- Volume 52, Issue 4, 2002

Five coccoid, Gram-positive strains were isolated from the air of the 'Virgilkapelle' in Vienna. A representative of these five strains, V-108T, shared 99.0 and 98.4% 16S rDNA sequence similarity, respectively, with Agrococcus jenensis DSM 9580 and Agrococcus citreus DSM 12453T. Colonies of the five strains were white when grown in the dark and turned yellow in the light. The strains displayed highly similar biochemical and physiological characteristics and showed only small differences in their protein patterns obtained after SDS-PAGE. Based on Fourier-transform infra-red (FT-IR) spectra, the five strains were grouped together and separated from the other members of the genus, A. jenensis and A. citreus. Chemotaxonomic characteristics analysed from selected members of the five isolates, including polar lipids, quinone systems, polyamine patterns, cell wall composition and fatty acid profiles, were in good agreement with those of the two species of the genus Agrococcus described to date. The G+C content of the genomic DNA was determined to be within the narrow range of 73.8-74.9 mol%. The results of DNA-DNA hybridization with A. citreus DSM 12453T and A. jenensis DSM 9580T, as well as differences in biochemical/physiological characteristics, peptidoglycan composition, fatty acids, polar lipid profiles and FT-IR spectra, demonstrated that the five isolates represent a novel species of the genus Agrococcus. The name Agrococcus baldri sp. nov. is proposed for the novel species, of which strain V-108T (= DSM 14215T = CCM 4953T) is the type strain.

A strictly anaerobic, moderately thermophilic, sporulating rod, designated strain Lup 33T, was isolated from an upflow anaerobic sludge blanket (UASB) reactor in Mexico. Strain Lup 33T possessed a few laterally inserted flagella, had a DNA G+C content of 32.2 mol % and grew optimally at pH 7.4 and 40 degrees C. Growth was observed at temperatures of up to 50 degrees C and was inhibited in the presence of 5% NaCl. Strain Lup 33T is heterotrophic and utilized some sugars, peptides and various single amino acids. Gelatin and casein were not used as energy sources. It performed the Stickland reaction and reduced elemental sulfur to sulfide. Acetate was the only fatty acid detected from glucose fermentation, whereas acetate together with isobutyrate and isovalerate were found as end products from peptone fermentation. Phylogenetically, strain Lup 33T branched with members of cluster XII of the order Clostridiales, with Clostridium hastiforme as the closest relative (similarity of 93%). On the basis of the phenotypic, genotypic and phylogenetic characteristics of the isolate, it is proposed as a novel species of a new genus, Sporanaerobacter acetigenes gen. nov., sp. nov. The type strain is strain Lup 33T (= DSM 13106T = CIP 106730T).

A carboxydotrophic actinomycete strain, AT10T (= DSM 41779T = KCTC 9909T), was the subject of a polyphasic study. The morphological and chemical properties of the strain were found to be consistent with its assignment to the genus Streptomyces. The organism formed a distinct phyletic line within the 16S rDNA Streptomyces tree, and DNA-DNA relatedness experiments further confirmed that it formed a distinct genomic species. The strain was also distinguished from related species using phenotypic properties. Strain AT10T, therefore, merits species status within the genus Streptomyces; the name Streptomyces thermospinisporus sp. nov. is proposed for this new taxon.

Three rod-shaped, Gram-positive strains were isolated from the air of the chapel 'Virgilkapelle' in Vienna. A representative of these three strains, strain V-73T, shared the highest 16S rDNA sequence similarities with members of the genus Microbacterium, in particular Microbacterium foliorum, Microbacterium testaceum, Microbacterium esteraromaticum, Microbacterium keratanolyticum and Microbacterium arabinogalactanolyticum. The strains displayed almost identical biochemical and physiological characteristics and showed no differences in their protein patterns obtained after SDS-PAGE. On the basis of Fourier-transform infra-red (FT-IR) spectra and genomic fingerprints, the three strains were grouped together and separated from the other relevant members of the genus Microbacterium. The chemotaxonomic characteristics analysed, including polar lipids, quinone systems, cell wall composition and fatty acid profiles, were in good agreement with the characteristics described for the genus Microbacterium. The G+C content of the DNAs was determined to be in the narrow range 69.3-69.7 mol %. The results of DNA-DNA hybridization, biochemical/physiological characterization, ERIC-PCR-generated genomic fingerprints and FT-IR spectra demonstrated that the three isolates represent a novel species of the genus Microbacterium. The name Microbacterium aerolatum sp. nov. is proposed for the novel species, of which strain V-73T (= DSM 14217T = CCM 4955T) is the type strain.

A strain of Streptosporangium with an unusual phospholipid pattern was isolated from Yunnan Province, a region in China. The isolate, designated CY-7113T, was identified by morphological and physiological properties, cell chemistry, genomic DNA G+C content, DNA-DNA hybridization and phylogenetic analysis. Based on 16S rRNA gene sequencing, DNA-DNA hybridization, phenotypic characteristics and its unusual phospholipid pattern, it was concluded that strain CY-7113T belongs to a novel Streptosporangium species, for which the name Streptosporangium subroseum sp. nov. is proposed. Strain CY-7113T (= CCTCC 97008T = CRC 16302T) is the type strain.

Phenotypic characterization of bacteria from diseased and healthy horses identified 18 isolates as Bisgaard taxon 9 and 11 isolates as Actinobacillus lignieresii. All strains of taxon 9 were alpha-galactosidase- and raffinose-positive and showed variable fermentation of (+)L-arabinose and (-)D-sorbitol. Strains of A. lignieresii were negative for these characteristics, with the exception of raffinose. Two strains from the (-)D-sorbitol-negative group of taxon 9 showed a 16S rRNA similarity of 99-6%, while 99.5% similarity was found between two strains of the (-)D-sorbitol-positive group. DNA-DNA hybridization between the two strains representing the (-)D-sorbitol-negative group showed 98% binding, and their closest relationship was to a strain of A. lignieresii (64%). The two strains of the (-)D-sorbitol-positive group showed 83% binding and were related to the (-)D-sorbitol-negative group at a 76% DNA binding level. Actinobacillus arthritidis sp. nov. is proposed for 12 strains of the (-)D-sorbitol-positive group. Actinobacillus genomospecies 2 is suggested for the six strains of the (-)D-sorbitol-negative group. Phenotypically, strains of A. arthritidis and Actinobacillus genomospecies 2 differ in (-)D-sorbitol fermentation and can be separated from Actinobacillus equuli by being trehalose-negative, while a positive reaction for alpha-galactosidase separates the taxa from A. lignieresii. The type strain of A. arthritidis, CCUG 24862T, was isolated from a joint of a horse. Three equine isolates of A. lignieresii that could not be separated from the type strain by means of phenotypic characteristics showed 98.6-100% 16S rRNA similarity, but only 96.4-96.7% similarity to the type strain. DNA-DNA hybridization between two strains of this group showed 92% binding but only 70% binding to the type strain of A. lignieresii. Consequently, these equine isolates of A. lignieresii represent a new genomospecies of Actinobacillus, suggested as genomospecies 1 because phenotypic characteristics are not presently available to separate it from the type strain of A. lignieresii.

The taxonomic dissection of the Streptococcus bovis-Streptococcus equinus group was carried out upon obtaining sequences for the manganese-dependent superoxide dismutase gene (sodA) of the type strains of S. bovis, Streptococcus caprinus, S. equinus, Streptococcus gallolyticus, Streptococcus infantarius, Streptococcus macedonicus and Streptococcus waius. The sodA sequences of 29 streptococcal strains of animal and human origin that were related to S. bovis were also sequenced. A phylogenetic analysis of the sodA sequences revealed that the S. bovis-S. equinus group comprises five different clusters that correspond to five distinct species. The type strains of S. bovis and S. equinus were associated in the same cluster, corresponding to the species S. equinus. The type strains of S. caprinus, S. gallolyticus, S. macedonicus and S. waius were associated in the same cluster, which defined a single species containing S. gallolyticus and its junior synonym S. caprinus, and S. macedonicus and its junior synonym S. waius. The two subspecies thought to constitute the species S. infantarius, namely S. infantarius subsp. infantarius and 'S. infantarius subsp. coli', were located in two distinct clusters. One of these clusters defined the species S. infantarius and included the type strain of S. infantarius subsp. infantarius. The other cluster defined 'S. infantarius subsp. coli', leading to the proposal of its reclassification as the novel species Streptococcus lutetiensis (NEM 782T = CIP 106849T). The remaining cluster comprised all of the strains previously identified as belonging to S. bovis biotype 11.2, leading to the proposal to reassign these strains to the novel species Streptococcus pasteurianus (NEM 1202T = CIP 107122T). The results of the phylogenetic analysis were confirmed by DNA-DNA hybridization experiments, thus demonstrating that sequence databases of defined DNA targets, such as sodA, may constitute a valuable alternative approach for modern bacterial systematics.

A taxonomic study was carried out on two strains that came from kimchi, a traditional Korean fermented-vegetable food. The DNA G+C content of these strains was 37 mol %. Both strains contained Lys-Ala-Ser in the cell walls. On the basis of morphological, physiological and chemotaxonomic characteristics, together with data from 16S rDNA sequence comparisons and DNA-DNA reassociation, it is proposed that these strains represent a novel species of the genus Weissella, Weissella koreensis sp. nov. The type strain is strain S-5623T (= KCTC 3621T KCCM 41516T = JCM 11263T).

An unknown, strictly anaerobic, Gram-positive, rod-shaped bacterium (strain MOL361T) was isolated from a blood culture of a febrile patient with acute appendicitis and characterized using phenotypic and molecular methods. Fatty acid analysis and biochemical examination indicated that the isolate most closely resembles members of the Gram-positive bacteria with low DNA G+C content. 16S rDNA sequencing revealed a relatively high overall similarity (97%) to an uncultured bacterium, but these two strains both exhibit low (<87%) 16S rDNA similarity to other bacteria. Phylogenetic analysis with different treeing methods showed that this strain forms a novel line of descent within the Gram-positive bacteria with low G+C content. Strain MOL361T is described as the type strain of a novel species within a new genus, Turicibacter sanguinis gen. nov., sp. nov.

This work is the completion of a series of reports describing the nitrogen-fixing bacterial symbionts of sulla (Hedysarum coronarium L., Leguminosae) and providing the grounds for their proposal as a new taxon. The introduction summarizes a large amount of previous evidence gathered on the physiology, genetics and ecology of such organisms, which have in the past been referred to provisionally as 'Rhizobium hedysari'. Upon adding 16S RNA sequencing, amplified rDNA restriction analysis of the rrn operon, DNA-DNA hybridization homology and analysis of low-molecular-mass RNA species, it is concluded that the group of strains that specifically nodulate sulla consists of a coherent set of isolates that differ from previously described rhizobia to an extent that warrants the constitution of the species boundary. The name Rhizobium sullae sp. nov. is proposed, with isolate 1S123T (=USDA 4950T = DSM 14623T) as the type strain.

A novel bacterium from the Mediterranean Sea was isolated under oligotrophic conditions at in situ temperature after prolonged continuous culture. The isolates were initially characterized by partial 16S rRNA gene sequencing. Similarity searches of one of the isolates, QMT2T, indicated high sequence identity to the well-characterized Rhodospirillum rubrum, [Aquaspirillum] itersonii and [Oceanospirillum] pusillum micro-organisms, which are representatives of the alpha-subclass of the Proteobacteria. The highest level of similarity of the complete 165 rRNA gene with respect to these microorganisms was 89%. Features such as the low similarities of 165 rRNA of QMT2T with its phylogenetically close neighbours, the distinct G+C content, and the differences in phenotypic features, including pigmentation, fatty acid composition, salt tolerance, the lack of bacteriochlorophyll a, and the capacity to use carbohydrates as carbon sources, are indicative of the novel nature of the isolate QMT2T among the alpha-Proteobacteria. This report describes the classification of strain QMT2T (= DSM 14000T = CECT 5390T) as a new genus and species, Thalassospira lucentensis gen. nov, sp. nov., in the family Rhodospirillaceae.

Six deep-yellow-pigmented strains were isolated from soil after enrichment on plasticized acetylated starch granules as a source of carbon. They showed very similar and unique fatty acid profiles, consisting almost exclusively of branched fatty acids. The strains consisted of small, motile rods, were oxidase- and catalase-positive, did not ferment sugars and were able to depolymerize starch and suspended acetylated starch in overlayer plates. The 16S rDNA sequence of a representative strain, strain LMG 19981T, showed 96.7% sequence similarity to that of Rhodanobacter lindaniclasticus, 96.0% to that of Frateuria aurantia and less than 92% to sequences of other members of the gamma-Proteobacteria. Repetitive extragenic palindromic DNA PCR fingerprinting revealed two groups, representatives of which showed 93% DNA-DNA reassociation with each other and less than 10% with Frateuria aurantia LMG 1558T. On the basis of phenotypic characteristics and the G+C content of the DNA, the strains could be differentiated from Frateuria aurantia and Rhodanobacter lindaniclasticus. The name Fulvimonas soli gen. nov., sp. nov. is proposed, with the type strain LMG 19981T (= DSM 14263T).

Two novel psychrophilic, halophilic, Psychrobacter-like bacteria, strains KMM 225T and KMM 277T, were isolated from sea water and the internal tissues of an ascidian Polysyncraton sp. specimen, respectively, and characterized using a polyphasic approach, which included phenotypic, genotypic, chemotaxonomic and phylogenetic analyses. The novel marine isolates were Gram-negative, aerobic, coccoid, oxidase- and catalase-positive, non-pigmented, non-motile, psychrophilic and halophilic and they utilized a restricted spectrum of carbon sources. Strains KMM 225T and KMM 277T required sea water or sodium ions for growth and were tolerant of up to 12-15% (w/v) NaCl. Growth of strains KMM 225T and KMM 277T was observed at 4-35 and 7-35 degrees C, respectively. The DNA G+C contents of KMM 225T and KMM 277T were respectively 46-8 and 50.7 mol %. Comparison of almost complete 16S rDNA sequences of strains KMM 225T and KMM 277T revealed that both strains were phylogenetically most closely related to each other (99.9% sequence similarity) and slightly less related to Psychrobacter glacincola, with 97.2 and 97.8% similarity, respectively. DNA-DNA reassociation between KMM 225T and KMM 277T revealed 15% similarity, whereas similarity to other Psychrobacter species was 14-25%. Strains KMM 225T and KMM 277T differed from one another in their growth temperature, organic substrate utilization, antibiotic sensitivity and DNA G+C content. Both strains examined could be distinguished from all previously described Psychrobacter species by their physiological, genotypic and phylogenetic characteristics. On the basis of the physiological and molecular properties of the novel isolates, the names Psychrobacter submarinus sp. nov. (type strain KMM 225T = DSM 14161T) and Psychrobacter marincola sp. nov. (type strain KMM 277T = DSM 14160T) are proposed.

A novel, strictly anaerobic, thermophilic sulfur-reducing bacterium, strain 525T, was isolated from tubes of the deep-sea hydrothermal vent polychaete Alvinella pompejana, collected on the East Pacific Rise (13 degrees N). This organism grew in the temperature range 37-68 degrees C, the optimum being 53 degrees C, and in the pH range 6.4-7.4, the optimum being 6.8-7.0. The NaCl range for growth was 0.8-5.0%, the optimum being 3.0%. Strain 525T grew lithoautotrophically with H2 as energy source, S0 as electron acceptor and CO2 as carbon source. Alternatively, strain 525T was able to use formate as an energy source. The G+C content of the genomic DNA was 34.7 mol%. Phylogenetic analysis of the 16S rDNA gene sequence placed strain 525T in the epsilon-subclass of the Proteobacteria, where it forms a deep cluster with recently isolated relatives. On the basis of phenotypic and phylogenetic differences between strain 525T and its closest phylogenetic relatives, it is proposed that the new isolate should be described as a member of a new genus, Nautilia, for which the name Nautilia lithotrophica gen. nov., sp. nov. is proposed. The type strain is strain 525T (= DSM 13520T).

The growth characteristics, DNA G+C content and sequences of 16S rDNA and the transcribed 16S-23S rDNA internal spacer were determined for Desulfomonas pigra ATCC 29098T, Desulfovibrio desulfuricans subsp. desulfuricans strains Essex 6T (= ATCC 29577T) and MB (= ATCC 27774) and 'Desulfovibrio fairfieldensis' ATCC 700045. Despite phenotypic differences (shape and motility) between Desulfomonas pigra and Desulfovibrio strains, the molecular analysis suggests that Desulfomonas pigra should be reclassified within the genus Desulfovibrio. Thus, the reclassification is proposed of Desulfomonas pigra, the type and only species of the genus, as Desulfovibrio piger comb. nov., which implies the emendation of the description of the genus Desulfovibrio.

The phenotypic and genotypic characteristics of 15 strains of Eikelboom type 021 N bacteria isolated from wastewater treatment plants were investigated. The strains shared many characters with Thiothrix species. However, the Eikelboom type 021N bacteria had only 88.3-92.0% 16S rDNA sequence similarity to members of the Thiothrix nivea group, including T. nivea, 'Thiothrix ramosa', Thiothrix unzii and Thiothrix fructosivorans, and were differentiated from them in sugar utilization and other properties, suggesting that the Eikelboom type 021N bacteria belong to species distinct from the T. nivea group. The 15 Eikelboom type 021N bacteria that were investigated were divided into three distinct groups (I to III) on the basis of their genotypic and phenotypic characteristics. The creation of two novel species is proposed, Thiothrix disciformis sp. nov. for the group I strains (type strain B3-1T = JCM 11364T = DSM 14473T) and Thiothrix flexilis sp. nov. for the group III strains (type strain EJ2M-BT = JCM 11135T = DSM 14609T). Thiothrix eikelboomii AP3T was included in group II and shared many characters with the other group II strains. The inclusion of all group II strains within the species T. eikelboomii is proposed,together with emendation of the description of T. eikelboomii.

A novel thermophilic, anaerobic, hydrogen-oxidizing bacterium, designated strain AM1116T, was isolated from an East Pacific Rise hydrothermal vent sample. The cells were rod-shaped (1.01-5 x 0.5 microm), motile with polar flagella. They grew at temperatures between 50 and 70 degrees C (optimum 60 degrees C; doubling time approximately 1.5 h), at between pH 5.0 and 7.5 (optimum around pH 5.5-6.0) and in between 10 and 40 g NaCl l(-1) (optimum 20-25 g l(-1)). Cells grew chemolithoautotrophically in a H2/CO2 atmosphere (80:20; 200 kPa). Poor heterotrophic growth was observed on complex organic substrates. Elemental sulphur and nitrate served as electron acceptors, respectively yielding hydrogen sulphide and ammonia (doubling times were equal with the two electron acceptors). In contrast, when cystine was used as electron acceptor, growth was poor. The G+C content of the genomic DNA was 29 +/- 1 mol %. Phylogenetic analyses of the 16S rRNA gene located the strain within the epsilon-Proteobacteria, in the bacterial domain. On the basis of 16S rDNA sequence comparisons, physiological and biochemical characteristics, it is proposed that the isolate should be described as the type species of a new genus, Caminibacter gen. nov., as Caminibacter hydrogeniphilus sp. nov. The type strain is strain AM1116T (= DSM 14510T = CIP 107140T).

Two Gram-negative, aerobic, heterotrophic, marine bacteria, isolated from Mediterranean sea water off the coast near Valencia (Spain), were the object of this study. These non-motile, yellow-pigmented, rod-shaped strains have been studied by means of DNA-DNA hybridization, 16S rRNA sequencing and cultural and physiological features. Phylogenetic analysis showed that both strains belong to the phylum Cytophaga-Flavobacterium-Bacteroides, and their closest neighbour is the psychrophilic bacterium Gelidibacter algens. The two strains differ from G. algens in their mesophilic behaviour, hydrolytic pattern and use of different carbon sources. There is 31% DNA-DNA hybridization between the proposed type strain and G. algens, and both isolates show 97.5% 16S rDNA similarity to G. algens. They represent a novel species of the genus Gelidibacter, for which the name Gelidibacter mesophilus sp. nov. is proposed, with strain 2SM29T (= CECT 5103T = DSM 14095T) as the type strain.

A thermophilic, anaerobic, piezophilic, chemo-organotrophic sulfur-reducing bacterium, designated as KA3T, was isolated from a deep-sea hydrothermal chimney sample collected at a depth of 2630 m on the East-Pacific Rise (13 degrees N). When grown under elevated hydrostatic pressure, the cells are rod-shaped with a sheath-like outer structure, motile, have a mean length of 1-1.5 microm and stain Gram-negative. They appear singly or in short chains. When grown at lower, or atmospheric, pressures, the cells elongate and become twisted. Growth is enhanced by hydrostatic pressure; the optimal pressure for growth is 40 MPa (26 MPa pressure at sampling site). The temperature range for growth is 45-70 degrees C, the optimum being around 65 degrees C (doubling time is approximately 20 min at 40 MPa). Growth is observed from pH 5 to pH 8, the optimum being at pH 6. The salinity range for growth is 10-50 g NaCl l(-1), the optimum being at 30 g l(-1). The isolate is able to grow on a broad spectrum of carbohydrates or complex proteinaceous substrates, and growth is stimulated by L-cystine and elemental sulfur. The G+C content of the genomic DNA is 29 +/- 1 mol%. According to phylogenetic analysis of the 16S rDNA gene, the strain is placed within the order Thermotogales, in the bacterial domain. On the basis of 16S rDNA sequence comparisons and morphological, physiological and genotypic characteristics, it is proposed that the isolate be described as a novel species of the genus Marinitoga, with Marinitoga piezophila sp. nov. as the type species. The type strain is KA3T (= DSM 14283T = JCM 11233T).