Wolfgang Ludwig

Complete 23S Ribosomal RNA Sequences of Gram-positive Bacteria with a Low DNA G+C Content

Summary The complete 23S rRNA primary structures of 14 gram-positive bacteria with a low DNA G+C content were determined. The sequences were compared with 50 published as well as unpublished complete 23S rRNA sequences from bacteria. Based on previously published models, higher order structure analyses were performed and a consensus higher order structure model of the 23S rRNA from gram-positive bacteria with a low DNA G+C content was established. A tree reflecting the phylogenetic relationships among gram-positive bacteria with a low DNA G+C content was reconstructed and compared with a phylogenetic tree based on a comparable data set of 16S rRNA sequences. The topologies of the trees are in good agreement.

Geovibrio ferrireducens, a phylogenetically distinct dissimilatory Fe(III)-reducing bacterium

Abstract A new, phylogenetically distinct, dissimilatory, Fe(III)-reducing bacterium was isolated from surface sediment of a hydrocarbon-contaminated ditch. The isolate, designated strain PAL-1, was an obligately anaerobic, non-fermentative, motile, gram-negative vibrio. PAL-1 grew in a defined medium with acetate as electron donor and ferric pyrophosphate, ferric oxyhydroxide, ferric citrate, Co(III)-EDTA, or elemental sulfur as sole electron acceptor. PAL-1 also used proline, hydrogen, lactate, propionate, succinate, fumarate, pyruvate, or yeast extract as electron donors for Fe(III) reduction. It is the first bacterium known to couple the oxidation of an amino acid to Fe(III) reduction. PAl-1 did not reduce oxygen, Mn(IV), U(VI), Cr(VI), nitrate, sulfate, sulfite, or thiosulfate with acetate as the electron donor. Cell suspensions of PAL-1 exhibited dithionite-reduced minus air-oxidized difference spectra that were characteristic of c-type cytochromes. Analysis of the 16S rRNA gene sequence of PAL-1 showed that the strain is not related to any of the described metal-reducing bacteria in the Proteobacteria and, together with Flexistipes sinusarabici, forms a separate line of descent within the Bacteria. Phenotypically and phylogenetically, strain PAl-1 differs from all other described bacteria, and represents the type strain of a new genus and species, Geovibrioferrireducens.

Comparative sequence analysis of 23S rRNA from Proteobacteria

Summary 23S rRNA genes of 17 strains representing the α, s, γ, δ and µ subclasses of the Proteobacteria were completely sequenced. The sequences were aligned to about 120 published as well as unpublished complete or almost complete primary structures of 23S rRNAs from other members of the domain Bacteria representing all known phyla. Primary and higher order structure analyses revealed remarkable differences of predicted 23S rRNA structures from members of the different subclasses. A phylogenetic tree reflecting the relationships among proteobacteria was reconstructed based on 23S rRNA sequence comparison. The topology of the tree is similar to that of a tree based on an equivalent 16S rRNA sequence data set.

Isolation and Taxonomic Characterization of a Halotolerant, Facultatively Iron-reducing Bacterium

Summary The isolation of a halotolerant, Fe(III)-reducing, Gram-negative bacterium from surface sediments of the Sippewisset marsh in Woodshole (USA) will be described. Detailed molecular taxonomic studies such as comparative 16S rRNA sequence analysis and DNA-DNA hybridization experiments revealed that the newly isolated strain is closely related to the previously isolated strain BrY. Both strains belong to the DNA-DNA similarity group IV of Shewanella putrefaciens which has recently been described as Shewanella alga . Thus, the ability to reduce Fe(III) is no longer restricted to S. putrefaciens within the genus but is also found among strains of S. alga . A 16S rRNA targeted probe has been designed that enabled us to rapidly differentiate strains of S. alga from those of S. putrefaciens and other bacteria.

Pure culture of Syntrophus buswellii, definition of its phylogenetic status, and description of Syntrophus gentianae sp. nov.

Summary The syntrophically benzoate-oxidizing anaerobic bacterium Syntrophus bustvellii was grown in pure culture in a defined mineral medium with crotonate as sole substrate, which was fermented stoichiometrically to acetate and butyrate. This pure culture, as well as that of another benzoate-oxidizing syntrophic bacterium, strain HQGo1, both were analyzed for possible phylogenetic relatedness on the basis of total 16S rRNA sequence analysis. Both strains turned out to be closely related and clustered in the δ subgroup of the Proteobacteria with sulfate-reducing bacteria. Strain HQGo1, which can be grown in pure culture with either hydroquinone or gentisic acid, is described as a new species of the genus Syntrophus, S. gentianae sp. nov.

Ferrimonas balearica gen. nov., spec. nov., a New Marine Facultative Fe(III)-reducing Bacterium

Summary The isolation of a new Fe(III)-reducing organism from a Mediterranean marine sediment at the coast of Mallorca (Spain) is described. Comparative 16S rRNA data analysis showed that the new isolate is a member of the gamma subclass of Proteobacteria and indicated a potential moderate phylogenetic affiliation to Shewanella species, Vibrio marinus and Alteromonas haloplanktis . Fe(III)-reduction was first described for members of the latter group. The low level of relatedness of the isolate to its closest relatives justifies the proposal of a new genus and species, namely Ferrimonas balearica gen. nov. spec. nov. .

Species Specific Oligonucleotide Probe for the Identification of Streptococcus thermophilus

Summary Sequences of 23S rRNA specific for the type strains of Streptococcus thermophilus and Streptococcus salivarius were identified and complementary oligonucleotides synthesized. The specifity of the probes was checked by dot blot hybridization. The probes reacted only with strains of S. thermophilus and S. salivarius, respectively. Other lactic acid bacteria tested did not react with these oligonucleotide probes.

The Phylogenetic Positions of Pelobacter acetylenicus and Pelobacter propionicus

Summary Almost complete 16S rRNA gene primary structures of Pelobacter acetylenicus strain WoAcyl (DSM 2348) and Pelobacter propionicus strain OttBd14 (DSM2379) were determined by direct sequencing of in vitro amplified DNA. Both species are members of the δ-subclass of Proteobacteria. Pelobacter acetylenicus is phylogenetically closer related to Pelobacter acidigallici, Pelobacter carbinolicus, Pelobacter venetianus and to Desulfuromonas species than to Pelobacter propionicus.

A 23S rRNA Targeted Specific Hybridization Probe for Bradyrhizobium japonicum

Summary The complete nucleotide sequences of 23S rRNA genes from Bradyrhizobium japonicum DSM 30131 and from closely related Rhodopseudomonas palustris DSM 126 were determined. A specific hybridization probe for Bradyrhizobium japonicum was designed and tested. The probe hybridized to nucleic acids from all Bradyrhizobium japonicum strains tested and did not react with nucleic acids from other reference bacteria.

The fermenting bacterium Malonomonas rubra is phylogenetically related to sulfur-reducing bacteria and contains a c-type cytochrome similar to those of sulfur and sulfate reducers

Malonomonas rubra is a microaerotolerant fermenting bacterium which can maintain its energy metabolism for growth by decarboxylation of malonate to acetate. 16S rRNA sequence analysis revealed that M. rubra is closely related to the cluster of mesophilic sulfur-reducing bacteria within the delta subclass of the Proteobacteria, with the fermenting bacterium Pelobacter acidigallici and the sulfur reducers Desulfuromusa kysingii, D. bakii and D. succinoxidans as closest relatives. The cells contain high amounts (up to 12% of the total cell protein content) of a c-type cytochrome which is present mainly (> 60%) in the cytoplasm and to minor parts in the periplasm (> 20%) and associated with the membrane fraction (> 10%), independent of the growth substrate. This cytochrome is a tetraheme cytochrome of 13,700 Da molecular mass with a midpoint redox potential of -0.210 V.M. rubra does not reduce sulfur or ferric iron compounds. Since this cytochrome appears not to be involved in the energy metabolism it is concluded that it is a remnant of sulfur-reducing ancestors of this bacterium, without a conceivable physiological function in its present energy metabolism.