- Volume 57, Issue 11, 2007

Two coccoid phototrophic purple sulfur bacteria were isolated from marine habitats (marine aquaculture pond near Bheemli, Visakhapatnam and marine tidal waters from a fishing harbour, Kakinada) in a medium that contained 3 % NaCl (w/v). Strains JA132T and JA130T are Gram-negative, motile cocci with a single flagellum. Both have an obligate requirement for NaCl. Intracellular photosynthetic membranes are of the vesicular type. Bacteriochlorophyll a and most probably carotenoids of the spirilloxanthin series were present as photosynthetic pigments. Both strains were able to grow photolithoautotrophically and photolithoheterotrophically. Chemotrophic and fermentative growth could not be demonstrated. There is no vitamin requirement for strain JA132T, while strain JA130T requires niacin, biotin and pantothenate as growth factors. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that both strains cluster with species of the genus Thiorhodococcus belonging to the Gammaproteobacteria. The DNA G+C contents of strains JA132T and JA130T were 65.5 and 57.5 mol%, respectively. Based on the 16S rRNA gene sequence analysis, morphological and physiological characteristics, strains JA132T and JA130T are significantly different from each other and from other species of the genus Thiorhodococcus and are recognized as two novel species, for which the names Thiorhodococcus bheemlicus sp. nov. and Thiorhodococcus kakinadensis sp. nov. are proposed. The type strains of T. bheemlicus sp. nov. and T. kakinadensis sp. nov. are JA132T (=MTCC 8120T=ATCC BAA-1362T=JCM 14149T=DSM 18805T) and JA130T (=ATCC BAA-1353T=DSM 18858T=JCM 14150T), respectively.

A diazotroph capable of accumulating significant amounts of polyhydroxyalkanoate was isolated in New Zealand from a bioreactor treating nitrogen-deficient pulp and paper-mill effluent. Strain Y88T is Gram-negative, rod-shaped and positive for catalase, nitrate reductase and urease activities. The complete 16S rRNA gene sequence was most similar to those of other members of the genus Novosphingobium, the highest level of similarity (94.7 %) being found with respect to the type strain of Novosphingobium stygium. The combined phenotypic, chemotaxonomic and sequence data show that while strain Y88T belongs to the genus Novosphingobium, it is distinct from all currently recognized Novosphingobium species. Therefore, strain Y88T represents the first nitrogen-fixing species of the genus Novosphingobium, for which the name Novosphingobium nitrogenifigens sp. nov. is proposed. The type strain is Y88T (=ICMP 16470T=DSM 19370T).

A Gram-negative, non-motile, coccobacilli-shaped bacterium, DS-48T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by means of a polyphasic study. Strain DS-48T grew optimally at 25 °C and pH 7.0–8.0 in the presence of 0.5 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C18 : 1 2-OH as the major fatty acids. The DNA G+C content was 69.3 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-48T fell within the genus Roseomonas, clustering with Roseomonas lacus TH-G33T (at a bootstrap confidence level of 100 %). The levels of similarity between the 16S rRNA gene sequence of strain DS-48T and those of the type strains of recognized Roseomonas species were in the range 93.2–98.0 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness of DS-48T, revealed that this strain differs from recognized Roseomonas species. On the basis of phenotypic, phylogenetic and genetic data, therefore, strain DS-48T represents a novel species within the genus Roseomonas, for which the name Roseomonas terrae sp. nov. is proposed. The type strain is DS-48T (=KCTC 12874T=JCM 14592T).

A Gram-negative, motile, rod-shaped, Idiomarina-like bacterial strain, ISL-52T, was isolated from a marine solar saltern of the Yellow Sea in Korea and was subjected to a polyphasic taxonomic investigation. Strain ISL-52T grew optimally at pH 7.0–8.0 and at 30–37 °C. It contained Q-8 as the predominant ubiquinone. The major fatty acids (>10 % of total fatty acids) were iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1 ω9c. The DNA G+C content was 53.9 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-52T fell within the genus Idiomarina, joining the type strain of Idiomarina homiensis at a bootstrap resampling value of 100 %. Strain ISL-52T exhibited 16S rRNA gene sequence similarity values of 94.9–96.7 % with respect to the type strains of eight recognized Idiomarina species. The differential phenotypic properties of ISL-52T, together with its phylogenetic distinctiveness, demonstrated that this strain is distinguishable from the recognized Idiomarina species. On the basis of phenotypic, phylogenetic and genetic data, therefore, strain ISL-52T represents a novel species of the genus Idiomarina, for which the name Idiomarina salinarum sp. nov. is proposed. The type strain is ISL-52T (=KCTC 12971T=CCUG 54359T).

Three Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from clinical specimens between 1992 and 2000. On the basis of 16S rRNA gene sequence similarities, these strains (CCUG 30717T, CCUG 43892 and CCUG 38531T) were shown to belong to the Alphaproteobacteria, most closely related to Ochrobactrum grignonense (99.0 and 98.2 % similarity to the type strain). Chemotaxonomic data (major ubiquinone Q-10; major polyamines spermidine, sym-homospermidine and putrescine; major polar lipids phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine; major fatty acids C18 : 1 ω7c and C19 : 0 cyclo ω8c) supported the affiliation of the isolates to the genus Ochrobactrum. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the isolates from described Ochrobactrum species. Isolates CCUG 30717T and CCUG 43892 were closely related on the basis of DNA–DNA reassociation experiments and therefore represent one novel species, for which the name Ochrobactrum pseudogrignonense sp. nov. is proposed, with the type strain CCUG 30717T (=CIP 109451T). Isolate CCUG 38531T was different from these strains and also from other Ochrobactrum species. For this strain, the name Ochrobactrum haematophilum sp. nov. is proposed, with the type strain CCUG 38531T (=CIP 109452T).

A Gram-negative, non-motile, oval to rod-shaped, psychrotolerant, phototrophic, purple non-sulfur bacterium (designated strain JA139T) was isolated from a snow sample from Changla Pass in the Indian Himalayas. Strain JA139T had vesicular-type intracytoplasmic membrane structures and contained bacteriochlorophyll a and most probably spheroidene-like carotenoids. Biotin, niacin and thiamine were required for growth of strain JA139T. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that the strain clustered with species of the genus Rhodobacter but was distinctly separate from all recognized members of the family Rhodobacteraceae. Based on the genotypic and phenotypic differences observed between strain JA139T and recognized Rhodobacter species, strain JA139T is considered to represent a novel species of the genus, for which the name Rhodobacter changlensis sp. nov. is proposed. The type strain is JA139T (=DSM 18774T =CCUG 53722T =JCM 14338T).

A strain of heterotrophic, facultatively anaerobic, marine bacterium, designated strain c121T, was isolated from coastal sediment of Luoyuan Bay, in Fujian province, PR China. Analysis of the 16S rRNA gene sequence revealed an affiliation with the genus Pseudidiomarina; the sequence similarity between c121T and Pseudidiomarina taiwanensis PIT1T was 97 %. Cells of the novel strain were non-pigmented, Gram-negative rods, 0.3 μm wide and 1.2–1.8 μm long. Cells grown in broth cultures were non-motile, lacking flagella. Growth of the strain was observed at salinities ranging from 0.5 to 15 % NaCl, and the optimal concentration was about 1–8 %. The temperature range for growth was rather broad and was high for a marine bacterium: the strain grew at 13–42 °C, showed good growth at 20–40 °C and had an optimum between 30 and 40 °C. The major cellular fatty acids were iso-C15 : 0 (24.2 %), C16 : 1 ω7c/iso-C15 : 0 2-OH (15.3 %) and iso-C17 : 1 ω9c (11.9 %). The DNA G+C content was 50.0 mol%. Phylogeny based on 16S rRNA gene sequences, together with data from phenotypic and chemotaxonomic characterization, revealed that strain c121T could be classified within a novel species of the genus Pseudidiomarina, for which the name Pseudidiomarina sediminum sp. nov. is proposed, with the type strain c121T (=CICC 10319T =LMG 24046T).

Several strains of the fungus Rhizopus microsporus harbour endosymbiotic bacteria for the production of the causal agent of rice seedling blight, rhizoxin, and the toxic cyclopeptide rhizonin. R. microsporus and isolated endobacteria were selected for freeze–fracture electron microscopy, which allowed visualization of bacterial cells within the fungal cytosol by their two parallel-running envelope membranes and by the fine structure of the lipopolysaccharide layer of the outer membrane. Two representatives of bacterial endosymbionts were chosen for phylogenetic analyses on the basis of full 16S rRNA gene sequences, which revealed that the novel fungal endosymbionts formed a monophyletic group within the genus Burkholderia. Inter-sequence similarities ranged from 98.94 to 100 %, and sequence similarities to members of the Burkholderia pseudomallei group, the closest neighbours, were 96.74–97.38 %. In addition, the bacterial strains were distinguished from their phylogenetic neighbours by their fatty acid profiles and other biochemical characteristics. The phylogenetic studies based on 16S rRNA gene sequence data, together with conclusive DNA–DNA reassociation experiments, strongly support the proposal that these strains represent two novel species within the genus Burkholderia, for which the names Burkholderia rhizoxinica sp. nov. (type strain, HKI 454T=DSM 19002T=CIP 109453T) and Burkholderia endofungorum sp. nov. (type strain, HKI 456T=DSM 19003T=CIP 109454T) are proposed.

A micro-organism, DCY12T, comprising Gram-negative, non-motile, pale-yellow rods was isolated from soil from a ginseng field in South Korea and was investigated to determine its taxonomic status. It grew optimally at 30 °C and at pH 7.0, the G+C content of its DNA was 40.5 mol%, the major components of the fatty acid profile were C16 : 0 and C18 : 1 and the major ubiquinone was Q-8. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate was most closely related to Hydrocarboniphaga effusa AP103T (89.2 %), Nevskia ramosa Soe1 (88.8 %) and Pseudomonas aeruginosa ATCC 10145T (83.2 %). The phenotypic, physiological, metabolic and phylogenetic properties of DCY12T suggest that it represents a novel genus (class Gammaproteobacteria) and species, for which the name Solimonas soli gen. nov., sp. nov. is proposed. The type strain of Solimonas soli is DCY12T (=KCTC 12834T =LMG 24014T).

A seawater bacterium, designated IMCC3195T, was isolated from the Antarctic coast. Cells of the novel strain were Gram-negative, rusty-coloured, strictly aerobic, chemoheterotrophic, non-budding and non-motile rods or vibrioids that possessed a thin prostheca. Based on 16S rRNA gene sequence comparisons, the novel strain was most closely related to the genera Hyphomonas (89.4–90.9 %), Maricaulis (90.1–90.4 %), Hirschia (89.0 %) and Oceanicaulis (87.9 %) of the family Hyphomonadaceae. Phylogenetic analyses also showed the Antarctic isolate to be only distantly related to the genera of stalked bacteria of marine origin in the family Hyphomonadaceae. The DNA G+C content of the novel strain was 60.3 mol% and the predominant cellular fatty acids were C18 : 1 ω7c (41.9 %), C17 : 1 ω8c (21.4 %) and C17 : 0 (14.3 %). The major quinone was Q-10. Several phenotypic and chemotaxonomic characteristics, including optimum temperature and salinity range for growth, cell morphology, pigmentation and fatty acid content, differentiated the novel strain from other related genera in the family Hyphomonadaceae. From the taxonomic evidence collected in this study, it is suggested that strain IMCC3195T (=KCCM 42687T=NBRC 103098T) represents a new genus and novel species in the family Hyphomonadaceae, for which the name Robiginitomaculum antarcticum gen. nov., sp. nov. is proposed.

Two Gram-negative, cold-adapted, aerobic bacteria, designated strains M8T and M6, were isolated from soil collected from the South Shetland Islands. The organisms were rod-shaped, catalase- and oxidase-positive and motile by means of polar flagella. These two psychrotolerant strains grew between −4 and 30 °C. 16S rRNA gene sequence analysis placed strains M8T and M6 within the genus Pseudomonas. DNA–DNA hybridization experiments between the Antarctic isolate M8T and type strains of phylogenetically related species, namely Pseudomonas peli and Pseudomonas anguilliseptica, revealed levels of relatedness of 33 and 37 %, respectively. Strain M6 showed 99 % DNA similarity to strain M8T. Several phenotypic characteristics, together with data on cellular fatty acid composition, served to differentiate strains M8T and M6 from related pseudomonads. On the basis of the polyphasic taxonomic evidence presented in this study, it can be concluded that strains M8T and M6 belong to the same genospecies, representing a novel species of the genus Pseudomonas, for which the name Pseudomonas guineae sp. nov. is proposed. The type strain is M8T (=LMG 24016T=CECT 7231T).

The taxonomic status of a yellow-coloured bacterial isolate from an oil-contaminated soil sample was determined using a polyphasic taxonomic approach. Comparative analysis of 16S rRNA gene sequences showed that the novel isolate formed a distinct phyletic line within the genus Sphingobium. The generic assignment was confirmed by chemotaxonomic data, which revealed: a fatty acid profile that is characteristic of the genus Sphingobium consisting of straight-chain saturated and unsaturated as well as 2-OH fatty acids; a ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone; a polar lipid pattern consisting of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine and sphingoglycolipid, and spermidine as the major polyamine component. Genotypic and phenotypic data show that the new isolate merits classification as a representative of a novel species of the genus Sphingobium, for which the name Sphingobium olei sp. nov. is proposed. The type strain is IMMIB HF-1T (=DSM 18999T=CCUG 54329T).

A Gram-negative, rod-shaped, non-spore-forming bacterium (strain NS11T) was isolated from a lichen-colonized rock surface. On the basis of 16S rRNA gene sequence similarity, strain NS11T was shown to belong to the Betaproteobacteria, and was most closely related to Herminiimonas arsenicoxydans ULPAs1T (98.8 %), Herminiimonas aquatilis CCUG 36956T (98.0 %) and Herminiimonas fonticola S-94T (98.0 %). Major whole-cell fatty acids were C16 : 0, C17 : 0 cyclo and C16 : 1 ω7c. Strain NS11T also contained high proportions of C10 : 0 3-OH and C18 : 1 ω7c. This pattern is typical for members of the genus Herminiimonas. The results of DNA–DNA hybridization experiments and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain NS11T from the three recognized Herminiimonas species. It is therefore concluded that strain NS11T represents a novel species of the genus Herminiimonas, for which the name Herminiimonas saxobsidens sp. nov. is proposed. The type strain is NS11T (=DSM 18748T=CCM 7436T).

Three Gram-negative, rod-shaped, non-spore-forming bacteria (strains CCUG 52769T, CCUG 52770 and CCUG 52771) isolated from haemodialysis water were characterized taxonomically, together with five strains isolated from industrial waters (CCUG 52428, CCUG 52507, CCUG 52575T, CCUG 52590 and CCUG 52631). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these isolates belonged to the class Betaproteobacteria and were related to the genus Pelomonas, with 16S rRNA gene sequence similarities higher than 99 % with the only species of the genus, Pelomonas saccharophila and to Pseudomonas sp. DSM 2583. The type strains of Mitsuaria chitosanitabida and Roseateles depolymerans were their closest neighbours (97.9 and 97.3 % 16S rRNA gene sequence similarity, respectively). Phylogenetic analysis was also performed for the internally transcribed spacer region and for three genes [hoxG (hydrogenase), cbbL/cbbM (Rubisco) and nifH (nitrogenase)] relevant for the metabolism of the genus Pelomonas. DNA–DNA hybridization, major fatty acid composition and phenotypical analyses were carried out, which included the type strain of Pelomonas saccharophila obtained from different culture collections (ATCC 15946T, CCUG 32988T, DSM 654T, IAM 14368T and LMG 2256T), as well as M. chitosanitabida IAM 14711T and R. depolymerans CCUG 52219T. Results of DNA–DNA hybridization, physiological and biochemical tests supported the conclusion that strains CCUG 52769, CCUG 52770 and CCUG 52771 represent a homogeneous phylogenetic and genomic group, including strain DSM 2583, clearly differentiated from the industrial water isolates and from the Pelomonas saccharophila type strain. On the basis of phenotypic and genotypic characteristics, these strains belong to two novel species within the genus Pelomonas, for which the names Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are proposed. The type strains of Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are CCUG 52769T (=CECT 7234T) and CCUG 52575T (=CECT 7233T), respectively.

Ten isolates of an unknown Campylobacter species were isolated from cloacal swabs obtained from captive adult whooping cranes (Grus americana). All isolates were identified as Campylobacter based on generic PCR and grouped with other Campylobacter species based on 23S rRNA gene sequence. None of the isolates could be identified by species-specific PCR for known taxa, and all ten isolates formed a robust clade that was very distinct from known Campylobacter species based on 16S rRNA, rpoB and cpn60 gene sequences. The results of 16S rRNA gene nucleotide sequence (≤92 % sequence similarity to recognized Campylobacter species) and genomic DNA (no detectable relatedness) analyses were consistent with novel species status. Cells of the Campylobacter from whooping cranes were uniflagellar and typically sigmoid to allantoid in shape (0.48 μm wide and 2.61 μm long), but also spheroid to coccoid (0.59 μm wide and 0.73 μm long). The bacterium was oxidase-positive, able to reduce nitrite, able to grow at 3 ° and 42 °C, and grew anaerobically, as well as in an atmosphere devoid of H2, and on MacConkey agar. It was not α-haemolytic and was negative for hippurate and indoxyl acetate hydrolysis and alkaline phosphatase. It also was susceptible to cephalotin and was unable to grow on nutrient agar, on a medium containing 3.5 % NaCl or in ambient O2. The bacterium was unable to grow at 25 °C and growth was negative or very restricted at 30 °C. Fluorescent amplified fragment length polymorphism analysis indicated that nine of the recovered isolates were genetically distinct. A species-specific primer set targeting the cpn60 gene was developed. The name Campylobacter canadensis sp. nov. is proposed for the novel species, with the type strain L266T (=CCUG 54429T =LMG 24001T).

A Gram-negative, coccobacillus-shaped, aerobic bacterium, designated strain UST040201-002T, was isolated in February 2004 from seawater at the outlet of a sandfilter in Port Shelter, Hong Kong SAR, China. This strain possessed ubiquinone-8; its 16S rRNA gene sequence shared only 91 % similarity with the sequence from Caedibacter taeniospiralis and 89–90 % similarity with sequences from Francisella tularensis, Francisella novicida, Francisella philomiragia and Wolbachia persica. 16S rRNA gene sequence analysis showed that the strain formed a distinct clade with C. taeniospiralis. This subcluster formed a tight coherent group with members of the family Francisellaceae and W. persica. Combined phylogenetic and physiological data suggest that strain UST040201-002T represents a novel genus and species within the order Τhiotrichales. The name Fangia hongkongensis gen. nov., sp. nov. is proposed; the type strain is UST040201-002T (=JCM 14605T=NRRL B-41860T).

A novel species, strain P2S11T, was isolated from the mucus of a puffer fish caught off the coast of Kaneohe Bay, O'ahu, Hawai'i. A phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was most closely related to Ferrimonas marina DSM 16917T and Ferrimonas balearica DSM 9799T with 93.5 % and 82.9 % sequence similarities, respectively, which established the novel strain as belonging to the genus Ferrimonas. The strain formed off-white coloured colonies on marine agar and cells were Gram-negative, non-motile rods. H2S was produced when strain P2S11T was grown on TSI medium with added salt. Strain P2S11T had a DNA G+C content of 54.9 mol% and the dominant fatty acids were C16 : 1 ω9c, C16 : 0 and C17 : 1 ω8c. On the basis of this polyphasic study, strain P2S11T (=ATCC BAA-1480T=DSM 18821T) represents a novel species of the genus Ferrimonas, for which the name Ferrimonas senticii sp. nov. is proposed.

Small Gram-negative cocco-bacilli resembling Brucella strains have been reported from marine mammals since the mid-1990s. Their placement in the genus Brucella has been supported by the following characteristics: they are aerobic, non-motile and catalase-positive, do not produce acid from carbohydrates and have a DNA–DNA relatedness value of >77 % with the six established members of the genus. Twenty-eight European isolates of the genus Brucella from marine mammals were distinguished from the six recognized species by their pattern of utilization of eleven substrates in oxidative metabolism tests and phage lysis. The 28 strains could be further separated into two groups with cetaceans and seals as their respective preferred hosts on the basis of molecular methods and on differences in the metabolism of l-arabinose, d-galactose and d-xylose. The names Brucella ceti sp. nov. and Brucella pinnipedialis sp. nov. are proposed for the isolates from cetaceans and seals, respectively. The type strain of Brucella ceti sp. nov. is NCTC 12891T (=BCCN 94-74T) and the type strain of Brucella pinnipedialis sp. nov. is NCTC 12890T (=BCCN 94-73T).

A novel anaerobic, long-chain alkene-degrading, sulfate-reducing bacterium, strain LM2801T, was isolated from brackish sediment of a wastewater decantation facility of an oil refinery (Berre lagoon, France). Cells of strain LM2801T were Gram-negative, motile, slightly curved or vibrioid rods. Its optimum growth conditions were 30–36 °C, 6–10 g NaCl l−1 and pH 7.5. Strain LM2801T incompletely oxidized long-chain alkenes (from C14 to C23) and fatty acids (C14 to C24). The DNA G+C content was 45.5 mol%. Sequence analyses of the 16S rRNA and dsrAB genes indicated that the strain was a member of the family Desulfobacteraceae within the Deltaproteobacteria. This novel isolate possesses phenotypic and phylogenetic traits that do not allow its classification as a member of any previously described genus. Therefore, strain LM2801T is described as a member of a new genus, Desulfatiferula gen. nov., of which Desulfatiferula olefinivorans sp. nov. is the type species. The type strain of Desulfatiferula olefinivorans is LM2801T (=DSM 18843T =JCM 14469T).