Role of pigmentation in protecting Bacillus sp. endospores against environmental UV radiation

Bacillus endospores show different kinds of pigmentation. Red-pigmented spores of Bacillus atrophaeus DSM 675, dark-gray spores of B. atrophaeus(T) DSM 7264 and light-gray spores of B. subtilis DSM 5611 were used to study the protective role of the pigments in their resistance to defined ranges of environmental UV radiation. Spores of B. atrophaeus DSM 675 possessing a dark-red pigment were 10 times more resistant to UV-A radiation than those of the other two investigated strains, whereas the responses to the more energetic UV-B and UV-C radiation were identical in all three strains. The methanol fraction of the extracted pigment from the spores absorbs in the associated wavelength area. These results indicate that the carotene-like pigment of spores of B. atrophaeus DSM 675 affects the resistance of spores to environmental UV-A radiation.     

Frequent genetic recombination in natural populations of the marine cyanobacterium Microcoleus chthonoplastes

A culture-independent method for multilocus sequence typing of Microcoleus chthonoplastes was developed based on mechanical separation of individual cyanobacterial filaments from natural microbial mat populations through micromanipulation, subsequent polymerase chain reaction (PCR) amplification and sequence analysis of three genetic loci (kaiC, petB/D, rDNA-ITS). Among 81 individuals sampled from intertidal sand flats of the North Sea and Baltic Sea, we found 8-14 different sequences (alleles) per genetic locus, resulting in 36 distinct genotypes with unique allele profiles. Non-congruent phylogenetic gene trees for the three loci analysed and split decomposition analysis indicated the occurrence of horizontal genetic exchange. The index of association determined for the entire population was 0.096, indicating that recombination occurs frequently enough to cause almost random association (linkage equilibrium) among alleles. Analysing individuals from three different locations in the North Sea and Baltic Sea, we did not find evidence for geographic subdivisions between populations.     

Genome organization and localization of the pufLM genes of the photosynthesis reaction center in phylogenetically diverse marine Alphaproteobacteria

Genome organization, plasmid content and localization of the pufLM genes of the photosynthesis reaction center were studied by pulsed-field gel electrophoresis (PFGE) in marine phototrophic Alphaproteobacteria. Both anaerobic phototrophs (Rhodobacter veldkampii and Rhodobacter sphaeroides) and strictly aerobic anoxygenic phototrophs from the Roseobacter-Sulfitobacter-Silicibacter clade (Roseivivax halodurans, Roseobacter litoralis, Staleya guttiformis, Roseovarius tolerans, and five new strains isolated from dinoflagellate cultures) were investigated. The complete genome size was estimated for R. litoralis DSM6996(T) to be 4,704 kb, including three linear plasmids. All strains contained extrachromosomal elements of various conformations (linear or circular) and lengths (between 4.35 and 368 kb). In strain DFL-12, a member of a putative new genus isolated from a culture of the toxic dinoflagellate Prorocentrum lima, seven linear plasmids were found, together comprising 860 kb of genetic information. Hybridization with probes against the pufLM genes of the photosynthesis gene cluster after Southern transfer of the genomic DNAs showed these genes to be located on a linear plasmid of 91 kb in R. litoralis and on a linear plasmid of 120 kb in S. guttiformis, theoretically allowing their horizontal transfer. In all other strains, the pufLM genes were detected on the bacterial chromosome. The large number and significant size of the linear plasmids found especially in isolates from dinoflagellates might account for the metabolic versatility and presumed symbiotic association with eukaryotic hosts in these bacteria.     

Phylogenetically Diverse New Sulfur Chemolithotrophs of α-Proteobacteria Isolated from Indian Soils

Five facultative sulfur chemolithotrophs were isolated from soils to study the diversity of sulfur lithotrophy. Phenotypic characteristics, including sulfur lithotrophic properties and chemotaxonomic features of the isolates, were similar to those of the members of the colorless sulfur bacteria. 16S rDNA sequence analyses rendered placing the isolates to three distinct phylogenetic clusters of -proteobacteria. Three isolates, AS001, AS002, and KCT002, were identified as members of the genus Paracoccus. The strains AS001 and AS002, having identical 16S-rDNA sequence, showed significant 16S rDNA sequence similarity (99.1%) to Paracoccus versutus. The strain KCT002 showed highest (98%) 16S rDNA sequence similarity to P. alcaliphilus and 96% similarity to the pair AS001 and AS002. Isolate KCT001 appeared to be closely related to Pseudaminobacter salicylatoxidans, although sulfur lithotrophy of P. salicylotoxidans is not known. The other isolate, TCK, showed almost identical 16S rDNA (99.9%) sequence with two recently described unclassified chemolithoautotrophic arsenite oxidizing strains. Physiological and chemotaxonomic characteristics and phylogenetic analyses of the five new strains emphasize the need of polyphasic bacterial taxonomy of sulfur lithotrophs.     

Morphological,physiological, and molecular characterization of actinomycetes isolated from dry soil,rocks, and monument surfaces

In an extended study on the biodiversity of rock-dwelling bacteria, the colony and cell morphology, physiology, protein patterns, and 16S rDNA sequences of 17 bacterial strains isolated from different surfaces of rocks, stones, and monuments and from various geographical locations were characterized. All except one strain, which was found to be a Bacillus, were members of the order Actinomycetales. The majority of the strains either were closely related to Geodermatophilus obscurus, which was also analyzed in this study, or formed a closely related sister taxon. All of these strains were isolated from the surface of marble in Namibia and Greece and from limestone from the Negev desert, Israel. One strain, G10, of Namibia origin was equidistantly related to Geodermatophilus obscurus, Frankia alni, Sporichthya polymorpha, and Acidothermus cellulolyticus. Three strains from rock varnish in the Mojave desert, California, were found to be highly related to Arthrobacter (formerly Micrococcus) agilis. All clusters could be confirmed from results of studies on morphological and physiological properties and from banding patterns of whole cell proteins. Based on the results of tests, four additional strains were assigned to the lineage defined by strain G10. Received: 16 October 1995 / Accepted: 4 April 1996     

Holophaga foetida gen. nov., sp. nov., a new,homoacetogenic bacterium degrading methoxylated aromatic compounds

A polyphasic approach was used in which genotypic and phenotypic properties of a gram-negative, obligately anaerobic, rod-shaped bacterium isolated from a black anoxic freshwater mud sample were determined. Based on these results, the name Holophaga foetida gen. nov., sp. nov. is proposed. This microorganism produced dimethylsulfide and methanethiol during growth on trimethoxybenzoate or syringate. The only other compounds utilized were pyruvate and trihydroxybenzenes such as gallate, phloroglucinol, or pyrogallol. The aromatic compounds were degraded to acetate. Although comparison of the signature nucleotide pattern of the five established subclasses of Proteobacteria with the 16S rDNA sequence of Holophaga foetida revealed a relationship to members of the -subclass, the phylogenetic position within the radiation of this class is so deep and dependent upon the number and selection of reference sequences that its affiliation to the Proteobacteria must be considered tentative. The type strain is H. foetida strain TMBS4 (DSM 6591).F. Bak died on 27 December 1992. A very promising and productive career thus ended much too early     

Phylogenetic relationship of the fish pathogenic Renibacterium salmoninarum to Arthrobacter, Micrococcus and related taxa

Abstract The phylogenetic position of the obligate fish pathogenic Gram-positive eubacterium Renibacterium salmoninarum was determined by the 16S ribosomal RNA cataloguing approach. Comparison of the catalogue to those of more than 165 Gram-positive organisms from 50 genera revealed that R. salmoninarum is a member of the actinomycetes subdivision. As derived from similarity coefficients (S_AB values), this organism is related to a subgroup harbouring morphologically and chemotaxonomically rather heterogeneous taxa, including Anthrobacter, Micrococcus, Cellulomonas, Jonesia, Promicromonospora, Stomatococcus and Brevibacterium . Thus, the inclusion of organisms characterized by regular rods increases the phenotypic variability of this phylogenetically coherent group.     

Phylogenetic evidence for the classification of Acidothermus cellulolyticus into the subphylum of actinomycetes

Abstract The primary structure of the 16S rDNA of Acidothermus cellulolyticus , a cellulolytic, asporogenous rod isolated from a hot spring, was determined by automated sequence analysis. This Gram-variable organism is not related to members of other aerobic thermophilic genera found in similar environments, such as Thermus and Thermomicrobium , but clusters within the phylogenetically defined radiation of the actinomycetes where it represents an individual subline of descent.