A survey of flagellate diversity at four deep-sea hydrothermal vents in the Eastern Pacific Ocean using structural and molecular approaches

Eighteen strains of flagellated protists representing nine species were isolated and cultured from four deep-sea hydrothermal vents: Juan de Fuca Ridge (2,200 m), Guaymas Basin (2,000 m), 21 degrees N (2,550 m) and 9 degrees N (2,000 m). Light and electron microscopy were used to identify flagellates to genus and, when possible, species. The small subunit ribosomal RNA genes of each vent species and related strains from shallow-waters and the American Type Culture Collection were sequenced then used for comparative analysis with database sequences to place taxa in an rDNA tree. The hydrothermal vent flagellates belonged to six different taxonomic orders: the Ancyromonadida, Bicosoecida, Cercomonadida, Choanoflagellida, Chrysomonadida, and Kinetoplastida. Comparative analysis of vent isolate and database sequences resolved systematic placement of some well-known species with previously uncertain taxonomic affinities, such as Ancyromonas sigmoides, Caecitellus parvulus, and Massisteria marina. Many of these vent isolates are ubiquitous members of marine, freshwater, and terrestrial ecosystems worldwide, suggesting a global distribution of these flagellate species.     

The microbial composition of three limnologically disparate hypersaline Antarctic lakes

16S rRNA clone library analysis was used to examine the biodiversity and community structure within the sediments of three hypersaline Antarctic lakes. Compared to sediment of low to moderate salinity Antarctic lakes the species richness of the hypersaline lake sediments was 2-20 times lower. The community of Deep Lake (32% salinity, average sediment temperature -15 degrees C) was made up almost entirely of halophilic Archaea. The sediment communities of two meromictic hypersaline lakes, Organic Lake (20% salinity, -7 degrees C) and Ekho Lake (15% salinity, 15 degrees C) were more complex, containing phylotypes clustering within the Proteobacteria and Cytophagales divisions and with algal chloroplasts. Many phylotypes of these lakes were related to taxa more adapted to marine-like salinity and perhaps derive from bacteria exported into the sediment from the lower salinity surface waters. The Ekho Lake clone library contained several major phylotypes related to the Haloanaerobiales, the growth of which appears to be promoted by the comparatively high in situ temperature of this lake.     

Development of molecular methods for identification of Streptococcus bovis from human and ruminal origins

Streptococcus bovis has been identified as a causative agent in humans for a variety of diseases, including endocarditis, meningitis, and septicemia. Identification of S. bovis strains of human origin in clinical settings has been problematic due to variations in biochemical tests as compared to ruminal strains of S. bovis, and other streptococcal species. DNA-DNA hybridization with chromosomal DNA from various S. bovis strains indicates that strains of human origin are different from those of ruminal origin. Specific probes have been designed from S. bovis 16S rDNA gene sequences that differentiate strains of human and ruminal origin by direct hybridization and PCR analyses. These techniques now allow for rapid identification of S. bovis strains for clinical and other scientific investigations.     

A cadmium resistance plasmid, pXU5, in Staphylococcus aureus, strain ATCC25923

A 25.9-kb plasmid, pXU5, encoding high level cadmium resistance was isolated from Staphylococcus aureus strain ATCC25923. A labelled cadA probe from plasmid pI258 hybridised to a 2.3-kb EcoRI fragment of pXU5. pXU5 was incompatible with an S. aureus incompatibility group 1 plasmid.     

Bifidobacterium lactis Meile et al. 1997 is a subjective synonym of Bifidobacterium animalis (Mitsuoka 1969) Scardovi and Trovatelli 1974

Bifidobacterium lactis JCM 10602T (T = type strain) and Bifidobacterium animalis JCM 1190T were found to be phenotypically similar. These strains were subjected to investigation of their genetic relationships. The 16S rRNA sequence of B. animalis JCM 1190T was aligned with that of other Bifidobacterium species. B. animalis and B. lactis were the most closely related species in the phylogenetic tree and showed a high similarity in sequences (98.8%). The levels of DNA-DNA hybridization between the type strains of B. lactis and B. animalis ranged from 85.5 to 92.3%, showing that they represent a single species. It is proposed that B. lactis should be considered as a junior subjective synonym of B. animalis.     

Coprobacillus catenaformis gen. nov., sp. nov., a new genus and species isolated from human feces

Three strains of Eubacterium-like isolates from human feces were characterized by biochemical tests and 16S rDNA analysis. The phenotypic characteristics of the three strains resembled those of the genus Collinsella transferred from the genus Eubacterium recently. However, Eubacterium-like strains were phylogenetically members of the Clostridium subphylum of gram-positive bacteria, and these showed a specific phylogenetic association with Clostridium ramosum and C. spiroforme. C. ramosum and C. spiroforme are gram-positive, anaerobic, spore-forming bacteria that belong to the genus Clostridium, and the G + C contents are 26.0 and 27.4 mol%, respectively. However, the three Eubacterium-like strains had G + C contents of 32.1 to 33.1 mol% and were non-spore-forming rods. Based on phenotypic characteristics, we can differentiate these species, and furthermore, a 16S rDNA sequence divergence of greater than 9% with a new related genus, Coprobacillus, is proposed for the three strains, with one species, Coprobacillus catenaformis. The type strain of C. catenaformis is JCM 10604T.     

Localization of major, high molecular weight proteins in Bacteroides forsythus

Bacteroides forsythus produces species-specific major proteins with high molecular weights of 270 and 230-kDa (270K and 230K). A specific antibody raised against 270K was used for Western blot analysis and immunoelectron microscopy. Western blot analysis showed that the 270K and 230K proteins were immunologically similar. Immunogold labeling of ultrathin-sectioned bacterial cells and biochemical fractionation revealed that these proteins were localized at the outermost cell surface, not in the cytoplasm. These results suggest that major proteins ubiquitous to this species may form the S-layer.     

Comparison of the oral bacterial flora in saliva from a healthy subject and two periodontitis patients by sequence analysis of 16S rDNA libraries

The oral bacterial flora in the saliva from two patients with periodontitis and from a periodontally healthy subject were compared using a sequence analysis of 16S rDNA libraries without cultivation. 16S rDNAs were amplified from salivary DNA by PCR and cloned. Randomly selected clones were partially sequenced. On the basis of sequence similarities, the clones were classified into several clusters corresponding to the major phylum of the domain Bacteria. The major phylum in the libraries was the low G+C Gram-positive bacteria. There was no clonal sequence affiliated with periodontopathic bacteria in the salivary sample from the healthy subject, while a number of periodontal pathogens such as Campylobacter rectus, Prevotella intermedia, Porphyromonas gingivalis and Treponema socranskii were detected in the salivary samples from the patients with periodontitis. In addition, a number of previously uncharacterized and uncultured microorganisms were recognized. These organisms may have some role in periodontal disease. This study reveals some potential for a molecular-biological technique to analyze the oral microflora associated with periodontal disease, including previously uncharacterized and uncultured microorganisms, without cultivation.     

Enhanced calcium transients in glial cells in neonatal cerebellar cultures derived from S100B null mice

S100B is the major low-affinity Ca(2+)-binding protein in astrocytes. In order to study the role of S100B in the maintenance of Ca(2+) homeostasis, we generated S100B null mice by a targeted inactivation of the S100B gene. Absence of S100B expression was demonstrated by Northern and Western blotting for S100B mRNA and protein, respectively, and immunoperoxidase staining of sections of various brain regions. S100B null mice were viable, fertile, and exhibited no overt behavioral abnormalities up to 12 months of age. On the basis of light microscopy and immunohistochemical staining, there were no discernable alterations in the distribution and morphology of astrocytes or neurons in sections of adult brains of these mice. Astrocytes in cerebellar cultures derived from 6-day-old S100B null mice exhibited enhanced Ca(2+) transients in response to treatment with KCl or caffeine. On the other hand, granule neurons, in the same cultures, exhibited normal Ca(2+) transients in response to treatment with KCl, caffeine, or N-methyl-d-aspartate. These results demonstrate a specific decrease in Ca(2+)-handling capacity in astrocytes derived from S100B null mice and suggest that S100B plays a role in the maintenance of Ca(2+) homeostasis in astrocytes.