- Volume 55, Issue 4, 2005

Thirteen bacterial isolates from lake sediment, capable of degrading cyanobacterial hepatotoxins microcystins and nodularin, were characterized by phenotypic, genetic and genomic approaches. Cells of these isolates were Gram-negative, motile by means of a single polar flagellum, oxidase-positive, weakly catalase-positive and rod-shaped. According to phenotypic characteristics (carbon utilization, fatty acid and enzyme activity profiles), the G+C content of the genomic DNA (66·1–68·0 mol%) and 16S rRNA gene sequence analysis (98·9–100 % similarity) the strains formed a single microdiverse genospecies that was most closely related to Roseateles depolymerans (95·7–96·3 % 16S rRNA gene sequence similarity). The isolates assimilated only a few carbon sources. Of the 96 carbon sources tested, Tween 40 was the only one used by all strains. The strains were able to mineralize phosphorus from organic compounds, and they had strong leucine arylamidase and chymotrypsin activities. The cellular fatty acids identified from all strains were C16 : 0 (9·8–19 %) and C17 : 1 ω7c (<1–5·8 %). The other predominant fatty acids comprised three groups: summed feature 3 (<1–2·2 %), which included C14 : 0 3-OH and C16 : 1 iso I, summed feature 4 (54–62 %), which included C16 : 1 ω7c and C15 : 0 iso OH, and summed feature 7 (8·5–28 %), which included ω7c, ω9c and ω12t forms of C18 : 1. A more detailed analysis of two strains indicated that C16 : 1 ω7c was the main fatty acid. The phylogenetic and phenotypic features separating our strains from recognized bacteria support the creation of a novel genus and species, for which the name Paucibacter toxinivorans gen. nov., sp. nov. is proposed. The type strain is 2C20T (=DSM 16998T=HAMBI 2767T=VYH 193597T).

A Gram-negative, non-spore-forming, short rod-shaped bacterium (UST010723-006T) was isolated from the surface of the sponge Mycale adhaerens in Hong Kong waters. Cells of UST010723-006T did not have flagella and were non-motile. Colonies were pale orange in colour, 2–4 mm in diameter, convex with a smooth surface and an entire translucent margin. Gas bubbles were observed in the colonies and also in the agar matrix underneath and adjacent to the colonies. UST010723-006T was heterotrophic, strictly aerobic and required NaCl for growth (2·0–6·0 %). It grew at pH 5·0–10·0 and between 12 and 44 °C. Phylogenetic analysis of the 16S rRNA gene sequence placed UST010723-006T within the genus Pseudoalteromonas of the γ-subclass of the Proteobacteria. The DNA G+C content is 40·6 mol% and the dominant fatty acids were 12 : 0 3-OH, 14 : 0, 15 : 0 iso 2-OH, 16 : 0, 16 : 1ω7, 17 : 1ω8 and 18 : 1ω7 (altogether representing 75·9 % of the total).These data supported the affiliation of UST010723-006T to the genus Pseudoalteromonas. The closest relatives were Pseudoalteromonas luteviolacea, P. phenolica, P. rubra and P. ruthenica with similarity values ranging from 95·4 to 96·8 %. UST010723-006T differed from these closest relatives by 9–19 traits. Molecular evidence, together with phenotypic characteristics, suggests that UST010723-006T constitutes a novel species within the genus Pseudoalteromonas. The name Pseudoalteromonas spongiae sp. nov. is proposed for this bacterium. The type strain is UST010723-006T (=NRRL B-41100T=JCM 12884T).

Eight strains of Gram-negative bacteria able to form ring-like cells were isolated from Mahoney Lake, a meromictic lake in south-central British Columbia, Canada. All strains were pink–purple and contained bacteriochlorophyll a incorporated into the light-harvesting 1 and 2 and reaction-centre pigment–protein complexes. Growth did not occur anaerobically under illuminated conditions; these strains were obligately aerobic, prompting their designation as members of the aerobic phototrophic bacteria. Physiological characterization revealed that these isolates share a similar tolerance to high levels of salinity and pH, as would be expected of bacteria from a highly saline lake; however, the strains exhibited marked differences in their ability to utilize organic substrates for aerobic heterotrophic growth. 16S rRNA sequence analysis showed that the strains are closely related to members of the non-phototrophic genera Octadecabacter (92·0–92·9 %) and Ketogulonicigenium (92·2–92·6 %), as well as to aerobic phototrophs of the genera Roseivivax (92·2–92·9 %) and Roseovarius (91·7–92·4 %) within the ‘Alphaproteobacteria’. The DNA G+C content was 66·2 mol%. The unusual light-harvesting complex 2, the distinct morphological features and physiological traits of these strains as well as the phylogenetic data support the proposal of the novel genus and species Roseicyclus mahoneyensis gen. nov., sp. nov., with ML6T (=DSM 16097T=VKM B-2346T) as the type strain.

A bacterial strain (designated BB4T), which has β-glucosidase activity, was isolated from soil around the roots of bamboo plants. Cells were Gram-negative, aerobic, non-motile and straight-rod-shaped. Phylogenetic analysis of 16S rRNA gene sequences revealed a clear affiliation with members of the family ‘Xanthomonadaceae’. The 16S rRNA gene sequence of strain BB4T showed the following sequence similarities: 97·7 % to Dyella japonica XD53T, 97·1 % to Frateuria aurantia LMG 1558T, 96·2 % to Fulvimonas soli LMG 19981T, 94·3 % to Rhodanobacter lindaniclasticus RP5575T and <90 % to other members of the ‘Gammaproteobacteria’. The G+C content of the genomic DNA was 63·8 mol%. The major fatty acids were branched forms, especially large proportions of iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1 ω9c, similar to the profile of the genus Dyella. The results of DNA–DNA hybridization with D. japonica XD53T and Frateuria aurantia LMG 1558T, in combination with phenotypic characteristics and 16S rRNA gene sequence analysis, demonstrated that strain BB4T should be classified as a novel Dyella species. The name Dyella koreensis sp. nov. is proposed, with strain BB4T (=KCTC 12359T=NBRC 100831T) as the type strain.

The taxonomic identity of the hereditary prokaryotic symbiont of the olive fly Bactrocera oleae (Diptera: Tephritidae) was investigated. In order to avoid superficial microbial contaminants and loosely associated saprophytic biota, flies were surface-sterilized at the larval stage and reared under aseptic conditions until adult emergence. B. oleae flies originating from different geographical locations and collected at different times of the year were tested. Bacterial isolation was undertaken from the cephalic oesophageal bulb, which is known to be a specific site of accumulation for the hosted microsymbionts in the adult insect. Despite evidence of multiplication cycles taking place within the insect, attempts at cultivation of the isolated bacteria ex situ were not productive at any stage, leading to the choice of unculturable status definition. PCR amplification and nucleotide sequencing of the entire 16S rRNA gene consistently yielded a single sequence that displayed marked similarity with enterobacterial lineages, with closest matches (97 %) to Erwinia persicina and Erwinia rhapontici. The novel taxon differs from common intestinal bacterial species of fruit flies and from instances of culturable bacteria previously described in B. oleae raised without sterility precautions, which we also observed as minority occupants or occasional contaminants. The symbiont's identity is also distinct from Pseudomonas savastanoi. In all observations, the numerically dominant inhabitant of the olive fly oesophageal organ was the same unculturable organism, whose presence at later stages was also regularly observed in the midgut. A novel species is proposed, by virtue of its unique properties, under the designation ‘Candidatus Erwinia dacicola’.

A Gram-negative, short rod- to coccus-shaped, non-spore-forming bacterium (Ch05T) was isolated from granules in an upflow anaerobic sludge blanket (UASB) reactor. On the basis of 16S rRNA gene sequence similarity, strain Ch05T was shown to belong to the subclass α-Proteobacteria, being related to Paracoccus solventivorans (97·5 %), Paracoccus alkenifer (96·9 %) and Paracoccus kocurii (96·4 %). The phylogenetic distance from Paracoccus species with validly published names was always less than 96 %. Physiological and chemotaxonomic data (major ubiquinone, Q-10; major fatty acids, C18 : 1 and C18 : 0) supported the affiliation of strain Ch05T to the genus Paracoccus. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Ch05T from the 17 Paracoccus species with validly published names. Ch05T therefore represents a novel species, for which the name Paracoccus koreensis sp. nov. is proposed. The type strain is Ch05T (=KCTC 12238T=IAM 15216T).

A Gram-negative, motile, rod-shaped, psychrophilic and weakly halophilic bacterial strain, SL13T, was isolated from deep-sea sediments (1450 m depth) of Edison Seamount in the western Pacific Ocean. Optimal growth of SL13T requires the presence of 1·5 % (w/v) NaCl, a pH of 6·0 and a temperature of 14 °C. The whole-cell fatty acid profile of the isolate includes C16 : 1 and C16 : 0 as major fatty acids and contains C20 : 5ω3. This is consistent with corresponding data for Photobacterium profundum. The DNA G+C content of strain SL13T is 43·8 mol%. Phylogenetic analyses of 16S rRNA gene sequences place this bacterium in the ‘Gammaproteobacteria’, within the genus Photobacterium. Sequence similarity analysis indicates that the closest relatives of strain SL13T are Photobacterium indicum (99·3 %), P. profundum (98·5 %) and Photobacterium lipolyticum (98·2 %). The DNA–DNA hybridization levels between the isolate and its closest known phylogenetic relatives, P. indicum, P. profundum and P. lipolyticum, are 27·1, 52·4 and 20·2 %, respectively. Thus strain SL13T represents a novel species of the genus Photobacterium, for which the name Photobacterium frigidiphilum sp. nov. is proposed. The type strain is SL13T (=KCTC 12384T=JCM 12947T).

Fe(III)-reducing isolates were recovered from two aquifers in which Fe(III) reduction is known to be important. Strain BemT was enriched from subsurface sediments collected in Bemidji, MN, USA, near a site where Fe(III) reduction is important in aromatic hydrocarbon degradation. Strains P11, P35T and P39 were isolated from the groundwater of an aquifer in Plymouth, MA, USA, in which Fe(III) reduction is important because of long-term inputs of acetate as a highway de-icing agent to the subsurface. All four isolates were Gram-negative, slightly curved rods that grew best in freshwater media. Strains P11, P35T and P39 exhibited motility via means of monotrichous flagella. Analysis of the 16S rRNA and nifD genes indicated that all four strains are δ-proteobacteria and members of the Geobacter cluster of the Geobacteraceae. Differences in phenotypic and phylogenetic characteristics indicated that the four isolates represent two novel species within the genus Geobacter. All of the isolates coupled the oxidation of acetate to the reduction of Fe(III) [iron(III) citrate, amorphous iron(III) oxide, iron(III) pyrophosphate and iron(III) nitrilotriacetate]. All four strains utilized ethanol, lactate, malate, pyruvate and succinate as electron donors and malate and fumarate as electron acceptors. Strain BemT grew fastest at 30 °C, whereas strains P11, P35T and P39 grew equally well at 17, 22 and 30 °C. In addition, strains P11, P35T and P39 were capable of growth at 4 °C. The names Geobacter bemidjiensis sp. nov. (type strain BemT=ATCC BAA-1014T=DSM 16622T=JCM 12645T) and Geobacter psychrophilus sp. nov. (strains P11, P35T and P39; type strain P35T=ATCC BAA-1013T=DSM 16674T=JCM 12644T) are proposed.

A Gram-negative, aerobic bacterium, designated CG20106T, was isolated from the surface tissues of rusty root lesions of Korean ginseng. Phylogenetic analysis of the 16S rRNA gene sequence revealed that this isolate represents a hitherto unknown subline within the genus Pseudomonas. Strain CG20106T was catalase- and oxidase-positive, motile and rod-shaped. The overall phenotypic features of the ginseng isolate were similar to those of Pseudomonas cedrina, Pseudomonas migulae and Pseudomonas azotoformans. However, several physiological and chemotaxonomic properties can be weighted to distinguish the isolate from these organisms. The major fatty acids were C16 : 1 ω7c and/or iso-C15 : 0 2-OH (summed feature 3, 36·4±0·4 %), C16 : 0 (27·5±0·7 %) and C18 : 1 ω7c (19·4±0·2 %). The DNA G+C content was 61·4 mol%. On the basis of the polyphasic results revealed in this study, the name Pseudomonas panacis sp. nov. is proposed for strain CG20106T. The type strain is CG20106T (=IMSNU 14100T=CIP 108524T=KCTC 12330T).

A Gram-positive, non-motile, non-spore-forming coccus (strain JST) was isolated from kimchi (a traditional Korean food) and investigated using a polyphasic taxonomic approach. The 16S rRNA gene sequence similarity between strain JST and its closest relative, Tetragenococcus halophilus IAM 1676T, was 98·1 %. The level of DNA–DNA relatedness between the two strains was 9·7 %. Strain JST had a DNA G+C content of 38·3 % and a cellular fatty acid profile containing 16 : 0, 18 : 1 and cyclo fatty acids. Phylogenetic data and genomic and phenotypic features demonstrated that strain JST represents a novel species, for which the name Tetragenococcus koreensis sp. nov. is proposed. The type strain is JST (=KCTC 3924T=DSM 16501T=LMG 22864T).

A group of 21 bacterial strains was isolated from samples of biofilm formation in the Servilia tomb (necropolis of Carmona, Spain) and the Saint-Catherine chapel (castle at Herberstein, Austria). A polyphasic taxonomic study of these isolates, including morphological, biochemical and chemotaxonomic characterization, rep-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA base ratio and DNA–DNA relatedness studies, allocated them to the genus Arthrobacter. The isolates represent six novel species, for which the names Arthrobacter castelli sp. nov., Arthrobacter monumenti sp. nov., Arthrobacter parietis sp. nov., Arthrobacter pigmenti sp. nov., Arthrobacter tecti sp. nov. and Arthrobacter tumbae sp. nov. are proposed. The respective type strains are LMG 22283T (=DSM 16402T), LMG 19502T (=DSM 16405T), LMG 22281T (=DSM 16404T), LMG 22284T (=DSM 16403T), LMG 22282T (=DSM 16407T) and LMG 19501T (=DSM 16406T).

A novel actinomycete strain YIM 33361T was isolated from a soil sample collected from Yunnan, China. Comparative 16S rRNA gene sequencing showed that the strain constituted a distinct subclade within the genus Nocardia, displaying more than 3 % sequence divergence from established species. Based on its morphological, chemotaxonomic, phenotypic and genotypic characteristics, strain YIM 33361T (=CCTCC AA 204004T=KCTC 19027T) is proposed as the type strain of a novel species, Nocardia polyresistens sp. nov.

The crude-oil-degrading strain BAS3T represents a novel Nocardioides species, according to a taxonomic study. The 16S rRNA gene sequence of strain BAS3T was most similar to that of Nocardioides ganghwensis (IMSNU 14028T; 99 % similarity), but the DNA–DNA relatedness to this type strain was only 32 %. The physiological properties of strain BAS3T differ from those of N. ganghwensis (IMSNU 14028T) and other species of Nocardioides. The diamino acid in the cell-wall peptidoglycan of strain BAS3T is ll-diaminopimelic acid and the major menaquinone is MK-8(H4). The name Nocardioides oleivorans sp. nov. is proposed for the novel Nocardioides species, since its type strain, BAS3T (=DSM 16090T=NCIMB 14004T), is able to degrade crude oil.

Two bacterial isolates from the sputa of a patient with a pulmonary infection were subjected to a polyphasic taxonomic study. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and mycolic acids consistent with the profile for the genus Nocardia. Comparative 16S rRNA gene sequencing showed that these isolates constitute a distinct subline within the genus Nocardia, displaying 99·6–95·5 % sequence similarities with established species. However, DNA–DNA hybridization studies demonstrated unambiguously that the isolates are genealogically distinct from closely related species, namely Nocardia veterana and Nocardia africana, which show high levels of 16S rRNA sequence similarity (99·2 and 99·6 % sequence similarity, respectively). On the basis of both phenotypic and phylogenetic evidence, it is proposed that these isolates be classified as a novel species of the genus Nocardia, for which the name Nocardia elegans sp. nov. is proposed. The type strain is IMMIB N-402T (=CCUG 50200T=CIP 108553T).

A halotolerant, obligately alkaliphilic bacterium, R-2T, was isolated from the skin of a rainbow trout (Oncorhynchus mykiss), a freshwater fish. The strain is Gram-positive, ferments several carbohydrates, is rod-shaped and motile by peritrichous flagella and produces ellipsoidal spores. The isolate grows at pH 9–10 but not at pH 7–8. This micro-organism grows in 0–22 % (w/v) NaCl at pH 10. Its major cellular fatty acids are iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, the major isoprenoid quinone is MK-7 and the DNA G+C content is 38·5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicates that strain R-2T is a member of the genus Oceanobacillus. DNA–DNA hybridization reveals low relatedness between the isolate and Oceanobacillus iheyensis (21·0 %). On the basis of phenotypic characteristics, phylogenetic data and DNA–DNA relatedness data, the isolate should be designated as a novel species, for which the name Oceanobacillus oncorhynchi sp. nov. is proposed. The type strain is R-2T (=JCM 12661T=NCIMB 14022T).

Three indigo-reducing obligately alkaliphilic strains, M3T, 41A and 41C, were isolated. The isolates grew at pH 9–12, but not at pH 7–8. They were Gram-positive, facultatively anaerobic, straight rod-shaped strains with peritrichous flagella. The isolates grew in 0–14 % (w/v) NaCl, with optimum growth at 3–13 %. They grew at temperatures between 10 and 45 °C, with optimum growth at around 30–37 °C. They did not hydrolyse starch or gelatin. dl-lactate was the major end-product from d-glucose. No quinones could be detected. The peptidoglycan type was A4β, Orn–d-Asp. The major cellular fatty acids were C16 : 0, C16 : 17c and C18 : 19c. The DNA G+C content was 42·6–43·2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence data indicated that the isolates belong to the genus Alkalibacterium. DNA–DNA hybridization revealed low similarity (less than 16 %) of the isolates with respect to the two closest phylogenetically related strains, Alkalibacterium olivapovliticus and Alkalibacterium psychrotolerans. On the basis of phenotypic and chemotaxonomic characteristics, phylogenetic data and DNA–DNA relatedness, the isolates merit classification as a novel species of the genus Alkalibacterium, for which the name Alkalibacterium iburiense is proposed. The type strain is M3T (=JCM 12662T=NCIMB 14024T).

Four staphylococcal isolates from clinical and necropsy specimens from a cat, a dog, a horse and a parrot (Psittacus erithacus timneh) were found to constitute a distinct taxon. 16S rRNA gene sequence analysis revealed that its closest phylogenetic relatives are Staphylococcus intermedius and Staphylococcus delphini. Growth characteristics, biochemical features and DNA–DNA hybridizations demonstrated that the strains differ from these and other known species and that they represent a single, novel Staphylococcus species for which the name Staphylococcus pseudintermedius sp. nov. is proposed. The novel species is commonly confused with S. intermedius in routine diagnostic veterinary bacteriology. Although the strains described were isolated from lesions and show several characteristics typical of pathogenic staphylococci, such as coagulase, DNase and β-haemolysin production, the pathogenic significance of the novel species remains unclear. The type strain, LMG 22219T (=ON 86T=CCUG 49543T), was isolated from lung tissue of a cat.

Two bacterial isolates, strains IMMIB RIV-085T and IMMIB RIV-095, isolated from a blood-sucking bug of the genus Triatoma, were characterized by phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and mycolic acids consistent with the genus Rhodococcus. Comparative 16S rRNA gene sequencing showed that the two isolates are genealogically highly related (100 % sequence similarity) and constitute a new subline within the genus Rhodococcus, with Rhodococcus corynebacteroides and Rhodococcus rhodnii as their nearest phylogenetic neighbours (98·4 and 98·3 % sequence similarity, respectively). However, DNA–DNA hybridization experiments demonstrated unambiguously that the isolates are genealogically distinct from R. corynebacteroides and R. rhodnii (32 and 43 % relatedness, respectively). The isolates could be distinguished from their phylogenetic relatives and other members of the genus Rhodococcus by means of biochemical tests. On the basis of both phenotypic and phylogenetic evidence, it is proposed that these isolates be classified as a novel species, Rhodococcus triatomae sp. nov. The type strain is strain IMMIB RIV-085T (=CCUG 50202T=DSM 44892T).

A soil actinomycete, strain 80-133T, with the non-validly published name ‘Microstreptospora cinerea’, was the subject of a polyphasic study designed to clarify its taxonomic status. Comparative 16S rRNA gene sequence studies indicated that the organism belonged to the genus Streptomyces, a result in line with previous chemotaxonomic and morphological data. The strain belonged to the Streptomyces griseus clade, but could be distinguished from representatives of species assigned to this taxon by using DNA–DNA relatedness and phenotypic data. In light of these findings, it is proposed that the organism should be recognized as a novel species of the genus Streptomyces. The name proposed for this taxon is Streptomyces yanii sp. nov., with isolate 80-133T (=AS 4.1146T=JCM 3331T) as the type strain. It was also shown that representative strains of Streptomyces argenteolus, Streptomyces caviscabies, S. griseus and Streptomyces setonii belong to the same genomic species and have key phenotypic properties in common. It is proposed that S. caviscabies and S. setonii should be considered as later heterotypic synonyms of S. griseus and that S. argenteolus AS 4.1693T should also be assigned to this taxon.