Flavobacterium aquaticum sp. nov., a member of the Bacteroidetes isolated from a freshwater reservoir

A novel bacterial strain, designated ARSA-111^T, was isolated from a freshwater reservoir in Cheonan, Korea. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the isolate belonged to the genus Flavobacterium of phylum Bacteroidetes. The 16S rRNA gene sequence of strain ARSA-111^T showed a high degree of sequence similarity to those of Flavobacteium cheonanense KACC 14972^T (97.3%), F. aquatile JCM 20475^T (97.1%), and other type strains of the genus Flavobacterium (< 97.0%). The phylogenetic tree and network analysis (i.e. median-joining) based on 16S rRNA gene sequences showed that strain ARSA-111^T is most closely related to F. aquatile JCM 20475^T. DNA-DNA hybridization experiment revealed 70% of genomic relatedness among strain ARSA-111^T, F. aquatile JCM 20475^T and F. cheonanense KACC 14972^T. The isolate had iso-C_15:1, iso-C_15:0, and iso-C_15:0 3-OH as predominant cellular fatty acids and MK-6 as a predominant menaquinone. The genomic DNA G+C content of the isolate was 35.6 mol%. On the basis of these data, strain ARSA-111^T is considered to be a novel species of the genus Flavobacterium, for which the name Flavobacterium aquaticum sp. nov. is proposed. The type strain is strain ARSA-111^T (=KACC 14973^T =KCTC 23185^T = JCM 17070^T).     

Flavobacterium ginsengiterrae sp. nov., isolated from a ginseng field

A novel strain of Flavobacterium, DCY55(T), a Gram-negative, yellow-pigmented, rod-shaped, non-spore-forming and gliding-motile bacterium, was isolated from the soil of a ginseng field in South Korea. Phylogenetic analysis, based on the 16S rRNA sequence, demonstrated that strain DCY55(T) belongs to the genus Flavobacterium within the family Flavobacteriaceae. Strain DCY55(T) showed the highest similarity with F. johnsoniae UW101(T) (97.1%), F. ginsenosidimutans THG 01(T) (96.8%), F. defluvii EMB 117(T) (96.6%), F. banpakuense 15F3(T) (96.3%) and F. anhuiense D3(T) (95.8%). Chemotaxonomic results showed that strain DCY55(T) predominantly contains menaquinone MK-6, that its DNA G+C content is 36.1mol%, and that its major cellular fatty acids are iso-C(15:0), summed feature 3 (comprising iso-C(15:0) 2-OH and/or C(16:1) ω 7c) and C(16:0). The chemotaxonomic and genotypic characteristics support the taxonomic classification of strain DCY55(T) to the genus Flavobacterium. The results of physiological and biochemical tests confirmed that strain DCY55(T) is distinct from previously validated species. We conclude that strain DCY55(T) should be classified as a novel species of the genus Flavobacterium, for which the name Flavobacterium ginsengiterrae sp. nov. is proposed, with the type strain DCY55(T) (=KCTC 23319(T) = JCM 17337(T)).     

Flavobacterium frigidimaris sp. nov., isolated from Antarctic seawater

We described the polyphasic characterization of the psychrotolerant isolated from Antarctic seawater. The strain was closely related to Flavobacterium hydatis, F. pectinovorum, and F. saccharophilum on the basis of the 16S rDNA sequence analysis. However, DNA–DNA hybridization experiments showed that the DNA-similarities between strain KUC-1^T and the reference strains of Flavobacterium were less than 30%. Therefore, we can definite a new species of Flavobacterium phylogenetically, and strain KUC-1^T can be considered to be a new species of Flavobacterium. i.e. F. frigidimaris (KUC-1^T: JCM 12218^T and DSM 15937^T; mol% G+C of DNA of the type strain is 34.5 mol%). Useful phenotypical features for discrimination of F. frigidimaris from other Flavobacterium species, such as a resistance to NaCl, optimum growth temperature, and cellular fatty acid composition, were also determined.     

Flavobacterium kyungheensis sp. nov., isolated from soil of a ginseng field

A Gram-staining negative, strictly aerobic, motile by gliding, non-spore-forming, pale yellow pigmented and rod-shaped bacterium designated strain THG-107^T was isolated from soil of a ginseng field on Ganghwa Island in the Republic of Korea and its taxonomic position was investigated by using a polyphasic study. Growth of strain THG-107^T was found to occur at 4–37 °C (optimum, 20–30 °C), at pH 5.5–10 (optimum, pH 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum, absence) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain THG-107^T was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium denitrificans ED5^T (99.1 % similarity). The G+C content of the genomic DNA was determined to be 34.2 mol%. These results are consistent with characteristics of members of the genus Flavobacterium. The only isoprenoid quinone detected in strain THG-107^T was menaquinone-6 (MK-6) and the major polyamine was identified as homospermidine (82.9 %). The major polar lipid detected was phosphatidylethanolamine and the major cellular fatty acids were identified as iso-C_15:0 (26.3 %), iso-C_17:0 3OH (12.6 %) and summed feature 3 (comprising C_16:1 ω7c and/or C_16:1 ω6c; 11.6 %). Flexirubin-type pigments were found to be present. Strain THG-107^T has β-glucosidase activity to convert ginsenosides Rb₁ and Rd into Gyp17 and F₂. DNA-DNA hybridization with F. denitrificans ED5^T was 52 %. Strain THG-107^T could be distinguished from F. denitrificans ED5^T and the other species of the genus Flavobacterium by its phylogenetic and genetic distinctiveness and by several phenotypic properties. Therefore, strain THG-107^T is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium kyungheensis sp. nov. is proposed (type strain THG-107^T = KACC 16219^T = LMG 26575^T).     

Arenimonas aquaticum sp. nov., a member of the gammaproteobacterium, isolated from a freshwater reservoir

A novel bacterial strain, designated NA-09^T, was isolated from a freshwater sample collected from the Cheonho reservoir, Republic of Korea. Colonies were creamy-white pigmented, translucent, and circular with convex shape. The isolate was Gram-staining negative, strictly aerobic, motile, and rod-shaped. The 16S rRNA gene sequence analysis revealed that strain NA-09^T belonged to the genus Arenimonas and showed the highest sequence similarities with Arenimonas malthae CC-JY-1^T (95.4%), A. oryziterrae YC6267^T (94.9%), A. composti P2-12-1^T (94.8%), and A. donghaensis H03-R19^T (94.1%). The major fatty acids were iso-C_16:0 (20.8%), iso-C_15:0 (16.9%), summed feature 1 (13.2%), and iso-C_16:1 ω7c alcohol (10.2%). The major isoprenoid quinone of the isolate was ubiquionone-8. On the basis of the data from the polyphasic characterization, the strain NA-09^T represents a novel species, for which the name Arenimonas aquaticum sp. nov. is proposed (type strain NA-09^T =KACC 14663^T =NBRC 106550^T).     

Flavobacterium circumlabens sp. nov. and Flavobacterium cupreum sp. nov., two psychrotrophic species isolated from Antarctic environmental samples

A taxonomic study of 24 Gram-stain-negative rod-shaped bacteria originating from the Antarctic environment is described. Phylogenetic analysis using 16S rRNA gene sequencing differentiated isolated strains into two groups belonging to the genus Flavobacterium. Group I (n = 20) was closest to Flavobacterium aquidurense WB 1.1-56^T (98.3% 16S rRNA gene sequence similarity) while group II (n = 4) showed Flavobacterium hydatis DSM 2063^T as its nearest neighbour (98.5–98.9% 16S rRNA gene sequence similarity). Despite high 16S rRNA gene sequence similarity, these two groups represented two distinct novel species as shown by phenotypic traits and low genomic relatedness assessed by rep-PCR fingerprinting, DNA-DNA hybridization and whole-genome sequencing. Common to representative strains of both groups were the presence of major menaquinone MK-6 and sym-homospermidine as the major polyamine. Common major fatty acids were C_15:0 iso, C_15:1 iso G, C_15:0 iso 3-OH, C_17:0 iso 3OH and Summed Feature 3 (C_16:1 ω7c/C_16:1 ω6c). Strain CCM 8828^T (group I) contained phosphatidylethanolamine, three unidentified lipids lacking a functional group, three unidentified aminolipids and single unidentified glycolipid in the polar lipid profile. Strain CCM 8825^T (group II) contained phosphatidylethanolamine, eight unidentified lipids lacking a functional group, three unidentified aminolipids and two unidentified glycolipids in the polar lipid profile. These characteristics corresponded to characteristics of the genus Flavobacterium. The obtained results showed that the analysed strains represent novel species of the genus Flavobacterium, for which the names Flavobacterium circumlabens sp. nov. (type strain CCM 8828^T = P5626^T = LMG 30617^T) and Flavobacterium cupreum sp. nov. (type strain CCM 8825^T = P2683^T = LMG 30614^T) are proposed.     

Fibrivirga algicola gen. nov., sp. nov., an algicidal bacterium isolated from a freshwater river

An aerobic, gram-stain-negative, pink-colored, non-motile and rod-shaped algicidal bacterium, designated as JA-25^T was isolated from freshwater in Geumgang River, Republic of Korea. Strain JA-25^T grew at 15–30 °C and pH 6–9, and did not require NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JA-25^T belongs to the family ‘Spirosomaceae’ and is most closely related to Fibrella aestuarina BUZ 2^T (93.6%). Strain JA-25^T showed?<?90% sequence similarity to other members of the family ‘Spirosomaceae’. The average nucleotide identity(ANI), in silico DNA-DNA hybridization and average amino acid identity(AAI) values based on the genomic sequences of JA-25^T and F. aestuarina BUZ 2^T were 74.4, 20.5, and 73.6%, respectively. Strain JA-25^T showed an algicidal effect on the marine flagellate alga Heterocapsa triquetra, but no effect on fresh water cyanobacterium (Nostoc). In genome analysis, RIPP-like peptides were detected and predicted to resemble the indolmycin biosynthetic gene cluster, which possibly influence its algicidal effect. Furthermore, a bacteriorhodopsin gene with photoheterotrophic characteristics was detected. The genomic DNA G?+?C content was 52.5 mol%. The major cellular fatty acids were summed feature 3 (C16:1 ω6c/C16:1 ω7c), C16:1 ω5c, C16:0 (>?10%). The major respiratory quinone was menaquinone 7 and major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two phospholipids, and five unidentified lipids. Considering the phylogenetic inference, phenotypic, and chemotaxonomic data, strain JA-25^T should be classified as a novel species in the novel genus Fibrivirga, with the proposed name Fibrivirga algicola sp. nov. The type strain is JA-25^T (=?KCCM 43334^T?=?NBRC 114259^T).

     

Flavobacterium ahnfeltiae sp. nov., a new marine polysaccharide-degrading bacterium isolated from a Pacific red alga

A Gram-negative, aerobic, rod-shaped, motile by gliding and yellow-pigmented bacterium, designated strain 10Alg 130^T, that displayed the ability to destroy polysaccharides of red and brown algae, was isolated from the red alga Ahnfeltia tobuchiensis. The phylogenetic analysis based on 16S rRNA gene sequence placed the novel strain within the genus Flavobacterium, the type genus of the family Flavobacteriaceae, the phylum Bacteroidetes, with sequence similarities of 96.2 and 95.7 % to Flavobacterium jumunjiense KCTC 23618^T and Flavobacterium ponti CCUG 58402^T, and 95.3–92.5 % to other recognized Flavobacterium species. The prevalent fatty acids of strain 10Alg 130^T were iso-C_15:0, iso-C_15:0 3-OH, iso-C_17:0 3-OH, C_15:0 and iso-C_17:1ω9c. The polar lipid profile consisted of phosphatidylethanolamine, two unknown aminolipids and three unknown lipids. The DNA G+C content of the type strain was 34.3 mol%. The new isolate and the type strains of recognized species of the genus Flavobacterium could strongly be distinguished by a number of phenotypic characteristics. A combination of the genotypic and phenotypic data showed that the algal isolate represents a novel species of the genus Flavobacterium, for which the name Flavobacterium ahnfeltiae sp. nov. is proposed. The type strain is 10Alg 130^T (=KCTC 32467^T = KMM 6686^T).     

The fish pathogen Flavobacterium columnare represents four distinct species: Flavobacterium columnare,Flavobacterium covae sp. nov., Flavobacterium davisii sp. nov. and Flavobacterium oreochromis sp. nov., and emended description of Flavobacterium columnare

Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish and four discrete genetic groups exist within the species, suggesting that the species designation requires revision. The present study determined the taxonomic status of the four genetic groups of F. columnare using polyphasic and phylogenomic approaches and included five representative isolates from each genetic group (including type strain ATCC 23463^T; genetic group 1). 16S rRNA gene sequence analysis revealed genetic group 2 isolate AL-02-36^T, genetic group 3 isolate 90-106^T, and genetic group 4 isolate Costa Rica 04-02-TN^T shared less than <98.8 % sequence identity to F. columnare ATCC 23463^T. Phylogenetic analyses of 16S rRNA and gyrB genes using different methodologies demonstrated the four genetic groups formed well-supported and distinct clades within the genus Flavobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) values between F. columnare ATCC 23463^T, genetic group 2 isolate AL-02-36^T, genetic group 3 isolate 90-106^T, and genetic group 4 isolate Costa Rica 04-02-TN^T were less than 90.84% and 42.7%, respectively. Biochemical and physiological characteristics were similar among the four genetic groups; however, quantitative differences in fatty acid profiles were detected and MALDI-TOF analyses demonstrated numerous distinguishing peaks unique to each genetic group. Chemotaxonomic, MALDI-TOF characterization and ANI/GGDC calculations afforded differentiation between the genetic groups, indicating each group is a discrete species. Herein, the names F. covae sp. nov. (AL-02-36^T), F. davisii sp. nov. (90-106^T), and F. oreochromis sp. nov. (Costa Rica 04-02-TN^T) are proposed to represent genetic groups 2, 3, and 4, respectively.     

Ferruginibacter profundus sp. nov., a novel member of the family Chitinophagaceae,isolated from freshwater sediment of a reservoir

A Gram-negative, aerobic, non-motile, and rod-shaped bacterium, designated strain DS48-5-3^T, was isolated from a 48 m sediment sample taken from Daechung Reservoir, Republic of Korea. Comparative 16S rRNA gene sequence studies showed a clear affiliation of this strain to the Bacteroidetes, notably most closely related to Ferruginibacter alkalilentus HU1-GD23^T, Ferruginibacter lapsinanis HU1-HG42^T and Ferruginibacter yonginensis HME8442^T, showing 16S rRNA gene sequence similarities to the type strains of these species of 95.2–96.4 % similarity. The predominant ubiquinone was identified as MK-7. The major fatty acids were identified as iso-C_15:0, iso-C_17:0 3-OH, and iso-C_15:1 G. The G+C content of the genomic DNA of strain DS48-5-3^T was determined to be 37.2 %. On the basis of polyphasic evidence, it is proposed that strain DS48-5-3^T should belong to a novel species, for which the name Ferruginibacter profundus sp. nov. (type strain DS48-5-3^T = KCTC 32478^T = JCM 19431^T), is proposed.