The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and amino acid sequence data as well. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or worldwide networks. A phylogenetic tree visualized in the main window can be used for data access and visualization. The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridization probe design and evaluation and other components for data analysis. Currently, the package is used by numerous working groups worldwide.

Uncultivated Nitrospira-like bacteria in different biofilm and activated-sludge samples were investigated by cultivation-independent molecular approaches. Initially, the phylogenetic affiliation of Nitrospira-like bacteria in a nitrifying biofilm was determined by 16S rRNA gene sequence analysis. Subsequently, a phylogenetic consensus tree of the Nitrospira phylum including all publicly available sequences was constructed. This analysis revealed that the genus Nitrospira consists of at least four distinct sublineages. Based on these data, two 16S rRNA-directed oligonucleotide probes specific for the phylum and genus Nitrospira, respectively, were developed and evaluated for suitability for fluorescence in situ hybridization (FISH). The probes were used to investigate the in situ architecture of cell aggregates of Nitrospira-like nitrite oxidizers in wastewater treatment plants by FISH, confocal laser scanning microscopy, and computer-aided three-dimensional visualization. Cavities and a network of cell-free channels inside the Nitrospira microcolonies were detected that were water permeable, as demonstrated by fluorescein staining. The uptake of different carbon sources by Nitrospira-like bacteria within their natural habitat under different incubation conditions was studied by combined FISH and microautoradiography. Under aerobic conditions, the Nitrospira-like bacteria in bioreactor samples took up inorganic carbon (as HCO 3 ؊ or as CO 2 ) and pyruvate but not acetate, butyrate, and propionate, suggesting that these bacteria can grow mixotrophically in the presence of pyruvate. In contrast, no uptake by the Nitrospira-like bacteria of any of the carbon sources tested was observed under anoxic or anaerobic conditions. Nitrification, the oxidation of ammonia to nitrate catalyzed by bacteria, is a key part of global nitrogen cycling (37). In the first step of nitrification, chemolithoautotrophic ammonia oxidizers transform ammonia to nitrite, which is subsequently oxidized to nitrate by the nitrite-oxidizing bacteria (8). All isolated chemolithoautotrophic, nitrite-oxidizing bacteria belong to one of four different genera (7) Nitrobacter (alpha subclass of Proteobacteria), Nitrococcus (gamma subclass of Proteobacteria), Nitrospina (delta subclass of Proteobacteria), and Nitrospira (phylum Nitrospira). While species of the genus Nitrobacter have been isolated from a variety of environments, including soil and fresh water, it was long assumed that the other three genera were confined to marine environments (7). In recent studies, however, bacteria related to the genus Nitrospira were also found to occur in different nonmarine habitats. While the first described species of this genus, Nitrospira marina, was isolated from ocean water (49), the second isolated species, N. moscoviensis, was cultured from an iron pipe of a heating system in Moscow, Russia (16). These two species are the only cultivated representatives of the genus Nitrospira, but numerous related bacteria have recently been detected by comparative analy...

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Thirty-two strains originally identified as Lactobacillus acidophilus and L. gasseri were screened for their taxonomic homogeneity by SDS-PAGE of whole-cell proteins. After numerical comparison of the resulting protein electrophoretic fingerprints, two well-delineated clusters were detected. The majority of the strains grouped in one electrophoretic cluster, which contained the type strain of L. acidophilus and corresponds to DNA group A1 of Johnson, J. L., Phelps, C. F., Cummins, C. S., London, J. & Gasser, F. (1980; Znternational Journalof Systematic Bacteriology 30, 53-68). Another cluster corresponded to DNA group B. It contained two subclusters, which agreed perfectly with DNA subgroups B l (L. gasseri) and B2 (A. johnsonii), respectively. The 23s rRNA genes were partially sequenced and 23s-rRNA-targeted oligonucleotide probes were designed for identification of DNA groups Al, B1 and B2. Probe Lbg reacted with all strains of electrophoretic cluster B1 (L. gasseri), probe Lbj hybridized with strains of cluster B2 (L. johnsonii) and probe Lba with strains of cluster A1 (authentic L. acidophilus). The probes were successfully used for the identification of strains belonging to the respective species. The phylogenetic relationship of a representative of L. johnsonii was determined by comparative sequence analysis of the 16s rRNA genes. It is very closely related to L. gasseri.

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