- Volume 53, Issue 1, 2003

A heterotrophic, pigmented, agarolytic, gliding bacterium was isolated from a seawater sample collected from the Gulf of Peter the Great, Sea of Japan, during June 2000. 16S rDNA sequence analysis indicated that the novel bacterium, strain KMM 3525T, was a member of the phlyum Cytophaga–Flavobacterium–Bacteroides. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, it is proposed that the marine bacterium represents the sole species of a novel genus, Reichenbachia, the type species of which is Reichenbachia agariperforans (KMM 3525T =IFO 16625T =JCM 11238T).

A Gram-negative, rod-shaped, non-spore-forming, yellow-pigmented bacterium (strain B2T) isolated from wastewater of a sequence batch reactor showing enhanced phosphorus removal was investigated to determine its taxonomic status. Complete 16S rRNA gene sequence analysis indicated that the organism should be placed in the genus Chryseobacterium. The strain contained a polyamine pattern with sym-homospermidine as the major compound, menaquinone MK-6 as the predominant menaquinone and ai-C15 : 0, i-C15 : 0 and C16 : 1 as the major fatty acids. Phosphatidylethanolamine and several unidentified lipids were detected in the polar lipid profile. Phylogenetically, strain B2T was most closely related to Chryseobacterium indoltheticum and Chryseobacterium gleum (96·2 and 95·9 % 16S rRNA gene sequence similarity, respectively). The phylogenetic distance from any validly described species within the genus Chryseobacterium, as indicated from 16S rRNA gene sequence similarities, and its phenotypic properties demonstrate that strain B2T represents a novel species, for which the name Chryseobacterium defluvii sp. nov. is proposed; the type strain is B2T (=DSM 14219T =CIP 107207T).

A novel strictly anaerobic, cellobiose-degrading bacterium, strain CelloT, was isolated from a human faecal sample by combining enrichments in liquid and soft-agar basal media. A noteworthy characteristic was its inability to grow on normal agar plates and in roll tubes. The cells were coccus shaped and non-motile, with an extracellular slime layer. Growth of strain CelloT occurred between 20 and 40 °C, with optimal growth at 37 °C. The pH range for growth was 5–7·5 with an optimum at 6·5. In pure culture, strain CelloT could only grow on a variety of sugars. Glucose was converted to acetate, ethanol and H2. The doubling time on glucose was 0·5 h. In a syntrophic co-culture with Methanospirillum hungatei strain JF-1T, strain CelloT converted glucose to acetate and H2. The G+C content was 59·2 mol%. 16S rDNA analysis revealed that the closest relatives of strain CelloT were two uncultured bacteria from anaerobic digesters, both with 94 % 16S rDNA sequence similarity. The closest cultured representatives belong to genera of the bacterial division ‘Verrucomicrobia’. The name Victivallis vadensis gen. nov., sp. nov. is proposed for strain CelloT (=DSM 14823T =ATCC BAA-548T).

A novel, moderately thermophilic, strictly anaerobic, mixotrophic bacterium, designated strain LF13T, was isolated from a deep-sea hydrothermal chimney sample that was collected at a vent site at 14° 45′ N, 44° 59′ W on the Mid-Atlantic Ridge. Cells were Gram-negative, thin, non-motile rods of variable length. Strain LF13T grew optimally at pH 6·8–7·0 and 60 °C with 2·5 % (w/v) NaCl. It grew chemo-organoheterotrophically, fermenting proteinaceous substrates, pyruvate and Casamino acids. The strain was able to grow by respiration, utilizing molecular hydrogen (chemolithoheterotrophically) or acetate as electron donors and nitrate as an electron acceptor. Ammonium was formed in the course of denitrification. One-hundred milligrams of yeast extract per litre were required for growth of the strain. The G+C content of the genomic DNA of strain LF13T was 42·5 mol%. Neither 16S rDNA sequence similarity values nor phylogenetic analysis unambiguously related strain LF13T with members of any recognized bacterial phyla. On the basis of 16S rDNA sequence comparisons, and in combination with physiological and morphological traits, a novel genus, Caldithrix, is proposed, with strain LF13T (=DSM 13497T =VKM B-2286T) representing the type species, Caldithrix abyssi.

On the basis of phenotypic and DNA relatedness data, three novel species of the genus Bosea are proposed, Bosea massiliensis (63287T =CIP 106336T =CCUG 43117T), Bosea vestrisii (34635T =CIP 106340T =CCUG 43114T) and Bosea eneae (34614T =CIP 106338T =CCUG 43111T). The original description of the genus Bosea included thiosulphate oxidation as a phenotypic feature, when the sole and type species of the genus, Bosea thiooxidans, was proposed. The three novel species described herein were not able to oxidize thiosulphate; thus, it is proposed that this characteristic be removed from the description of the genus and considered as specific for B. thiooxidans. The novel species of the genus Bosea proposed here form a well-separated cluster in the Bradyrhizobium group of the α-2 subclass of the Proteobacteria, on the basis of 16S rDNA gene sequence analysis. However, 16S rDNA gene sequence analysis was not sufficient to delineate the species; hence, DNA–DNA relatedness and phenotypic data were also required. All of the novel species described in this study are fastidious bacteria isolated from a hospital water supply, using co-cultivation with amoebae. This group of bacteria are hypothesized to be a potential cause of nosocomial infections. For treatment of infections caused by these novel bacteria, doxycycline appears to be the sole antibacterial compound with a consistently low MIC value.

Among Pseudomonas strains isolated from Korean agricultural soils, four strains (Ps 9-14 group: Ps 1-2, Ps 1-10, Ps 5-5 and Ps 9-14T) from the Suwon, Goesan and Samchok regions, three strains (Ps 3-10 group: Ps 2-22, Ps 3-1 and Ps 3-10T) from Umsong Region and four strains (Pss 26 group: Pss 14, Pss 25, Pss 26T and Pss 27) from Jinju Region were identified as three independent groups on the basis of 16S rDNA sequence analysis. While, on the basis of 16S rDNA sequence analysis, Ps 9-14T and Ps 3-10T form a phyletic line with Pseudomonas jessenii CIP 105274T, ‘Pseudomonas pavonaceae’ IAM 1155 and Pseudomonas graminis DSM 11363T, Pss 26T is grouped with Pseudomonas citronellolis ATCC 13674T and Pseudomonas nitroreducens IAM 1439T. According to DNA–DNA hybridization studies, strain Ps 9-14T shows high DNA relatedness to strain Ps 3-10T (52 %) and Pseudomonas migulae CIP 105470T (49 %) and strain Ps 3-10T reveals high relatedness to strain Ps 9-14T (48 %) and P. jessenii CIP 105274T (45 %). Strain Pss 26T shows high relatedness to P. citronellolis LMG 18378T (54 %), P. nitroreducens ATCC 33634T (48 %) and Pseudomonas aeruginosa LMG 1242T (48 %). On the basis of phenotypic and genotypic analyses, three novel species of the genus Pseudomonas are proposed: Pseudomonas koreensis sp. nov. (type strain Ps 9-14T =LMG 21318T =KACC 10848T) for the Ps 9-14 group, Pseudomonas umsongensis sp. nov. (type strain Ps 3-10T =LMG 21317T =KACC 10847T) for the Ps 3-10 group and Pseudomonas jinjuensis sp. nov. (type strain Pss 26T =LMG 21316T =KACC 10760T) for the Pss 26 group.

Two strains of a novel aerobic, bacteriochlorophyll a-containing species of the α-4 subclass of the Proteobacteria were isolated from the hot spring at Alcafache in central Portugal. 16S rRNA gene sequence-based phylogenetic analyses showed the two novel isolates to be phylogenetically related to members of the genera Erythrobacter, Erythromicrobium and Porphyrobacter. The strains produce reddish-orange-pigmented colonies, have an optimum growth temperature of about 50 °C and could be distinguished from the species Porphyrobacter tepidarius, which also has a high growth temperature, primarily on the basis of the fatty acid composition. The novel species does not grow anaerobically in the presence or absence of a light source. The strains of the novel species utilize several single carbon sources for growth, most of which are also used by P. tepidarius. The species status of strains ALC-2T and ALC-3 was confirmed by low reassociation values of the DNA with species of the genera Erythrobacter, Erythromicrobium and Porphyrobacter. Phenotypic characteristics and 16S rRNA gene sequence analyses also show that strains ALC-2T (=DSM 12079T =ATCC BAA-386T) and ALC-3 (=DSM 12080) represent a novel species, for which the name Porphyrobacter cryptus sp. nov. is proposed.

An oestradiol-degrading bacterium isolated at a sewage treatment plant in Tokyo was studied phenotypically, genotypically and phylogenetically. Analysis of its 16S rDNA sequence, DNA base composition, whole-cell fatty acid profile and isoprenoid quinone composition, as well as the presence of sphingoglycolipid, revealed that the isolate is a member of the genus Novosphingobium. However, the sequence similarity of its 16S rDNA to those of known Novosphingobium species was no higher than 97 %, implying that the isolate is distinctive. The results of DNA–DNA hybridization experiments and physiological characterization also indicated that the isolate represents a novel Novosphingobium species, for which the name Novosphingobium tardaugens sp. nov. is proposed; strain ARI-1T (=JCM 11434T =ATCC BAA-531T =IFO 16725T) is the type strain.

A Gram-negative, non-motile, non-spore-forming, moderately halophilic rod (strain SM-1T) was isolated from salt marsh around the junction of the Youngsan River and the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. This organism grew optimally at 37 °C and was able to grow at 10 and 45 °C. It grew optimally in the presence of 2–3 % (w/v) NaCl. The major fatty acids in strain SM-1T were iso-C15 : 0 and C16 : 0. Strain SM-1T and Microbulbifer hydrolyticus DSM 11525T were characterized by having ubiquinone-8 as the predominant respiratory lipoquinone. The DNA G+C content of strain SM-1T was 59 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strain SM-1T formed a coherent cluster with M. hydrolyticus; this relationship was supported by a bootstrap resampling value of 100 %. The level of 16S rDNA identity between strain SM-1T and the type strain of M. hydrolyticus was 98·6 %. The mean level of DNA–DNA relatedness between strain SM-1T and the type strain of M. hydrolyticus was 20·6 %. Therefore, on the basis of phenotypic properties, phylogeny and genomic data, strain SM-1T should be placed in the genus Microbulbifer as a member of a novel species, for which the name Microbulbifer salipaludis sp. nov. is proposed. The type strain of the novel species is strain SM-1T (=KCCM 41586T =JCM 11542T).

Three Legionella-like micro-organisms, isolated from cooling tower water of a building in Busan, Korea, were characterized by a variety of biochemical and molecular phylogenetic tests. Analyses of whole-cell fatty acids and results of biochemical tests revealed that these three isolates are distinct from previously described Legionella species. Furthermore, results of comparative analyses of 16S rDNA (1476–1488 bp), mip (408 bp) and rpoB (300 bp) sequences also confirmed that these strains represent a novel species within the genus Legionella. The 16S rDNA sequences of the three Korean isolates had similarities of less than 95·8 % to other Legionella species. Phylogenetic trees formed by analysis of the 16S rRNA, rpoB and mip genes revealed that the isolates formed a distinct cluster within the genus Legionella. Based on the evaluated phenotypic and phylogenetic characteristics, it is proposed that these Korean isolates from water be classified as a novel species, Legionella busanensis sp. nov.; the type strain is strain K9951T (=KCTC 12084T =ATCC BAA-518T).

Arbuscular mycorrhizal fungi are obligate endosymbionts that colonize the roots of almost 80 % of land plants. The present paper describes morphological and molecular data on a bacterial endosymbiont living in the cytoplasm of dormant or germinating spores and symbiotic mycelia of the fungal species Gigaspora margarita, Scutellospora persica and Scutellospora castanea. PCR amplification of almost the entire 16S rRNA gene of the Gigaspora margarita BEG 34 endosymbiont, using universal bacterial primers, and subsequent sequence analysis demonstrated that this organism occupies a very distinct phylogenetic position within the β-Proteobacteria, with the genera Burkholderia, Pandoraea and Ralstonia as its closest neighbours. Primers specific to the 16S rDNA of the endosymbiotic bacteria of BEG 34 allowed amplification of spore DNA from endosymbionts of Gigaspora margarita, Gigaspora decipiens, S. persica and S. castanea, but not from the Gigaspora gigantea endosymbiont (which was morphologically different) or from the cytoplasm of Gigaspora rosea (which did not contain endosymbiotic bacteria). These specific primers were successfully used as a probe for the in-situ hybridization of endobacteria in Gigaspora margarita spores. The overall rod-shaped morphology of the Gigaspora margarita, Gigaspora decipiens, S. persica and S. castanea endosymbionts was similar, and amplification and sequence analysis of the almost-complete 16S rRNA genes of several Gigaspora margarita, S. persica and S. castanea endosymbionts revealed over 98 % sequence similarity. These morphological and genomic characteristics were used to assign the endosymbionts of these three species (five isolates) of arbuscular mycorrhizal fungi as ‘Candidatus Glomeribacter gigasporarum’ gen. nov., sp. nov.

The phenotypic, genomic and phylogenetic characteristics of four aerobic, Gram-negative, non-fermentative, motile, non-pigmented, agarolytic Pseudoalteromonas-like bacteria, isolated from marine environments, have been investigated. These bacteria share DNA–DNA similarities above 86 %. Comparative 16S rDNA sequence analysis of strain KMM 255T revealed its membership of the genus Pseudoalteromonas; it shares 99·9 % sequence similarity with Pseudoalteromonas distincta, Pseudoalteromonas elyakovii, Pseudoalteromonas atlantica and Pseudoalteromonas espejiana. DNA–DNA reassociation levels obtained for strain KMM 255T and type strains of these four species and other Pseudoalteromonas species were below 45 %. The marine isolates differed from known species of the genus by the fact that the cells are motile by means of a single flagellum or two to four polar unsheathed flagella and by an inability to utilize most organic compounds. On the basis of phenotypic, DNA–DNA hybridization and phylogenetic data, it is concluded that the isolates represent a novel species within the genus Pseudoalteromonas, for which the name Pseudoalteromonas agarivorans sp. nov. is proposed. The type strain is strain KMM 255T (=DSM 14585T).

A facultatively denitrifying bacterium, strain K601T, was isolated at 30 °C from a municipal sewage plant on cyclohexanol as sole carbon source and nitrate as electron acceptor. Under aerobic conditions this strain used acetate, fumarate, lactate, pyruvate, crotonate, indole, glucose, vanillate, 4-hydroxybenzoate, m-cresol, o-cresol and p-cresol. Under denitrifying conditions the strain used cyclohexanol, cyclohexanone, 1,3-cyclohexanedione, 2-cyclohexenone, 1,3-cyclohexanediol (cis and trans), monocarboxylic acids (C2–C7), adipate, pimelate, 5-oxocaproate, citrate, 2-oxoglutarate, succinate, malate, crotonate, lactate, pyruvate and fumarate. Cells were short rods, 0·6 μm wide and 1–2 μm long, motile, non-spore-forming, Gram-negative, and catalase- and oxidase-positive. Strain K601T used nitrate, nitrite and oxygen as electron acceptors, but not sulfate, sulfite or fumarate. The DNA G+C content of strain K601T was 66 mol%. Phylogenetic analysis, based on 16S rDNA sequencing, showed that strain K601T represents a separate lineage of the family Comamonadaceae in the β-subclass of Proteobacteria. Based on the high 16S rDNA sequence divergence and phenotypic characteristics, the name Alicycliphilus denitrificans gen. nov., sp. nov. is proposed for this strain. The type strain is K601T (=DSM 14773T =CIP 107495T).

Microbial mats developing in the hypersaline lagoons of a commercial saltern in the Salin-de-Giraud (Rhône delta) were found to contain a red layer fully dominated by spirilloid phototrophic purple bacteria underlying a cyanobacterial layer. From this layer four strains of spirilloid purple bacteria were isolated, all of which were extremely halophilic. All strains were isolated by using the same medium under halophilic photolithoheterotrophic conditions. One of them, strain SG 3105 was a purple non-sulfur bacterial strain closely related to Rhodovibrio sodomensis with a 16S rDNA sequence similarity of 98·8 %. The three other isolated strains, SG 3301T, SG 3302 and SG 3304, were purple sulfur bacteria and were found to be very similar. The cells were motile by a polar tuft of flagella. Photosynthetic intracytoplasmic membranes of the lamellar stack type contained BChl a and spirilloxanthin as the major carotenoid. Phototrophic growth with sulfide as electron donor was poor; globules of elemental sulfur were present outside the cells. In the presence of sulfide and CO2 good growth occurred with organic substrates. Optimum growth occurred in the presence of 9–12 % (w/v) NaCl at neutral pH (optimal pH 6·8–7) and at 30–35 °C. The DNA base composition of strains SG 3301T and SG 3304 were 74·5 and 74·1 mol% G+C, respectively. According to the 16S rDNA sequences, strains SG 3301T and SG 3304 belonged to the genus Halorhodospira, but they were sufficiently separated morphologically, physiologically and genetically from other recognized Halorhodospira species to be described as a new species of the genus. They are, therefore, described as Halorhodospira neutriphila sp. nov. with strain SG 3301T as the type strain (=DSM 15116T).

Mesophilic, hydrogenotrophic, sulfate-reducing bacteria were isolated from a deep-sea hydrothermal chimney sample collected at 13° N on the East-Pacific Rise at a depth of 2600 m. Two strains (BL5 and H9) were found to be phylogenetically similar to Desulfovibrio profundus (similarity >99 %), whereas two other strains (H1 and AM13T) were found to be phylogenetically distinct (similarity 96·4 %) from Desulfovibrio zosterae, their closest relative. Strain AM13T was characterized further. It was a barophilic, Gram-negative, non-sporulating, motile, vibrio-shaped or sigmoid bacterium possessing desulfoviridin. It grew at temperatures ranging from 20 to 40 °C, with an optimum at 35 °C in the presence of 2·5 % NaCl. The pH range for growth was 6·7–8·2 with an optimum around 7·8. Strain AM13T utilized H2/CO2, lactate, formate, ethanol, choline and glycerol as electron donors. Electron acceptors were sulfate, sulfite and thiosulfate, but not elemental sulfur or nitrate. The G+C content of DNA was 47 mol%. Strain AM13T (=DSM 14728T =CIP107303T) differed from D. zosterae not only phylogenetically, but also genomically (DNA–DNA reassociation value between the two bacteria was 23·8 %) and phenotypically. This isolate is therefore proposed as the type strain of a novel species of the genus Desulfovibrio, Desulfovibrio hydrothermalis sp. nov.

On the basis of morphological, physiological and genotypic properties ‘Blastobacter viscosus’ 7d and ‘Blastobacter aminooxidans’ 14a are proposed as new species of the genus Xanthobacter, Xanthobacter viscosus (type strain 7dT =VKM B-2253T =ATCC BAA-298T) and Xanthobacter aminoxidans corrig. (type strain 14aT =VKM B-2254T =ATCC BAA-299T).

Two strains of a novel myxobacterium (designated SIR-1T and SHI-1) were isolated from Japanese coasts located in the Pacific subtropical zone. Cells of both strains were Gram-negative, rod-shaped and motile by gliding. The strains were chemoheterotrophic and strictly aerobic. They had the common characteristics associated with myxobacteria, such as bacteriolytic action and fruiting-body formation. The characteristic feature of the strains was a NaCl growth requirement with an optimum concentration of 2·0–3·0 % (w/v), comparable to that of sea water. In addition, other cationic components of sea water, such as Mg2+, Ca2+ and K+, were needed for growth. The major respiratory quinone was MK-8(H2). The cellular fatty acid profile was characterized by the predominance of iso-C15 : 0. Characteristic fatty acids anteiso-C16 : 0 and anteiso-C17 : 0, and a long-chain polyunsaturated fatty acid (C20 : 4), were also detected. The G+C content of the genomic DNA of strains SIR-1T and SHI-1 was between 69·3 and 70·0 mol% (as determined by HPLC). Strains SIR-1T and SHI-1 shared almost identical 16S rDNA sequences, and clustered with the genus Nannocystis as their closest relative upon phylogenetic analysis. However, the phylogenetic distance between the novel strains and the genus Nannocystis was large enough to warrant their different generic allocation. This finding was supported by significant phenotypic differences between the novel strains and Nannocystis. Thus, strains SIR-1T and SHI-1 represent a novel genus and species, for which the names Plesiocystis and Plesiocystis pacifica, respectively, are proposed. The type strain of the species is SIR-1T (=JCM 11591T =DSM 14875T =AJ 13960T).