The phylogenetic diversity of thermophilic members of the genus Bacillus as revealed by 16S rDNA analysis

Abstract Sixteen thermophilic strains of the genus Bacillus , representing eight validly described and six invalidly described species, as well as one unassigned strain, were investigated by comparative 16S rDNA analyses and the sequences compared to the existing database for the genera Bacillus and Alicyclobacillus . The majority of strains were found to cluster in two groups represented by B. stearothermophilus and B. pallidus. Bacillus smithii, B. thermocloacae , and B. thermoruber are phylogenetically well separated and cluster within the radiation of mesophilic bacilli. The as yet undescribed taxon 'B. flavothermus' warrants species status. B. schlegelii and B. tusciae group peripherally with members of Alicyclobacillus and may be reclassified when more phenotypic data support their phylogenetic position.     

Acetobacterium tundrae sp. nov., a new psychrophilic acetogenic bacterium from tundra soil

A new psychrophilic, anaerobic, acetogenic bacterium from the tundra wetland soil of Polar Ural is described. The organism fermented H2/CO2, formate, methanol, and several sugars to acetate as the sole end-product. The temperature range for growth was 1-30 degrees C with an optimum at 20 degrees C. The bacterium showed no growth at 32 degrees C. Cells were gram-positive, oval-shaped, flagellated rods 0.7-1.l x 1.1-4.0 microm in size when grown at 1-20 degrees C. At 25-30 degrees C, the cell size increased up to 2-3 x 10-15 microm due to a defect in cell division. The DNA G+C content of the organism was 39.2 mol%. Based upon 16S rDNA analysis and DNA-DNA reassociation studies, the organism was classified in the genus Acetobacterium as a new species, for which the name Acetobacterium tundrae sp. nov. is proposed. The type strain is Z-4493 (=DSM 9173T).     

Design and application of two oligonucleotide probes for the identification of Geodermatophilaceae strains using fluorescence in situ hybridization (FISH)

Bacteria of the family of Geodermatophilaceae are actively involved in the decay processes [Urzì, C. and Realini, M. (1998) Int Biodeterior Biodegrad 42: 45-54; Urzì, C., Salamone, P., Schumann, P., and Stackebrandt, E. (2000) Int J Syst Evol Microbiol 50: 529-536] of stone monuments. Characterization of isolates includes phenotypic, chemotaxonomic and genetic analysis often requiring long-term procedures. The use of specific probes for members of Geodermatophilaceae family could be useful for the easy detection of those strains colonizing rock surfaces and involved in the biodeterioration. Two 16S rRNA-targeted oligonucleotide probes were designed for the specific detection of members of the family Geodermatophilaceae using fluorescence in situ hybridization (FISH); one probe specific for members of the two genera Geodermatophilus/Blastococcus and the second for members of the genus Modestobacter.     

Brucella abortus 16S rRNA and lipid A reveal a phylogenetic relationship with members of the alpha-2 subdivision of the class Proteobacteria

On the basis of ribosomal 16S sequence comparison, Brucella abortus has been found to be a member of the alpha-2 subdivision of the class Proteobacteria (formerly named purple photosynthetic bacteria and their nonphototrophic relatives). Within the alpha-2 subgroup, brucellae are specifically related to rickettsiae, agrobacteria, and rhizobiae, organisms that also have the faculty or the obligation of living in close association to eucaryotic cells. The composition of Brucella lipid A suggests a close phylogenetical relationship with members of the alpha-2 group. The chemical analysis of the lipid A fraction revealed that Brucella species contain both glucosamine and diaminoglucose, thus suggesting the presence of a so-called mixed lipid A type. The serological analysis with polyclonal and monoclonal antibodies is in agreement with the existence of mixed lipid A type in B. abortus. The amide-linked fatty acid present as acyl-oxyacyl residues were 3-O-C(16:0)12:0, 3-O-C(16:0)13:0, 3-O-C(16:0)14:0, and 3-O-C(18:0)14:0. The only amide-linked unsubstituted fatty acid detected was 3-OH-C16:0. The ester-linked fatty acids are 3-OH-C16:0, 3-OH-C18:0, C16:0, C17:0, and C18:0. Significant amounts of the large-chain 27-OH-C28:0 were detected together with traces of 25-OH-C26:0 and 29-OH-C30:0. Comparison of the Brucella lipid composition with that of the other Proteobacteria also suggests a close phylogenetical relationship with members of the alpha-2 subdivision. The genealogical grouping of Brucella species with pericellular and intracellular plant and animal pathogens as well as with intracellular plant symbionts suggests a possible evolution of Brucella species from plant-arthropod-associated bacteria.     

Biosurfactant Production by Halotolerant Rhodococcus fascians from Casey Station, Wilkes Land, Antarctica

Isolate A-3 from Antarctic soil in Casey Station, Wilkes Land, was characterized for growth on hydrocarbons. Use of glucose or kerosene as a sole carbon source in the culture medium favoured biosynthesis of surfactant which, by thin-layer chromatography, indicated the formation of a rhamnose-containing glycolipid. This compound lowered the surface tension at the air/water interface to 27 mN/m as well as inhibited the growth of B. subtilis ATCC 6633 and exhibited hemolytic activity. A highly hydrophobic surface of the cells suggests that uptake occurs via a direct cell–hydrocarbon substrate contact. Strain A-3 is Gram-positive, halotolerant, catalase positive, urease negative and has rod–coccus shape. Its cell walls contained meso-diaminopimelic acid. Phylogenetic analysis based on comparative analysis of 16S rRNA gene sequences revealed that strain A-3 is closely related to Rhodococcus fascians with which it shares 100% sequence similarity. This is the first report on rhamnose-containing biosurfactant production by Rhodococcus fascians isolated from Antarctic soil.     

High-pressure tuning of primary photochemistry in bacterial photosynthesis: membrane-bound versus detergent-isolated reaction centers

Photosynthesis Research - While photosynthesis thrives at close to normal pressures and temperatures, it is presently well known that life is similarly commonplace in the hostile environments of...     

An alphaproteobacterium capable of both aerobic and anaerobic anoxygenic photosynthesis but incapable of photoautotrophy: <Emphasis Type="Italic">Charonomicrobium ambiphototrophicum</Emphasis>, gen. nov., sp. nov.

A facultatively aerobic deep brown coccoid to ovoid bacterium, strain EG17^T, was isolated from a saline effluent stream in the NaCl-dominated brine spring system known as East German Creek in the province of Manitoba, Canada. The strain produced BChl a incorporated into a functional reaction center and two light-harvesting complexes with absorption peaks at 802, 850, and 879 nm. EG17^T is the first reported anoxygenic phototroph capable of photoheterotrophic growth under both oxic and anoxic conditions. It yielded proportionally the greatest aerobic photosynthetic biomass under oligotrophic conditions. The results of 16S rRNA gene sequence comparisons revealed that EG17^T was related most closely to the aerobic anoxygenic phototrophs Roseibacterium elongatum (98.3%) and quite distantly to both Dinoroseobacter shibae (95.2%) and Roseicyclus mahoneyensis (94.7%). The DNA G + C content was 65.6 mol%. On the basis of the unique dual aerobic/anaerobic photosynthetic capability, the distinctive spectrophotometric absorption of the photosynthetic apparatus, diagnostic physiological and biochemical traits, and the moderate phylogenetic separation between EG17^T and its nearest relatives, it is concluded that this microorganism should be classified as a novel genus and species, Charonomicrobium ambiphototrophicum gen. nov., sp. nov., with EG17^T as the type strain.     

The phylogenetic significance of peptidoglycan types: Molecular analysis of the genera Microbacterium and Aureobacterium based upon sequence comparison of gyrB, rpoB, recA and ppk and 16SrRNA genes

The type strains of 27 species of the genus Microbacterium, family Microbacteriaceae, were analyzed with respect to the phylogeny of the housekeeping genes coding for DNA gyrase subunit B (gyrB), RNA-polymerase subunit B (rpoB), recombinase A (recA) and polyphosphate kinase (ppk). The resulting gene trees were compared to the 16S rRNA gene phylogeny of the same species. The topology of neighbour-joining and maximum parsimony phylogenetic trees based upon nucleic acid sequences and protein sequences of housekeeping genes differed among each other and no gene tree was identical to that of the 16S rRNA gene tree. Only some species showed consistent clustering by all genes analyzed, but the majority of species branched with different neighbours in most gene trees. The failure to phylogenetically cluster type strains into two groups based upon differences in the amino acid composition of peptidoglycan on the basis of 16S rRNA gene sequence similarity, once leading to the union of the genera Microbacterium and Aureobacterium, was also seen in the analysis of recA, rpoB and gyrB gene and protein phylogenies. Analysis of the pkk gene and protein as well as of a concatenate tree, combining sequences of all five genes (total of 3.700 nucleotides), sees members of the former genus Aureobacterium and other type strains with lysine as diagnostic diamino acid to form a coherent cluster that branches within the radiation of Microbacterium species with ornithine in the peptidoglycan.     

Methods development for diffraction and spectroscopy studies of metalloenzymes at X-ray free-electron lasers

X-ray free-electron lasers (XFELs) open up new possibilities for X-ray crystallographic and spectroscopic studies of radiation-sensitive biological samples under close to physiological conditions. To facilitate these new X-ray sources, tailored experimental methods and data-processing protocols have to be developed. The highly radiation-sensitive photosystem II (PSII) protein complex is a prime target for XFEL experiments aiming to study the mechanism of light-induced water oxidation taking place at a Mn cluster in this complex. We developed a set of tools for the study of PSII at XFELs, including a new liquid jet based on electrofocusing, an energy dispersive von Hamos X-ray emission spectrometer for the hard X-ray range and a high-throughput soft X-ray spectrometer based on a reflection zone plate. While our immediate focus is on PSII, the methods we describe here are applicable to a wide range of metalloenzymes. These experimental developments were complemented by a new software suite, cctbx.xfel. This software suite allows for near-real-time monitoring of the experimental parameters and detector signals and the detailed analysis of the diffraction and spectroscopy data collected by us at the Linac Coherent Light Source, taking into account the specific characteristics of data measured at an XFEL.