- Volume 56, Issue 1, 2006

An aerobic, Gram-negative bacterial strain, TH-G33T, was isolated from freshwater sediment of Taihu Lake in China. The taxonomy of strain TH-G33T was studied by using phenotypic and phylogenetic methods. Cells of strain TH-G33T were coccoid rods or rods and formed colourless to pale-pink colonies on nutrient agar. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences showed that strain TH-G33T was related to Roseomonas mucosa (94·4 %), Roseomonas gilardii subsp. gilardii (94·1 %), Roseomonas gilardii subsp. rosea (94·8 %) and Roseomonas cervicalis (93·9 %). Cells contained ubiquinone 10 (Q-10) as the major quinone and the G+C content was 71·9 mol%. Thus, strain TH-G33T represents a novel species of the genus Roseomonas, for which the name Roseomonas lacus sp. nov. is proposed. The type strain is TH-G33T (=CGMCC 1.3617T=JCM 13283T).

A novel Colwellia-like bacterial strain, SMK-10T, was isolated from a tidal flat sediment in Korea and subjected to a polyphasic taxonomic analysis. Cells of strain SMK-10T were Gram-negative, motile, greyish yellow-pigmented, curved rods. Optimal growth occurred at 25–30 °C and in the presence of 2–3 % (w/v) NaCl. Strain SMK-10T contained Q-8 as the predominant ubiquinone and C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C17 : 1, C15 : 1 and iso-C16 : 0 as major fatty acids. The DNA G+C content was 39·3 mol%. Phylogenetic trees based on 16S rRNA gene sequence analysis showed that strain SMK-10T belonged to the genus Colwellia. 16S rRNA gene sequence similarity values (94·7–96·7 %) to the type strains of all other Colwellia species and various differential phenotypic properties were sufficient to distinguish strain SMK-10T from recognized Colwellia species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain SMK-10T (=KCTC 12480T=DSM 17314T) is classified as the type strain of a novel Colwellia species, for which the name Colwellia aestuarii sp. nov. is proposed.

A slightly halophilic alphaproteobacterium, designated CL-SP26T, was isolated from hypersaline water of a solar saltern located in Seosin, Korea. 16S rRNA gene sequence analysis revealed an affiliation with the genus Jannaschia. Sequence similarities between CL-SP26T and type strains of members of the genus Jannaschia were 94·9–97·2 %. Cells were rod-shaped and motile with one or more monopolar flagella. Strain CL-SP26T grew on solid media as circular red colonies. It was able to grow in 3–10 % sea salt; however, no growth occurred in media containing NaCl as the only salt. Strain CL-SP26T grew at 5–35 °C and pH 7–10. The major fatty acids were 18 : 1ω7c (64 %) and 18 : 0 (12·0 %). Three fatty acids, 3-OH 14 : 0/iso 16 : 1 (3·6 %), 18 : 3ω6c (2·2 %) and 10-methyl 19 : 0 (1·9 %), found in minor quantities in CL-SP26T, are unique among Jannaschia species. The DNA G+C content was 63 mol%. According to physiological data, fatty acid composition and 16S rRNA gene sequence analysis, CL-SP26T was assigned to the genus Jannaschia, but could be distinguished from recognized species of the genus. Strain CL-SP26T (=KCCM 42114T=JCM 13035T) therefore represents a novel species, for which the name Jannaschia seosinensis sp. nov. is proposed.

Strain CP2CT was isolated from biological soil crusts in the Colorado Plateau, USA. The isolate was aerobic, facultatively fermentative, Gram-negative, non-motile and red-pigmented (due to the presence of carotenoids), but did not contain bacteriochlorophyll a. The strain tested positive for catalase, oxidase and urease and was negative for lysine and ornithine decarboxylases and arginine dihydrolase. The major fatty acids present were C18 : 1 ω7c and C16 : 0. It had a high DNA G+C content of 75 mol%. Comparisons of 16S rRNA gene sequences identified bacteriochlorophyll a-producing strains of Paracraurococcus ruber (94·9 %), Craurococcus roseus (92·2 %) and Roseococcus thiosulfatophilus (92·3 %), as well as non-bacteriochlorophyll a-producing bacteria Muricoccus roseus (94·9 %), Roseomonas gilardii (94·2 %) and Roseomonas mucosa (93·8 %), as the bacteria most closely related to strain CP2CT. Phylogenetically, CP2CT was placed roughly equidistantly from the above organisms. Based on its phylogenetic placement and morphological and physiological characteristics, strain CP2CT is assigned to a new genus in the α-1 subgroup of the Proteobacteria, for which the name Belnapia gen. nov. is proposed. Strain CP2CT (=ATCC BAA-1043T=DSM 16746T) is proposed as the type strain of the type species of this genus, with the name Belnapia moabensis gen. nov., sp. nov.

A Gram-negative, aerobic and halophilic bacterium designated strain mano18T was isolated from a tidal flat area of Dae-Chun, Chung-Nam, Korea. This strain was motile by means of polar flagella, occasionally forming rosette-like aggregates, reduced nitrate to nitrite, required sodium ions for growth, exhibited catalase and oxidase activities and contained Q-10 as the major quinone and C18 : 1 ω7c as the dominant cellular fatty acid. Analysis of the 16S rRNA gene sequence revealed that this strain is affiliated with a cluster within the Alphaproteobacteria. Strain mano18T synthesized bacteriochlorophyll under aerobic conditions. The 16S rRNA gene sequence similarity between strain mano18T and the most closely related species, Stappia aggregata DSM 13394T, was 98·5 %. Levels of DNA–DNA relatedness between strain mano18T and the type strains of S. aggregata and Stappia stellulata were respectively 6·2–11·2 and 3·3–7·6 %. Strain mano18T, like other Stappia strains, possesses carbon monoxide dehydrogenase genes. The results of DNA–DNA hybridization and the polyphasic data confirmed that strain mano18T can be considered to represent a novel taxon in the genus Stappia. The name Stappia marina sp. nov. is proposed for the tidal flat isolate; the type strain is strain mano18T (=KCTC 12288T=DSM 17023T).

A Gram-negative, rod-shaped, non-spore-forming bacterium (TR6-01T) was isolated from compost near Daejeon city in South Korea. On the basis of 16S rRNA gene sequence similarity, strain TR6-01T was shown to belong to the class Gammaproteobacteria, related to Stenotrophomonas acidaminiphila (97·1 %) and Stenotrophomonas maltophilia (96·9 %); the phylogenetic distance from any other established species within the genus Stenotrophomonas was less than 97·0 %. Phenotypic and chemotaxonomic data (major ubiquinone Q-8; fatty acid profile) supported the affiliation of strain TR6-01T to the genus Stenotrophomonas. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain TR6-01T from the five Stenotrophomonas species with validly published names. TR6-01T therefore represents a novel species, for which the name Stenotrophomonas koreensis sp. nov. is proposed, with the type strain TR6-01T (=KCTC 12211T=JCM 13256T).

Three strains of bacteria that degrade the cyanobacterial hepatotoxin microcystin, Y2T, MDB2 and MDB3, were isolated from a eutrophic lake, Lake Suwa, and the Tenryu River, Japan, and characterized. These strains were aerobic and chemo-organotrophic and their cells were Gram-negative, non-spore-forming rods, motile by means of single polar flagella. Yellow-pigmented colonies were formed on nutrient agar media. The strains assimilated only citrate among the organic compounds tested as carbon sources. The G+C content of genomic DNA ranged from 63·6 to 63·7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolates formed a tight cluster within the family Sphingomonadaceae but were clearly separate from established genera of this family, e.g. Sphingomonas, Sphingobium, Novosphingobium and Sphingopyxis; sequence similarities between the new isolates and type strains from established genera ranged from 90·9 to 94·9 %. Chemotaxonomic and phenotypic data supported the conclusion that these strains were members of the family Sphingomonadaceae. The major components of the cellular fatty acids were 18 : 1ω7c (36–41 %) and 16 : 1ω7c (33–36 %). Hydroxy fatty acids were mainly 2-OH 14 : 0 (11–13 %), and 3-OH fatty acids were absent. Glycosphingolipids were detected. Ubiquinone-10 and homospermidine were present as the major quinine and polyamine, respectively. Thus, it is proposed that the three strains represent a new genus and species of the family Sphingomonadaceae with the name Sphingosinicella microcystinivorans gen. nov., sp. nov. The type strain is Y2T (=KCTC 12019T=JCM 13185T).

The bacterial strain SJTT, along with 15 other mesophilic, neutrophilic and facultatively sulfur-oxidizing chemolithotrophic isolates, was isolated by enrichment on reduced sulfur compounds as the sole energy and electron source from soils immediately adjacent to the roots of Clitoria ternatea, a slender leguminous herb of the Lower Gangetic plains of India. Strain SJTT was able to oxidize thiosulfate and elemental sulfur for chemolithoautotrophic growth. 16S rRNA and recA gene sequence-based phylogenetic analyses showed that the Gram-negative rod-shaped bacterium belonged to the genus Mesorhizobium and was most closely related to Mesorhizobium loti, Mesorhizobium plurifarium, Mesorhizobium amorphae and Mesorhizobium chacoense. Unequivocally low 16S rRNA (<97 %) and recA (⩽88 %) gene sequence similarities to all existing species of the most closely related genera, a unique fatty acid profile, a distinct G+C content (59·6 mol%) and phenotypic characteristics all suggested that strain SJTT represents a novel species. DNA–DNA hybridization and SDS-PAGE analysis of whole-cell proteins also confirmed the taxonomic uniqueness of SJTT. It is therefore proposed that isolate SJTT (=LMG 22697T=MTCC 7001T) be classified as the type strain of a novel species, Mesorhizobium thiogangeticum sp. nov.

A Gram-negative, rod-shaped, non-motile, non-spore forming bacterium (SV96T) was isolated from wetland soil near Ny-Ålesund, Svalbard. On the basis of 16S rRNA gene sequence similarity, strain SV96T was shown to belong to the Gammaproteobacteria, related to Methylobacter psychrophilus Z-0021T (99·1 %), Methylobacter luteus ATCC 49878T (97·3 %), Methylobacter marinus A45T (97·0 %) and Methylobacter whittenburyi ATCC 51738T (95·8 %); the closest related species within the genus Methylomicrobium with a validly published name was Methylomicrobium album ATCC 33003T (95·0 %). Chemotaxonomic data (including the major fatty acids: 16 : 1ω8, 16 : 1ω7 and 16 : 1ω5t) supported the affiliation of strain SV96T to the genus Methylobacter. The results of DNA–DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain SV96T from the four Methylobacter species mentioned above. Strain SV96T therefore represents a novel species, for which the name Methylobacter tundripaludum sp. nov. is proposed (type strain SV96T=DSM 17260T=ATCC BAA-1195T).

Zymomonas mobilis strains recently isolated from French ‘framboisé’ ciders were compared with collection strains of the two defined subspecies, Z. mobilis subsp. mobilis and Z. mobilis subsp. pomaceae, using a polyphasic approach. Six strains isolated from six different regions of France were compared with three strains of Z. mobilis subsp. mobilis, including the type strain LMG 404T, and four strains of Z. mobilis subsp. pomaceae, including the type strain LMG 448T, using phenotypic and genotypic methods. For phenotypic characterization, both physiological tests and SDS-PAGE protein profiles revealed significant differences between the two known subspecies and the French isolates; three distinct groups were observed. These findings were further confirmed by random amplified polymorphic DNA and repetitive extragenic palindromic-PCR genotyping methods in which the French isolates were clearly distinguished from the other two subspecies. Sequence analysis of a fragment ranging from 604 to 617 nucleotides corresponding to the 16S–23S rRNA gene intergenic spacer region (ISR), a 592 nucleotide HSP60 gene fragment and a 1044 nucleotide gyrB gene fragment confirmed the presence of three distinct groups. The French strains exhibited almost 94 % similarity to the ISR, 90 % to HSP60 and 86 % to gyrB sequences of the three collection strains of Z. mobilis subsp. mobilis and 87, 84 and 80 % sequence similarity, respectively, was observed with the four Z. mobilis subsp. pomaceae strains. Based on both the phenotypic and genotypic results, the French strains are proposed to represent a novel subspecies, Zymomonas mobilis subsp. francensis subsp. nov. Strain AN0101T (=LMG 22974T=CIP 108684T) was designated as the type strain.

Two Gram-negative, motile, non-spore-forming and rod-shaped bacterial strains, DS-123T and DS-140, were isolated from soil and their taxonomic positions were investigated by a polyphasic study. Strains DS-123T and DS-140 grew optimally at 30 °C and pH 6·5 without NaCl. They contained Q-8 as the predominant ubiquione and iso-C17 : 1 ω9c, iso-C17 : 0 and iso-C15 : 0 as the major fatty acids. Major polar lipids detected in the two strains were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an amino-group-containing lipid that was ninhydrin-positive. Their DNA G+C contents were 71·0 mol%. Strains DS-123T and DS-140 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 92 %. Phylogenetic trees based on 16S rRNA gene sequences showed that strains DS-123T and DS-140 formed a distinct evolutionary lineage within the Gammaproteobacteria. The 16S rRNA gene sequences of strains DS-123T and DS-140 exhibited similarity values of less than 94·1 % to members of the Gammaproteobacteria. Strains DS-123T and DS-140 were distinguished from phylogenetically related genera by differences in some phenotypic properties. On the basis of phenotypic, phylogenetic and genetic data, it is proposed that strains DS-123T (=KCTC 12396T=DSM 17203T) and DS-140 be classified in a novel genus and species, Dokdonella koreensis gen. nov., sp. nov.

Indigenous bacteria found in the sediment of the Emerald Basin (depth of 215 m, Atlantic Ocean) located offshore of Halifax Harbour (Nova Scotia, Canada) were previously found to be able to degrade the explosive compound hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). In the present study, a novel obligately respiratory, denitrifying and RDX-mineralizing bacterium, designated strain HAW-EB4T, was isolated from the marine sediment. This bacterium utilized peptone, yeast extract, Casamino acids, esters (Tweens 20, 40 and 80), sugars (N-acetyl-d-glucosamine, ribose), several C2 and C3 acids (acetate, pyruvate, lactate, propionate) and amino acids (serine, proline) as sole carbon and energy sources. Aerobically grown cells (in marine broth 2216 at 10 °C) contained C14 : 0 (6 %), iso-C15 : 0 (12 %), C16 : 0 (20 %), C16 : 1 ω7 (37 %), C18 : 1 ω7 (7 %) and C20 : 5 ω3 (7 %) as major membrane fatty acids, and Q7 (28·1 %) and MK-7 (60·9 %) as dominant respiratory quinones, consistent with deep-sea species of Shewanella. The novel bacterium had a DNA G+C content of 45 mol% and showed similarity to Shewanella species in terms of 16S rRNA and gyrB gene sequences (93–99 and 67·3–88·4 % similarity, respectively), with Shewanella pealeana being the most closely related species. Genomic DNA–DNA hybridization between strain HAW-EB4T and S. pealeana revealed a level of relatedness of 17·9 %, lower than the 70 % species cut-off value, indicating that strain HAW-EB4T (=NCIMB 14093T=DSM 17350T) is the type strain of a novel species of Shewanella, for which the name Shewanella halifaxensis sp. nov. is proposed.

Strain Dae16T, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from the soil of a ginseng field in South Korea and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Dae16T belongs to the Gammaproteobacteria and had the highest degree of sequence similarity to Lysobacter gummosus ATCC 29489T (97·1 %), Lysobacter antibioticus DSM 2044T (96·6 %), Lysobacter enzymogenes DSM 2043T (96·2 %), Lysobacter concretionis KCTC 12205T (94·7 %) and Lysobacter brunescens ATCC 29482T (93·7 %). Chemotaxonomic data revealed that strain Dae16T possesses a quinone system with Q-8 as the predominant compound and C15 : 0 iso, C16 : 0 iso and C17 : 1 iso ω9c as the predominant iso-branched fatty acids, all of which corroborated the assignment of the strain to the genus Lysobacter. Results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain Dae16T represents a distinct species. Based on these data, it is proposed that Dae16T (=KCTC 12204T=NBRC 101156T) should be classified as the type strain of a novel Lysobacter species, Lysobacter koreensis sp. nov.

Two novel species belonging to the genus Shewanella are described on the basis of their phenotypic characteristics, phylogenetic analyses of 16S rRNA and gyrB gene sequences and levels of DNA–DNA hybridization. A total of 47 strains belonging to two novel Gram-negative, psychrotolerant, H2S-producing bacterial species were isolated from marine fish (cod and flounder) caught from the Baltic Sea off Denmark. The phenotypic characteristics of strains belonging to group 1 (14 strains) indicated that these represented a non-sucrose-assimilating variant of Shewanella baltica with a DNA G+C content of 47·0 mol%. Strains of group 2 (33 isolates) did not utilize the carbon substrates assimilated by S. baltica except gluconate, N-acetylglucosamine and malate. Their DNA G+C content was 44·0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence data placed the two novel species within the genus Shewanella. Group 1 strains showed greatest sequence similarity to Shewanella putrefaciens ATCC 8071T (99·0 %) and with S. baltica NCTC 10375T (98·3 %). However, gyrB gene sequence analysis showed these isolates to share only 90·0 % sequence similarity with S. putrefaciens ATCC 8071T and 93·9 % with S. baltica NCTC 10375T. Similarly, DNA–DNA hybridization experiments revealed DNA relatedness levels of 38 % between the group 1 isolates and S. putrefaciens ATCC 8071T and 43 % with S. baltica NCTC 10375T. The group 2 strains shared less than 97 % 16S rRNA gene sequence similarities with recognized Shewanella species. Comparisons between the two novel species indicated 16S rRNA gene sequence similarity of ∼98 %, gyrB gene sequence similarity of ∼89 % and DNA–DNA reassociation values of 20–34 %. Based on the evidence presented, two novel species, Shewanella hafniensis sp. nov. (type strain P010T=ATCC BAA-1207T=NBRC 100975T) and Shewanella morhuae sp. nov. (type strain U1417T=ATCC BAA-1205T=NBRC 100978T), are described.

Among basidiomycetous yeast strains isolated from wilting leaves of various plants in China, two groups of Pseudozyma strains were distinguished from the others by morphological and physiological characterization. Molecular taxonomic analysis based on sequencing of the large subunit (26S) rRNA gene D1/D2 domain and internal transcribed spacer (ITS) region confirmed that the two groups represent two novel species. They are proposed as Pseudozyma hubeiensis sp. nov. (type strain WS 6.4T=AS 2.2493T=CBS 10077T) and Pseudozyma shanxiensis sp. nov. (type strain SH 64T=AS 2.2523T=CBS 10075T). The phylogenetic relationships of the novel species with described Pseudozyma species and related ustilagomycetous teleomorphs were analysed based on the combined sequences of ITS and D1/D2. The phenotypic diagnosis of Pseudozyma was emended because of the negative inositol assimilation reaction of P. hubeiensis sp. nov., which was closely related to the type species of the genus, Pseudozyma prolifica.

A novel species of the genus Rhodotorula was isolated from sediments collected on the deep-sea floor in the north-west Pacific Ocean. Strains SY-96T, isolated from the Yap Trench, and SY-246, isolated from the Iheya Ridge, had almost identical nucleotide sequences for their internal transcribed spacers and their 5·8S rDNA. Their physiological characteristics were also almost identical. The strains were assumed to be related to Rhodotorula mucilaginosa and Rhodotorula dairenensis based on sequence similarities in the D1/D2 region of the 26S rDNA. The low DNA–DNA relatedness and sequence similarity between strain SY-96T and related species revealed that strains SY-96T and SY-246 represent a hitherto unknown species. As ballistoconidia and sexual reproduction were not observed in strains SY-96T and SY-246, these strains are described as Rhodotorula pacifica sp. nov. The type strain is SY-96T (=JCM 10908T=CBS 10070T).

Two strains of a novel yeast species were isolated from different habitats, from soil in an alluvial zone national park in Austria and from a drain in a Turkish soft drinks factory. Analysis of the nucleotide sequences of the D1/D2 region of their large-subunit rDNAs and PCR fingerprints show that the strains are members of the same species, described as Geotrichum vulgare sp. nov. Analysis of nucleotide sequences showed that this species is related to the ascogenous genus Galactomyces. The closest phylogenetic relative is Geotrichum silvicola, a recently described species. The type strain of Geotrichum vulgare is HA1379T (=CBS 10073T=NRRL Y-27915T).

The protozoan genus Cochlosoma includes parasitic intestinal flagellates of birds and mammals of uncertain taxonomic classification. The presence of an adhesive disc, superficially similar to that of Giardia, led to a proposal that Cochlosoma should be classified as diplomonads. Careful morphological and ultrastructural observations, however, revealed conspicuous homologies to trichomonads. We addressed the question of classification and phylogenetic affiliation of Cochlosoma using the methods of molecular phylogenetics. Analyses based on the 16S rRNA gene sequence of the species Cochlosoma anatis very robustly placed Cochlosoma in the clade of the parabasalid subfamilies Trichomonadinae, Trichomitopsiinae and Pentatrichomonoidinae of the order Trichomonadida (bootstraps >94 %). The data did not provide robust support for any particular position of Cochlosoma within this clade because the sequence suffered from mutational saturation and produced a long branch. The most probable sister taxon of Cochlosoma is the genus Pentatrichomonas, because their relationship was supported specifically by the slowest-mutating, least-saturated positions as determined using the method slow–fast. Classification of the order Trichomonadida was revised to accommodate knowledge about its phylogeny – the family Cochlosomatidae and subfamilies Trichomitopsiinae and Pentatrichomonoidinae were abandoned, Trichomonadidae was amended and new families Tritrichomonadidae (formerly a subfamily) and Trichomitidae were proposed.

Two yeast strains, 153MT and NCYC 3133, isolated from clinical sources in separate hospitals were found to be almost identical in the sequences of the D1/D2 domain of large-subunit rDNA, the PCR fingerprinting profiles and physiological characteristics. The isolates are phenotypically similar, although not identical, to Candida glabrata and Kluyveromyces delphensis (recently renamed Nakaseomyces delphensis). Sequence analysis of the 26S rDNA D1/D2 gene variable region revealed that the two clinical isolates were closely related phylogenetically to C. glabrata and K. delphensis, but differed sufficiently to justify their assignment as representatives of a separate species. The name Candida bracarensis sp. nov. is proposed for the novel species with the type strain 153MT (=CBS 10154T=NCYC D3853T=CECT 12000T).