Euzebya tangerina gen. nov., sp. nov., a deeply branching marine actinobacterium isolated from the sea cucumber Holothuria edulis, and proposal of Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov.

Abstract

Euzebya tangerina gen. nov., sp. nov., a deeply branching marine actinobacterium isolated from the sea cucumber Holothuria edulis, and proposal of Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov. A tangerine-coloured, Gram-positive actinobacterial strain, designated F10 T , was isolated from the abdominal epidermis of a sea cucumber, Holothuria edulis, collected in seawater off the coast of Japan. A 16S rRNA gene sequence analysis indicated that strain F10 T was a member of the class Actinobacteria and was most closely related to Nitriliruptor alkaliphilus ANL-iso2 T (87.4 % sequence similarity). Phylogenetic analyses showed that strain F10 T represented a novel, deeprooted, and distinct phylogenetic lineage within the class Actinobacteria and clustered with N. alkaliphilus and uncultured bacteria. The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and rhamnose and galactose as the diagnostic cell-wall sugars. Strain F10 T contained C 16 : 1 v7c, C 16 : 0 and C 17 : 1 v8c as the major cellular fatty acids. The predominant isoprenoid quinone was MK-9 (H 4 ). The G+C content of the DNA was 68.3 mol%. Based on data from the current polyphasic study, it is proposed that the new marine isolate be placed in a novel genus and be considered a novel species designated Euzebya tangerina gen. nov., sp. nov. within the new family, order and subclass Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov. in the class Actinobacteria. The type strain of Euzebya tangerina is F10 T (5NBRC 105439 T 5KCTC 19736 T ).In the course of searching for novel lineages of bacteria from the intestine and epidermis of marine creatures, a novel bacterial strain, F10 T , was isolated, and this strain was shown to form a deep branch in the class Actinobacteria. As the field of marine actinobacterial research is still in its early stages (Bull et al., 2005), the isolation and taxonomic characterization of strain F10 T promises to increase our understanding of marine actinobacteria. Stackebrandt et al. (1997) proposed a hierarchical classification system for the actinobacteria by conducting 16S rRNA gene sequence analyses and by distinguishing between patterns of signature nucleotides. As a result, the phylum Actinobacteria was classified into 5 subclasses within one class Actinobacteria Stackebrandt et al. 1997: Acidimicrobidae Stackebrandt et al. 1997, Rubrobacteridae Stackebrandt et al. 1997, Coriobacteridae Stackebrandt et al. 1997, Actinobacteridae Stackebrandt et al. 1997 and Sphaerobacteridae Stackebrandt et al. 1997. Sphaerobacter thermophilus was originally described by Demharter et al. (1989) and was subsequently placed in the subclass Sphaerobacteridae, which contains only the order Sphaerobacterales, the family Sphaerobacteraceae, the genus Sphaerobacter, and one species, S. thermophilus. More recently, Hugenholtz & Stackebrandt (2004) proposed the reclassification of S. thermophilus from the subclass Sphaerobacteridae...

Egicoccus halophilus gen. nov., sp. nov., a halophilic, alkalitolerant actinobacterium and proposal of Egicoccaceae fam. nov. and Egicoccales ord. nov.

“…Furthermore, strain EGI 80432 T differs greatly from N. alkaliphilus ANL-iso2 T by the following chemotaxonomic characteristics: (1) wholecell sugars (glucose, galactose, mannose and three unknown sugars for strain EGI 80432 T , glucose and galactose for N. alkaliphilus ANL-iso2 T ); and (2) fatty acid profile (Table S1) [C 18 : 1 v9c and iso-C 15 : 0 for strain EGI 80432 T , C 16 : 0 and iso-C 14 : 0 as major fatty acids (.10 %) for N. alkaliphilus NBRC 105792 T ], although both have C 17 : 1 v8c and summed feature 3 as main components (.10 %). The fatty acid profile of N. alkaliphilus NBRC 105792 T determined herein differs from previous reports (Sorokin et al, 2009;Kurahashi et al, 2010), which indicates that different media and temperatures for growth greatly influence the fatty acid compositions of this strain. In addition, strain EGI 80432 T had distinct signature nucleotides of the 16S rRNA gene sequence from those of N. alkaliphilus ANL-iso2 T and E. tangerina F10 T at positions 47 : 396 (U-C) and 841 : 845 (G-A), as given in the description of the family.…”

“…Characteristics that distinguish strain EGI 80432 T from its closest phylogenetic neighbours N. alkaliphilus ANL-iso2 T and E. tangerina F10 T Strains: 1, EGI 80432 T ; 2, N. alkaliphilus ANL-iso2 T ; 3, E. tangerina F10 T . Data for strain EGI 80432 T are from this study, data for N. alkaliphilus ANL-iso2 T are from Sorokin et al (2009) and data for E. tangerina F10 T are from Kurahashi et al (2010). All have cell-wall peptidoglycan type A1c and MK-9(H 4 ) as the predominant menaquinone.…”

“…The cell-wall peptidoglycan of strain EGI 80432 T contained meso-diaminopimelic acid, alanine and glutamic acid as major amino acids, which indicated the presence peptidoglycan type A1c (Schleifer & Kandler, 1972;Sorokin et al, 2009;Kurahashi et al, 2010). Strain EGI 80432 T had a complex cell-wall sugar composition, which contained glucose, galactose, mannose and three unknown sugars as major sugars, and fucose, arabinose, xylose, ribose and rhamnose as minor sugars.…”

“…At the time of writing, the class comprises only two orders, Nitriliruptorales (Sorokin et al, 2009) and Euzebyales (Kurahashi et al, 2010), and two validly published species names, Nitriliruptor alkaliphilus (Sorokin et al, 2009) and Euzebya tangerina (Kurahashi et al, 2010), which are from a soda lake sediment and a sea cucumber, respectively. The characteristics that distinguish Nitriliruptoria from other classes of the phylum 'Actinobacteria' are its phyletic lineage and signature nucleotides of the 16S rRNA gene sequence, Gram-stain-positive rod-shaped cells and cellwall peptidoglycan type A1c (Sorokin et al, 2009;Kurahashi et al, 2010). Beside the orders described above, few taxa have been reported due to limited knowledge on nutrient requirements and the physiology of the class.…”

“…The class Nitriliruptoria was originally proposed by Kurahashi et al (2010) as the subclass Nitriliruptoridae based on its distinct phyletic lineage and signature nucleotides of the 16S rRNA gene, and it was later elevated to the rank of the class (Ludwig et al, 2012). At the time of writing, the class comprises only two orders, Nitriliruptorales (Sorokin et al, 2009) and Euzebyales (Kurahashi et al, 2010), and two validly published species names, Nitriliruptor alkaliphilus (Sorokin et al, 2009) and Euzebya tangerina (Kurahashi et al, 2010), which are from a soda lake sediment and a sea cucumber, respectively.…”