Halobium palmae gen. nov., sp. nov., an extremely halophilic archaeon isolated from a solar saltern

A novel and extremely halophilic archaeon, designated strain 2a_47_2T, was isolated from a solar saltern sample collected in Indonesia. Cells of the strain were Gram-stain-negative, non-motile and pleomorphic and formed orange–red pigmented colonies. Strain 2a_47_2TC (optimum 38–41_grew at 20–48C),  pH 6.0–8.5 (optimum pH 7.5), >1.7 M NaCl (optimum 2.6 M) and <0.5 M MgCl (optimum 0.3 M). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two phospholipids and sulfated diglycosyl diether. The cells mainly contained menaquinone-8. The G+C content in the genomic DNA of the strain was 67.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 2a_47_22 represents a member of the family Halorubraceae and is different from any other known halophilic archaea. This finding was also demonstrated by phylogenetic analyses based on deduced RpoB¢ amino acid sequences. Collectively, these results show that strain 2a_47_2T represents a novel genus and species in the family Halorubraceae, and the name Halobium palmae gen. nov., sp. nov. is proposed. The type strain is 2a_47_2T (=NBRC 111368T = InaCC Ar34T).

International Journal of Systematic and Evolutionary Microbiology (2016), 66, 3799–3804

DOI 10.1099/ijsem.0.001267

Haloarchaeobius baliensis sp. nov., isolated from a solar saltern

A novel halophilic archaeon, designated strain 2b_61_3T, was isolated from a solar saltern in Indonesia. Cells of the strain were Gram-stain-negative, motile, pleomorphic rods that formed orange–red-pigmented colonies on solid medium. The isolate grew optimally at 42-44 8C, pH 6.5–7.0, and with 2.6 M NaCl, and MgCl2 was required for growth. Strain 2b_61_3 two differential 16S rRNA genes (rrnA and rrnB), and phylogenetic analysis revealed that the strain belonged to the genus Haloarchaeobius. The rrnA and rrnB sequence similarities between strain 2b_61_3T and species of the genus Haloarchaeobius were 98.4–99.2 % and 98.5–98.8 %, respectively. The ndings from the 16S rRNA gene analysis were supported by sequence analysis of rpoB9, the B9 subunit of RNA polymerase. On the basis of the phenotypic characteristics and phylogenetic analyses, as well as DNA–DNA hybridization experiments with Haloarchaeobius iranensis NBRC 110930T, strain 2b_61_3T represents a novel species of the genus Haloarchaeobius, for which the name Haloarchaeobius baliensis sp. nov. is proposed. The type strain is 2b_61_3 T (=NBRC 110517T = InaCC Ar2T).

International Journal of Systematic and Evolutionary Microbiology (2016), 66, 38–43.DOI 10.1099/ijsem.0.000672

Bacteroides caecigallinarum sp. nov., isolated from caecum of an Indonesian chicken

Three strains of anaerobic Gram-stain-negative, short to longer rod-shaped bacteria isolated from the caecum of chicken in Indonesia were studied using a polyphasic taxonomic approach. These strains belonged to the genus Bacteroides, based on sequence analysis of 16S rRNA and hsp60 (groEL) genes, with similarities of 93.2–94.1 and 89.8–90.8 %, respectively, to the closest recognized species, Bacteroides coprocola JCM 17929T. Sugar fermentation and enzyme characteristics, cellular fatty acid pro?les, menaquinone pro?les and metabolic end products were also investigated. Furthermore, DNA–DNA hybridization studies conformed that the three novel strains are different from the closest related species. The strains were also found to be distinct from each other on the basis of ribotype pro?les. The DNA G+C contents of the three strains were 41.1–41.8 mol%. Based on phenotypic and phylogenetic characteristics, a novel species, Bacteroides caecigallinarum sp. nov., is proposed (type strain C13EG111 = LIPI12-4-Ck773 = JSAT12-4-Ck773 = InaCC B455 = NBRC 110959)

International Journal of Systematic and Evolutionary Microbiology (2015), 65, 4341–4346

DOI 10.1099/ijsem.0.000573

Cryptosporangium cibodasense sp. nov., isolated from leaf litter in Indonesia

A novel actinomycete strain, designated LIPI11-2-Ac046, was isolated from a leaf litter sample obtained from Cibodas Botanical Garden, West Java, Indonesia, using the rehydration and centrifugation method. The taxonomic status of this organism was established using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain LIPI11-2-Ac046 had the closest sequence similarities with members of the genus Cryptosporangium (97.99–98.90 %). The strain grew well on ISP 4 and ISP 5 media and formed sporangia. Spores of this strain were motile. The strain grew in the presence of 0–2 % (w/v) NaCl and the temperature range of 15–28 8C. The cell-wall hydrolysate contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysate contained mannose, glucose, galactose, ribose and xylose, together with one unidentified O-methyl-pentose. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H), and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were C818 : 1 v9c, iso-C and Cv9c. These phenotypic characteristics corresponded to those of the genus Cryptosporangium. Meanwhile, the results of DNA–DNA hybridization as well as physiological and biochemical analyses distinguished strain LIPI11-2-Ac04617 : 1T from known members of the genus Cryptosporangium. On the basis of these data, it is proposed that strain LIPI11-2-Ac046 represents a novel species of the genus Cryptosporangium, with the name Cryptosporangium cibodasense sp. nov. The type strain is LIPI11-2-Ac046T (=InaCC A457T 16 : 0, C 16 : 0 = NBRC 110976T).

International Journal of Systematic and Evolutionary Microbiology (2015), 65, 4632–4637

DOI 10.1099/ijsem.0.000625

Actinoplanes tropicalis sp. nov. and Actinoplanes cibodasensis sp. nov., isolated from leaf litter

Two actinomycete strains, designated LIPI11-2-Ac034T and LIPI11-2-Ac042, were isolated from leaf litter collected from Cibodas Botanical Garden, West Java, Indonesia. Phylogenetic analysis based on 16S rRNA gene sequences suggested that both isolates belong to the genus Actinoplanes. These isolates were closely related to Actinoplanes ferrugineus and Actinoplanes durhamensis with similarity values of 98.2 % and 97.7 % respectively, for strain LIPI11-2Ac034T, and 99.0 % and 97.4–97.7 % respectively for strain LIPI11-2-Ac042. Both isolates grew well on ISP 7 medium with brown soluble pigment production. Spores were motile and sporangia were irregular. The isolates contained meso-diaminopimelic acid in cell-wall hydrolysates, and mannose, glucose and galactose in whole-cell hydrolysates. The predominant menaquinone of strain LIPI11-2-Ac034 was MK-9(H4) while that of strain LIPI11-2-Ac042 was MK-9(H6). The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C for strain LIPI11-2-Ac034, and iso-C16 : 0, anteiso-C15 : 0, iso-C15 : 0 and anteiso-C for strain LIPI11-2-Ac042. Phosphatidylethanolamine was detected as the diagnostic polar lipid. The DNA G+C contents of strains LIPI11-2-Ac034 and LIPI11-2-Ac042 were 71.5 and 70.7 mol%, respectively. Based on the differential phenotypic characteristics and the results of DNA–DNA hybridization and phylogenetic analysis, it is proposed that strains LIPI11-2-Ac034 and LIPI11-2-Ac042 represent two novel species of the genus Actinoplanes, for which the names Actinoplanes tropicalis sp. nov. (type strain LIPI11-2-Ac034 = InaCC A459 = NBRC 110973T) and Actinoplanes cibodasensis sp. nov. (type strain LIPI11-2-Ac042=InaCCA458T=NBRC 110974T) are proposed.

International Journal of Systematic and Evolutionary Microbiology (2015), 65, 3824–3829

DOI 10.1099/ijsem.0.000499

Tropicihabitans flavus gen. nov., sp. nov., a new member of the family Cellulomonadaceae

Two novel Gram-stain positive actinobacteria, designated PS-14-16T and RS-7-1, were isolated from the rhizosphere of a mangrove and sea sediment, respectively, and their taxonomic positions were investigated by a polyphasic approach. Both strains were observed to form vegetative hyphae in the early phase of growth but the hyphae eventually fragment into short rods to coccoid cells. The peptidoglycan type of both strains was found to be A4a. Their predominant menaquinone was identified as MK9(H4) and the major fatty acid as anteiso-C. The DNA G?C content was determined to be 68.4–68.5 mol%. 16S rRNA gene sequencing revealed that strains PS-14-16T and RS-7-1 were related to members of the family Cellulomonadaceae. Their nearest phylogenetic neighbour was found to be Sediminihabitans luteus, which is currently the only species of the genus Sediminihabitans, with a similarity of 97.94 %. However, strains PS-14-16T and RS-7-1 were distinguishable from the members of the genus Sediminihabitans and the other genera within the family Cellulomonadaceae in terms of chemotaxonomic characteristics and phylogenetic relationship. The results of DNA–DNA hybridization experiments indicated that strains PS-14-16 and RS7-1 belong to the same species. Strains PS-14-16 and RS-7-1 are concluded to represent a novel genus and species of the family Cellulomonadaceae, for which the name Tropicihabitans flavus gen. nov., sp. nov. is proposed. The type strain of T. flavus is PS-14-16 (=NBRC 110109T= IanCC A 516T).
Keyword: Actinobacteria, Mangrove, Cellulomonadaceae, Tropicihabitans flavus, Polyphasic taxonomy

Antonie van Leeuwenhoek (2015) 107:1299–1306

DOI 10.1007/s10482-015-0424-4

Serinibacter tropicus sp. nov., an actinobacterium isolated from the rhizosphere of a mangrove, and emended description of the genus Serinibacter

A novel Gram-stain-positive actinobacterium, designated PS-14-7T, was isolated from the rhizosphere of a mangrove on Pramuka Island, Indonesia, and its taxonomic position was investigated using a polyphasic approach. The peptidoglycan type of strain PS-14-7 and lysine was the diagnostic diamino acid of the peptidoglycan. The predominant menaquinone was MK-8(H4) and the major fatty acids were anteiso-C 15 : 0,C16 : 0 and iso-C. The DNA G+C content was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain PS-14-7T was closely related to Serinibacter salmoneus Kis428T (99.6 %). However, DNA–DNA hybridization and phenotypic characteristics revealed that strain PS-14-7T differed from Serinibacter salmoneus. Therefore, strain PS-14-7 represents a novel species of the genus Serinibacter, for which the name Serinibacter tropicus sp. nov. is proposed. The type strain is PS-14-7T (5NBRC 110108T=InaCC A 515). An emended description of the genus Serinibacter is also proposed.

International Journal of Systematic and Evolutionary Microbiology (2015), 65, 1151–1154

DOI 10.1099/ijs.0.000068

Actinoplanes bogoriensis sp. nov., a novel actinomycete isolated from leaf litter

A novel actinomycete, designated LIPI11-2-Ac043(T), was isolated from leaf litter collected in Indonesia. According to phylogenetic analysis based on the 16S rRNA gene sequence comparisons, strain LIPI11-2-Ac043(T) was closely related to Actinoplanes abujensis A4029(T) (99.3%) and Actinoplanes brasiliensis DSM 43805(T) (98.8%). Spores of strain LIPI11-2-Ac043(T) were motile and the sporangia were spherical. The predominant menaquinone was MK-9(H6) and the principal polar lipids were phosphatidylinositol, phosphatidylethanolamine, phosphatidylglycerol and diphospatidylglycerol. The whole-cell sugars were galactose, glucose and mannose; rhibose, arabinose and xylose were also detected as minor components. The major fatty acids were anteiso-C15:0, iso-C16:0, iso-C15:0 and anteiso-C17:0. These data supported the affiliation of strain LIPI11-2-Ac043(T) to the genus Actinoplanes. Meanwhile, the results of DNA-DNA hybridization and physiological and biochemical tests indicated that strain LIPI11-2-Ac043(T) can be distinguished from its closest related species. Therefore, strain LIPI11-2-Ac043(T) represents a novel species of the genus Actinoplanes, for which the name Actinoplanes bogoriensis sp. nov. is proposed. The type strain is LIPI11-2-Ac043(T) (=InaCC A522(T)=NBRC 110975(T)).The Journal of Antibiotics advance online publication, 5 August 2015; doi:10.1038/ja.2015.81
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