Strain KMM Research Articles

Winogradskyella echinorum sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius

The taxonomic position of a novel marine, yellow-pigmented bacterium, designated strain KMM 6211(T), was examined by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KMM 6211(T) is a member of the family Flavobacteriaceae, phylum Bacteroidetes. The closest relative of strain KMM 6211(T) was Winogradskyella eximia KMM 3944(T), the sequence similarity being 97.1 %. The DNA G+C content of KMM 6211(T) was 33.6 mol%. The strain was motile by gliding and grew with 1-6 % NaCl and at 4-37 degrees C. Aesculin, casein and gelatin were hydrolysed, but agar, starch, DNA and chitin were not degraded. On the basis of phylogenetic data and phenotypic differences between the isolate and recognized Winogradskyella species, strain KMM 6211(T) represents a novel species of the genus Winogradskyella, for which the name Winogradskyella echinorum sp. nov. is proposed. The type strain is KMM 6211(T) (=KCTC 22026(T)=LMG 24757(T)).

Pseudozobellia thermophila gen. nov., sp. nov., a bacterium of the family Flavobacteriaceae, isolated from the green alga Ulva fenestrata

Two novel aerobic, dark-orange-pigmented, Gram-negative bacterial strains, designated KMM 3531(T) and KMM 3953, were isolated from the green alga Ulva fenestrata. Analysis of the 16S rRNA gene sequences showed that the strains represented a novel lineage within the family Flavobacteriaceae. The most closely related genera with validly published names were Costertonia, Flagellimonas, Kriegella, Maribacter, Muricauda and Zobellia, with 16S rRNA gene sequence similarities of 93.3-91.8 %. Cells of strains KMM 3531(T) and KMM 3953 were rod-shaped, motile by gliding and grew at temperatures up to 49 degrees C. They produced acid from carbohydrates and possessed oxidase, catalase, beta-galactosidase and agarase activities. The predominant cellular fatty acids were iso-C(15 : 0,) iso-C(17 : 0) 3-OH, iso-C(15 : 1) G, summed feature 3 (comprising C(16 : 1)omega7c and/or iso-capital ES, Cyrillic(15 : 0) 2-OH), iso-C(17 : 1)omega9c and iso-C(15 : 0) 3-OH. The DNA G+C content was 47-49 mol%. On the basis of phenotypic and genotypic characteristics, strains KMM 3531(T) and KMM 3953 represent a novel genus and species, for which the name Pseudozobellia thermophila gen. nov., sp. nov. is proposed. The type strain is KMM 3531(T) (=DSM 19858(T)=JCM 11733(T)=KCTC 22016(T)).

Pseudochrobactrum glaciei sp. nov., isolated from sea ice collected from Peter the Great Bay of the Sea of Japan

An aerobic, Gram-negative, non-pigmented, non-motile bacterium, KMM 3858(T), was isolated from a sea-ice sample collected from Peter the Great Bay of the Sea of Japan, Russia, and subjected to a phenotypic and phylogenetic study. Comparative analyses based on the 16S rRNA and recA gene sequences placed strain KMM 3858(T) within the genus Pseudochrobactrum. The major chemotaxonomic characteristics were found to be the presence of phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unknown aminolipid and phosphatidylcholine, major fatty acids C(18 : 1)omega7c and C(19 : 0) cyclo, and ubiquinone Q-10, confirming the affiliation of strain KMM 3858(T) to the genus Pseudochrobactrum. On the basis of the phylogenetic analysis and the physiological and biochemical characterization, strain KMM 3858(T) should be classified as representing a novel species of the genus Pseudochrobactrum, for which the name Pseudochrobactrum glaciei sp. nov. is proposed. The type strain is strain Pi26(T) (=KMM 3858(T)=NRIC 0733(T)=JCM 15115(T)).

Structure of the repeat unit of the Alteromonas addita type strain KMM 3600T O-specific polysaccharide

The O-specific polysaccharide of Alteromonas addita type strain KMM 3600T is constructed of trisaccharide repeat units containing L-rhamnose, D-glucose, and D-galactose. It was established that the O-specific polysaccharide consists of trisaccharide repeat units with the structure →3)-α-D-Galp-(1→3)-α-L-Rhap-(1→3)-α-D-Glcp-(1→ based on monosaccharide analysis, Smith degradation, PMR and 13C NMR spectroscopy, and two-dimensional COSY, HSQC, and HMBC.

Pseudomonas marincola sp. nov., isolated from marine environments

An aerobic, Gram-negative, motile, non-pigmented bacterium, strain KMM 3042(T), isolated from a deep-sea brittle star in the Fiji Sea, was subjected to a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed marine Mn(II)-oxidizing isolate S185-2B as the closest neighbour of strain KMM 3042(T) (99.9 % sequence similarity). The two strains formed a distinct lineage within the genus Pseudomonas adjacent to the members of the Pseudomonas borbori cluster, sharing highest sequence similarity of 97.4 and 97.0 %, respectively, with P. borbori DSM 17834(T) and Pseudomonas flavescens DSM 12071(T). The DNA-DNA hybridization value (71 %) between strains KMM 3042(T) and S185-2B confirmed their assignment to the same species. On the basis of phylogenetic analysis, DNA-DNA hybridization and physiological and biochemical characterization, strains KMM 3042(T) and S185-2B should be assigned to a novel species of the genus Pseudomonas, for which the name Pseudomonas marincola sp. nov. is proposed. The type strain is KMM 3042(T) (=NRIC 0729(T) =JCM 14761(T)).

Lysobacter spongiicola sp. nov., isolated from a deep-sea sponge

An aerobic, Gram-negative bacterium, strain KMM 329(T), was isolated from a deep-sea sponge specimen from the Philippine Sea and subjected to a polyphasic taxonomic investigation. Comparative 16S rRNA gene sequence analysis showed that strain KMM 329(T) clustered with the species of the genus Lysobacter. The highest level of 16S rRNA gene sequence similarity (97.0 %) was found with respect to Lysobacter concretionis KCTC 12205(T); lower values (96.4-95.2 %) were obtained with respect to the other recognized Lysobacter species. The value for DNA-DNA relatedness between strain KMM 329(T) and L. concretionis KCTC 12205(T) was 47 %. Branched fatty acids 16 : 0 iso, 15 : 0 iso, 11 : 0 iso 3-OH and 17 : 1 iso were found to be predominant. Strain KMM 329(T) had a DNA G+C content of 69.0 mol%. On the basis of the phenotypic, chemotaxonomic, DNA-DNA hybridization and phylogenetic data, strain KMM 329(T) represents a novel species of the genus Lysobacter, for which the name Lysobacter spongiicola sp. nov. is proposed. The type strain is KMM 329(T) (=NRIC 0728(T) =JCM 14760(T)).

Maribacter polysiphoniae sp. nov., isolated from a red alga

A novel gliding, heterotrophic, Gram-negative, yellow-orange-pigmented, aerobic, oxidase- and catalase-positive bacterium, designated strain KMM 6151(T), was isolated from the Pacific red alga Polysiphonia japonica. Analysis of the 16S rRNA gene sequence of the strain revealed that it formed a distinct lineage within the genus Maribacter, family Flavobacteriaceae, with sequence similarities in the range 94.6-96.9 %. On the basis of phenotypic, genotypic and phylogenetic data, strain KMM 6151(T) represents a novel species of the genus Maribacter, for which the name Maribacter polysiphoniae sp. nov. is proposed. The type strain is KMM 6151(T) (=KCTC 22021(T)=LMG 23671(T)).

Arenibacter echinorum sp. nov., isolated from the sea urchin Strongylocentrotus intermedius

Two marine, heterotrophic, aerobic, pigmented and gliding bacteria, isolated from the sea urchin Strongylocentrotus intermedius were subjected to a polyphasic taxonomy study. The 16S rRNA gene sequence analysis revealed that strains KMM 6032T and KMM 6047 formed a distinct branch within the genus Arenibacter, a member of the family Flavobacteriaceae. The level of sequence similarity between the novel isolates and members of the genus Arenibacter was 94.5-98.9%. The DNA G+C content was 39-40 mol%. The dominant fatty acids were iso-C15:1, iso-C15:0, C15:0, C15:1omega6c, iso-C15:0 3-OH, iso-C17:1omega9c, iso-C17:0 3-OH and summed feature 3 (comprising iso-C15:0 2-OH and/or C16:1omega7c). The results of DNA-DNA hybridization experiments supported by phenotypic data indicated that the isolates represent a novel species within the genus Arenibacter, for which the name Arenibacter echinorum sp. nov. is proposed. The type strain is KMM 6032T (=KCTC 22013T=LMG 22574T).

Structure of teichoic acid from the marine proteobacterium Sulfitobacter brevis KMM 6006

A glycopolymer was isolated from the marine gram-negative bacterium Sulfitobacter brevis strain KMM 6006 and found to be teichoic acid containing ribitol, glycerine, and N-acetyl-D-glucosamine. The polymeric chain consisted of alternating 1,5-poly(4-N-acetyl-β-D-glucosaminylribitophosphate) and 1,3-poly(glycerophosphate) based on 13C and 31P NMR spectroscopy of the native polymer and the glycoside obtained by its dephosphorylation.

Algibacter mikhailovii sp. nov., a novel marine bacterium of the family Flavobacteriaceae, and emended description of the genus Algibacter

A novel marine bacterium, designated strain KMM 6171(T), was subjected to taxonomic analysis by using a polyphasic approach. Colonies were yellow-pigmented and cells were Gram-negative, heterotrophic rods displaying slow gliding motility. 16S rRNA gene sequence analysis indicated that strain KMM 6171(T) was closely related to the genus Algibacter, a member of the family Flavobacteriaceae, with sequence similarity of 96.7-96.8 %. The predominant cellular fatty acids were iso-C15 : 1, iso-C15 : 0, anteiso-C15 : 0, C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3, comprising C16 : 1omega7c and/or iso-C15 : 0 2-OH. The DNA G+C content was 35.1 mol%. On the basis of the phenotypic, genotypic, chemotaxonomic and phylogenetic data, strain KMM 6171(T) represents a novel species of the genus Algibacter, for which the name Algibacter mikhailovii sp. nov. is proposed. The type strain is KMM 6171(T) (=KCTC 12710(T)=LMG 23988(T)). An emended description of the genus Algibacter based on the new data is also given.

Proposal of Algoriphagus vanfongensis sp. nov., transfer of members of the genera Hongiella Yi and Chun 2004 emend. Nedashkovskaya et al. 2004 and Chimaereicella Tiago et al. 2006 to the genus Algoriphagus, and emended description of the genus Algoriphagus Bowman et al. 2003 emend. Nedashkovskaya et al. 2004

A taxonomic study of a novel marine, heterotrophic, non-gliding, halotolerant and light-pink-pigmented bacterium was carried out using a polyphasic approach. 16S rRNA gene sequence analysis revealed that strain KMM 6241(T) is a member of the phylum Bacteroidetes. Strain KMM 6241(T) formed a cluster with the genera Algoriphagus, Chimaereicella and Hongiella with sequence similarities of 94.0-98.2 %. Hongiella ornithinivorans was the closest relative of the novel isolate. Comparative analysis of phenotypic, chemotaxonomic and genotypic characteristics of strain KMM 6241(T) and representatives of the genera Algoriphagus, Chimaereicella and Hongiella revealed many similar features. Consequently, phylogenetic evidence supported by phenotypic and genotypic similarities support the transfer of members of the genera Chimaereicella and Hongiella to the genus Algoriphagus and the establishment of a novel species, Algoriphagus vanfongensis sp. nov., with strain KMM 6241(T) (=DSM 17529(T)=KCTC 12716(T)) as the type strain.

Fulvivirga kasyanovii gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from seawater in a mussel farm

A novel, strictly aerobic, heterotrophic, gliding, Gram-negative, oxidase-, catalase-, beta-galactosidase- and alkaline phosphatase-positive marine bacterium, designated strain KMM 6220(T), was isolated from seawater and studied by using a polyphasic taxonomic approach. The DNA G+C content of strain KMM 6220(T) was 59.9 mol%. The predominant fatty acids were iso-C(15 : 1), iso-C(15 : 0), iso-C(15 : 0) 3-OH, iso-C(17 : 0) 3-OH and C(16 : 1)omega7/iso-C(15 : 0) 2-OH. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain KMM 6220(T) formed a cluster with the misclassified strains [Flexibacter] aggregans NBRC 15974 and [Flexibacter] tractuosus NBRC 16035 and with the type strains of Reichenbachiella agariperforans and Roseivirga ehrenbergii with levels of similarity of 95.9, 94.4, 92.0 and 91.8 %, respectively. On the basis of its phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, strain KMM 6220(T) is considered to represent a novel species of a new genus in the phylum Bacteroidetes, for which the name Fulvivirga kasyanovii gen. nov., sp. nov. is proposed. The type strain of the type species is KMM 6220(T) (=CCTCC AB 206119(T)=KCTC 12832(T)).

Echinicola vietnamensis sp. nov., a member of the phylum Bacteroidetes isolated from seawater

The taxonomic position of a novel marine, heterotrophic, gliding, halotolerant and light-pink-pigmented bacterium, designated strain KMM 6221(T), was examined by using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain KMM 6221(T) is affiliated with the genus Echinicola, a member of the phylum Bacteroidetes, with levels of similarity of 94.7-95.0 % to strains of Echinicola pacifica. Growth of strain KMM 6221(T) was observed with 0-15 % NaCl and at 6-44 degrees C. The DNA G+C content of strain KMM 6221(T) was 45.9 mol%. On the basis of molecular distinctiveness supported by phenotypic and chemotaxonomic data, strain KMM 6221(T) is considered to represent a novel species of the genus Echinicola, for which the name Echinicola vietnamensis sp. nov. is proposed. The type strain is KMM 6221(T) (=DSM 17526(T)=LMG 23754(T)).

Marixanthomonas ophiurae gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a deep-sea brittle star

An aerobic, Gram-negative, non-motile, yellow-pigmented bacterium, strain KMM 3046(T), was isolated from a deep-sea brittle star from the Fiji Sea and was subjected to a polyphasic taxonomic analysis. Strain KMM 3046(T) grew at 5-32 degrees C and in the presence of 1-12 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and 3-OH i16 : 0, 3-OH i17 : 0 and 3-OH a17 : 0 as the major fatty acids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KMM 3046(T) forms a distinct evolutionary lineage within the family Flavobacteriaceae (phylum Bacteroidetes), displaying 92.3-91.9 % sequence similarity with respect to Salegentibacter species. On the basis of the phenotypic and phylogenetic data, strain KMM 3046(T) represents a novel genus and species of the family Flavobacteriaceae, for which the name Marixanthomonas ophiurae gen. nov., sp. nov. is proposed. The type strain of Marixanthomonas ophiurae is KMM 3046(T) (=NRIC 0684(T)=JCM 14121(T)).

The Outer Membrane of the Marine Gram‐Negative Bacterium Alteromonas addita is Composed of a Very Short‐Chain Lipopolysaccharide with a High Negative Charge Density

AbstractThe complete structure of the lipopolysaccharide isolated from the Gram‐negative marine bacterium Alteromonas addita, type strain KMM 3600T = R10SW13T, has been elucidated by means of a combined chemical approach and state‐of‐the‐art NMR and MS analyses. Isolation and characterisation of the lipid A moiety and the core oligosaccharide were pursued separately after either acid or alkaline treatment of the lipopolysaccharide. The structure detected was identified as a novel, highly negatively charged, deep‐rough lipopolysaccharide in which a trisaccharide subunit is connected to a typical lipid A glucosamine backbone. Within the core oligosaccharide, a phosphodiester bridge connects a glucose unit to a heptose residue.(© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2007)

Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity

An aerobic, Gram-negative, yellow-pigmented, non-motile bacterium, designated strain KMM 3882T, was isolated from a marine bivalve (Anadara broughtoni) collected from Peter the Great Bay, Sea of Japan, and was subjected to phenotypic and phylogenetic analyses. Strain KMM 3882T was found to exert a remarkable inhibitory activity against a number of Gram-positive micro-organisms. Phylogenetic analysis based on 16S rRNA gene sequences placed strain KMM 3882T within the genus Sphingomonas, as an independent lineage adjacent to Sphingomonas dokdonensis DS-4T and Sphingomonas panni DSM 15761T. Strain KMM 3882T showed the highest 16S rRNA gene sequence similarity to Sphingomonas dokdonensis DS-4T (97.3 %); similarities of 96.5-96.7 % were obtained with Sphingomonas pituitosa DSM 13101T, Sphingomonas azotifigens NBRC 15497T, Sphingomonas asaccharolytica NBRC 15499T, Sphingomonas trueperi DSM 7225T and Sphingomonas panni DSM 15761T. Chemotaxonomically, strain KMM 3882T contained sphingoglycolipid, C(16 : 0) and C(18 : 1) as predominant fatty acids and 2-OH C(14 : 0) as a major 2-hydroxy fatty acid, confirming the affiliation of strain KMM 3882T with the genus Sphingomonas. On the basis of phylogenetic analysis, DNA-DNA hybridization and physiological and biochemical characterization, strain KMM 3882T should be classified as representing a novel species of the genus Sphingomonas, for which the name Sphingomonas molluscorum sp. nov. is proposed. The type strain is KMM 3882T (=An 18T=NRIC 0685T=JCM 14122T=CIP 109223T).

Mesonia mobilis sp. nov., isolated from seawater, and emended description of the genus Mesonia

The taxonomic position of a novel marine, heterotrophic, strictly aerobic, gliding and yellow-pigmented bacterium, designated strain KMM 6059(T), was determined. 16S rRNA gene sequence analysis revealed that this strain represents a member of the genus Mesonia. Phenotypic and chemotaxonomic data showed that the isolate represents a novel species of the genus Mesonia, for which the name Mesonia mobilis sp. nov. is proposed. The type strain is KMM 6059(T) (=KCTC 12708(T)=LMG 23670(T)). An emended description of the genus Mesonia based on the new data is also given.

Aquimarina intermedia sp. nov., reclassification of Stanierella latercula (Lewin 1969) as Aquimarina latercula comb. nov. and Gaetbulimicrobium brevivitae Yoon et al. 2006 as Aquimarina brevivitae comb. nov. and emended description of the genus Aquimarina

A heterotrophic, aerobic, Gram-negative, pigmented and gliding bacterium, strain KMM 6258(T), was isolated from the sea urchin Strongylocentrotus intermedius and investigated using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis revealed that the closest relatives of the novel strain are Aquimarina muelleri, Stanierella latercula and Gaetbulimicrobium brevivitae, members of the family Flavobacteriaceae, with sequence similarities of 96.3, 96.4 and 96.2 %, respectively. Phylogenetic evidence, supported by chemotaxonomic and phenotypic data, assigned strain KMM 6258(T) to the genus Aquimarina as Aquimarina intermedia sp. nov. (type strain KMM 6258(T)=DSM 17527(T)=JCM 13506(T)=LMG 23204(T)). The reclassification of Stanierella latercula as Aquimarina latercula comb. nov. and Gaetbulimicrobium brevivitae as Aquimarina brevivitae comb. nov. is proposed.

Mariniflexile gromovii gen. nov., sp. nov., a gliding bacterium isolated from the sea urchin Strongylocentrotus intermedius

A marine bacterium, designated strain KMM 6038(T), was subjected to taxonomic analysis via a polyphasic approach. Cells of the strain were heterotrophic, orange-pigmented, Gram-negative and motile by means of gliding. 16S rRNA gene sequence analysis indicated that strain KMM 6038(T) was closely related to the type species of the genera Algibacter and Yeosuana, members of the family Flavobacteriaceae, with sequence similarities of 93.8 and 93.6 % to the respective type strains. However, several chemotaxonomic and phenotypic characteristics, such as the cellular fatty acid profile (iso-C(15 : 0), anteiso-C(15 : 0), iso-C(15 : 1), C(15 : 0), C(15 : 1)omega6c, iso-C(15 : 0) 3-OH and iso-C(17 : 0) 3-OH) and the low G+C content of the DNA (35.7 mol%), indicated that the strain should be separated from these two genera. From the results of phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, the bacterium should be classified as representing a novel genus and species, for which the name Mariniflexile gromovii gen. nov., sp. nov. is proposed. The type strain of Mariniflexile gromovii is KMM 6038(T) (=KCTC 12570(T)=LMG 22578(T)).

Echinicola pacifica gen. nov., sp. nov., a novel flexibacterium isolated from the sea urchin Strongylocentrotus intermedius

The taxonomic position of three novel marine, heterotrophic, pigmented and agarolytic bacteria with gliding motility, isolated from the sea urchin Strongylocentrotus intermedius, was investigated. 16S rRNA gene sequence analysis revealed that strains KMM 6166, KMM 6172T and KMM 6173 are members of the phylum Bacteroidetes; their nearest neighbours were Belliella baltica and Hongiella marincola (similarities of 94.5 and 93.6 %, respectively). The DNA G+C content of the strains was 44-45 mol%. The predominant fatty acids were C15 : 0 iso, C16:1omega5c, C17:1 iso omega9c, C17:0 iso 3-OH and summed feature 3 (C16:1omega7c and/or C15:0 iso 2-OH). The major respiratory quinone was MK-7. Results of molecular experiments supported by phenotypic and chemotaxonomic data enabled the isolates to be classified as representatives of a novel species in a new genus, for which the name Echinicola pacifica gen. nov., sp. nov. is proposed. Echinicola pacifica is the type species of the genus Echinicola, and its type strain is KMM 6172T (=KCTC 12368T=LMG 23350T).