Family Sphingobacteriaceae Research Articles

Pelobium manganitolerans gen. nov., sp. nov., isolated from sludge of a manganese mine.

A Gram-staining-negative, rod-shaped, motile by gliding and facultative anaerobic bacterial strain, YS-25T, was isolated from a sludge of a manganese mine. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YS-25T formed a single branch within the strains of the family Sphingobacteriaceae and showed low similarities to Pedobacter arcticus CCTCC AB 2010223T (91.7 %), 'Pedobacter zeaxanthinifaciens' TDMA-5 (91.5 %), Pedobacter terricola DS-45T (90.9 %), Pedobacter ureilyticus THG-T11T (90.9 %), Pseudopedobacter beijingensis MCCC 1A01299T (90.8 %) and Pedobacter heparinus CCTCC AB 209030T (88.5 %). Strain YS-25T had some unique physiological and biochemical characteristics: facultative anaerobic, able to hydrolyse Tween 40, positive for cystine arylamidase and negative for mannose assimilation and β-galactosidase. The polar lipids of strain YS-25T were phosphatidylethanolamine, aminolipid, two unknown lipids and two glycolipids. The presence of glycolipids and absence of sphingolipid were different from the Pedobacter and Pseudopedobacter strains. The major fatty acids (>5 %) were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), unknown ECL 13.565, iso-C17 : 0 3-OH, iso-C17 : 1ω9c and anteiso-C15 : 0. The genomic DNA G+C content was 42.0 mol%, and the only respiratory quinone was menaquinone 7. On the basis of polyphasic taxonomic analyses, strain YS-25T is considered to represent a novel genus and species, for which the name Pelobium manganitolerans gen. nov., sp. nov. is proposed. The type strain is YS-25T (=KCTC 52203T=CCTCC AB 2016051T).

Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost.

A Gram-stain-negative, strictly aerobic, non-motile, light yellow, short-rod bacterium (designated GJ30-7T) isolated from compost, was characterized using a polyphasic approach, in order to clarify its taxonomic position. Strain GJ30-7T was observed to grow optimally at 30 °C and at pH 7.0 on R2A agar medium. Strain Gsoil GJ30-7T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1 and Rc (the two main active components of ginseng) to ginsenoside F2. Phylogenetic analysis, based on 16S rRNA gene sequence similarities, indicated that GJ30-7T belongs to the genus Sphingobacterium of the family Sphingobacteriaceae and was most closely related to Sphingobacterium yanglingense JCM 30166T (92.6 %), Sphingobacterium psychroaquaticum KACC 18188T (92.6 %), and Sphingobacterium thermophilum KCTC 23708T (92.0 %). The DNA G+C content was 43 mol% and MK-7 was the major isoprenoid quinone. The main polar lipids were phosphatidylethanolamine, one unidentified phospolipid and one unknown polar lipid. In contrast to standard and reference strains, unidentified sphingolipid was also present. The predominant fatty acids of strain GJ30-7T were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and iso-C17 : 1ω9c and/or C16 : 0 10-methyl (summed feature 9), supporting the affiliation of strain GJ30-7T to the genus Sphingobacterium. However, strain GJ30-7T could be distinguished genotypically and phenotypically from species of the genus Sphingobacterium with validly published names. The novel isolate therefore represents a novel species, for which the name Sphingobacterium jejuense sp. nov. is proposed, with the type strain GJ30-7T (=KACC 18625T=JCM 30948T).

Mucilaginibacter pocheonensis sp. nov., with ginsenoside-converting activity, isolated from soil of a ginseng-cultivating field.

A Gram-reaction-negative, aerobic, heterotrophic, non-motile, non-spore-forming, rod-shaped bacterial strain, designated Gsoil 032T, was isolated from soil of a ginseng field in Pocheon Province, South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain Gsoil 032T grew at 10-42 °C and at pH 5.0-10.0 on R2A agar medium. Strain Gsoil 032T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to compound K. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 032T was shown to belong to the family Sphingobacteriaceae and to be related to Mucilaginibacter sabulilitoris SMS-12T (97.6 % sequence similarity) and Mucilaginibacter lappiensis ANJLI2T (97.1 %) The G+C content of the genomic DNA was 44.4 mol%. The predominant respiratory quinone was menaquinone MK-7 and the major fatty acids were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipid detected was phosphatidylethanolamine, while the minor polar lipids were various unidentified aminophospholipids, unidentified phospholipids and unidentified polar lipids. DNA and chemotaxonomic data supported the affiliation of strain Gsoil 032T to the genus Mucilaginibacter. Strain Gsoil 032T could be differentiated genotypically and phenotypically from recognized species of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter pocheonensis sp. nov. is proposed, with the type strain Gsoil 032T (=KCTC 12641T=LMG 23495T).

Pedobacter humicola sp. nov., a member of the genus Pedobacter isolated from soil.

An aerobic, Gram-stain-negative, oxidase-negative, catalase-positive, non-motile, non-spore-forming, rod-shaped, light pink-pigmented bacterium, designated strain R135T, was isolated from soil in Hwaseong, South Korea. Flexirubin-type pigments were absent. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain R135T formed a lineage within the family Sphingobacteriaceae of the phylum Bacteroidetes. It was distinct from various species of the genus Pedobacter, including P. terrae DS-57T (98.13 % sequence similarity), P. alluvionis NWER-II11T (97.76 %), P. suwonensis 15-52T (97.71 %), P. kyungheensis KACC 16221T (97.37 %), P. roseus CG-GP80T (97.24 %), P. soli 15-51T (97.23 %) and P. sandarakinus DS-27T (97.09 %). The major isoprenoid quinone was menaquinone-7 (MK-7), and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0. The DNA G+C content of strain R135T was 40.4 mol%. Levels of DNA-DNA hybridization similarities between strain R135Tand other members of the genus Pedobacter ranged from 25 % to 43 %. On the basis of phenotypic, genotypic and phylogenetic analysis, strain R135T represents a novel species of the genus Pedobacter, for which the name Pedobacter humicola sp. nov. is proposed. The type strain is R135T (=KEMB 9005-332T=KACC 18452T=JCM 31010T).

Anseongella ginsenosidimutans gen. nov., sp. nov., isolated from soil cultivating ginseng.

A Gram-stain-negative, rod-shaped, non-spore-forming, oxidase and catalase-positive, strictly aerobic bacterium, designated strain Gsoil 524T, was isolated from the soil of a ginseng field and subjected to polyphasic taxonomic analysis. Phylogenetic analysis, based on the 16S rRNA gene sequence, placed Gsoil 524T in a distinct lineage in the family Sphingobacteriaceae, sharing 87.2-88.0 % sequence similarity with members of the closely related genera Pedobacter, Mucilaginibacter and Solitalea. Strain Gsoil 524T contained MK-7 as the predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 1ω5c as the major fatty acids. Strain Gsoil 524T could be distinguished from the other members of the family Sphingobacteriaceae by a number of chemotaxonomic and phenotypic characteristics. The major polar lipids in strain Gsoil 524T were phosphatidylethanolamine and two unidentified polar lipids. Compared with the standard and reference strains unidentified sphingolipid was also found. Based on this polyphasic taxonomic analysis, strain Gsoil 524T represents a novel species within a novel genus, for which the name Anseongella ginsenosidimutans gen. nov., sp. nov. is proposed. The type strain of Anseongella ginsenosidimutans is Gsoil 524T ( = KACC 14636T = KCTC 22261T = LMG 24494T).

Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica.

A red-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, strain R2-28T, was isolated from a soil sample collected from Ardley Island, South Shetland Islands, Antarctica, and was characterized taxonomically by using a polyphasic approach. The organism grew optimally at 18 °C in TSB. On the basis of phylogenetic analyses of the 16S rRNA gene sequence, strain R2-28T was most closely related to the genus Pedobacter of the family Sphingobacteriaceae. The highest levels of 16S rRNA gene sequence similarity were found with respect to Pedobacter alluvionis NWER-II11T (95.6 %) and Pedobacter terrae DS-57T (95.2 %). The DNA G+C content was 39.9 mol%, and MK-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine and a sphingolipid. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). These chemotaxonomic and phylogenetic data supported the allocation of strain R2-28T to the genus Pedobacter. Additionally, the results of physiological and biochemical tests allowed phenotypic differentiation of strain R2-28T from species of the genus Pedobacter with validly published names. Therefore, strain R2-28T represents a novel species within the genus Pedobacter, for which the name Pedobacter ardleyensis sp. nov. is proposed. The type strain is R2-28T ( = CCTCC AB 2013365T = LMG 28255T).

Mucilaginibacter vulcanisilvae sp. nov., isolated from a volcanic forest.

A Gram-stain-negative, strictly aerobic, pale-pink-pigmented bacterium, designated strain G27(T), was isolated from a volcanic forest of Jeju Island, South Korea. Cells were catalase- and oxidase-positive, non-motile rods producing exopolysaccharide and flexirubin-type and pale pink pigments. Growth of strain G27(T) was observed at 4-30 °C (optimum, 25 °C) and pH 5.0-8.0 (optimum, pH 7.0). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain G27(T) formed a phyletic lineage within the genus Mucilaginibacter of the family Sphingobacteriaceae. Strain G27(T) was related most closely to Mucilaginibacter gossypii Gh-67(T) at 96.5% 16S rRNA gene sequence similarity. Strain G27(T) contained menaquinone 7 (MK-7) as the sole isoprenoid quinone and summed feature 3 (comprising C16:1ω7c/C16:1ω6c), iso-C15:0, C16:0, C16:1ω5c and C16:1ω5c as the major cellular fatty acids. Phosphatidylethanolamine was identified as the major polar lipid. The G+C content of the genomic DNA was 46.5 mol%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G27(T) represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter vulcanisilvae sp. nov. is proposed. The type strain is G27(T) ( = KACC 18231(T) = JCM 30363(T)).

Sphingobacterium yamdrokense sp. nov., isolated from Lake Yamdrok.

A strictly aerobic and facultatively psychrophilic bacterium, strain 3-0-1(T), was isolated from Lake Yamdrok on the Tibetan Plateau, China. Cells were Gram-negative and short-rod-shaped. Strain 3-0-1(T) formed circular, opaque, yellow colonies, and grew at 0-5% (w/v) NaCl, pH 5.0-11.0 and 5-35 °C. Phylogenetic analysis based on 16S rRNA gene sequences of various species with validly published names showed that strain 3-0-1(T) belongs to the genus Sphingobacterium, family Sphingobacteriaceae, sharing the highest similarity with Sphingobacterim nematocida M-SX103(T) (96.62%) and less than 95% similarity with all the other species in the genus Sphingobactrium. The predominant isoprenoid quinone of strain 3-0-1(T) was identified as menaquinone 7 (MK-7), the major polar lipid was identified as phosphatidylethanolamine and the DNA G+C content was determined to be 42.5 mol%. The predominant cellular fatty acids were identified as summed feature 3 (C(16:1) ω7c and/or C(16:1) ω6c) (>30%), iso-C(15:0) (>20%) and iso-C(17:0) 3-OH (>10%). Based on the variability of phylogenetic and phenotypic characteristics, strain 3-0-1(T) represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium yamdrokense sp. nov. is proposed. The type strain is 3-0-1(T) (=JCM 19397(T) = CGMCC 1.12560(T)).

Pedobacter pituitosus sp. nov., isolated from a waterfall.

A taxonomic study was carried out on a novel bacterial strain, designated MIC2002(T), which was isolated from Wibong falls in Korea. Cells were Gram-stain-negative, aerobic, non-motile and rods, 0.3-0.5 µm wide and 4.0-5.0 µm long. The optimum temperature and pH range for growth were 25 °C and pH 6.5-7.0, respectively. Catalase and oxidase activities were positive. Flexirubin pigments were not produced. Comparison of the 16S rRNA gene sequences indicated that the isolate belonged to the genus Pedobacter, with Pedobacter daechungensis as its closest relative, with a similarity of 94.4%. It contained iso-C(15:0), anteiso-C(15:0), C(16:0), summed feature 3 (C(16:1)ω6c and/or C(16:1)ω7c) and iso-C(17:0) 3-OH as the major fatty acids and menaquinone MK-7 as isoprenoid quinone. The polar lipid profile of strain MIC2002(T) revealed the presence of phosphatidylethanolamine and an unknown lipid. The DNA G+C content of the strain was 34.7 mol%. On the basis of the evidences presented, it was concluded that strain MIC2002(T) represents a novel species of the genus Pedobacter within the family Sphingobacteriaceae, for which the name Pedobacter pituitosus sp. nov. is proposed. The type strain is MIC2002(T) ( =KACC 17064(T) =JCM 18729(T)).

High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6(T)), a diphenol degrader with genes involved in the catechol pathway.

Olivibacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae, phylum Bacteroidetes. Members of the genus Olivibacter are phylogenetically diverse and of significant interest. They occur in diverse habitats, such as rhizosphere and contaminated soils, viscous wastes, composts, biofilter clean-up facilities on contaminated sites and cave environments, and they are involved in the degradation of complex and toxic compounds. Here we describe the features of O. sitiensis AW-6T, together with the permanent-draft genome sequence and annotation. The organism was sequenced under the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project at the DOE Joint Genome Institute and is the first genome sequence of a species within the genus Olivibacter. The genome is 5,053,571 bp long and is comprised of 110 scaffolds with an average GC content of 44.61%. Of the 4,565 genes predicted, 4,501 were protein-coding genes and 64 were RNA genes. Most protein-coding genes (68.52%) were assigned to a putative function. The identification of 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase-coding genes indicates involvement of this organism in the catechol catabolic pathway. In addition, genes encoding for β-1,4-xylanases and β-1,4-xylosidases reveal the xylanolytic action of O. sitiensis.

Mucilaginibacter ginsenosidivorax sp. nov., with ginsenoside converting activity isolated from sediment

A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming, and rod-shaped bacterial strain designated KHI28(T) was isolated from sediment in Gapcheon (river) and its taxonomic position was investigated using a polyphasic approach. Strain KHI28(T) grew at 10-42°C and at pH 5.5-8.5 on R2A and nutrient agar without additional NaCl as a supplement. Strain KHI28(T) possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1 and Re (ones of the dominant active components of ginseng) to C-K and Rg2, respectively. On the basis of 16S rRNA gene sequence similarity, strain KHI28(T) was shown to belong to the family Sphingobacteriaceae and to be related to Mucilaginibacter dorajii DR-f4(T) (97.9% sequence similarity), M. polysacchareus DRP28(T) (97.3%), and M. lappiensis ANJLI2(T) (97.2%). The G+C content of the genomic DNA was 45.8%. The predominant respiratory quinone was MK-7 and the major fatty acids were summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c), iso-C15:0 and C16:0. DNA and chemotaxonomic data supported the affiliation of strain KHI28(T) to the genus Mucilaginibacter. Strain KHI28(T) could be differentiated genotypically and phenotypically from the recognized species of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter ginsenosidivorax sp. nov. is proposed, with the type strain KHI28(T) (=KACC 14955(T) =LMG 25804(T)).

Mucilaginibacter calamicampi sp. nov., a member of the family Sphingobacteriaceae isolated from soil at a field of reeds

A Gram-negative, aerobic, non-flagellated, non-gliding, rod-shaped bacterial strain, designated WR-R1Y(T), was isolated from soil at a field of reeds in South Korea. Strain WR-R1Y(T) grew optimally at 30°C, at pH 7.0-7.5 and in the absence of NaCl. Neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain WR-R1Y(T) fell within the clade comprising Mucilaginibacter species, coherently clustering with the type strain of Mucilaginibacter composti, with which it exhibited the highest 16S rRNA gene sequence similarity value of 97.6%. Sequence similarities to the type strains of the other Mucilaginibacter species and the other species used in the phylogenetic analysis were 93.1-96.9% and <91.1%, respectively. Strain WR-R1Y(T) contained MK-7 as the predominant menaquinone and iso-C15:0, summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C16:0 and iso-C17:0 3-OH as the major fatty acids. The major polar lipids were phosphatidylethanolamine and one unidentified aminophospholipid. The DNA G+C content of strain WR-R1Y(T) was 43.1mol% and its mean DNA-DNA relatedness value with M. composti KACC 14956(T) was 17%. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain WR-R1Y(T) is separate from other Mucilaginibacter species. On the basis of the data presented, strain WR-R1Y(T) represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter calamicampi sp. nov. is proposed. The type strain is WR-R1Y(T) (= KCTC 32214(T)=CCUG 63418(T)).

Pedobacter namyangjuensis sp. nov. isolated from soil and reclassification of Nubsella zeaxanthinifaciens Asker et al. 2008 as Pedobacter zeaxanthinifaciens comb. nov.

A Gram-stain-negative, non-motile, strictly aerobic, yellow-pigmented bacterium, designated strain 5G38(T), was isolated from a field cultivated with Chinese cabbage in Korea. The strain grew at 5-40°C and at pH 6.0-8.0. 16S rRNA gene sequence analysis revealed that strain 5G38(T) represented a distinct lineage within the family Sphingobacteriaceae and showed the highest 16S rRNA gene sequence similarity of 95.2% with Pedobacter koreensis WPCB189(T), followed by Pedobacter agri PB92(T) (94.6%), Pedobacter suwonensis 15-52(T) (94.4%), Pedobacter rhizosphaerae 01-96(T) (94.4%), Pedobacter sandarakinus DS-27(T) (94.4%), and Nubsella zeaxanthinifaciens TDMA-5(T) (94.3%). Strain 5G38(T) formed monophyletic clade with Nubsella zeaxanthinifaciens in the cluster comprised of species of the genus Pedobacter. Chemotaxonomic characteristics of the novel strains, including DNA G+C content of genomic DNA (37.0 mol%), the predominant respiratory quinine (MK-7), and the major fatty acids which were iso-C15:0, summed feature 3 (comprising C16:1 ω7c and/or iso-C15:0 2-OH) and iso-C17:0 3-OH, are similar to those of the genus Pedobacter. However, the novel strains can be distinguished from the other species of Pedobacter by physiological properties. The name Pedobacter namyangjuensis sp. nov. is therefore proposed for strain 5G38(T) (KACC 13938(T) =NBRC 107692(T)) as the type strain. Furthermore, the reclassification of Nubsella zeaxanthinifaciens as Pedobacter zeaxanthinifaciens comb. nov. is proposed.

Sphingobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside-converting activity isolated from the soil of a ginseng field

A Gram-staining-negative, aerobic, non-motile, non-spore-forming, and rod-shaped bacterium designated THG 07(T) was isolated from the soil of a ginseng field of Pocheon in South Korea, and its taxonomic position was investigated by using a polyphasic study. Strain THG 07(T) grew optimally at 25-30°C and at pH 6.5-7.0 and in the absence of NaCl on nutrient agar. Strain THG-T17(T) displayed β-glucosidase activity that was responsible for its ability to transform ginsenoside Rb1 (one of the dominant ginsenosides of ginseng) to compound C-K. On the basis of 16S rRNA gene sequence similarity, strain THG 07(T) was shown to belong to the family Sphingobacteriaceae and was related to Sphingobacterium canadense CR11(T) (98.7%), S. cladoniae No.6(T) (98.1%), S. detergens 6.2S(T) (98.0%), S. multivorum IAM14316(T) (97.9%), S. siyangense SY1(T) (97.8%) and S. thalpophilum DSM11723(T) (96.9%). The G+C content of the genomic DNA was 40.6 mol%. The major menaquinone, MK-7, and major fatty acids, iso-C₁₅:₀ and C₁₆:₁ ω7c and/or ω6c, supported the affiliation of strain THG 07(T) to the genus Sphingobacterium. The DNA-DNA relatedness values between strain THG 07(T) and its closest phylogenetic neighbors were below 26.9%. The results of physiological and biochemical tests enabled strain THG 07(T) to be differentiated phenotypically from the recognized species of the genus Sphingobacterium. Therefore the isolate represents a novel species, for which the name Sphingobacterium ginsenosidimutans sp. nov. is proposed, with the type strain THG 07(T) (=KACC 14526(T)=JCM 16722(T)).

Olivibacter oleidegradans sp. nov., a hydrocarbon-degrading bacterium isolated from a biofilter clean-up facility on a hydrocarbon-contaminated site

A novel hydrocarbon-degrading, Gram-negative, obligately aerobic, non-motile, non-sporulating, rod-shaped bacterium, designated strain TBF2/20.2(T), was isolated from a biofilter clean-up facility set up on a hydrocarbon-contaminated site in Hungary. It was characterized by using a polyphasic approach to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate is affiliated with the genus Olivibacter in the family Sphingobacteriaceae. It was found to be related most closely to Olivibacter ginsengisoli Gsoil 060(T) (93.3% 16S rRNA gene sequence similarity). Strain TBF2/20.2(T) grew at pH 6-9 (optimally at pH 6.5-7.0) and at 15-42 °C (optimally at 30-37 °C). The major fatty acids were iso-C(15:0) (39.4%), summed feature 3 (iso-C(15:0) 2-OH and/or C(16:1)ω7c; 26.0%), iso-C(17:0) 3-OH (14.5%) and C(16:0) (4.5%). The major menaquinone was MK-7 and the predominant polar lipid was phosphatidylethanolamine. The DNA G+C content of strain TBF2/20.2(T) was 41.2 mol%. Physiological and chemotaxonomic data further confirmed the distinctiveness of strain TBF2/20.2(T) from recognized members of the genus Olivibacter. Thus, strain TBF2/20.2(T) is considered to represent a novel species of the genus Olivibacter, for which the name Olivibacter oleidegradans sp. nov. is proposed. The type strain is TBF2/20.2(T) (=NCAIM B 02393(T) =CCM 7765(T)).

Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113).

Pedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus Pedobacter within the family Sphingobacteriaceae. The species is of interest for its isolated location in the tree of life. Like other members of the genus P. saltans is heparinolytic. Cells of P. saltans show a peculiar gliding, dancing motility and can be distinguished from other Pedobacter strains by their ability to utilize glycerol and the inability to assimilate D-cellobiose. The genome presented here is only the second completed genome sequence of a type strain from a member of the family Sphingobacteriaceae to be published. The 4,635,236 bp long genome with its 3,854 protein-coding and 67 RNA genes consists of one chromosome, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Mucilaginibacter composti sp. nov., with ginsenoside converting activity, isolated from compost

The Gram-negative, strictly aerobic, non-motile, non-spore-forming, rod shaped bacterial strain designated TR6-03(T) was isolated from compost, and its taxonomic position was investigated by using a polyphasic approach. Strain TR6-03(T) grew at 4-42°C and at pH 6.0-8.0 on R2A and nutrient agar without NaCl supplement. Strain TR6-03(T) had β-glucosidase activity, which was responsible for its ability to transform ginsenoside Re (one of the dominant active components of ginseng) to Rg(2). On the basis of 16S rRNA gene sequence similarity, strain TR6-03(T) was shown to belong to the family Sphingobacteriaceae and to be related to Mucilaginibacter lappiensis ANJLI2(T) (96.3% sequence similarity), M. dorajii FR-f4(T) (96.1%), and M. rigui WPCB133(T) (94.1%). The G+C content of the genomic DNA was 45.6%. The predominant respiratory quinone was MK-7 and the major fatty acids were summed feature 3 (comprising C(16:1) ω7c and/or iso-C(15:0) 20H), iso-C(16:0) and iso-C(17:0) 3OH. DNA and chemotaxonomic data supported the affiliation of strain TR6-03(T) to the genus Mucilaginibacter. Strain TR6-03(T) could be differentiated genotypically and phenotypically from the recognized species of the genus Mucilaginibacter. The isolate therefore represents a novel species, for which the name Mucilaginibacter composti sp. nov. is proposed, with the type strain TR6-03(T) (=KACC 14956(T) = KCTC 12642(T) =LMG 23497(T)).

Pedobacter bauzanensis sp. nov., isolated from soil

A Gram-negative, aerobic, rod-shaped, non-motile bacterium, designated BZ42(T), was isolated from the soil of an industrial site. Strain BZ42(T) was able to grow at 5-25 °C. The major fatty acids were iso-C(15 : 0) (46.2 %), C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH (23.2 %) and iso-C(17 : 0) 3-OH (9.1 %). The predominant menaquinone was MK-7. The genomic DNA G+C content was 36.5 mol% (HPLC). 16S rRNA gene sequence phylogenetic analysis revealed that strain BZ42(T) was a member of the genus Pedobacter, family Sphingobacteriaceae, and 16S rRNA gene sequence similarities between strain BZ42(T) and the type strains of species of the genus Pedobacter with validly published names were 90.4-93.2 %. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain BZ42(T) was considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter bauzanensis sp. nov. is proposed. The type strain is BZ42(T) (=DSM 22554(T) =CGMCC 1.10187(T) =CIP 110134(T)).

Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T)

Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum ‘Bacteroidetes’. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Solitalea koreensis gen. nov., sp. nov. and the reclassification of [Flexibacter] canadensis as Solitalea canadensis comb. nov.

A Gram-negative, rod-shaped, non-spore-forming bacterium, designated strain R2A36-4T, was isolated from greenhouse soil and subjected to a polyphasic taxonomic analysis. 16S rRNA gene sequence analysis revealed that the strain represented a novel member of the family Sphingobacteriaceae. Its nearest phylogenetic neighbour was the type strain of [Flexibacter] canadensis CIP 104802T (93.2% 16S rRNA gene sequence similarity). Strain R2A36-4T and [F.] canadensis CIP 104802T fell in a distinct cluster within the family Sphingobacteriaceae. Strain R2A36-4T contained MK-7 as the predominant quinone. Strain R2A36-4T and [F.] canadensis CIP 104802T had iso-C15:0, iso-C17:0 3-OH, summed feature 3 and C15:1omega6c as the major fatty acids. Strain R2A36-4T could be distinguished from [F.] canadensis on the basis of several physiological properties and fatty acid compositions. Based on phenotypic characterization and 16S rRNA gene sequence analysis, strain R2A36-4T represents a novel species within a new genus, for which the name Solitalea koreensis gen. nov., sp. nov. is proposed. The type strain of Solitalea koreensis is strain R2A36-4T (=KACC 12953T=DSM 21342T). It is also proposed that [F.] canadensis be transferred to this genus as Solitalea canadensis comb. nov. (type strain UASM 9DT=ATCC 29591T=CIP 104802T=DSM 3403T=NBRC 15130T=JCM 21819T=KACC 13276T=LMG 8368T).