- Volume 49, Issue 2, 1999

The phylogenetic relationships among members of the family Comamonadaceae and several unclassified strains were studied by direct sequencing of their PCR-amplified 16S rRNA genes. Based on the 16S rRNA gene sequence analysis, members of the family formed a coherent group. The closest relatives are species of the Rubrivivax sub-group: Leptothrix discophora, Ideonella dechloratans and Rubrivivax gelatinosus. The genus Hydrogenophaga formed two subclusters, as did the species of Acidovorax, whereas the five species of the genus [Aquaspirillum] were polyphyletic. Comamonas acidovorans was phylogenetically distant from the type species of Comamonas, Comamonas terrigena. On the basis of this work and previous studies, Comamonas acidovorans is removed from the genus Comamonas and renamed as Delftia acidovorans gen. nov., comb. nov. Descriptions of the new genus Delftia and of the type species Delftia acidovorans, for which the type strain is ATCC 15668T, are presented.

Phenotypic and phylogenetic studies were performed with two strains (OCh 239T and OCh 210T, T = type strain) of aerobic bacteriochlorophyll-containing bacteria isolated from the charophytes and the epiphytes on the stromatolites, respectively, of a saline lake located on the west coast of Australia. Both strains were chemoheterotrophic, Gram-negative and motile rods with subpolar flagella. Catalase and oxidase were produced. ONPG reaction was positive. Cells utilized d-glucose, acetate, butyrate, citrate, dl-lactate, dl-malate, pyruvate, succinate, l-aspartate and l-glutamate. Acids were produced from d-fructose and d-glucose. Bacteriochlorophyll a was synthesized under aerobic conditions. Strain OCh 239T had nitrate reductase and phosphatase. Acids were produced from l-arabinose, d-galactose, lactose, maltose, d-ribose and sucrose. The strain could grow in 0·20–0% (w/v) NaCI. Strain OCh 210T had urease. Hydrolysis of gelatin was positive. Acids were produced from d-xylose. The strain could grow in 0·5–20·0% (w/v) NaCI. The results of 16S rRNA sequence comparisons revealed that strains OCh 239T and OCh 210T formed a new cluster within the α-3 group of the α subclass of the class Proteobacteria. The similarity value of the 16S rRNA sequences between strains OCh 239T and OCh 210T was 95·8%. Therefore, it was concluded that these two strains should be placed in a new genus, Roseivivax gen. nov., as the new species Roseivivax halodurans sp. nov. and Roseivivax halotolerans sp. nov. The type species of the genus is Roseivivax halodurans. The type strains of Roseivivax halodurans and Roseivivax halotolerans are OCh 239T (= JCM 10272T) and OCh 210T (= JCM 10271T), respectively.

A sulfate-reducing bacterium, strain HDvT(T = type strain), was isolated from an anoxic ricefield soil. Cells were Gram-negative, non-sporulating curved rods motile by means of a single polar flagellum. Cytochrome c 3 and desulfoviridin were present. In the presence of sulfate, glycerol, 1,2- and 1,3-propanediol, dihydroxyacetone, pyruvate, lactate, fumarate, maleate, malate and succinate were incompletely oxidized mainly to acetate. Sulfite, thiosulfate, elemental sulfur, fumarate, maleate and malate were utilized as alternative electron acceptors. In the absence of added electron acceptors, pyruvate, fumarate, maleate, malate and dihydroxyacetone were fermented. The DNA base composition was 67 mol% G+C. The phylogenetic, phenotypic and physiological characteristics of strain HDvTindicate that it is a new species of the genus Desulfovibrio, for which the name Desulfovibrio burkinensis sp. nov is proposed; the type strain is HDvT(= DSM 6830T). Phylogenetic analysis confirmed that Desulfovibrio alcoholivorans was a distinct species supporting the previously published phenotypic data.

Comparison of both 16S rRNA coding sequences and DNA-DNA hybridization of ten strains of α-subclass of Proteobacteria currently classified as strains of Paracoccus denitrificans has shown that they fall into two groups which are distinct from each other at the species level. Comparison with published data on the cytochrome c profiles and other 16S rRNA coding sequences in the literature has confirmed these observations and enabled several other strains also to be assigned to these two groups. Group A comprises strains ATCC 1774T (the type strain of P. denitrificans), LMD 22.2V, DSM 413T, ATCC 19367, ATCC 13543, DSM 1404, DSM 1405, Pd 1222 (a genetic modification of DSM 4131) and NCIMB 8944. Group B comprises ATCC 35512T (the original type strain of Thiosphaera pantotropha), LMD 82.5T, LMD 92.63, DSM 65, LMG 4218, IAM 12479, JCM 6892, DSM 11072, DSM 11073 and DSM 11104. In light of these findings, it is proposed that: (1) strains of group A are retained as P. denitrificans, with ATCC 17741T as the type strain of the type species; and (2) all strains of group B are assigned to the new species combination Paracoccus pantotrophus comb, nov., with strain ATCC 35512T as the type strain. Comparative 16S rRNA sequence analysis and DNA-DNA hybridization of strains of Paracoccus versutus confirm that this species is distinct from both P. denitrificans and P. pantotrophus, but that its nearest phylogenetic neighbour is P. pantotrophus.

An integrated genotypic and phenotypic analysis of 12 Centers for Disease Control (CDC) group IVc-2 strains revealed that this taxon represents a novel species belonging to the genus Ralstonia. Comparative 16S rDNA sequence analysis allocated a representative CDC group IVc-2 strain to the Ralstonia branch of the ß subclass of the Proteobacteria. DNA–DNA hybridizations did not detect significant binding levels towards any presently known Ralstonia species, including Ralstonia pickettii. Its DNA base ratio is between 65 and 67 mol%. The name Ralstonia paucula sp. nov. is proposed, with strain LMG 3244 ( = CDC E6793), isolated from a human respiratory tract, as the type strain. R. paucula can be differentiated from other Ralstonia species by wholecell protein analysis, amplified rDNA restriction analysis and a variety of classical biochemical tests. Strains have been isolated from various human clinical and environmental sources.

A new purple sulfur bacterium was isolated from microbial films on decaying plant mass in the near-shore area of the soda lake Malyi Kasytui (pH 9·5, 0·2% salinity) located in the steppe of the Chita region of south-east Siberia. Single cells were vibrioid- or spiral-shaped (3–4μm wide and 7–20 μm long) and motile by means of a polar tuft of flagella. Internal photosynthetic membranes were of the lamellar type. Lamellae almost filled the whole cell, forming strands and coils. Photosynthetic pigments were bacteriochlorophy II a and carotenoids of the spirilloxanthin group. The new bacterium was strictly anaerobic. Under anoxic conditions, hydrogen sulfide and elemental sulfur were used as photosynthetic electron donors. During growth on sulfide, sulfur globules were formed as intermediate oxidation products. They were deposited outside the cytoplasm of the cells, in the peripheral periplasmic space and extracellularly. Thiosulfate was not used. Carbon dioxide, acetate, pyruvate, propionate, succinate, fumarate and malate were utilized as carbon sources. Optimum growth rates were obtained at pH 9·0 and optimum temperature was 30 °C. Good growth was observed in a mineral salts medium containing 5 g sodium bicarbonate I–1 without sodium chloride. The new bacterium tolerated up to 60 g sodium chloride I–1 and up to 80 g sodium carbonates I–1. Growth factors were not required. The DNA G+C composition was 56·0–57·4 mol %. Based on physiological, biochemical and genetic characteristics, the newly isolated bacterium is recognized as a new species of a new genus with the proposed name Thiorhodospira sibirica.

The genus Shewanella has been studied since 1931 with regard to a variety of topics of relevance to both applied and environmental microbiology. Recent years have seen the introduction of a large number of new Shewanella-like isolates, necessitating a coordinated review of the genus. In this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them into a consensus classification. Based on information generated from this study and obtained from the literature, a scheme for the identification of Shewanella species has been compiled. Key phenotypic characteristics were sulfur reduction and halophilicity. Fatty acid and quinone profiling were used to impart an additional layer of information. Molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in some cases. As a result, DNA-DNA hybridization and sequence analyses of a more rapidly evolving molecule (gyrB gene) were performed. Species-specific PCR probes were designed for the gyrB gene and used for the rapid screening of closely related strains. With this polyphasic approach, in addition to the ten described Shewanella species, two new species, Shewanella oneidensis and ‘Shewanella pealeana’, were recognized; Shewanella oneidensis sp. nov. is described here for the first time.

Two new strains of marine purple bacteria, N1T and N2T, were isolated from coastal sediment of the North Sea (Germany) with ferrous iron as the only electron donor for anoxygenic photosynthesis. The isolates are the first saltdependent, ferrous-iron-oxidizing purple bacteria characterized so far. Analysis of 16S rRNA gene sequences revealed an affiliation with the genus Rhodovulum, which until now comprises only marine species. The sequence similarity of both strains was 95·2 %, and their closest relative was Rhodovulum adriaticum. Like all known Rhodovulum species, the new strains had ovoid to rod-shaped cells, contained bacteriochlorophyll a and carotenoids of the spheroidene series, and were able to oxidize sulfide and thiosulfate. Like Rhodovulum adriaticum, both strains were unable to assimilate sulfate ; for growth they needed a reduced sulfur source, e.g. thiosulfate. In contrast to the new strains, none of the known Rhodovulum species tested was able to oxidize ferrous iron or iron sulfide. In growth experiments, strains N1T and N2T oxidized 65 and 95%, respectively, of the ferrous iron supplied. Electron diffraction analysis revealed ferrihydrite as the main product of ferrous iron oxidation. In addition, traces of magnetite were formed. Strains N1T (= DSM 12328T) and N2T (= DSM 12329T) are described as Rhodovulum iodosum sp. nov. and Rhodovulum robiginosum sp. nov., respectively.

Three bacterial strains isolated from biofilms of the Berlin drinking water system were characterized with respect to their morphological and physiological properties and their taxonomic position. Phenotypically, the bacteria investigated were motile, Gram-negative rods, oxidase-positive and catalase-negative, and contained polyalkanoates and polyphosphate as storage polymers. They displayed a microaerophilic growth behaviour and used oxygen and nitrate as electron acceptors, but not nitrite, chlorate, sulfale or ferric iron. The substrates metabolized included a broad range of organic acids but no carbohydrates at all. The three species can be distinguished from each other by their substrate utilization, ability to hydrolyse urea and casein, cellular protein patterns and growth on nutrient-rich media as well as their temperature, pH and NaCI tolerances. Phylogenetic analysis, based on 16S rRNA gene sequence comparison, revealed that the isolates are affiliated to the β1-subclass of Proteobacteria. The isolates constitute three new species with internal levels of DNA relatedness ranging from 44·9 to 51·3%. It is proposed that a new genus, Aquabacterium gen. nov., should be created, including Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov. and Aquabacterium commune sp. nov. The type species of the new genus is Aquabacterium commune. The type strain of A. citratiphilum is strain B4T(= DSM 11900T), the type strain of A. parvum is strain B6T(= DSM 11968Tand the type strain of A. commune is strain B8T(= DSM 11901T).

The phylogenetic position of Gram-negative, strictly anaerobic, non-spore-forming bacteria, representing four different genera, was determined by analysis of their 16S rDNA sequences. Formivibrio citricus and Propionivibrio dicarboxylicus are members of the β-subclass of the class Proteobacteria. While Formivibrio citricus stands phylogenetically isolated, Propionivibrio dicarboxylicus is moderately related to members of the genus Rhodocyclus. Succinimonas amylolytica and Succinivibrio dextrinosolvens are members of the γ-subclass of the class Proteobacteria in which they, together with members of the genus Anaerobiospirillum and Ruminobacter amylophilus, form a separate line of descent. This phylogenetic group is described as Succinivibrionaceae fam. nov.

The taxonomic positions of ‘Pseudomonas hydrogenothermophila’ strain TH-1 and ‘Flavobacterium autothermophilum’ strain TH-4 were studied by 16S rDNA sequencing. These organisms are Gram-negative, strictly aerobic, thermophilic facultatively chemolithoautotrophic hydrogen-oxidizing rods and have a DNA G+C content of 63–65 mol%. The major isoprenoid quinone is ubiquinone-8 an 3-hydroxy decanoic acid (3-OH C10:0) is the major 3-hydroxy cellular fatty acid, phylogenetic analysis based on 16S rDNA sequences placed strains TH-1Tand TH-4 in the β-subclass of the Proteobacteria. The taxonomic characteristics of these organisms are different from those of previously described aerobic, facultatively chemolithoautotrophic, hydrogen-oxidizing bacteria that belong to the β-subclass of Proteobacteria. On the basis of the information described above, a new genus and species, Hydrogenophilus thermoluteolus gen. nov., sp. nov., is described to include both strains. The type strain is strain TH-1T(= IFO 14978T).

Twenty-one exopolysaccharide-producing strains were isolated from the 5–20 μm fraction of a vertisol in the south-east of the island of Martinique in the French West Indies. Although these strains were phenotypically identifie as Burkholderia cepacia or as Burkholderia glathei using BIOLOG microplates they did not cluster genotypically by amplified rDNA restriction analysis (ARDRA) with any described Burkholderia species. A phylogenetic analysis revealed that the rrs (16S rDNA) sequences of three representative strains clustered in a single branch within the genus Burkholderia and distantly from all of the previously described species of Burkholderia for which rrs sequences were available. DNA–DNA hybridization data as well as phenotypic analyses indicated that the 21 isolates represented a single and new species for which the name Burkholderia caribensis sp. nov. is proposed (type strain MWAP64TLMG 18531T).

A sulfate-reducing bacterium, designated strain lacT, was isolated from surface-sterilized roots of the benthic macrophyte Zostera marina. Cells were motile by means of a single polar flagellum. Strain lacTutilized lactate, pyruvate, malate, ethanol, l-alanine, fumarate, choline and fructose with sulfate as electron acceptor. In addition, fumarate, pyruvate and fructose were also degraded without an external electron acceptor. Sulfate could be substituted with thiosulfate, sulfite and elemental sulfur. Optimal growth was observed between 32·5 and 34·5 °C, at an NaCl concentration of 0·2 M and in a pH range between 6·8 and 7·3. The G+C content of the DNA was 42·7±0·2 mol%. Desulfoviridin and catalase were present. Strain lacTcontained c-type cytochromes. Comparative 16S rRNA gene sequence analysis and the fatty acid pattern grouped this isolate into the genus Desulfovibrio. However, strain lacTdiffers from all other described Desulfovibrio species on the bases of its 16S rRNA gene sequence, the G+C content, its cellular lipid pattern and the utilization pattern of substrates. These characteristics establish strain lacT(= DSM 11974T) as a novel species of the genus Desulfovibrio, for which the name Desulfovibrio zosterae sp. nov. is proposed.

Taxon 1502 was originally described as a Riemerella anatipestifer-like bacterium causing exudative septicaemia in ducks and geese. In the present study, an integrated genotypic and phenotypic approach was used to elucidate the phylogenetic affiliation and taxonomic relationships of 12 strains of taxon 1502. Whole-cell protein and fatty acid analyses and an extensive biochemical examination by using conventional tests and several API microtest systems indicated that all isolates formed a homogeneous taxon, which was confirmed by DNA–DNA hybridizations. 16S rDNA sequence analysis of a representative strain (LMG 14382T) indicated that this taxon belongs to the Cytophaga–Flavobacterium–Bacteroides phylum and revealed a moderate but distinct relationship to species of the genus Capnocytophaga (overall 16S rDNA sequence identities were 88·8–90·2 %). Taxon 1502 is concluded to represent a single species that should be allocated to a novel genus, and the name Coenonia anatina gen. nov., sp. nov. is proposed. The DNA G+C content of representative strains was 35–36 mol% and the type strain is LMG 14382T.

A new member of the genus Thiomicrospira, which utilizes thiosulfate as the electron donor and CO2 as the carbon source, was isolated from a sediment sample dominated by the filamentous sulfur bacterium Thioploca. Although the physiological properties investigated are nearly identical to other described species of the genus, it is proposed that strain Ch-1Tis a member of new species, Thiomicrospira chilensis sp. nov., on the basis of differences in genotypic characteristics (16S rRNA sequence, DNA homology, G+C content). Strain Ch-1Twas highly motile with a slight tendency to form aggregates in the stationary growth phase. The organism was obligately autotrophic and strictly aerobic. Nitrate was not used as an electron acceptor. Chemolithoautotrophic growth was observed with thiosulfate, tetrathionate, sulfur and sulfide. The isolate was not able to grow heterotrophically. Growth of strain Ch-1Twas observed between pH 5·3 and 8·5 with an optimum at pH 7·0. The temperature range for growth was between 3·5 and 42 °C; the optimal growth temperature was between 32 and 37 °C. The mean maximum growth rate on thiosulfate was 0·4 h-1. This is the second Thiomicrospira species described that has a rodshaped morphology; therefore discrimination between vibrio-shaped Thiomicrospira and rod-shaped Thiobacilli is no longer valid.

An aerobic bacterium, strain BN12T, which degrades substituted naphthalenesulfonates and substituted salicylates was isolated from a 6-aminonaphthalene-2-sulfonate-degrading microbial consortium originating from the River Elbe, Germany. Chemotaxonomic investigations of quinones, polyamines and polar lipids allowed allocation of this strain to the α-subclass of the Proteobacteria and revealed similarity to species of the genera Aminobacter, Chelatobacter and Mesorhizobium. This was confirmed by typing with 16S rRNA-targeted oligonucleotide probes and 16S rDNA sequencing and phylogenetic analysis, indicating that BN12T clusters most closely with a strain ‘ Thiobacillus’ THI 051T and with the above genera but comprising a separate branch. DNA–DNA hybridizations demonstrated that strain BN12T is different from all species of Aminobacter currently described and recognized. The fatty acid patterns, substrate utilization profile and biochemical characteristics displayed no obvious similarity to the characteristics of Aminobacter and Chelatobacter species. ‘Thiobacillus’ THI 051T, however, revealed phenotypic similarities to BN12T. Furthermore, 16S rRNA sequences of Chelatobacter heintzii showed a high similarity to the 16S rRNA sequences of all currently recognized Aminobacter species. On the basis of these and previously published results, the new genus Pseudaminobacter is proposed, harbouring the two new species Pseudaminobacter salicylatoxidans sp. nov. and Pseudaminobacter defluvii sp. nov. The type strains are BN12T ( = DSM 6986T) and THI 051T (= IFO 1457T), respectively.

A novel pathogen from Asian pears (Pyrus pyrifolia Nakai) was analysed by sequencing the 16S rDNA and the adjacent intergenic region, and the data were compared to related Enterobacteriaceae. The 16S rDNA of the Asian pear pathogen was almost identical with the sequence of Erwinia amylovora, in contrast to the 16S–23S rRNA intergenic transcribed spacer region of both species. A dendrogram was deduced from determined sequences of the spacer regions including those of several related species such as Erwinia amylovora, Enterobacter pyrinus, Pantoea stewartii subsp. stewartii and Escherichia coli. Dendrograms derived from 121 biochemical characteristics including Biotype 100 data placed the Asian pear pathogen close to Erwinia amylovora and more distantly to other members of the species Erwinia and to the species Pantoea and Enterobacter. Another DNA relatedness study was performed by DNA hybridizations and estimation of ΔT m values. The Asian pear strains constituted a tight DNA hybridization group (89–100%) and were barely related to strains of Erwinia amylovora (40–50%) with a ΔT m in the range of 5·2–6·8. The G+C content of DNA from the novel pathogen is 52 mol %. Therefore, it is proposed that strains isolated from Asian pears constitute a new species and the name Erwinia pyrifoliae is suggested; the type strain is strain Ep16/96T (= CFBP 4172T = DSM 12163T).

Comparison of phenotypic, chemotaxonomic and genomic properties of the type strains of Kocuria rosea and Kocuria erythromyxa indicates that these taxa are members of the same species. The conclusion is based upon 16S rDNA similarity of 99·9% [Rainey, F. A., et al. (1997). Int J Syst Barteriol 47, 510-514], DNA-DNA reassociation of 95%, identical fatty acid patterns and almost identical physiological reactions against substrates provided by the BIOLOG plate. According to Rule 42 of the International Code of Nomenclature of Bacteria, which requires that the oldest legitimate epithet be retained when taxa of equal rank are united, Kocuria (Micrococcus) rosea (Flügge 1886) has priority over Kocuria (Deinococcus) erythromyxa (Brooks and Murray 1981).