- Volume 52, Issue 3, 2002

Phylogenetic analysis of the 16S rRNA gene of bacterial isolates from garden soil showed relatedness to Weissella kandleri and Weissella confusa. However, the sequences had notable differences, and DNA-DNA hybridizations confirmed that the isolates are separate from these two species. The isolates could be further distinguished from all previously described Weissella species by electrophoretic analysis of whole-cell proteins, as well as by the results from different biochemical tests. The name Weissella soli is proposed for the new species, the type strain being Mi268T (= LMG 20113T = DSM 14420T).

Chelatobacter heintzii, which was described as a nitrilotriacetate-utilizing organism, was re-investigated in order to clarify its taxonomic position. On the basis of 16S rDNA sequence comparisons, it is obvious that this species clusters phylogenetically with species of the genus Aminobacter. The results of investigations of the fatty acid patterns, polar lipid profiles, polyamine patterns and quinone system supported this placement. The substrate-utilization profiles and fatty acid patterns of four strains (belonging to two different genomovars) revealed homogeneous results and showed high levels of similarity to Aminobacter aminovorans. DNA-DNA similarity studies confirmed that both genomovars of Chelatobacter heintzii belong to Aminobacter aminovorans. It could be shown that all species of this group are highly interrelated. On the basis of these data and previously published results, it is obvious that Chelatobacter heintzii is a later subjective synonym of Aminobacter aminovorans.

The characteristics of the fusiform species Bacteroides forsythus, isolated from human periodontal pockets, were examined. 165 rDNA sequence analysis confirmed that B. forsythus was not a species within the genus Bacteroides sensu stricto. Although B. forsythus was phylogenetically related to Bacteroides distasonis and Bacteroides merdae in the phylogenetic tree, the ratio of anteiso-15:0 to iso-15:0 in whole-cell methanolysates of B. forsythus was different from those of B. distasonis, B. merdae and other Bacteroides species. B. forsythus did not grow on medium containing 20% bile, but members of the Bacteroides fragilis group did. B. forsythus was the only species tested that was trypsin-positive in API ZYM tests. The dehydrogenase enzyme pattern was of no use for the differentiation of B. forsythus and the B. fragilis group. On the basis of these data, a new genus, Tannerella, is proposed for Bacteroides forsythus, with one species, Tannerella forsythensis corrig., gen. nov., comb. nov. The type strain of Tannerella forsythensis is JCM 10827T (= ATCC 43037T).

A marine methylotroph, designated strain MB2T, was isolated for its ability to grow on methyl bromide as a sole carbon and energy source. Methyl chloride and methyl iodide also supported growth, as did methionine and glycine betaine. A limited amount of growth was observed with dimethyl sulfide. Growth was also noted with unidentified components of the complex media marine broth 2216, yeast extract and Casamino acids. No growth was observed on methylated amines, methanol, formate, acetate, glucose or a variety of other substrates. Growth on methyl bromide and methyl iodide resulted in their oxidation to CO2 with stoichiometric release of bromide and iodide, respectively. Strain MB2T exhibited growth optima at NaCl and Mg2+ concentrations similar to that of seawater. Phylogenetic analysis of the 16S rDNA sequence placed this strain in the alpha-Proteobacteria in proximity to the genera Ruegeria and Roseobacter. It is proposed that strain MB2T (= ATCC BAA-92T = DSM 14336T) be designated Leisingera methylohalidivorans gen. nov., sp. nov..

To investigate the genetic diversity of the genus Arthrospira and to compare it with other cyanobacteria, sequences of 670 nt from the phycocyanin operon were determined for 23 natural, cultivated or commercial strains of Arthrospira and compared with sequences from 20 other non-Arthrospira cyanobacterial strains. The sequenced DNA fragment comprises the last 255 nt of cpcB, the cpcB-cpcA spacer and the first 304 nt of cpcA. The resulting phylogenetic tree confirms that the genus Arthrospira is not related to Spirulina. So far, cpcB-cpcA data suggest that the closest relative of Arthrospira is Planktothrix. Based on this locus, the genus Arthrospira consists of three genetically clustered lineages. However, the distribution of nucleotide substitutions indicates that these three lineages are not the result of a simple cladogenesis characterized by the accumulation of independent substitutions. Instead, the observed clustering is the result of horizontal transfers of blocks of sequences. Analysis of the distribution of substitutions in the sequenced fragment indicates a point of intragenic recombination close to the stop codon of cpcB. The capacity of exchange of genetic material among strains probably explains why morphology and geographical origin do not correlate with the cpcB-cpcA clusters. Nevertheless, this study shows for the first time that the genus Arthrospira, represented here by cultivated and wild specimens, is clearly monophyletic. Moreover, the cpcB-cpcA DNA fragment, comprising both highly and moderately variable regions, allows (1) a strict differentiation of the taxon Arthrospira from other cyanobacteria (using the coding regions only) and (2) the study of relationships inside Arthrospira (using both the coding and non-coding regions).

A facultatively anaerobic bacterium, designated strain COOI3B(T) (= ATCC BAA 136T = DSM 13966T), was isolated from the waters emitted by a bore well tapping the deep subterranean thermal waters of the Great Artesian Basin of Australia. The cells were straight to slightly curved rods (0.5-0.8 x 2-25 microm) that occurred singly and rarely in pairs or in chains. Strain COOI3B(T) was motile by peritrichous flagella. It stained gram-negative, but electron micrographs showed a gram-positive-type cell wall. Spores were never observed and cells were heat-sensitive. Yeast extract at 0.02% (w/v) was required for growth and could also be used as a sole carbon and energy source at concentrations higher than 0.1% (w/v). The strain utilized amorphous iron(III), manganese(IV), nitrate, nitrite and fumarate as electron acceptors in the presence of yeast extract, glucose, sucrose, fructose, maltose, xylose, starch, glycerol, ethanol or lactate. Electron acceptors were not obligately required and growth was better in the presence of nitrate than in its absence. Acid was not produced from growth on carbohydrates. Tryptophan deaminase, H2S, arginine dihydrolase, lysine decarboxylase, beta-galactosidase, arabinosidase, glucuronidase, glucosaminidase, nitroanilidase, xylosidase and ornithine decarboxylase were not produced. Starch and gelatin, but not casein, were hydrolysed. Aesculin and catalase, but not oxidase and urease, were produced. Strain COOI3B(T) grew optimally at temperatures between 37 and 40 degrees C (the temperature growth range was 25-45 degrees C) and at pH 7.0-9.0 (the pH growth range was 6.0 to 9.5) with 5% (w/v) NaCl (the NaCl concentration growth range was 0.9%, w/v). The DNA base composition was 43 +/- 1 mol % G+C. Phylogenetic analysis indicated that it was a member of the family Bacillaceae, Bacillus infernus and Bacillus firmus being the closest phylogenetic neighbours (having a mean similarity value of 96%); hence, strain COOI3B(T) is designated as a novel species, Bacillus subterraneus sp. nov.

Two bacterial strains, designated 1A-C(T) and 3A-1, were studied and, using these results and previously published data, taxonomically classified. Cells of the strains exhibited a rod-coccus cycle. The peptidoglycan determined for 1A-C(T) was of type A4alpha with lysine as the diagnostic cell-wall diamino acid and an interpeptide bridge of L-Lys <-- L-Glu. The menaquinone systems of the two strains contained MK-8(H4) (82-94%) and MK-7(H4) (3-11%). The polar lipid profiles consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, two unidentified phospholipids and an unidentified glycolipid. The fatty acid profiles contained predominantly ai-C15:0 and significant amounts of i-C14:0 and i-C15:1 fatty acids. Genomic fingerprints clearly distinguished strains 1A-C(T) and 3A-1 from each other. DNA-DNA relatedness between the two strains (92%) demonstrated that they are members of a single species. Analyses of the 16S rDNA sequences of strains IA-C(T) and 3A-1, which were almost identical (99.6% sequence similarity), and comparison with corresponding sequences demonstrated that they represent a novel lineage within the suborder Micrococcineae, most closely related to species of the genera Beutenbergia, Bogoriella and Cellulomonas (94.7-95.7% sequence similarity). The results demonstrate that the two strains are members of a single new genus and a single novel species. Thus, the name Georgenia muralis gen. nov., sp. nov. is proposed. The type strain is strain 1A-C(T) (= DSM 14418T = CCM 4963T). Another strain of the species is strain 3A-1 (= DSM 14419 = CCM 4964).

A new meso-diaminopimelic acid-containing, gram-positive bacterium was isolated from an activated sludge reactor showing enhanced biological phosphorus removal activity. The isolate was an asporogenous oval to rod-shaped bacterium, but occasionally formed clumps. The Neisser staining was positive, suggesting intracellular polyphosphate granules. The isolate was an aerobic chemoheterotroph which was capable of utilizing various sugars, sugar alcohols and organic acids. It contained anteiso-C15:0, iso-C15:0, iso-C14:0 and C16:0 as the major cellular fatty acids, and menaquinone-8(H4) as the major quinone. The G+C content of the genomic DNA was 69.6 mol%. Analysis of the 16S rDNA sequence revealed that the isolate is a new member of the family Intrasporangiaceae. The closest relatives were Tetrasphaera species. On the basis of the phenotypic and phylogenetic distinctiveness of the isolate, it was concluded that the organism represents a new species in the genus Tetrasphaera, for which the name Tetrasphaera elongata sp. nov. is proposed. The type strain is strain Lp2T (= JCM 11141T = DSM 14184T).

The taxonomic positions of two thermophilic actinomycetes isolated from soil were established in a polyphasic taxonomic study. The organisms were shown to have phenotypic properties typical of members of the genus Amycolatopsis and formed a distinct phyletic line in the Amycolatopsis methanolica 16S rDNA subclade. They also had many phenotypic properties in common and formed a genomic species that was closely related to, albeit distinct from, the type strain of A. methanolica. A range of phenotypic properties distinguished the isolates from representatives of all validly described species of Amycolatopsis. Genotypic and phenotypic data show that the two strains should be classified in the genus Amycolatopsis as a novel species, Amycolatopsis eurytherma sp. nov.; the type strain is strain NT202T (= DSM 44348T = NCIMB 13795T).

A poly(3-hydroxybutyrate) (PHB)-degrading, gram-negative, aerobic bacterium, strain HS(T), was isolated from a hot spring and chemotaxonomically and phylogenetically characterized. The oxidase-positive, weakly catalase-positive, non-pigmented cells (0.6 x 2.6 microm) exhibited a single polar flagellum and accumulated PHB granules. Strain HS(T) was capable of manganese oxidation. Highest growth rate was attained at 50 degrees C. The optimum pH for growth was 7-8. The major respiratory quinone was ubiquinone-8 and major cellular fatty acids were C16:0, C16:1 and C18:1. The G+C content of the DNA was 66.2 mol%. Comparative 16S rDNA analysis indicated that strain HS(T) is related to the Rubrivivax subgroup and the family Comamonadaceae. The nearest phylogenetic relatives were Ideonella dechloratans (92.1% similarity), Leptothrix discophora (93.6%), Roseateles depolymerans (92.4%) and Rubrivivax gelatinosus (92.2%). On the basis of its phylogenetic and phenotypic properties, it is proposed that this isolate be designated Caldimonas manganoxidans gen. nov., sp. nov.; the type strain is HS(T) (= JCM 10698T = IFO 16448T = ATCC BAA-369T).

A bacterial isolate, ME102T, was obtained from an n-hexadecane enrichment culture of seawater/sediment samples collected in the harbour of Messina (Italy). This gram-negative, aerobic, motile, rod-shaped bacterium used a narrow spectrum of organic compounds, including aliphatic hydrocarbons, alkanoates and alkanoles, as carbon and energy sources. None of the sugars, organic acids or amino acids tested was used. During cultivation on n-alkanes as the sole source of carbon and energy, the cells formed a biofilm on the surface of the alkane droplets. Large-scale (sometimes >50% of the cell mass) intracellular accumulation of alkanoates occurred in cells adsorbed on the alkane surface and under nitrogen-limiting conditions. 16S rRNA gene sequence analysis showed that this isolate represents a distinct lineage in the gamma-Proteobacteria and has about 91% sequence identity to members of Marinobacter and Alcanivorax, the closest genera. Four different types of polar lipid could be detected, phosphatidyl glycerol, phosphatidyl ethylamine, phosphatidyl dimethylethylamine and lipids belonging to an unknown type of phospholipid (m/z between 861 and 879). The principal fatty acids in the polar lipid fatty acid profile were 16:0 and 16:1. The putative gene encoding the key enzyme of alkane catabolism, alkane hydroxylase (AlkB), has been cloned. The protein sequence of the putative AlkB of the isolate ME102T was related to the AlkB of Pseudomonas oleovorans and Alcanivorax borkumensis, showing about 60% sequence identity. On the basis of physiological studies and taking into account the distant phylogenetic position of isolate ME102T relative to previously described organisms, a novel genus and species is proposed, Oleiphilus messinensis gen. nov., sp. nov., within a new family, Oleiphilaceae fam. nov. Strain ME102T (= DSM 13489T = LMG 20357T) is the type and only strain of O. messinensis.

Two strains of haloalkaliphilic, obligately autotrophic, sulfur-oxidizing bacteria were isolated from the oxygen-sulfide interface water layer of stratified alkaline and saline Mono Lake, California, USA. Strain ALM 1T was a dominant species in enrichment on moderate-saline, carbonate-buffered medium (0.6 M total Na+, pH 10) with thiosulfate as an energy source and nitrate as a nitrogen source. Cells of ALM 1T are open ring-shaped and are non-motile. It has a high growth rate and activity of thiosulfate and sulfide oxidation and very low sulfur-oxidizing activity. Genetic comparison and phylogenetic analysis suggested that ALM 1T (= DSM 14477T = JCM 11371T) represents a new species of the genus Thioalkalimicrobium in the gamma-Proteobacteria, for which the name Thioalkalimicrobium cyclicum sp. nov. is proposed. Another Mono Lake isolate, strain ALM 2T, dominated in enrichment on a medium containing 2 M total Na+ (pH 10). It is a motile vibrio which tolerates up to 4 M Na+ and produces a membrane-bound yellow pigment. Phylogenetic analysis placed ALM 2T as a member of genus Thioalkalivibrio in the gamma-Proteobacteria, although its DNA hybridization with the representative strains of this genus was only about 30%. On the basis of genetic and phenotypic properties, strain ALM 2T (= DSM 14478T = JCM 11372T) is proposed as Thioalkalivibrio jannaschii sp. nov..

An obligately anaerobic, lactate-fermenting bacterium (strain G17T) was isolated from the caeca of a 31-day-old chicken. Grown at neutral pH, cells were rod-shaped with tapered ends and showed no motility and no spore formation. Electron microscopy showed that the cell walls had a gram-positive structure. The DNA G+C content was 44.6 mol %. Based on 16S rDNA sequence analysis, strain G17T was considered to belong to the low-G+C-content gram-positive bacteria of cluster XIV subgroup b and most closely related to Clostridium propionicum (93.5%) and Clostridium neopropionicum (93.5%). The optimum temperature for growth was 41 degrees C and the optimum pH was pH 6.4-7.3. The optimum temperature of 41 degrees C suggests that strain G17T might have become adapted to the body temperature of chickens. Strain G17T was able to grow on a variety of organic compounds. Most of these compounds were converted to acetate, propionate and traces of butyrate and isovalerate. In media with mixtures of substrates, lactate was degraded by strain G17T before the other substrates. This indicates that strain G17T might be important in the fermentation of lactate in the caeca of chickens. Based on its physiological and phylogenetic characteristics, it is proposed that strain G17T should be assigned to the genus Clostridium as a novel species, Clostridium lactatifermentans sp. nov.

Lactic acid bacteria (LAB) are the predominant micro-organisms in tempoyak, a Malaysian acid-fermented condiment. In a study on the diversity of LAB in this product, three isolates could not be identified using SDS-PAGE of whole-cell proteins or API 50 CH. The taxonomic position of the three isolates was clarified in the present study. 16S rDNA sequencing classified a representative strain in the genus Lactobacillus, clearly separated from all known species, and most closely related to the Lactobacillus reuteri phylogenetic group. DNA-DNA hybridization experiments and an extensive phenotypic description confirm that the strains represent a single and separate novel species among the obligately heterofermentative lactobacilli. The three isolates are distinguished at the intra-species level by plasmid profiling, pulsed-field gel electrophoresis of macro-restriction fragments and biochemical features. The name Lactobacillus durianis sp. nov. is proposed for the novel taxon and the type strain is LMG 19193T (= CCUG 45405T).

A gram-type positive, motile, coccus-shaped organism was isolated from a radioactive work area. Strain SRS30216T is an orange-pigmented bacterium that is catalase-positive, oxidase-negative and urease-negative. The orange pigment is most likely a carotenoid with absorption peaks at approximately 444, 471 and 501 nm. Cells normally grew in clusters, but individual, motile, flagellated cells were also observed. Growth of strain SRS30216T occurred at temperatures between 11 and 41 degrees C, between pH 5 and 9 and at NaCl concentrations up to and including 5%. Fatty acid composition was limited, with >90% of the fatty acids being anteiso 15:0. Alkenes of 19-24 carbons in length were detected during examination of the neutral lipids. Strain SRS30216T demonstrated high levels of resistance to gamma-radiation and desiccation. The most closely related recognized species is Kineococcus aurantiacus RA 333T, which is 93% similar in 16S rDNA sequence. DNA-DNA hybridization revealed only 31% similarity between these two organisms. It is proposed that SRS30216T (= ATCC BAA-149T = DSM 14245T) represents the type strain of a novel species in the genus Kineococcus, Kineococcus radiotolerans sp. nov..

A facultatively anaerobic, mesophilic, non-motile, non-sporulating bacterium, designated strain B7, was isolated from an anaerobic digester fed with shea cake rich in tannins and aromatic compounds, after enrichment on tannic acid. The coccoid cells (less than 2 microm in diameter) occurred in pairs or short chains and stained gram-positive. Strain B7 fermented a wide range of carbohydrates (cellobiose, fructose, galactose, glucose, lactose, maltose, mannitol, melibiose, raffinose and trehalose), grew optimally at pH 7.0 and had a G+C content of 40.4+/-0.3 mol%. Strain B7 was closely related to Streptococcus gallolyticus ACM 3611T, a member of the Streptococcus bovis rRNA cluster, with a sequence similarity of 98% and a DNA hybridization value of 86 mol%. Isolate B7 hydrolysed tannic acid and decarboxylated gallic acid to pyrogallol, traits also observed in S. gallolyticus ACM 3611T. In addition, both strains decarboxylated protocatechuic acid to catechol, p-coumaric acid to 4-vinylphenol, caffeic acid to 4-vinylcatechol and ferulic acid to 4-vinylguaiacol. An unsubstituted para-hydroxyl group on the benzene ring was required for decarboxylation. Glucose addition markedly increased the conversion rate. As these traits were not described previously, emendation of the description of the species Streptococcus gallolyticus is proposed.

Two species of dairy streptococci, Streptococcus waius and Streptococcus macedonicus, were originally characterized by 16S-23S intergenic spacer sequence analysis, random amplified polymorphic DNA fingerprinting, PFGE analysis and DNA-DNA reassociation experiments. All genetic data suggested that S. waius strains belong to the previously described species S. macedonicus. Likewise, the phenotypic characterization showed that strains of S. macedonicus and S. waius were highly related and easily differentiated from the closest phylogenetic neighbour, Streptococcus bovis, principally by their failure to produce a blackening reaction in medium containing aesculin. The utilization of maltose and cellobiose by S. macedonicus/S. waius strains allowed their differentiation from the most studied dairy species, Streptococcus thermophilus. On the basis of genetic and phenotypic data S. macedonicus and S. waius species should be considered synonyms and S. macedonicus has the priority.

Thirty-three clinical, dairy and industrial isolates of aerobic endospore-forming bacteria which were unreactive in routine identification tests were characterized genotypically by using amplified rDNA restriction analysis (ARDRA), 16S rDNA sequencing and DNA-DNA reassociation, and phenotypically by using fatty acid methyl ester (FAME) analysis, SDS-PAGE of whole-cell proteins, API Biotype 100 assimilation tests and 16 other routine phenotypic tests. Three isolates were identified as strains of Bacillus badius, 12 as Brevibacillus agri, including 3 strains associated with an outbreak of waterborne illness, 4 as Brevibacillus centrosporus and 2 as Brevibacillus parabrevis; 12 strains contaminating an antibiotic production plant were recognized as members of a new species, for which the name Brevibacillus invocatus is proposed, with the type strain LMG 18962T (= B2156T = CIP 106911T = NCIMB 13772T).

The taxonomic position of Catellatospora ferruginea and 'Catellatospora ishikariense' was investigated by phylogenetic, chemotaxonomic and physiological characterization. The 16S rDNA sequences of the organisms were compared with those of members of the genus Catellatospora and other genera of the Micromonosporaceae and phylogenetic trees were inferred by using distance-matrix and parsimony methods. The organisms formed a distinct cluster within the radiation of this family that was supported by a high bootstrap value, of 100%. The nearest neighbours were members of the genera Catenuloplanes and Verrucosispora. The organisms were readily differentiated from all of the validly described genera of the family Micromonosporaceae by using a battery of chemical and morphological characters, and the name Asanoa gen. nov. is proposed. On the basis of phenotypic and DNA-DNA hybridization data, Asanoa ferruginea comb. nov. (type strain IMSNU 22009T = IFO 14496T DSM 44099T) and Asanoa ishikariensis sp. nov. (type strain IMSNU 22004T = IFO 14551T) are described.