- Volume 54, Issue 2, 2004

Halorubrum distributum (basonym, Halobacterium distributum) is an extremely halophilic, aerobic archaeon isolated from saline soils, which was described on the basis of phenotypic features of several strains. The designated type strain of the species (1mT=VKM B-1733T=JCM 9100T) was shown recently to differ from the other strains. In this study, Halorubrum distributum isolates have been characterized with regard to phenotypic features, polar lipid content, comparison of 16S rRNA gene sequences and DNA–DNA hybridization. On the basis of these data, a novel species that includes the other isolates is proposed, with the name Halorubrum terrestre sp. nov. The type strain of this novel species is 4pT (=VKM B-1739T=JCM 10247T). The DNA G+C content of this novel species is 64·2–64·9 mol% (64·4 mol% for the type strain).

Elm yellows group (16SrV) phytoplasmas, which are associated with devastating diseases in elm, grapevine, blackberry, cherry, peach and several other plant species in America, Europe and Asia, represent one of the most diverse phytoplasma clusters. On the basis of phylogenetic analysis of 16S rDNA sequences, elm yellows group phytoplasmas form a discrete subclade within the phytoplasma clade. Three phylogenetic parameters, namely 16S rRNA, ribosomal protein and secY genes, have been evaluated for their usefulness in differentiating elm yellows group phytoplasmas. RFLP analysis of 16S rRNA sequences differentiated the elm yellows group phytoplasmas into five subgroups. Twelve RFLP subgroups were differentiated on the basis of ribosomal protein and 13 were differentiated using secY gene sequences. Phylogenetic analysis of the ribosomal protein genes and secY gene alone or in combination indicated that the subgroups constitute 12 genetically distinct lineages, each of which appears to have evolved under different ecological constraints such as specific vector or plant hosts. On the basis of unique DNA and biological properties, it is proposed that the elm yellows phytoplasma EY1T represents a novel taxon, ‘Candidatus Phytoplasma ulmi’.

Eperythrozoon ovis, an erythrocytic agent that causes haemolytic anaemia in sheep and goats, occurs worldwide and is currently thought to be a rickettsia. To determine the relationship between this agent and other haemotrophic bacterial parasites, the 16S rRNA gene of this organism was sequenced. Phylogenetic analysis revealed that this wall-less bacterium is not a rickettsia, but a mycoplasma. This mycoplasma is related closely to several other uncultivated, epierythrocytic mycoplasmas that comprise a recently identified group, the haemotrophic mycoplasmas (haemoplasmas). The haemoplasma group is composed of former Eperythrozoon and Haemobartonella species, as well as newly identified epierythrocytic mycoplasmas. Haemoplasmas parasitize the surface of erythrocytes of a wide variety of vertebrate animal hosts and are transmitted mainly by blood-feeding arthropod vectors. Recognition that E. ovis is a mycoplasma provides a new approach to dealing with this bacterium. It is proposed that E. ovis should be reclassified as Mycoplasma ovis comb. nov.

A taxonomic study was performed on three strains isolated from microbial mats in Lake Fryxell, McMurdo Dry Valleys, Antarctica. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the family Flavobacteriaceae, in which they form a distinct lineage. The isolates are Gram-negative, chemoheterotrophic, aerobic, rod-shaped cells. They are psychrophilic and yellow-pigmented, with DNA G+C contents in the range 37·8–38·9 mol%. Whole-cell fatty acid profiles revealed mainly branched fatty acids and 17 : 0 2-OH. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenetic results, it is proposed that the isolates represent a novel species in a new genus, Gillisia limnaea gen. nov., sp. nov. The type strain is LMG 21470T (=DSM 15749T).

A number of bacteria were isolated from sea water in Skagerrak, Denmark, at 30 m depth. Two of the isolates, strains D28 and D30T, belonged to the Flavobacteriaceae within the Cytophaga–Flavobacterium–Bacteroides group. Sequencing of 16S rRNA genes of the two strains indicated strongly that they belonged to the genus Tenacibaculum and that they showed greatest similarity to the species Tenacibaculum amylolyticum and Tenacibaculum mesophilum. DNA–DNA hybridization values, DNA base composition and phenotypic characteristics separated the Skagerrak strains from the other species within Tenacibaculum. Thus, it is concluded that the strains belong to a novel species within the genus Tenacibaculum, for which the name Tenacibaculum skagerrakense sp. nov. is proposed, with strain D30T (=ATCC BAA-458T=DSM 14836T) as the type strain.

Intracellular bacteria were observed in the hepatopancreas of the terrestrial isopod Porcellio scaber. Comparative 16S rRNA gene sequence analysis and electron microscopic observations were used to determine the taxonomic position of these intracellular bacteria. Phylogenetic analysis and a complex developmental cycle affiliate these bacteria to the order Chlamydiales, within which they form a distinctive lineage, close to the family Simkaniaceae. They share <92 % 16S rRNA gene sequence similarity with their closest relative and <88 % similarity with other members of the order Chlamydiales. A specific signature oligonucleotide sequence was identified and used as a probe, enabling the identification of intracellular bacteria in infected hepatopancreatic tissue. According to the distinctive morphology of their elementary bodies, which are rod-shaped rather than spherical and contain translucent oblong structures, their genomic properties and their crustacean host, the name ‘Candidatus Rhabdochlamydia porcellionis' is proposed for intracellular bacteria in the hepatopancreas of P. scaber.

Sixty strains of Gram-negative, anaerobic, rod-shaped bacteria from human sources initially assigned to Leptotrichia buccalis (n=58) and ‘Leptotrichia pseudobuccalis’ (n=2) have been subjected to polyphasic taxonomy. Full-length 16S rDNA sequencing, DNA–DNA hybridization, RAPD, SDS-PAGE of whole-cell proteins, cellular fatty acid analysis and enzymic/biochemical tests supported the establishment of four novel Leptotrichia species from this collection, Leptotrichia goodfellowii sp. nov. (type strain LB 57T=CCUG 32286T=CIP 107915T), Leptotrichia hofstadii sp. nov. (type strain LB 23T=CCUG 47504T=CIP 107917T), Leptotrichia shahii sp. nov. (type strain LB 37T=CCUG 47503T=CIP 107916T) and Leptotrichia wadei sp. nov. (type strain LB 16T=CCUG 47505T=CIP 107918T). Light and electron microscopy showed that the four novel species were Gram-negative, non-spore-forming and non-motile rods. L. goodfellowii produced arginine dihydrolase, β-galactosidase, N-acetyl-β-glucosaminidase, arginine arylamidase, leucine arylamidase and histidine arylamidase. L. shahii produced α-arabinosidase. L. buccalis and L. goodfellowii fermented mannose and were β-galactosidase-6-phosphate positive. L. goodfellowii, L. hofstadii and L. wadei were β-haemolytic. L. buccalis fermented raffinose. With L. buccalis, L. goodfellowii showed 3·8–5·5 % DNA–DNA relatedness, L. shahii showed 24·5–34·1 % relatedness, L. hofstadii showed 27·3–36·3 % relatedness and L. wadei showed 24·1–35·9 % relatedness. 16S rDNA sequencing demonstrated that L. hofstadii, L. shahii, L. wadei and L. goodfellowii each formed individual clusters with 97, 96, 94 and 92 % similarity, respectively, to L. buccalis.

Three marine, heterotrophic, aerobic, agarolytic, pigmented and gliding bacteria were isolated in June 2000 from a sea water sample that was collected in the Gulf of Peter the Great, Sea of Japan, and analysed in a polyphasic taxonomic study. 16S rDNA sequence analysis indicated that strains KMM 3664T, KMM 3669 and KMM 3915 were members of the family Flavobacteriaceae. Based on phenotypic, chemotaxonomic, genotypic and phylogenetic data, the isolates were classified in the genus Cellulophaga as members of a novel species, Cellulophaga pacifica sp. nov. The type strain is KMM 3664T (=JCM 11735T=LMG 21938T).

Three bacterial strains were isolated from flowers collected in Bangkok, Thailand, by an enrichment-culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were located in the lineage of the genus Asaia but constituted a cluster separate from the type strains of Asaia bogorensis and Asaia siamensis. The DNA base composition of the isolates was 60·2–60·5 mol% G+C, with a range of 0·3 mol%. The isolates constituted a taxon separate from Asaia bogorensis and Asaia siamensis on the basis of DNA–DNA relatedness. The isolates had morphological, physiological, biochemical and chemotaxonomic characteristics similar to those of the type strains of Asaia bogorensis and Asaia siamensis, but the isolates grew on maltose. The major ubiquinone was Q10. On the basis of the results obtained, the name Asaia krungthepensis sp. nov. is proposed for the isolates. The type strain is isolate AA08T (=BCC 12978T=TISTR 1524T=NBRC 100057T=NRIC 0535T), which had a DNA G+C content of 60·3 mol% and was isolated from a heliconia flower (‘paksaasawan’ in Thai; Heliconia sp.) collected in Bangkok, Thailand.

Comparative 16S rDNA sequence analysis indicates that two distinct sublineages, with a sequence dissimilarity of >4 % (bootstrap value, 100 %), exist within the genus Ralstonia: the Ralstonia eutropha lineage, which comprises Ralstonia basilensis, Ralstonia campinensis, R. eutropha, Ralstonia gilardii, Ralstonia metallidurans, Ralstonia oxalatica, Ralstonia paucula, Ralstonia respiraculi and Ralstonia taiwanensis; and the Ralstonia pickettii lineage, which comprises Ralstonia insidiosa, Ralstonia mannitolilytica, R. pickettii, Ralstonia solanacearum and Ralstonia syzygii comb. nov. (previously Pseudomonas syzygii). This phylogenetic discrimination is supported by phenotypic differences. Members of the R. eutropha lineage have peritrichous flagella, do not produce acids from glucose and are susceptible to colistin, in contrast to members of the R. pickettii lineage, which have one or more polar flagella, produce acid from several carbohydrates and are colistin-resistant. Members of the R. pickettii lineage are viable for up to 6 days on tryptic soy agar at 25 °C, whereas members of the R. eutropha lineage are viable for longer than 9 days. It is proposed that species of the R. eutropha lineage should be classified in a novel genus, Wautersia gen. nov. Finally, based on the literature and new DNA–DNA hybridization data, it is proposed that Pseudomonas syzygii should be renamed Ralstonia syzygii comb. nov.

A Gram-negative, aerobic, halophilic bacterium, designated strain JC2041T, was isolated from a sediment sample of getbol, the Korean tidal flat. Results of 16S rDNA sequence analyses indicated a moderate relationship to Thalassomonas viridans within the γ-Proteobacteria (94·9 % similarity). Depending on the tree-making algorithm used, the isolate either formed a monophyletic clade with T. viridans or was recovered as a sister group of a class containing the genera Thalassomonas and Colwellia. Phenotypic features of the getbol isolate were similar to those of T. viridans, but several physiological and chemotaxonomic properties, including nitrate reduction, amylase, lecithinase, Tweenase and utilization of 13 carbon sources, distinguished strain JC2041T from T. viridans. The polyphasic data presented in this study indicate that the isolate should be classified as a novel species in the genus Thalassomonas. The name Thalassomonas ganghwensis sp. nov. is therefore proposed for the getbol isolate; the type strain is JC2041T (=IMSNU 14005T=KCTC 12041T=DSM 15355T).

A curved, ring-like bacterium, strain AS 1.1761T, isolated from the roots of Spartina anglica, was studied by a polyphasic approach. According to phylogenetic analysis, strain AS 1.1761T belongs to the genus Ancylobacter, with 99·21 % 16S rDNA sequence similarity to Ancylobacter aquaticus, the only species described so far in this genus. However, strain AS 1.1761T had no significant DNA–DNA binding with the type strain of A. aquaticus. In addition, strain AS 1.1761T differed from A. aquaticus in many phenotypic features. Based on molecular and phenotypic data, a novel species, Ancylobacter rudongensis sp. nov., is proposed. The type strain is AS 1.1761T (=JCM 11671T).

A rod-shaped, slightly curved sulfate reducer, designated strain P2T, was isolated from the sulfate–methane transition zone of a marine sediment. Cells were motile by means of a single polar flagellum. The strain reduced sulfate, thiosulfate and sulfite to sulfide and used propionate, lactate and 1-propanol as electron donors. Strain P2T also grew by fermentation of lactate. Propionate was oxidized incompletely to acetate and CO2. The DNA G+C content was 48·8mol%. Sequence analysis of the small-subunit rDNA and the dissimilatory sulfite reductase gene revealed that strain P2T was related to the genera Desulfonema, Desulfococcus, Desulfosarcina, ‘Desulfobotulus’, Desulfofaba, Desulfomusa and Desulfofrigus. These genera include incomplete as well as complete oxidizers of substrates. Strain P2T shared important morphological and physiological traits with Desulfofaba gelida and Desulfomusa hansenii, including the ability to oxidize propionate incompletely to acetate. The 16S rRNA gene similarities of P2T to Desulfofaba gelida and Desulfomusa hansenii were respectively 92·9 and 91·5%. Combining phenotypic and genotypic traits, we propose strain P2T to be a member of the genus Desulfofaba. The name Desulfofaba fastidiosa sp. nov. (type strain P2T=DSM 15249T=ATCC BAA-815T) is proposed, reflecting the limited number of substrates consumed by the strain. In addition, the reclassification of Desulfomusa hansenii as a member of the genus Desulfofaba, Desulfofaba hansenii comb. nov., is proposed. A common line of descent and a number of shared phenotypic traits support this reclassification.

On the basis of data from phenotypic and genotypic characterization and analysis of 16S rRNA gene sequences, two novel species belonging to the genus Sulfitobacter are described. Strains KMM 3584T, a pale-yellowish, non-motile strain isolated from a starfish (Stellaster equestris), and KMM 3554T, which is motile by means of a single subpolar flagellum and was isolated from sea grass (Zostera marina), are marine, Gram-negative, aerobic, rod-shaped organisms. Both strains have the ability to degrade gelatin, but not casein, chitin, agar, DNA, Tween 80 or starch. Strain KMM 3584T decomposed alginate and grew at NaCl concentrations of 1–8 % and temperatures of 12–37°C, whereas strain KMM 3554T grew in 1–12% NaCl and at temperatures of 10–30°C. The predominant fatty acid was 18:1ω7, amounting to up to 80% of the total fatty acids. The other characteristic feature was the presence of 18:2 isomers. The DNA G+C contents of KMM 3584T and KMM 3554T were respectively 60·0 and 63·7 mol%. The level of DNA similarity between the two strains was 33%. DNA from KMM 3584T and KMM 3554T had hybridization values of 5–24% and 10–41%, respectively, with DNA from the type strains of Sulfitobacter pontiacus, Sulfitobacter brevis, Sulfitobacter mediterraneus and Staleya guttiformis. It is proposed that strains KMM 3584T (=LMG 20554T=ATCC BAA-321T) and KMM 3554T (=LMG 20555T=ATCC BAA-320T) represent two novel species, Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively.

Two Aeromonas strains, IBS S6874T and IBS S6652, were isolated from the faeces of two healthy monkeys (Macaca fascicularis) from Mauritius that were kept in quarantine in the Centre for Primatology, Strasbourg, France. Phylogenetic analysis based on 16S rRNA gene sequences showed that the two isolates formed an unknown genetic lineage within the genus Aeromonas. The two isolates had nearly identical sequences (0·1 % nucleotide substitution) that were related closely to those of recognized Aeromonas species (1·7–3·5 % nucleotide substitution). DNA–DNA hybridization showed that strains IBS S6874T and IBS S6652 had high DNA–DNA similarity (89 %) to each other and a low level of DNA–DNA similarity to closely related taxa (18 % relatedness to Aeromonas trota and 16 % relatedness to Aeromonas schubertii). Phenotypically, the two monkey isolates differed from most previously described mesophilic Aeromonas species by their lack of haemolysis on sheep-blood agar and inability to produce indole, gas from glucose or acid from mannitol. They differed from the most closely related species, A. schubertii, by their ability to produce acid from d-cellobiose and d-sucrose and by their pyrazinamidase activity. The name Aeromonas simiae sp. nov. is proposed for these isolates; strain IBS S6874T (=CIP 107798T=CCUG 47378T) is the type strain.

A Gram-negative, motile, non-spore-forming, rod-shaped strain, TF-27T (=KCCM 41648T=JCM 11814T), was isolated from a tidal flat in Korea. This organism grew well at 25–35 °C, with optimum growth at 30 °C. Strain TF-27T grew optimally in the presence of 2 % NaCl; it did not grow without NaCl or in the presence of >8 % NaCl. Strain TF-27T simultaneously contained both menaquinones and ubiquinones as isoprenoid quinones. The predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acids in strain TF-27T were iso-C15 : 0 (20·6 %) and iso-C15 : 0 2-OH and/or C16 : 1 ω7c (21·1 %). The DNA G+C content of strain TF-27T was 42 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-27T falls within the radiation of the cluster that is encompassed by the genus Shewanella. Levels of 16S rDNA sequence similarity between strain TF-27T and the type strains of Shewanella species were 93·2–96·8 %. On the basis of phenotypic properties and phylogenetic data, strain TF-27T should be placed in the genus Shewanella as a novel species, for which the name Shewanella gaetbuli sp. nov. is proposed.

To assess the physiological and phylogenetic diversity of culturable halophilic bacteria in deep-sea hydrothermal-vent environments, six isolates obtained from low-temperature hydrothermal fluids, sulfide rock and hydrothermal plumes in North and South Pacific Ocean vent fields located at 1530–2580 m depth were fully characterized. Three strains were isolated on media that contained oligotrophic concentrations of organic carbon (0·002 % yeast extract). Sequencing of the 16S rRNA gene indicated that all strains belonged to the genus Halomonas in the γ-subclass of the Proteobacteria. Consistent with previously described species, the novel strains were slightly to moderately halophilic and grew in media containing up to 22–27 % total salts. The isolates grew at temperatures as low as −1 to 2 °C and had temperature optima of 30 or 20–35 °C. Both the minimum and optimum temperatures for growth were similar to those of Antarctic and sea-ice Halomonas species and lower than typically observed for the genus as a whole. Phenotypic tests revealed that the isolates were physiologically versatile and tended to have more traits in common with each other than with closely related Halomonas species, presumably a reflection of their common deep-sea, hydrothermal-vent habitat of origin. The G+C content of the DNA for all strains was 56·0–57·6 mol%, and DNA–DNA hybridization experiments revealed that four strains (Eplume1T, Esulfide1T, Althf1T and Slthf2T) represented novel species and that two strains (Eplume2 and Slthf1) were related to Halomonas meridiana. The proposed new species names are Halomonas neptunia (type strain Eplume1T=ATCC BAA-805T=CECT 5815T=DSM 15720T), Halomonas sulfidaeris (type strain Esulfide1T=ATCC BAA-803T=CECT 5817T=DSM 15722T), Halomonas axialensis (type strain Althf1T=ATCC BAA-802T=CECT 5812T=DSM 15723T) and Halomonas hydrothermalis (type strain Slthf2T=ATCC BAA-800T=CECT 5814T=DSM 15725T).