially expressed when grown at -2.5 degrees C, 10 degrees C, and 39 degrees C versus 28 degrees C, respectively. CONCLUSION: The results show that E. sibiricum is constitutively adapted to cold temperatures stressful to mesophiles since little differential gene expression was observed between 4 degrees C and 28 degrees C, but at the extremities of its Arrhenius growth profile, namely -2.5 degrees C and 39 degrees C, several physiological and metabolic adaptations associated with stress responses were observed.

Characterization of two novel saccharolytic, anaerobic thermophiles, Thermoanaerobacterium polysaccharolyticum sp. nov. and Thermoanaerobacterium zeae sp. nov., and emendation of the genus Thermoanaerobacterium.

Two anaerobic, thermophilic, Gram-positive, non-spore forming bacteria with an array of polysaccharide-degrading enzymes were isolated from the leachate of a waste pile from a canning factory in Hoopeston, East Central Illinois, USA. The results of 16S rDNA sequence homology indicated that their closest relatives belong to the saccharolytic, thermophilic and anaerobic genera of Thermoanaerobacterium and Thermoanaerobacter. Although, the evolutionary distances between these bacteria and their closest relatives are greater than 11%, there is no defining phenotypic characteristic for the creation of a new genus. It is proposed that these bacteria should be placed in the genus Thermoanaerobacterium, which requires emendment of the genus description with regard to the reduction of thiosulfate to sulfur, because neither isolate is capable of this reduction. Thermoanaerobacterium polysaccharolyticum reduces thiosulfate to sulfide, whereas Thermoanaerobacterium zeae is unable to reduce thiosulfate. The cells of both isolates are rod-shaped and exist as single cells or sometimes in pairs. Cells are motile by means of flagella. Growth occurs between 45 and 72 degrees C, with optimum temperature of 65-68 degrees C at pH 6.8. The pH range for growth is from 4 to 8 at a temperature of 65 degrees C. Both organisms ferment glucose, arabinose, maltose, mannose, rhamnose, sucrose, trehalose, xylose, cellobiose, raffinose, melibiose and melezitose. The major end products of fermentation with glucose are ethanol and CO2, with lesser amounts of acetate, formate, lactate and hydrogen. The DNA G+C contents of Thermoanaerobacterium polysaccharolyticum sp. nov. and Thermoanaerobacterium zeae sp. nov. are 46 and 42 mol%, respectively. The type strains are KMTHCJT (= ATCC BAA-17T = DSM 13641T) and mel2T (= ATCC BAA-16T = DSM 13642T), respectively.

Symbiobacterium thermophilum gen. nov., sp. nov., a symbiotic thermophile that depends on co-culture with a Bacillus strain for growth.

A Gram-negative and tryptophanase-positive thermophile, whose growth is dependent on co-culture with an associating Bacillus strain, had been reported and tentatively named Symbiobacterium thermophilum strain T(T). Axenic culture of strain T(T) was recently established by dialysing cultures with the supporting bacterial strains or adding their culture broth. Phylogenetic analysis of strain T(T), based on the 16S rDNA sequence, was conducted for the validation of S. thermophilum. The sequence of strain T(T) was located at the outermost position in the high-G+C Gram-positive group distinctly isolated from any other branches hitherto known. Ten sequences identical to that of strain T(T), and one sequence closely related to it, were identified for the first time from soil and compost samples. The outer membrane of strain T(T) had a three-layered structure, outside the cytoplasmic membrane, which is similar to the S-layer in the cells of members of the Bacillaceae. Chemical analysis of the cells revealed that menaquinone-6 is a major component of the quinone system. According to these results, along with several previous observations (i.e. a G+C DNA content of 65 mol% and the identification of iso-C15:0 and iso-C17:0 acids as major cellular fatty acids), the new taxon Symbiobacterium thermophilum gen. nov., sp. nov. is proposed. The type strain is S. thermophilum strain T(T) (= IAM 14863T).

Bulleidia extructa gen. nov., sp. nov., isolated from the oral cavity.

Five strains of anaerobic non-sporing Gram-positive bacilli isolated from advanced periodontitis (four strains) and a dentoalveolar abscess (one strain) that did not correspond to existing species were subjected to phenotypic and genetic characterization. Following 16S rDNA sequence analysis, they were found to constitute a novel branch of the low G+C Gram-positive division of the phylogenetic tree related to Erysipelothrix rhusiopathiae and Holdemania filiformis. A new genus Bulleidia, and the species Bulleidia extructa, are proposed. Growth of B. extructa in broth media was poor but was enhanced by the addition of fructose, glucose or maltose together with Tween 80. Glucose and maltose were fermented and arginine was hydrolysed. Acetate, lactate and trace amounts of succinate were the end products of glucose fermentation. The G+C content of the DNA of the type strain is 38 mol%. The type strain of Bulleidia extructa is DSM 13220T.

Cryptobacterium curtum gen. nov., sp. nov., a new genus of gram-positive anaerobic rod isolated from human oral cavities.

Novel Eubacterium-like isolates, strains 12-3T and KV43-B, which were isolated from the periodontal pocket of an adult patient with periodontal disease and necrotic dental pulp, respectively, were studied taxonomically and phylogenetically. The morphological and differential biochemical characteristics of these organisms are also described in this paper. These organisms were Gram-positive, anaerobic, non-spore-forming, rod-shaped bacteria that were inert in most of the conventional biochemical tests and closely resembled members of asaccharolytic oral Eubacterium species. On the other hand, protein profiles of whole cells in SDS-PAGE and Western immunoblotting reaction analysis distinguished these isolates from strains of the previously described genus Eubacterium. The G+C content of the DNAs from the novel isolates was 50 and 51 mol%, respectively. The levels of DNA-DNA relatedness to other asaccharolytic oral Eubacterium species, including Eubacterium brachy, Eubacterium lentum, Eubacterium nodatum, Eubacterium timidum, Eubacterium saphenum, Eubacterium minutum and Eubacterium exiguum, was less than 11%. These organisms also exhibited a very low level of reassociation with the DNA of Eubacterium limosum, the type species of the genus Eubacterium. The results of 16S rDNA sequence comparisons revealed that these organisms represent a novel lineage distinct from all previously described genera of Gram-positive, rod-shaped bacteria. On the basis of our results, it is suggested that strains 12-3T and KV43-B should be classified in a new genus and species, for which the name Cryptobacterium curtum gen. nov., sp. nov. is proposed. The type strain of Cryptobacterium curtum is 12-3T (= ATCC 700683T).

The molecular structure of the Na(+)-translocating F1F0-ATPase of Acetobacterium woodii, as revealed by electron microscopy, resembles that of H(+)-translocating ATPases.

The Na(+)-translocating F1F0-ATPase of Acetobacterium woodii was examined by electron microscopy. After reconstitution into proteoliposomes, knobs typical for the F1 domain were visible on the outside of the membrane. The F1-part of the isolated enzyme showed a hexagonal symmetry suggesting an alpha 3 beta 3 structure, and the F1F0 complex had molecular dimensions very similar to those of H(+)-translocating ATPases of E. coli, chloroplasts, and mitochondria.

The cytochrome composition of the meat spoilage bacterium Brochothrix thermosphacta: identification of cytochrome a3-and d-type terminal oxidases under various conditions.

Brochothrix thermosphacta, grown in batch culture in a yeast-dextrose broth, at temperatures from 30 degrees C to 10 degrees C, contained diverse membrane-bound respiratory cytochromes. Under conditions of moderate aeration, cytochromes of the a-, b- and d-type were detected at all growth temperatures, but the proportions changed as a function of temperature, with the spectra of cells grown at 10 or 15 degrees C being dominated by a-type cytochrome(s). Cytochrome a3 was detected by its reactions with CO and cyanide in cells from all growth conditions. An additional cytochrome a, which was not cyanide-reactive, was also detected, suggesting the presence of an aa3 oxidase complex. Cytochrome d was cyanide- and CO-reactive, but not detectable in photodissociation spectra, presumably because of the very rapid recombination of CO at the sub-zero temperatures used. Decreasing the oxygen transfer rates to batch cultures resulted in enhanced expression of cytochrome d and changed the proportion of the aa3-type oxidase that could be attributed to ligand-binding cytochrome a3; at the lowest oxygen transfer rates, no cytochrome a was detected, suggesting the presence of a cytochrome ba3 terminal oxidase complex. Intact cells showed no evidence of a c-type cytochrome and no haem C was detected in membrane preparations. After growth at 10 degrees C, the cytochrome composition of B. campestris was essentially identical to that of B. thermosphacta. The multiplicity of putative terminal oxidases in B. thermosphacta is discussed.