rRNA Gene Sequence Similarity Levels Research Articles

Chryseobacterium vrystaatense sp. nov., isolated from raw chicken in a chicken-processing plant

Yellow-pigmented, Gram-negative organisms isolated from raw chicken were investigated by means of a polyphasic taxonomic approach and were shown to represent a novel species in the genus Chryseobacterium, for which the name Chryseobacterium vrystaatense sp. nov. is proposed. Its nearest phylogenetic neighbours were Chryseobacterium joostei, Chryseobacterium indologenes and Chryseobacterium gleum, which showed 16S rRNA gene sequence similarity levels of 96.9, 97.1 and 96.1%, respectively. Levels of DNA-DNA hybridization between strains of C. vrystaatense and Chryseobacterium reference species were below 46%. Strain LMG 22846(T) (=CCUG 50970(T)) was chosen as the type strain and has a DNA G+C content of 37.1 mol%.

Algoriphagus locisalis sp. nov., isolated from a marine solar saltern

Two Gram-negative, rod-shaped, non-motile bacterial strains, MSS-170(T) and MSS-171, were isolated from sea water of a marine solar saltern of the Yellow Sea, Korea, and characterized by using a polyphasic taxonomic approach. The two isolates grew optimally at 30 degrees C and in the presence of 2% (w/v) NaCl. They were characterized chemotaxonomically as having MK-7 as the predominant menaquinone and major amounts of fatty acids iso-C(15:0) and C(16:1)omega7c and/or iso-C(15:0) 2-OH. The DNA G+C content of each of the two strains was 42 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the two strains fall within the evolutionary radiation enclosed by the genus Algoriphagus. Strains MSS-170(T) and MSS-171 had identical 16S rRNA gene sequences and exhibited a mean DNA-DNA relatedness level of 93%. The two strains exhibited 16S rRNA gene sequence similarity levels of 96.4-98.9% with respect to the type strains of recognized Algoriphagus species. DNA-DNA relatedness levels between the two strains and the type strains of six Algoriphagus species were less than 35%. On the basis of phenotypic data and phylogenetic and genetic distinctiveness, strains MSS-170(T) and MSS-171 were classified in the genus Algoriphagus as members of a novel species, for which the name Algoriphagus locisalis sp. nov. is proposed. The type strain is MSS-170(T) (=KCTC 12310(T)=JCM 12597(T)).

Psychrobacter aquimaris sp. nov. and Psychrobacter namhaensis sp. nov., isolated from sea water of the South Sea in Korea

Two Gram-negative, non-motile, non-spore-forming, slightly halophilic bacterial strains, SW-210(T) and SW-242(T), were isolated from sea water of the South Sea in Korea, and were characterized taxonomically by means of a polyphasic approach. The two isolates grew optimally at 25-30 degrees C and in the presence of 2-3 % (w/v) NaCl. Strains SW-210(T) and SW-242(T) contained Q-8 as the predominant respiratory lipoquinone and C(18 : 1)omega9c as the major fatty acid. The DNA G+C contents of strains SW-210(T) and SW-242(T) were 43.2 and 45.3 mol%, respectively. The 16S rRNA gene sequences of strains SW-210(T) and SW-242(T) were 98.9 % similar, and the mean DNA-DNA relatedness value between them was 24 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains SW-210(T) and SW-242(T) form distinct phylogenetic lineages within the radiation of the cluster comprising Psychrobacter species, having 16S rRNA gene sequence similarity levels of 95.9-99.2 % with respect to the type strains of Psychrobacter species. The levels of DNA-DNA relatedness between the two isolates and the type strains of 15 phylogenetically related Psychrobacter species were well below 70 %. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains SW-210(T) and SW-242(T) were classified in the genus Psychrobacter as representing two distinct novel species, for which the names Psychrobacter aquimaris sp. nov. (type strain, SW-210(T) = KCTC 12254(T) = DSM 16329(T)) and Psychrobacter namhaensis sp. nov. (type strain, SW-242(T) = KCTC 12255(T) = DSM 16330(T)) are proposed, respectively.

Tenacibaculum lutimaris sp. nov., isolated from a tidal flat in the Yellow Sea, Korea

Four Gram-negative, rod-shaped bacterial strains, TF-26(T), TF-28, TF-42 and TF-53, were isolated from a tidal flat in the Yellow Sea, Korea, and their taxonomic positions were determined by a polyphasic characterization. The strains grew optimally in the presence of 2-3 % (w/v) NaCl and at 30-37 degrees C. The predominant menaquinone detected in the four strains was MK-6. These strains contained large amounts of fatty acids C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH, iso-C(15 : 0), iso-C(16 : 0) 3-OH, C(15 : 0) and iso-C(17 : 0) 3-OH. The DNA G+C contents of the four strains were 32.3-32.8 mol%. Strains TF-26(T), TF-28, TF-42 and TF-53 showed 16S rRNA gene sequence similarity levels of 99.8-100 % and DNA-DNA relatedness levels of 82-87 %. The four strains exhibited 16S rRNA gene sequence similarity levels of 95.0-98.0 % to the type strains of the five current Tenacibaculum species, and DNA-DNA relatedness levels between the four strains and two phylogenetic relatives, Tenacibaculum mesophilum DSM 13764(T) and Tenacibaculum skagerrakense DSM 14836(T), were less than 21 %. On the basis of phenotypic, phylogenetic and genetic data, strains TF-26(T), TF-28, TF-42 and TF-53 were classified in the genus Tenacibaculum as members of a novel species, for which the name Tenacibaculum lutimaris sp. nov. (type strain, TF-26(T)=KCTC 12302(T)=DSM 16505(T)) is proposed.

Biochemical and genetic evidence for the transfer of Enterococcus solitarius Collins et al. 1989 to the genus Tetragenococcus as Tetragenococcus solitarius comb. nov.

Phylogenetic analysis of 16S rRNA gene sequences revealed that Enterococcus solitarius is not a member of the genus Enterococcus, but is related to species of the genus Tetragenococcus. On a phylogenetic tree, E. solitarius clustered with Tetragenococcus halophilus and Tetragenococcus muriaticus, with which it showed the highest 16S rRNA gene sequence similarity level (about 94 %). Phenotypic studies indicated that E. solitarius was also unable to produce acid from lactose, providing further evidence of its affiliation to the genus Tetragenococcus. DNA hybridization studies indicated that E. solitarius was clearly a separate species, different from T. halophilus and T. muriaticus (reassociation levels of about 23 and 54 %, respectively). As suggested in previous studies, E. solitarius is closely related to but clearly distinct from T. halophilus. Based upon properties that taxonomically distinguish it from species of the genus Enterococcus, it is proposed that E. solitarius be transferred to the genus Tetragenococcus and reclassified as Tetragenococcus solitarius comb. nov. (type strain, 885/78(T)=ATCC 49428(T)=CCUG 29293(T)=CIP 103330(T)=DSM 5634(T)=JCM 8736(T)=LMG 12890(T)=NCTC 12193(T)).

Nocardioides alkalitolerans sp. nov., isolated from an alkaline serpentinite soil in Korea

Four Gram-positive, rod- or coccus-shaped bacterial strains, KSL-1(T), KSL-9, KSL-10 and KSL-12, were isolated from an alkaline serpentinite soil in Korea, and their taxonomic positions were investigated in a polyphasic study. The four strains exhibited no difference in their 16S rRNA gene sequences. Phylogenetic analyses based on 16S rRNA gene sequences showed that the four strains were phylogenetically affiliated to the genus Nocardioides. The four strains had cell-wall peptidoglycan based on ll-diaminopimelic acid as the diamino acid, indicating wall chemotype I. The predominant menaquinone detected in the four strains was MK-8(H(4)). The major fatty acid components were iso-C(16 : 0), 10-methyl-C(18 : 0), C(18 : 1)omega9c and C(17 : 1)omega6c. The DNA G+C contents were 72.4-73.6 mol%. The four strains exhibited 16S rRNA gene sequence similarity levels of 94.0-96.3 % to the type strains of Nocardioides species with validly published names. DNA-DNA relatedness levels between the four strains were 85-91 %. On the basis of phenotypic properties, phylogenetic distinctiveness and genotypic relatedness, strains KSL-1(T), KSL-9, KSL-10 and KSL-12 were classified in the genus Nocardioides as members of a novel species, Nocardioides alkalitolerans sp. nov. The type strain is strain KSL-1(T) (=KCTC 19037(T)=DSM 16699(T)).

Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea

Two Gram-negative, motile, non-spore-forming, rod-shaped organisms, strains SW-117(T) and SW-120(T), were isolated from sea water of the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. Strains SW-117(T) and SW-120(T) simultaneously contained both menaquinones (MK) and ubiquinones (Q) as isoprenoid quinones; the predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acid detected in the two strains was iso-C(15 : 0). The DNA G+C content of strains SW-117(T) and SW-120(T) was 51 and 54 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-117(T) and SW-120(T) fall within the radiation of the cluster comprising Shewanella species. Strains SW-117(T) and SW-120(T) showed a 16S rRNA gene sequence similarity of 97.4 % and a DNA-DNA relatedness level of 10.1 %. Strains SW-117(T) and SW-120(T) exhibited 16S rRNA gene sequence similarity levels of 93.8-98.5 % and 92.4-97.0 %, respectively, to Shewanella species. Strain SW-117(T) exhibited DNA-DNA relatedness levels of 8.3-20.3 % to the type strains of six phylogenetically related Shewanella species. On the basis of phenotypic, phylogenetic and genetic data, strains SW-117(T) and SW-120(T) were classified in the genus Shewanella as two distinct novel species, for which the names Shewanella marisflavi sp. nov. (type strain, SW-117(T)=KCCM 41822(T)=JCM 12192(T)) and Shewanella aquimarina sp. nov. (type strain, SW-120(T)=KCCM 41821(T)=JCM 12193(T)) are proposed, respectively.

Janibacter melonis sp. nov., isolated from abnormally spoiled oriental melon in Korea

Two Gram-positive bacterial strains, CM2104(T) and CM2110, isolated from the inner part of abnormally spoiled oriental melon (Cucumis melo) in Korea, were subjected to a polyphasic taxonomic study. The cell-wall peptidoglycan of strains CM2104(T) and CM2110 contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was MK-8(H(4)). The major fatty acids detected in the two strains were iso-C(16 : 0), C(17 : 1)omega8c and C(18 : 1)omega9c or C(17 : 0). The DNA G+C content of the two strains was 73 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strains formed a coherent cluster with a clade comprising two Janibacter species, Janibacter limosus and Janibacter terrae. Strains CM2104(T) and CM2110 exhibited a 16S rRNA gene sequence similarity value of 99.7 % and a mean DNA-DNA relatedness level of 89 %. Strains CM2104(T) and CM2110 showed 16S rRNA gene sequence similarity levels of 97.8-98.4 % to the type strains of J. limosus and J. terrae. DNA-DNA relatedness between strains CM2104(T) and CM2110 and the type strains of these two Janibacter species was 7-11 %. On the basis of the phenotypic and phylogenetic data and genomic distinctiveness, strains CM2104(T) and CM2110 should be placed within the genus Janibacter as members of a novel species, for which the name Janibacter melonis sp. nov. is proposed. The type strain is CM2104(T) (=KCTC 9987(T)=DSM 16063(T)=JCM 12321(T)).

Kangiella koreensis gen. nov., sp. nov. and Kangiella aquimarina sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.

Two Gram-negative, non-motile, non-spore-forming, rod-shaped organisms, strains SW-125T and SW-154T, were isolated from tidal flat sediment of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. Strains SW-125T and SW-154T grew optimally at 30-37 degrees C and in the presence of 2-3 % (w/v) NaCl. They contained ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and iso-C(15 : 0) as the major fatty acid. The DNA G + C contents of strains SW-125T and SW-154T were 44 mol%. Phylogenetic trees based on 16S rRNA gene sequences revealed that the two strains form deep evolutionary lineages of descent within the gamma-Proteobacteria. Strains SW-125T and SW-154T exhibited 16S rRNA gene sequence similarity levels of less than 90 % to members of the gamma-Proteobacteria used in this analysis. Strains SW-125T and SW-154T showed a 16S rRNA gene sequence similarity level of 98.5 % and a mean DNA-DNA relatedness level of 9.4 %. Therefore, on the basis of phenotypic, phylogenetic and genomic data, a new genus, Kangiella gen. nov., is proposed to accommodate the novel strains, comprising two novel species, Kangiella koreensis sp. nov. (type strain, SW-125T = KCTC 12182T = DSM 16069T) and Kangiella aquimarina sp. nov. (type strain, SW-154T = KCTC 12183T = DSM 16071T).

Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov.

The phylogenetic relationships among marine Alteromonas-like bacteria of the genera Alteromonas, Pseudoalteromonas, Glaciecola, Thalassomonas, Colwellia, Idiomarina, Oceanimonas, Oceanisphaera, Shewanella, Moritella, Ferrimonas, Psychromonas and several other genera of the 'Gammaproteobacteria' were studied. Results of 16S rRNA gene sequence analyses revealed that some members of these genera formed several coherent groups at the family level. Characteristic signature oligonucleotides for studied taxa were defined. Signature positions are divided into three classes: (i) single compensatory mutations, (ii) double compensatory mutations and (iii) mutations affecting nucleotides not paired in the secondary structure. The 16S rRNA gene sequence similarity level within genera was 93 % or above. This value can be a useful additional criterion for genus discrimination. On the basis of this work and previous polyphasic taxonomic studies, the circumscription of the family Alteromonadaceae is limited to the genera Alteromonas and Glaciecola and the creation is proposed of the families Pseudoalteromonadaceae fam. nov. to accommodate bacteria of the genera Pseudoalteromonas and Algicola gen. nov. (formerly Pseudoalteromonas bacteriolytica) and Colwelliaceae fam. nov. to accommodate bacteria of the genera Colwellia and Thalassomonas. Bacteria of the genera Oceanimonas and Oceanisphaera formed a robust cluster and shared common signature oligonucleotides. Because of deep branching and lack of association with any other genus, the following families are proposed that include single genera: Idiomarinaceae fam. nov., Psychromonadaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov. and Shewanellaceae fam. nov. Finally, this study also revealed that [Hyphomicrobium] indicum should be reclassified as Photobacterium indicum comb. nov.

Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea.

Two Gram-negative, motile, non-spore-forming and slightly halophilic rods (strains SW-145T and SW-156T) were isolated from sea water of the Yellow Sea in Korea. Strains SW-145T and SW-156T grew optimally at 37 and 30-37 degrees C, respectively, and in the presence of 2-6 % (w/v) NaCl. Strains SW-145T and SW-156T were chemotaxonomically characterized as having ubiquinone-9 as the predominant respiratory lipoquinone and C(16 : 0), C(18 : 1)omega9c, C(16 : 1)omega9c and C(12 : 0) 3-OH as the major fatty acids. The DNA G + C contents of strains SW-145T and SW-156T were 58 and 57 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SW-145T and SW-156T fell within the evolutionary radiation enclosed by the genus Marinobacter. The 16S rRNA gene sequences of strains SW-145T and SW-156T were 94.8 % similar. Strains SW-145T and SW-156T exhibited 16S rRNA gene sequence similarity levels of 94.3-98.1 and 95.4-97.7 %, respectively, with respect to the type strains of all Marinobacter species. Levels of DNA-DNA relatedness, together with 16S rRNA gene sequence similarity values, indicated that strains SW-145T and SW-156T are members of two species that are distinct from seven Marinobacter species with validly published names. On the basis of phenotypic properties and phylogenetic and genotypic distinctiveness, strains SW-145T (= KCTC 12185T = DSM 16070T) and SW-156T (= KCTC 12184T = DSM 16072T) should be placed in the genus Marinobacter as the type strains of two distinct novel species, for which the names Marinobacter flavimaris sp. nov. and Marinobacter daepoensis sp. nov. are proposed.